cluster_id adjacent altsplice break_adj_entropy1 break_adj_entropy2 break_adj_entropy_min breakpoint_homology cdna_breakseqs_percident defuse_probability deletion est_breakseqs_percident estisland_breakseqs_percident eversion exonboundaries expression1 expression2 gene1 gene2 gene_align_strand1 gene_align_strand2 gene_chromosome1 gene_chromosome2 gene_end1 gene_end2 gene_location1 gene_location2 gene_name1 gene_name2 gene_start1 gene_start2 gene_strand1 gene_strand2 genome_breakseqs_percident genomic_break_pos1 genomic_break_pos2 genomic_strand1 genomic_strand2 interchromosomal interrupted_index1 interrupted_index2 inversion library_name max_map_count mean_map_count min_map_count num_multi_map num_splice_variants orf path_id path_score read_through repeat_list1 repeat_list2 repeat_proportion1 repeat_proportion2 repeat_proportion_max span_count span_coverage1 span_coverage2 span_coverage_max span_coverage_min splice_score splicing_index1 splicing_index2 10882 N Y 3.67952553980864 3.54292948342842 3.54292948342842 86 0 0.531992618191953 N 0 0.94507874015748 N N 0 317991 ENSG00000218014 ENSG00000171346 - + 6 17 72352330 36932191 intron upstream RP11-263F15.1 KRT15 72351145 36923523 + - 0 72351555 36946877 - - Y 1 - N HCC1954 2 1.5 1 3 2 N - - N - LINE 0 0.0279329608938547 0.0279329608938547 6 0.671324327033068 0.971277749749971 0.971277749749971 0.671324327033068 2 0 - 28336 N Y 3.33850347850287 3.43677165801469 3.33850347850287 185 0.907479572595852 0.00310049062469975 N 0.907479572595852 0.907479572595852 N N 90 5357 ENSG00000214814 ENSG00000171208 - + 8 16 125201483 45735409 downstream coding FER1L6 NETO2 125037406 45672943 + - 0.641483343808925 125223683 45719755 - - Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.45707188223528 0.771308801272036 0.771308801272036 0.45707188223528 1 - - 36275 Y Y 2.89840082667239 3.43933231109443 2.89840082667239 0 0 0.279105233686924 Y 0 0.983676915499895 N N 3 4 ENSG00000161798 ENSG00000167580 - + 12 12 48645701 48638926 intron downstream AQP5 AQP2 48641920 48630796 + + 0 48642648 48639605 - + N 1.14092276830491 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.442788385915428 0.292811674556976 0.442788385915428 0.292811674556976 1 0 - 42368 N Y 3.34673757434116 3.5774559507845 3.34673757434116 265 0 0.0518505776021045 Y 0 0 N N 0 0 ENSG00000201818 ENSG00000201818 - + 4 4 170163070 170163070 downstream downstream Y_RNA Y_RNA 170162975 170162975 + + 0.99233671988389 170171906 170170037 - + N - - N HCC1954 1 1 1 0 1 N - - N DNA SINE,SINE 0.492063492063492 0.936507936507937 0.936507936507937 5 0.771308801272036 0.692749571512847 0.771308801272036 0.692749571512847 1 - - 36346 Y Y 2.67758996018145 3.45447218342791 2.67758996018145 348 0 0.0165790064606434 Y 0 0.994202753274525 N N 1214 1982 ENSG00000185479 ENSG00000170454 + - 12 12 51132177 51114377 utr3p upstream KRT6B KRT75 51126704 51104121 - - 0 51126731 51116666 - + N 0.189659081728125 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 18 1.1141127129485 1.13553795742827 1.13553795742827 1.1141127129485 1 0 - 32800 N N 3.7788666418837 3.42633507561067 3.42633507561067 0 0 0.111379557353134 N 0 0 N N 11413 1476 ENSG00000112877 ENSG00000182247 - + 5 3 706664 23608288 coding upstream CEP72 UBE2E2 665405 23219788 + + 0 672107 23195420 - + Y - - N HCC1954 20 12 8 4 1 N - - N - SINE 0 1 1 4 0.328520415356608 0.371370904316165 0.371370904316165 0.328520415356608 1 - - 19067 Y Y 3.46704205511183 3.4267624394105 3.4267624394105 245 0 0.0492948282890953 Y 0.00408163265306116 0.979251700680272 N N 0 0 ENSG00000213353 ENSG00000198758 + - 1 1 110111760 110108093 upstream intron AL158847.22 EPS8L3 110111549 110094225 - - 0 110119217 110104095 - + N - 1 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.942710757110266 0.671324327033068 0.942710757110266 0.671324327033068 4 - 0 10122 Y Y 3.58337693299909 3.22167408707565 3.22167408707565 0 0 0.882952228102131 Y 0 0.984 N N 5477 1954 ENSG00000169992 ENSG00000205544 - - 17 17 7263903 7248142 coding upstream NLGN2 C17orf61 7252226 7247038 + - 0 7252712 7249655 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.489247311827957 0.489247311827957 4 0.799875793911741 0.792734045751814 0.799875793911741 0.792734045751814 2 - - 42012 N N 3.50016892023405 3.42783536197374 3.42783536197374 0 0 0.146868862806890 N 0 0.0258620689655172 N N 17935 14212 ENSG00000148180 ENSG00000085719 - + 9 8 123134942 87642842 utr5p intron GSN CPNE3 123009896 87566186 + + 0.0258620689655172 123033393 87596064 - + Y - 0.00415047150867838 N HCC1954 36 27.4 1 4 1 N - - N SINE - 0.857142857142857 0 0.857142857142857 5 0.39993789695587 0.742741808632331 0.742741808632331 0.39993789695587 1 - 0 13279 N Y 3.52936639476796 3.69681549006792 3.52936639476796 0 0 0.452123568442864 N 0 0.984432656826568 N N 0 7628 ENSG00000217878 ENSG00000133466 - - 6 22 165450902 35914276 downstream intron RP11-534P19.1 C1QTNF6 165450674 35906152 - - 0 164952387 35912033 + + Y - 1.24330007730118 N HCC1954 2 1.75 1 3 1 N - - N LTR,LTR,LTR - 0.580645161290323 0 0.580645161290323 4 0.835584534711372 0.799875793911741 0.835584534711372 0.799875793911741 0 - 0 47091 Y Y 3.66016945000958 3.36551102231762 3.36551102231762 196 0 0.0186920189546254 Y 0.978831958315241 0.978831958315241 N N 5408 4977 ENSG00000171466 ENSG00000171469 + - 19 19 9646734 9592899 downstream upstream ZNF562 ZNF812 9620363 9580140 - - 0 9616750 9604093 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE LTR 1 1 1 6 0.692749571512847 0.742741808632331 0.742741808632331 0.692749571512847 4 - - 37318 N N 3.61889661733171 3.46145674063593 3.46145674063593 0 0 0.184243682096051 N 0 0 N N 850768 3 ENSG00000075624 ENSG00000187537 - + 7 14 5536758 18654942 coding downstream ACTB POTEG 5533313 18623365 - + 0 5534816 18655370 + + Y - - N HCC1954 20 3.625 1 2 1 N 60 21.8076 N - - 0 0 0 8 0.821301038391519 0.849868031031224 0.849868031031224 0.821301038391519 3 - - 20620 N Y 3.52936639476796 3.23061038311659 3.23061038311659 216 0.52946127946128 0.0196971326974216 N 0.619949494949495 0.71043771043771 N N 0 6539 ENSG00000208232 ENSG00000009413 + + 1 6 191967737 111911125 downstream coding AL160001.10-1 REV3L 191967611 111726927 - - 0.656144781144781 191822944 111735926 - - Y - - N HCC1954 128 99 24 4 1 N - - N LINE LINE 1 1 1 4 0.264244681917271 0.521347615674617 0.521347615674617 0.264244681917271 3 - - 26694 N Y 3.27568462530678 3.57489529770476 3.27568462530678 217 0 0.0403033339096616 Y 0 0.98952219257822 N N 438 24977 ENSG00000140660 ENSG00000103342 - - 16 16 12054642 11917313 upstream upstream RUNDC2A GSPT1 11978103 11874040 + - 0 11977926 11939012 - + N - - N HCC1954 7 3 1 2 1 N - - N - - 0 0 0 6 0.392796148795944 0.914143764470561 0.914143764470561 0.392796148795944 3 - - 38720 N Y 3.32523140661629 3.75016368088976 3.32523140661629 0 0 0.0233676120048191 N 0.844658430232558 0.875726744186047 N N 73 4513 ENSG00000109743 ENSG00000196663 - - 4 14 15343508 102038562 upstream intron BST1 TECPR2 15313739 101899031 + + 0 15292111 102024477 - - Y - 1.74636121541759 N HCC1954 20 6.38709677419355 2 31 1 N - - N - SINE 0 1 1 31 1.12839620926835 0.34280391167646 1.12839620926835 0.34280391167646 1 - 0 14132 N Y 3.55657227767559 3.34000055658918 3.34000055658918 275 0.74602495543672 0.0150219767003724 N 0.726488413547237 0.74602495543672 N N 3467 81 ENSG00000104472 ENSG00000133424 + - 8 22 141596434 32646410 utr3p intron CHRAC1 LARGE 141590586 31998847 + - 0.74602495543672 141595571 32087073 + + Y - 0.692052643815131 N HCC1954 1 1 1 0 1 N - - N SINE SINE 0.258823529411765 1 1 4 0.592765097273879 0.28566992639705 0.592765097273879 0.28566992639705 3 - 0 13938 Y Y 3.50016892023405 2.97630611903947 2.97630611903947 249 0 0.0724733570633823 Y 0 0 N N 36 12539 ENSG00000128218 ENSG00000138869 - + 22 22 22426655 22440141 coding intron VPREB3 CHCHD10 22424855 22438021 - - 0 22425364 22440020 + - N - 3.29499755112089 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 4 0.557056356474248 0.585623349113953 0.585623349113953 0.557056356474248 1 - 0 38100 Y Y 3.47592491799029 3.44615838200292 3.44615838200292 274 0 0.0660108780128821 Y 0.00364963503649618 0.992029197080292 N N 312 0 ENSG00000139973 ENSG00000213572 - + 14 14 61638180 61402019 upstream downstream SYT16 AL137918.4 61532294 61401469 + + 0 61506602 61464441 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 1.09982921662864 0.799875793911741 1.09982921662864 0.799875793911741 1 - - 46733 N N 3.67849247003875 3.62295434849776 3.62295434849776 0 0 0.501307277089694 N 0.738391966956274 0.746830935764136 N N 9 7722 ENSG00000130377 ENSG00000090661 - - 19 19 6144112 8233302 intron intron ACSBG2 LASS4 6086710 8180257 + + 0 6128051 8221956 - - N 0.804797361816256 0.548773271345724 Y HCC1954 23 20.8 20 5 1 N - - N SINE - 1 0 1 5 0.349945659836387 0.542772860154395 0.542772860154395 0.349945659836387 3 0 0 5521 N Y 3.8333716936548 3.25463311832853 3.25463311832853 0 0 0.743358620608474 N 0.235540334855403 0.945395738203958 N N 3966 160 ENSG00000175772 ENSG00000009694 + - 2 X 110111006 123925347 upstream intron AC013268.5-1 ODZ1 110103138 123339504 + - 0 110102056 123715470 + + Y - 0.696874693837562 N HCC1954 60 40.3809523809524 24 42 1 N - - N - LINE 0 1 1 42 1.39978263934555 0.442788385915428 1.39978263934555 0.442788385915428 3 - 0 48090 N N 3.64081336021051 3.0292090395872 3.0292090395872 0 0 0.980617143683125 N 0 0 N N 12549 0 ENSG00000087206 ENSG00000212451 + + 5 8 176366358 127753081 coding downstream UIMC1 U11 176264612 127752949 - + 0 176270998 128092524 - + Y - - N HCC1954 1 1 1 0 5 N 573 7.11156 N - LINE 0 0.173076923076923 0.173076923076923 4 0.51420586751469 0.371370904316165 0.51420586751469 0.371370904316165 3 - - 38111 Y Y 3.39487633072086 3.33896748681929 3.33896748681929 264 0 0.0640456719635278 Y 0.625278009452321 0 N N 0 0 ENSG00000196183 ENSG00000179627 + + 14 14 104374266 104341846 downstream downstream RPS2P4 AL590327.3 104373376 104340133 - + 0 104358439 104354283 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.614678899082569 0.614678899082569 5 0.735600060472404 0.742741808632331 0.742741808632331 0.735600060472404 3 - - 9363 Y N 3.5482584762506 3.47336426491055 3.47336426491055 0 0 0.497043987210219 Y 0 0.102990033222591 N N 5176 7182 ENSG00000141562 ENSG00000178927 - - 17 17 78039430 78001983 upstream upstream NARF C17orf62 78009349 77990056 + - 0.102990033222591 78008664 78005480 - + N - - N HCC1954 20 5.85714285714286 1 4 2 N - - Y LTR Other 1 1 1 7 0.592765097273879 0.807017542071667 0.807017542071667 0.592765097273879 1 - - 47574 Y Y 3.41376841220351 3.56591914887046 3.41376841220351 0 0 0.260850523614871 Y 0.974438852943526 0.993609713235881 N N 106 70 ENSG00000142227 ENSG00000105479 - - 19 19 53525622 53516997 utr5p upstream EMP3 CCDC114 53520454 53491526 + - 0 53520679 53517045 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 1.23552243166724 1.15696320190805 1.23552243166724 1.15696320190805 1 - - 9333 Y N 3.30128837699106 3.61169707060223 3.30128837699106 0 0.0385890151515151 0.999999701009963 Y 0.0385890151515151 0.0385890151515151 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p intron ORMDL3 GSDMB 35330822 35314374 - - 0.0385890151515151 35331933 35327589 - + N 2.89217234889613 9.44764878355004 N HCC1954 1 1 1 0 14 N - - Y - LTR 0 0.44047619047619 0.44047619047619 15 1.08554572030879 0.599906845433805 1.08554572030879 0.599906845433805 1 0 0 43297 N N 3.6769648867289 3.38296880644625 3.38296880644625 17 0.0174967797337912 0.0477707159348182 N 0.0902747960498067 0.0174967797337912 N N 0 0 ENSG00000214285 ENSG00000179460 - + 10 7 129240925 22640794 upstream intron NPS AC002480.1-1 129237603 22516494 + - 0.0174967797337912 129212728 22516739 - - Y - 1 N HCC1954 6 5 4 4 1 N - - N - - 0 0 0 4 0.464213630395207 0.821301038391519 0.821301038391519 0.464213630395207 1 - 0 5810 N Y 3.8333716936548 3.1703920357936 3.1703920357936 0 0 0.753312514524277 N 0.161810762076492 0.927113979310999 N N 0 0 ENSG00000183846 ENSG00000206889 + - 2 3 110575338 118745848 upstream downstream AC112229.4-1 U6 110574935 118745742 - + 0 110576429 118983227 - - Y - - N HCC1954 40 32.4 2 10 1 N 518 16.6993 N - LINE 0 1 1 10 0.742741808632331 0.278528178237124 0.742741808632331 0.278528178237124 3 - - 24835 N N 3.1971966911171 3.57800808738356 3.1971966911171 0 0 0.428046416014563 N 0.00404858299595146 0 N N 2 17943 ENSG00000187323 ENSG00000105141 - + 18 19 49311780 15027900 intron downstream DCC CASP14 48121156 15024015 + + 0.0221567905778434 49307599 15029502 - + Y 0.937508762181025 - N HCC1954 5 4 3 5 1 N - - N SINE - 1 0 1 5 0.264244681917271 0.414221393275723 0.414221393275723 0.264244681917271 3 0 - 11083 N N 3.63345808064191 3.43937216388778 3.43937216388778 18 0.0146098163841807 0.097192698912523 N 0.0768449858757062 0.0146098163841807 N N 272 78560 ENSG00000204277 ENSG00000112493 - + 17 6 73786168 33390114 utr3p utr3p AC087645.19-2 TAPBP 73769025 33375449 - - 0.0146098163841807 73769314 33375989 + - Y - - N HCC1954 40 38.75 38 4 1 N 367 21.217 N SINE DNA 1 0.80327868852459 1 4 0.535631111994469 0.592765097273879 0.592765097273879 0.535631111994469 3 - - 29393 Y Y 3.50575423470996 3.71976530271662 3.50575423470996 147 0 0.395089981687957 Y 0 0.966529663735845 N Y 2351 667 ENSG00000111801 ENSG00000124549 - + 6 6 26561629 26540321 intron coding BTN3A3 BTN2A3 26548742 26529618 + + 0 26551589 26536992 - + N 0.586578293289147 - N HCC1954 2 2 2 5 1 N - - Y - SINE 0 0.0444444444444444 0.0444444444444444 5 0.657040830713216 0.871293275511003 0.871293275511003 0.657040830713216 4 0 - 27084 N Y 3.37655331069169 3.52039024593366 3.37655331069169 0 0 0.709131868576197 N 0.955937349576036 0.973562409745622 Y N 6304 0 ENSG00000196696 ENSG00000209917 - + 16 16 68657352 29458187 coding downstream PDXDC2 AC009086.6-1 68567713 29458086 - - 0 68587872 29446389 + - N - - N HCC1954 6 5.22222222222222 5 9 1 N - - N SINE - 0.583333333333333 0 0.583333333333333 9 0.34280391167646 0.607048593593732 0.607048593593732 0.34280391167646 3 - - 39269 N N 3.71976530271662 3.33205747752478 3.33205747752478 7 0 0.095083436416784 N 0.00378787878787878 0 N N 27074 14 ENSG00000137804 ENSG00000129673 - + 15 17 39460535 71977793 coding utr5p NUSAP1 AANAT 39412361 71961028 + + 0 39444983 71973594 - + Y - - N HCC1954 37 28 21 8 1 N - - N - SINE 0 1 1 8 0.528489363834543 0.264244681917271 0.528489363834543 0.264244681917271 1 - - 34090 N Y 3.28871850530713 3.21808036422602 3.21808036422602 5 0 0.0813842110332719 N 0 0 N N 0 0 ENSG00000220068 ENSG00000170217 - - 9 9 44934987 67376221 upstream intron RP11-374M1.6 FAM27E3 44934285 67375502 + + 0 44932907 67375559 - - N - 1 Y HCC1954 12 10.5 10 4 1 N 70 26.1434 N Satellite Satellite,Simple_repeat 1 0.75 1 4 0.557056356474248 1.02841173502938 1.02841173502938 0.557056356474248 1 - 0 29 Y Y 3.31592438821476 3.27920380024291 3.27920380024291 392 0 0.0194512412455378 Y 0.663781242834212 0.994396354047237 N N 4244 10409 ENSG00000177685 ENSG00000177666 - + 11 11 821985 815216 intron downstream EFCAB4A PNPLA2 817618 808902 + + 0.994396354047237 818226 816262 - + N 0.0149951451349141 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 445 1.55690109886392 1.37835739486577 1.55690109886392 1.37835739486577 1 0 - 42292 Y Y 3.26460248413936 3.68846183584958 3.26460248413936 229 0 0.453081934075282 Y 0.00436681222707425 0.986899563318777 N N 3530 1004 ENSG00000169762 ENSG00000007062 + - 4 4 15837259 15694766 downstream upstream TAPT1 PROM1 15771226 15574385 - - 0 15736493 15728199 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.942710757110266 0.471355378555133 0.942710757110266 0.471355378555133 1 - - 11051 N Y 3.12804628055249 3.6491271616355 3.12804628055249 1 0 0.222115473647423 N 0.898743424897721 0.797486849795441 N N 1649619 1936 ENSG00000141736 ENSG00000083123 - + 17 6 35138441 81112706 coding utr3p ERBB2 BCKDHB 35104766 80873083 + + 0 35122227 81110923 - + Y - - N HCC1954 23 21 1 10 1 N - - N - SINE 0 1 1 11 0.899860268150708 0.357087407996313 0.899860268150708 0.357087407996313 2 - - 9834 N Y 3.1117894000631 2.51851081481407 2.51851081481407 342 0 0.00359863767887281 Y 0 0.988269693842449 N N 4310 64784 ENSG00000183011 ENSG00000170004 - - 17 17 7701897 7756803 coding coding LSMD1 CHD3 7700730 7728849 - + 0 7701240 7729062 + - N - 0.13923419625232 N HCC1954 3 2.03636363636364 1 52 2 N - - N - - 0 0 0 55 0.642757334393363 0.807017542071667 0.807017542071667 0.642757334393363 1 - 0 38194 Y Y 3.58849823915857 3.62617734898681 3.58849823915857 289 0 0.00312919859301108 Y 0.992932341897961 0.992932341897961 N N 1 0 ENSG00000100453 ENSG00000100450 + - 14 14 24173313 24148704 downstream downstream GZMB GZMH 24170017 24145534 - - 0 24162016 24135050 - + N - - N HCC1954 6 1.33333333333333 1 1 1 N - - Y LINE LINE 1 1 1 15 0.93556900895034 1.04269523134923 1.04269523134923 0.93556900895034 1 - - 18464 Y Y 3.34718800228844 3.46401739371567 3.34718800228844 254 0 0.240762408414288 Y 0.850590551181102 0.987549212598425 N N 10984 0 ENSG00000136631 ENSG00000219469 - + 1 1 148384129 148293640 upstream upstream VPS45 RP11-458I7.1 148305966 148292470 + + 0 148305654 148289144 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.507064119354764 0.407079645115797 0.507064119354764 0.407079645115797 2 - - 6233 N Y 3.80144573217181 3.42680229220385 3.42680229220385 0 0 0.0478847811448042 N 0.76040814362035 0.886509120662271 N N 2742 147 ENSG00000196912 ENSG00000179082 + + 2 9 97572761 131127005 utr3p downstream ANKRD36B C9orf106 97475562 131123116 - + 0 97488022 131144161 - + Y - - N HCC1954 35 31.25 23 4 1 N - - N SINE - 1 0 1 4 0.299953422716903 0.414221393275723 0.414221393275723 0.299953422716903 0 - - 28005 N N 2.36095200887839 3.10125097279879 2.36095200887839 0 0 0.0844978030328883 N 0 0 N N 4500 10384 ENSG00000071859 ENSG00000149923 - - X 16 153332195 30004193 coding intron FAM50A PPP4C 153325698 29994839 + + 0 153325743 29995037 - - Y - 0.571957914005921 N HCC1954 16 9.6 1 3 1 N - - N Simple_repeat - 1 0 1 5 0.299953422716903 0.421363141435649 0.421363141435649 0.299953422716903 2 - 0 48888 Y Y 3.52361324642271 3.43784458057793 3.43784458057793 263 0 0.163566008157776 Y 0 0.978804303858911 N N 0 5996 ENSG00000222534 ENSG00000187678 + - 5 5 141894094 141684750 downstream upstream AC005215.2 SPRY4 141894004 141670189 - - 0 141823719 141763759 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 21 0.735600060472404 0.914143764470561 0.914143764470561 0.735600060472404 4 - - 46954 Y Y 3.28655907981151 3.42567593647813 3.28655907981151 318 0 0.0162890974998546 Y 0 0 N N 16692 12189 ENSG00000079432 ENSG00000105722 - - 19 19 47491789 47451093 upstream upstream CIC ERF 47480657 47443564 + - 0 47467765 47464585 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 31 1.24980592798709 0.907002016310634 1.24980592798709 0.907002016310634 1 - - 38200 Y Y 3.50272957331379 3.4748918482204 3.4748918482204 251 0.0937152291733966 0.127913821954569 Y 0.0937152291733966 0 N N 0 5310 ENSG00000200264 ENSG00000100814 + - 14 14 19881406 19871297 downstream utr5p RNaseP_nuc CCNB1IP1 19881074 19849369 - - 0 19880611 19867374 - + N - 9.38519983906003 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 18 0.742741808632331 0.821301038391519 0.821301038391519 0.742741808632331 2 - 0 21215 N N 3.53039946453785 3.22336950425484 3.22336950425484 14 0.0131255411255411 0.0531992271538252 N 0 0.108017316017316 N N 0 0 ENSG00000212679 ENSG00000222549 - + 1 3 559619 75314889 intron upstream RP5-857K21.10 SRP_euk_arch 558939 75314597 + - 0.108017316017316 559164 75347178 - - Y 1 - N HCC1954 14 9.2 4 5 1 N - - N - Simple_repeat,Simple_repeat,Simple_repeat 0 0.60233918128655 0.60233918128655 5 0.835584534711372 0.807017542071667 0.835584534711372 0.807017542071667 1 0 - 16043 N N 3.09719324163274 3.25459326553517 3.09719324163274 2 0 0.167474702757389 N 0 0.00243309002433079 N N 154774 0 ENSG00000122566 ENSG00000212679 - - 7 1 26206942 559619 coding intron HNRPA2B1 RP5-857K21.10 26196081 558939 - + 0.00243309002433079 26202041 559595 + - Y - 1 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.785592297591888 0.871293275511003 0.871293275511003 0.785592297591888 3 - 0 39508 N Y 3.46448140203209 3.18296190747752 3.18296190747752 0 0 0.360015956208634 N 0.813223938223938 0.922176640926641 N Y 2292 2334 ENSG00000099385 ENSG00000138604 - + 16 15 30812900 67351592 coding utr5p BCL7C GLCE 30753770 67240027 - + 0 30771144 67240150 + + Y - 0.263875777718692 N HCC1954 16 10.2222222222222 1 6 1 N - - N DNA - 0.804347826086957 0 0.804347826086957 9 0.328520415356608 0.28566992639705 0.328520415356608 0.28566992639705 4 - 0 31636 N N 3.68527868815389 3.5816815158199 3.5816815158199 1 0 0.0865465237820336 Y 0.00847457627118653 0.00847457627118653 N N 139 7313 ENSG00000206552 ENSG00000181061 - - 3 3 42959283 42820986 coding upstream C3orf41 HIGD1D 42952856 42800797 + - 0.00847457627118653 42957735 42826015 - + N - - N HCC1954 1 1 1 0 1 N - - N - LTR 0 1 1 8 0.864151527351077 0.51420586751469 0.864151527351077 0.51420586751469 2 - - 45659 N Y 3.66592259835483 3.3550912285595 3.3550912285595 0 0.181137845014887 0.0996925646897893 N 0.103886698318178 0.38199082642633 N N 1303 0 ENSG00000197573 ENSG00000219516 + + 19 X 46148403 64606985 intron upstream CYP2B7P1 RP3-323B6.1 46122010 64605692 + + 0.412891285105013 46135907 64593870 + + Y 0.938223076889623 - N HCC1954 21 6.75 2 4 1 N - - N - Other,Other 0 1 1 4 0.407079645115797 0.678466075192994 0.678466075192994 0.407079645115797 1 0 - 6587 N Y 3.8333716936548 3.25463311832853 3.25463311832853 0 0 0.747834846043554 N 0.232395024782568 0.973066492097634 N N 3966 1 ENSG00000175772 ENSG00000163092 + + 2 2 110111006 167824509 upstream intron AC013268.5-1 XIRP2 110103138 167453243 + + 0 110102056 167576278 + + N - 0.994285260734979 Y HCC1954 60 39.5348837209302 18 43 1 N 530 22.386 N - LINE 0 1 1 43 1.45691662462496 0.421363141435649 1.45691662462496 0.421363141435649 3 - 0 12439 N Y 3.71720464963688 3.07101108092519 3.07101108092519 0 0 0.576428928221747 N 0 0 N N 13563 1649619 ENSG00000163110 ENSG00000141736 - - 4 17 95808400 35138441 utr3p coding PDLIM5 ERBB2 95592061 35104766 + + 0 95804918 35125066 - - Y - 0.990793461175642 N HCC1954 22 21.75 21 16 2 N 453 21.9768 N SINE - 1 0 1 16 0.314236919036755 1.1141127129485 1.1141127129485 0.314236919036755 1 - 0 10233 Y Y 3.51935717616377 3.46038381807268 3.46038381807268 274 0 0.368166600520567 Y 0.991627307857449 0.991627307857449 N N 830 7432 ENSG00000185158 ENSG00000178691 - + 17 17 27404630 27352162 coding downstream LRRC37B SUZ12 27372156 27288185 + + 0.656719622155432 27372524 27359263 - + N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity 0 0.303030303030303 0.303030303030303 4 0.764167053112109 0.664182578873142 0.764167053112109 0.664182578873142 1 - - 3844 N N 3.66592259835483 3.46551447180198 3.46551447180198 1 0.311904761904762 0.0242810139387077 N 0.311904761904762 0 N N 9613 13100 ENSG00000136235 ENSG00000169398 - - 7 8 23281248 142080514 utr3p utr5p GPNMB PTK2 23252841 141737683 + - 0 23263609 142005022 - + Y - 3.15580822152054 N HCC1954 24 22.6 21 5 1 N - - N SINE SINE 1 1 1 5 0.292811674556976 0.45707188223528 0.45707188223528 0.292811674556976 1 - 0 46158 N N 3.46613696641793 2.71144473255841 2.71144473255841 0 0 0.171999613221467 N 0.405436081242533 0.0197729988052566 N N 4428 6438 ENSG00000099821 ENSG00000157693 - + 19 9 584568 116448517 utr5p utr5p POLRMT C9orf91 568223 116413527 - + 0.0197729988052566 584531 116413655 + + Y - - N HCC1954 4 2.25 1 3 1 N - - N - Simple_repeat 0 0.636363636363636 0.636363636363636 4 0.678466075192994 0.314236919036755 0.678466075192994 0.314236919036755 2 - - 46910 Y N 3.21232721588077 3.72079837248651 3.21232721588077 189 0.547859547859548 0.00586325988625314 Y 0.773929773929774 0.785233285233285 N N 231 513 ENSG00000213971 ENSG00000196081 + - 19 19 23237276 23206938 downstream coding AC092329.3-1 ZNF724P 23234603 23197360 - - 0.593073593073593 23224950 23206908 - + N - 7.1808078876352 N HCC1954 4 1.10344827586207 1 1 1 N - - Y - - 0 0 0 29 0.471355378555133 0.828442786551446 0.828442786551446 0.471355378555133 3 - 0 38815 N Y 3.57800808738356 3.46128890676658 3.46128890676658 1 0 0.39437387432658 N 0 0 N N 17943 435 ENSG00000105141 ENSG00000133962 + - 19 14 15027900 91268166 downstream intron CASP14 CATSPERB 15024015 91116871 + - 0 15029502 91258127 + + Y - 2.11902664700188 N HCC1954 5 3 1 7 1 N - - N - SINE 0 1 1 9 0.621332089913584 0.264244681917271 0.621332089913584 0.264244681917271 3 - 0 495 N Y 3.26824964015148 3.50000108636471 3.26824964015148 14 0 0.413247706904165 N 0.98972602739726 0.948630136986301 Y N 8014 22 ENSG00000149084 ENSG00000150672 - - 11 11 43834736 85015962 utr3p intron HSD17B12 DLG2 43658719 82843701 + - 0 43834016 83895065 - + N - 0.482043379748128 N HCC1954 46 19.5 1 3 1 N - - N - SINE,LTR 0 0.898148148148148 0.898148148148148 4 0.778450549431962 0.564198104634174 0.778450549431962 0.564198104634174 2 - 0 42333 Y Y 3.57332786160156 3.57912086274016 3.57332786160156 208 0 0.0698038712563613 Y 0.960192307692308 0.990048076923077 N N 73 5741 ENSG00000109743 ENSG00000118564 - - 4 4 15343508 15266111 upstream upstream BST1 FBXL5 15313739 15215252 + - 0 15292075 15270588 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.635615586233437 0.871293275511003 0.871293275511003 0.635615586233437 2 - - 33090 N N 3.01191908932792 3.34359427943881 3.01191908932792 0 0 0.104171454142743 N 0 0 Y N 171855 0 ENSG00000198886 ENSG00000210194 - - MT MT 12138 14743 coding intron MT-ND4 AF347015.1-22 10761 14675 + - 0 10857 14733 - + N 0.350439220498621 1 N HCC1954 2 1.4 1 2 1 N 189 4.09957 N - - 0 0 0 5 0.707033067832699 0.728458312312478 0.728458312312478 0.707033067832699 2 0 0 37727 N N 3.6491271616355 3.48809356209009 3.48809356209009 0 0 0.0932224347889681 N 0 0 N N 5503 45068 ENSG00000088808 ENSG00000205336 + + 14 16 103383680 56256445 intron upstream PPP1R13B GPR56 103269841 56220023 - + 0 103362036 56211646 - + Y 6.48539511254257 - N HCC1954 21 20.3333333333333 20 9 1 N - - N SINE - 1 0 1 9 0.321378667196682 0.492780623034912 0.492780623034912 0.321378667196682 1 0 - 44498 N Y 3.60103760561896 2.8073549220576 2.8073549220576 0 0.630769230769231 0.0240543099491781 N 0.630769230769231 0.630769230769231 N N 7 26927 ENSG00000203876 ENSG00000104738 - + 10 8 111755788 49052621 coding coding RP11-451M19.3 MCM4 111691019 49036047 - + 0 111701631 49042484 + + Y - 0.888157776514276 N HCC1954 25 21.8571428571429 21 7 1 N - - N SINE - 1 0 1 7 0.407079645115797 0.635615586233437 0.635615586233437 0.407079645115797 2 - 0 1322 N Y 3.47233119514066 3.37126417066287 3.37126417066287 1 0 0.114700762306952 N 0 0.924688057040998 N N 20739 0 ENSG00000143951 ENSG00000209698 - - 2 11 63669355 45804873 utr3p upstream C2orf86 AC044839.16-1 63202041 45804729 - - 0.894563279857398 63309485 45814582 + + Y - - N HCC1954 620 532 420 5 1 N - - N LINE LINE 1 1 1 5 0.45707188223528 0.364229156156239 0.45707188223528 0.364229156156239 4 - - 7337 N N 3.70512929149291 3.41315949795669 3.41315949795669 1 0 0.923849541965628 Y 0 0 N Y 8684 2286 ENSG00000055044 ENSG00000082146 - + 2 2 202876627 202053819 intron coding NOP58 STRADB 202838760 202024637 + + 0 202870347 202046044 - + N 1.02198008249922 - N HCC1954 2 1.58208955223881 1 117 1 N 512 4.03905 N - - 0 0 0 201 1.03555348318931 1.46405837278488 1.46405837278488 1.03555348318931 4 0 - 36643 Y Y 3.52361324642271 3.42680229220385 3.42680229220385 0 0 0.420198015773692 Y 0.98705222270177 0.98705222270177 N Y 1127 566 ENSG00000069493 ENSG00000214774 - + 12 12 9743306 9743306 coding upstream CLEC2D AC007068.17 9713576 9713576 + + 0 9731765 9724896 - + N - - N HCC1954 20 5.22222222222222 1 2 1 N - - Y - LTR 0 0.596385542168675 0.596385542168675 9 1.0069864905496 0.978419497909897 1.0069864905496 0.978419497909897 4 - - 30621 Y Y 3.4561676006071 3.56807857436608 3.4561676006071 22 0.0110673816001479 0.974651706112004 Y 0 0 N N 1195 0 ENSG00000173681 ENSG00000206663 - + X X 19898337 19913198 utr5p upstream CXorf23 Y_RNA 19841403 19913097 - - 0 19898337 19916018 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.942710757110266 0.949852505270192 0.949852505270192 0.942710757110266 4 - - 30604 Y Y 3.27192306858781 3.58424216889964 3.27192306858781 8 0 0.87605132711378 Y 0.977098571926158 0.977098571926158 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 coding coding STS HDHD1A 7147472 6976961 + - 0 7181238 7076116 - + N - 0.505076995171717 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 14 1.24980592798709 0.671324327033068 1.24980592798709 0.671324327033068 1 - 0 26306 N N 3.46551447180198 3.32679884271949 3.32679884271949 0 0 0.0794975865408415 N 0 0 N N 1307 313916 ENSG00000170100 ENSG00000131748 + + 16 17 87822471 35073248 intron intron ZNF778 STARD3 87811612 35046938 + + 0 87818116 35047020 + + Y 0.678899070140454 1.09830374749134 N HCC1954 3 2.11111111111111 1 8 1 N - - N SINE - 1 0 1 9 0.28566992639705 0.785592297591888 0.785592297591888 0.28566992639705 2 0 0 3574 N N 3.72192472821224 3.58527523866953 3.58527523866953 0 0 0.994959363058952 N 0 0 N N 5889 7284 ENSG00000198862 ENSG00000156299 + + 21 21 29287141 31853161 intron intron RNF160 TIAM1 29222337 31412607 - - 0 29274252 31517316 - - N 0.542453307584369 0.599488559832437 Y HCC1954 1 1 1 0 4 N 566 1.62267 N DNA - 1 0 1 4 0.635615586233437 0.749883556792257 0.749883556792257 0.635615586233437 2 0 0 3475 N N 3.3755202409218 3.4780843434859 3.3755202409218 3 0 0.974092334585183 N 0.0119535519125683 0 N N 5889 7284 ENSG00000198862 ENSG00000156299 + + 21 21 29287141 31853161 intron coding RNF160 TIAM1 29222337 31412607 - - 0 29282007 31511886 - - N 0.909108324021675 - Y HCC1954 20 7.71428571428571 1 3 4 N 566 1.62267 N DNA,SINE - 0.714285714285714 0 0.714285714285714 7 0.664182578873142 0.978419497909897 0.978419497909897 0.664182578873142 1 0 - 24441 N Y 3.26936241550807 3.64759957832565 3.26936241550807 1 0 0.0951729728654437 N 0 0.865098581805603 N N 10428 2814 ENSG00000114346 ENSG00000154839 + + 3 18 174021957 46174532 utr5p utr3p ECT2 C18orf24 173951207 46155390 + + 0.865098581805603 173954993 46173640 + + Y - - N HCC1954 36 29 21 7 1 N - - N - SINE 0 1 1 7 0.385654400636018 0.299953422716903 0.385654400636018 0.299953422716903 1 - - 41726 N N 3.57167229721571 3.55657227767559 3.55657227767559 13 0 0.089986279474997 Y 0 0.125165343915344 N N 4 25232 ENSG00000220279 ENSG00000156471 + + 8 8 105463585 97415950 downstream coding AP003471.2-2 PTDSS1 105462904 97343340 - + 0.125165343915344 105457288 97390973 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.871293275511003 0.549914608314322 0.871293275511003 0.549914608314322 1 - - 13760 Y Y 3.35719722089263 3.0897446761083 3.0897446761083 193 0 0.777569113551107 Y 0.186057465850212 0.988695242581253 N N 194 480 ENSG00000169325 ENSG00000159496 + + 22 22 22389508 22371363 downstream intron AP000347.1 RGL4 22386399 22360329 - + 0 22381321 22367707 - + N - 9.23377595712169 N HCC1954 4 1.5 1 1 4 N - - Y LINE Simple_repeat 1 0.441558441558442 1 6 0.585623349113953 0.549914608314322 0.585623349113953 0.549914608314322 2 - 0 5531 N N 3.43681151080804 3.63825270713077 3.43681151080804 0 0 0.0868376499797365 N 0 0 N N 1356 559 ENSG00000138378 ENSG00000102290 - + 2 X 191724561 91764885 coding intron STAT4 PCDH11X 191602547 90920960 - + 0 191721154 91128974 + + Y 23.1687693601909 7.54631183192038 N HCC1954 18 10 4 5 1 N - - N - SINE 0 0.936170212765957 0.936170212765957 5 0.392796148795944 0.335662163516534 0.392796148795944 0.335662163516534 2 0 0 17538 Y Y 3.42742478681981 3.20703807585194 3.20703807585194 0 0 0.268478474910395 Y 0 0 N N 2470 69209 ENSG00000143303 ENSG00000143320 - - 1 1 154973365 154942232 coding downstream C1orf66 CRABP2 154964902 154936034 + - 0 154968505 154926401 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 1.02841173502938 0.621332089913584 1.02841173502938 0.621332089913584 1 - - 15995 N Y 2.1510444457265 3.64553343878587 2.1510444457265 0 0 0.0637158938240089 N 0 0 N N 2784 101048 ENSG00000143643 ENSG00000127954 + + 1 7 229181207 87774145 intron utr3p TTC13 STEAP4 229108613 87743687 - - 0 229168337 87744842 - - Y 2.33740202700692 - N HCC1954 66 17.25 1 1 1 N 235 24.7296 N SINE SINE 1 1 1 4 0.264244681917271 0.349945659836387 0.349945659836387 0.264244681917271 1 0 - 27072 Y N 3.68680627146374 3.47336426491055 3.47336426491055 134 0.648889148509453 0.159138083322648 N 0.360476663356505 0 Y Y 9011 12607 ENSG00000157349 ENSG00000168872 - + 16 16 68925230 68964780 coding coding DDX19B DDX19A 68890573 68938322 + + 0 68915989 68938452 - + N - 0.40799316679032 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 76 1.17838844638783 1.20695543902754 1.20695543902754 1.17838844638783 4 - 0 46742 Y Y 3.6800200533486 3.4561676006071 3.4561676006071 310 0 0.167934690550318 Y 0.0744239631336406 0.982200460829493 N N 8022 746 ENSG00000126464 ENSG00000126460 - + 19 19 54821507 54785999 upstream downstream PRR12 PRRG2 54790591 54778280 + + 0.982200460829493 54788396 54786809 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.212328767123288 0.212328767123288 112 0.857009779191151 1.04269523134923 1.04269523134923 0.857009779191151 4 - - 31249 Y Y 3.74337746277462 3.69209541149257 3.69209541149257 328 0 0.0871973320051271 Y 0 0 N N 0 174 ENSG00000213216 ENSG00000163762 + - 3 3 150558022 150534160 downstream downstream AC073522.19 TM4SF18 150557682 150519452 - - 0 150554963 150485659 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR LTR,LTR 0.896174863387978 0.368421052631579 0.896174863387978 8 1.09982921662864 0.892718519990782 1.09982921662864 0.892718519990782 4 - - 36513 Y Y 3.49591284997512 3.65231965690101 3.49591284997512 107 0 0.840636017102148 Y 0 0.983667726939075 N N 4142 2004 ENSG00000135392 ENSG00000123353 + + 12 12 54509687 54501226 coding coding DNAJC14 ORMDL2 54501011 54498073 - + 0 54503478 54500416 - + N 0.840501507550749 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.842726282871298 0.999844742389676 0.999844742389676 0.842726282871298 4 0 - 19552 Y Y 3.7061623612628 3.44785379918211 3.44785379918211 136 0 0.366873561078781 Y 0.406338485134498 0.987759556394526 N N 6191 7120 ENSG00000169905 ENSG00000143337 - - 1 1 178113557 178157206 utr5p coding TOR1AIP2 TOR1AIP1 178080577 178117800 - + 0 178113131 178118576 + - N - 0.284301381699802 N HCC1954 1 1 1 0 1 N - - Y SINE,SINE - 0.456349206349206 0 0.456349206349206 7 1.05697872766909 1.21409718718746 1.21409718718746 1.05697872766909 4 - 0 4066 Y Y 3.5816815158199 3.51360402781852 3.51360402781852 272 0 0.0402201163016306 Y 0.992276561787506 0.992276561787506 N N 8965 4751 ENSG00000127359 ENSG00000006530 + + 7 7 141048422 141000678 downstream coding KIAA1147 AGK 141002997 140901712 - + 0 141002815 140999154 - + N - 2.0645784548917 N HCC1954 2 1.05882352941176 1 1 2 N - - Y - - 0 0 0 17 0.949852505270192 0.835584534711372 0.949852505270192 0.835584534711372 1 - 0 31258 N Y 3.71890006681607 3.71976530271662 3.71890006681607 0 0 0.598292308240313 Y 0.9390602752729 0.98984337921215 N N 0 37 ENSG00000212211 ENSG00000189283 + - 3 3 60817317 60497735 downstream upstream U3 FHIT 60817102 59712992 - - 0 60782655 60497754 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 0.714174815992626 0.685607823352921 0.714174815992626 0.685607823352921 1 - - 30475 N Y 3.70889084821189 3.61104682422314 3.61104682422314 5 0 0.681151358153991 Y 0 0 N N 0 0 ENSG00000219537 ENSG00000198354 - - X X 125434945 125127615 upstream upstream RP11-10B2.3 WDR40C 125434549 125126195 + - 0 125421604 125244662 - + N - - N HCC1954 8 4.33333333333333 1 5 1 N - - N LINE LTR 1 1 1 6 0.849868031031224 0.699891319672773 0.849868031031224 0.699891319672773 4 - - 41821 Y Y 3.50272957331379 3.52824003904223 3.50272957331379 1 0 0.599535275383042 Y 0.0320709105560033 0.775127585280688 N N 2650 3685 ENSG00000104231 ENSG00000164695 - - 8 8 82796090 82834305 coding coding ZFAND1 CHMP4C 82776513 82807243 - + 0 82796069 82807573 + - N - 0.890085394268759 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 13 1.15696320190805 0.921285512630487 1.15696320190805 0.921285512630487 3 - 0 44105 N Y 3.3984700535705 3.63296356710195 3.3984700535705 233 0.751072961373391 0.00315768019390728 N 0.782188841201717 0.823676680972818 N N 6060 249 ENSG00000079482 ENSG00000150076 - + X 10 67570372 33211797 utr3p intron OPHN1 C10orf68 67179440 32896657 - + 0.782188841201717 67179623 33113488 + + Y - 13.7178929359707 N HCC1954 32 27 23 19 1 N - - N LINE LINE 1 1 1 19 0.685607823352921 0.264244681917271 0.685607823352921 0.264244681917271 0 - 0 39919 Y Y 3.69209541149257 3.23168330567983 3.23168330567983 231 0 0.658158131569183 Y 0.663961038961039 0.975108225108225 N N 1136 38799 ENSG00000104147 ENSG00000187446 + + 15 15 39412111 39361377 downstream downstream OIP5 AC012652.1 39388762 39310729 - + 0.228354978354978 39377237 39365590 - + N - - N HCC1954 40 11.25 1 3 4 N - - Y SINE,SINE - 1 0 1 4 0.799875793911741 0.5713398527941 0.799875793911741 0.5713398527941 4 - - 41629 Y Y 3.50529022639353 3.42257672716845 3.42257672716845 245 0 0.050880364597044 Y 0.99133984028394 0.982679680567879 N N 0 2253 ENSG00000222694 ENSG00000156795 + + 8 8 124536528 124523441 upstream downstream U4 WDYHV1 124536402 124498146 - + 0.263886424134871 124548500 124529645 - + N - - N HCC1954 7 2 1 1 1 N - - Y SINE LTR 1 1 1 6 0.707033067832699 0.792734045751814 0.792734045751814 0.707033067832699 4 - - 33097 N Y 3.37023110089298 3.30757073399642 3.30757073399642 408 0 0.00572337697090952 Y 0 0.993349673202614 N N 0 544065 ENSG00000210191 ENSG00000198744 - + MT MT 12337 9988 intron coding AF347015.1-21 MT-CO3 12267 8367 + + 0 12290 9368 - + N 1 0.772099739223864 N HCC1954 2 1.22222222222222 1 2 2 N - - N - - 0 0 0 9 1.16410495006798 0.899860268150708 1.16410495006798 0.899860268150708 3 0 0 23048 N N 3.00762316627563 3.52936639476796 3.00762316627563 21 0 0.0108905998146069 N 0.896446078431373 0.109436274509804 N N 3891 11782 ENSG00000166295 ENSG00000142784 + + 10 1 73665622 27507322 intron upstream C10orf104 WDTC1 73645812 27433746 + + 0.109436274509804 73645904 27431625 + + Y 0.744979490524871 - N HCC1954 23 15.5 1 3 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.307095170876829 0.39993789695587 0.307095170876829 1 0 - 19727 N N 3.38489761734022 3.43152237077921 3.38489761734022 0 0 0.0744250085600824 N 0 0 N N 3336 11338 ENSG00000090447 ENSG00000157193 - + 16 1 4263002 53566409 utr5p intron TFAP4 LRP8 4247189 53483800 - - 0 4253059 53493212 + - Y - 0.670421615438839 N HCC1954 24 22.2222222222222 22 9 1 N - - N SINE - 1 0 1 9 0.271386430077198 0.385654400636018 0.385654400636018 0.271386430077198 2 - 0 14870 N N 3.61360747730288 3.32912610208445 3.32912610208445 2 0 0.0485764156595863 N 0.0805194805194804 0.278838808250573 N N 49089 7074 ENSG00000117450 ENSG00000052841 - + 1 11 45760196 43472069 coding intron PRDX1 TTC17 45749295 43337067 - + 0.278838808250573 45757256 43344575 + + Y - 0.567986789816757 N HCC1954 14 8 3 5 1 N - - N - SINE 0 1 1 5 0.564198104634174 0.357087407996313 0.564198104634174 0.357087407996313 1 - 0 34407 Y Y 3.04338104249449 3.49896801659482 3.04338104249449 309 0 0.000824091452752418 Y 0.475387497870891 0.99250553568387 N N 45208 0 ENSG00000119335 ENSG00000217628 - + 9 9 130498488 130454247 intron downstream SET RP11-216B9.4 130485996 130453098 + + 0 130486391 130465502 - + N 0.138517976927999 - N HCC1954 1 1 1 0 1 N - - Y LINE,LINE - 1 0 1 15 0.685607823352921 0.849868031031224 0.849868031031224 0.685607823352921 1 0 - 35934 N N 3.62568283544685 3.04030230740834 3.04030230740834 0 0.235671936758893 0.096817172718145 N 0.235671936758893 0.370553359683794 N N 14514 3886 ENSG00000139289 ENSG00000146416 - + 12 6 74711823 143703134 utr3p utr5p PHLDA1 AIG1 74705494 143423716 - + 0.370553359683794 74707779 143423744 + + Y - 1.02313547045226 N HCC1954 36 31.75 27 4 1 N - - N SINE - 1 0 1 4 0.357087407996313 0.578481600954027 0.578481600954027 0.357087407996313 3 - 0 12164 N N 2.66125853177855 2.8315550432675 2.66125853177855 0 0 0.233455226757935 N 0 0.257772530499803 N N 11059 0 ENSG00000160551 ENSG00000219507 - + 17 8 24895628 82597221 upstream intron TAOK1 AC023644.6 24742069 82596349 + - 0.257772530499803 24741971 82597062 - - Y - 1 N HCC1954 10 5.75 4 4 1 N - - N Low_complexity - 1 0 1 4 0.292811674556976 0.264244681917271 0.292811674556976 0.264244681917271 1 - 0 45722 N N 3.60578818941786 3.16828604346046 3.16828604346046 9 0 0.083368499906828 N 0 0.338199513381995 N N 837 3144 ENSG00000188315 ENSG00000171017 + + 3 19 49289456 7872906 utr3p utr5p C3orf62 LRRC8E 49281223 7859390 - + 0.0545707334028501 49283214 7859440 - + Y - 0.588263151374728 N HCC1954 29 23.25 21 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.421363141435649 0.421363141435649 0.28566992639705 2 - 0 45567 N N 3.40016547074969 2.82035397286018 2.82035397286018 6 0 0.0667786598418044 N 0 0 N N 24 1063 ENSG00000112562 ENSG00000131116 - + 6 19 168815214 48815846 downstream coding SMOC2 ZNF428 168584680 48803217 + - 0 168935487 48810295 - - Y - - N HCC1954 1 1 1 0 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.464213630395207 0.464213630395207 0.271386430077198 1 - - 28018 N Y 3.29553522864581 3.59425138750382 3.29553522864581 5 0 0.0622710106945767 N 0 0.905908568142611 N N 45068 2763 ENSG00000205336 ENSG00000184083 + - 16 X 56256445 54226439 upstream upstream GPR56 FAM120C 56220023 54111482 + - 0 56211562 54230635 + + Y - - N HCC1954 21 20.7142857142857 20 14 1 N 557 29.4452 N - SINE 0 1 1 14 0.45707188223528 0.349945659836387 0.45707188223528 0.349945659836387 1 - - 8321 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.119993787226896 N 0 0.893539581437671 N N 20739 365 ENSG00000143951 ENSG00000164398 - + 2 5 63669355 131375678 utr3p downstream C2orf86 ACSL6 63202041 131311207 - - 0.875796178343949 63309485 131259203 + - Y - - N HCC1954 620 485 400 4 1 N - - N LINE LINE 1 1 1 4 0.435646637755502 0.307095170876829 0.435646637755502 0.307095170876829 4 - - 2394 N Y 2.19305636934196 2.797350727049 2.19305636934196 0 0 0.344906580528799 N 0.453963739779595 0.761109136153573 N N 30552 10901 ENSG00000110400 ENSG00000130635 + + 11 9 119104645 136876510 intron intron PVRL1 COL5A1 119014018 136673473 - + 0.761109136153573 119024308 136746136 - + Y 0.0027997624808655 0.535025920034587 N HCC1954 2 1.28571428571429 1 2 1 N 177 8.81679 N Simple_repeat Simple_repeat 1 1 1 7 0.335662163516534 0.485638874874985 0.485638874874985 0.335662163516534 3 0 0 37296 N Y 2.62170675956394 3.1369689962243 2.62170675956394 249 0.566963506198708 0.0368741824748583 N 0.545311681508643 0 N N 15 5996 ENSG00000139767 ENSG00000187678 + + 12 5 118085240 141684750 utr3p utr3p KIAA1853 SPRY4 117903779 141670189 + - 0.566963506198708 118081176 141671693 + - Y - - N HCC1954 38 37.25 37 4 1 N 345 23.3169 N Simple_repeat - 1 0 1 4 0.328520415356608 0.314236919036755 0.328520415356608 0.314236919036755 3 - - 18762 Y Y 3.60426060610801 3.41422307295011 3.41422307295011 154 0 0.428373759675518 Y 0 0.967426016606344 N N 0 0 ENSG00000223181 ENSG00000217260 + - 1 1 683579 653390 downstream upstream U6 RP11-206L10.1 683476 651474 - - 0.446242282307856 671931 666343 - + N - - N HCC1954 336 241.6 56 5 4 N - - Y SINE SINE 1 1 1 5 0.607048593593732 0.51420586751469 0.607048593593732 0.51420586751469 0 - - 6076 N N 3.53039946453785 3.39487633072087 3.39487633072087 0 0 0.259275215469555 N 0 0 N N 9 355 ENSG00000178568 ENSG00000106066 + - 2 7 213111810 29201417 downstream intron ERBB4 CPVL 211948691 29001772 - - 0 211722419 29092886 - + Y - 7.57279579202011 N HCC1954 20 5.8 1 3 2 N - - N SINE - 1 0 1 5 0.299953422716903 0.307095170876829 0.307095170876829 0.299953422716903 2 - 0 34778 Y Y 3.56232542602083 2.77693106225651 2.77693106225651 0 0 0.995806780331532 Y 0.416087912087912 0.985758241758242 N N 4263 0 ENSG00000187764 ENSG00000218102 - - 9 9 91260688 91277427 utr5p downstream SEMA4D RP13-93L13.1 91181972 91276972 - + 0 91260688 91302654 + - N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity,Simple_repeat 0 0.474860335195531 0.474860335195531 7 0.885576771830856 0.956994253430118 0.956994253430118 0.885576771830856 4 - - 5780 N N 3.59784511035345 3.08507803069543 3.08507803069543 0 0 0.0634497688380867 N 0.161877394636015 0 N N 738 4140 ENSG00000132170 ENSG00000152117 + + 3 2 12450855 131995615 utr5p utr5p PPARG AC093838.3-2 12304070 131967133 + + 0 12395713 131975535 + + Y - 1.05981300116657 N HCC1954 30 28.5 24 4 1 N - - N SINE - 0.953488372093023 0 0.953488372093023 4 0.307095170876829 0.407079645115797 0.407079645115797 0.307095170876829 2 - 0 31487 N Y 3.64656650855576 3.54144175291192 3.54144175291192 258 0 0.0376149673395745 Y 0.983258419646929 0.991629209823464 N N 7179 30872 ENSG00000175792 ENSG00000058262 + + 3 3 129325332 129273215 intron intron RUVBL1 SEC61A1 129282493 129253902 - + 0 129298831 129266751 - + N 0.375964246825831 1.65832413471081 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 0.828442786551446 0.814159290231593 0.828442786551446 0.814159290231593 1 0 0 23416 N Y 3.2069447898961 3.36617336972692 3.2069447898961 225 0 0.012773413143917 N 0.633216374269006 0.84280701754386 N N 27 0 ENSG00000167383 ENSG00000220337 + + 19 1 49644505 142087113 upstream downstream ZNF229 BX571672.7 49622266 142086687 - + 0.84280701754386 49653484 142122031 - + Y - - N HCC1954 6 2.25 1 1 1 N 363 17.6919 N Satellite Satellite 1 1 1 4 0.307095170876829 0.528489363834543 0.528489363834543 0.307095170876829 1 - - 30424 Y Y 3.2729561383577 3.2359232648304 3.2359232648304 0 0 0.537296528921633 Y 0.224643998837547 0.224643998837547 N N 0 7010 ENSG00000217748 ENSG00000213401 + - X X 151704649 151688896 upstream upstream U82671.12 MAGEA3 151703833 151685309 - - 0.224643998837547 151710765 151690009 - + N - - N HCC1954 2 2 2 6 3 N - - Y LINE - 1 0 1 6 0.414221393275723 0.39993789695587 0.414221393275723 0.39993789695587 2 - - 24463 N N 3.660633458326 3.44719145177281 3.44719145177281 3 0 0.0832327508021705 N 0 0 N N 1673 92 ENSG00000212774 ENSG00000171791 - + 7 18 23644794 59138341 coding downstream AC006026.2-1 BCL2 23643291 58941559 - - 0 23644627 58874159 + - Y - - N HCC1954 160 62.5 26 4 1 N 131 21.29 N Other SINE 1 0.447368421052632 1 4 0.507064119354764 0.271386430077198 0.507064119354764 0.271386430077198 1 - - 34310 Y Y 3.24165267149067 3.26352956157612 3.24165267149067 334 0 0.124153431980144 Y 0 0.986881500157579 N N 7118 0 ENSG00000137145 ENSG00000218778 - - 9 9 19364139 19191044 upstream upstream DENND4C RP11-146N23.1 19280749 19190333 + - 0 19266156 19220831 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 74 1.20695543902754 1.05697872766909 1.20695543902754 1.05697872766909 4 - - 38633 N N 3.22280044280138 3.21960794753587 3.21960794753587 0 0.248480972177806 0.522991796149856 N 0.248480972177806 0.248480972177806 N N 51903 10273 ENSG00000137818 ENSG00000100934 + - 15 14 67534938 38642188 utr3p intron RPLP1 SEC23A 67532213 38570874 + - 0.248480972177806 67534911 38630077 + + Y - 0.768425359124689 N HCC1954 4 1.75 1 3 1 N - - N - - 0 0 0 8 0.742741808632331 0.28566992639705 0.742741808632331 0.28566992639705 2 - 0 17367 Y Y 3.50120199000394 3.65657572715995 3.50120199000394 120 0 0.579421189443775 Y 0 0 N N 14045 0 ENSG00000117859 ENSG00000218025 - - 1 1 52026729 51833157 utr5p intron OSBPL9 RP11-191G24.2 51815439 51800126 + - 0 51836452 51812390 - + N - 1 N HCC1954 21 3.875 1 2 2 N - - Y SINE - 0.684848484848485 0 0.684848484848485 8 1.15696320190805 0.978419497909897 1.15696320190805 0.978419497909897 2 - 0 49406 N N 3.60273302279816 3.39231567764112 3.39231567764112 0 0 0.172485160242535 N 0 0 N N 0 29 ENSG00000221436 ENSG00000092421 - - 5 5 109877515 115938529 downstream upstream hsa-mir-548f-3 SEMA6A 109877429 115807150 - - 0.0271096616388096 109720299 115998942 + + N - - Y HCC1954 1 1 1 0 1 N 123 7.17639 N - LTR 0 1 1 5 0.678466075192994 0.857009779191151 0.857009779191151 0.678466075192994 1 - - 30428 Y Y 3.57063922744582 3.46654754157187 3.46654754157187 307 0 0.0273989740066258 Y 0 0.98671009771987 N N 13 9759 ENSG00000182583 ENSG00000101846 - + X X 7772183 7282682 upstream downstream VCX STS 7770303 7147472 + + 0 7542815 7521835 - + N - - N HCC1954 4 1.5 1 1 1 N - - Y - LINE 0 0.696774193548387 0.696774193548387 6 0.757025304952183 0.671324327033068 0.757025304952183 0.671324327033068 4 - - 36394 Y Y 3.54768941479713 3.38383404234679 3.38383404234679 260 0 0.0861972904147647 Y 0.00384615384615372 0.991628959276018 N N 6150 34794 ENSG00000171792 ENSG00000111206 - - 12 12 2868885 2856564 intron intron C12orf32 FOXM1 2856650 2837113 + - 0 2864709 2855941 - + N 2.71188138455344 3.13632272952695 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.642757334393363 0.749883556792257 0.749883556792257 0.642757334393363 1 0 0 27147 Y Y 3.46079439322662 3.2965682984157 3.2965682984157 160 0.0279910779581687 0.0549935339712285 Y 0.987457949393009 0.993728974696504 N N 2689 0 ENSG00000184939 ENSG00000201164 - + 16 16 67158539 67127062 coding upstream ZFP90 U4 67130715 67126919 + + 0 67131228 67125257 - + N - - N HCC1954 15 2.06666666666667 1 9 1 N - - Y - SINE,LINE 0 0.771929824561403 0.771929824561403 45 1.4140661356654 1.22123893534739 1.4140661356654 1.22123893534739 2 - - 41873 N N 3.43681151080804 3.43614916339873 3.43614916339873 0 0 0.98840199370876 N 0 0 N N 29840 30 ENSG00000164830 ENSG00000212993 + + 8 8 107834093 128498621 intron upstream OXR1 POU5F1P1 107739270 128497039 + + 0 107740717 128160562 + + N 1.03655686692363 - Y HCC1954 1 1 1 0 4 N 607 3.86243 N SINE LINE,LINE 0.507352941176471 0.554455445544555 0.554455445544555 4 0.871293275511003 0.635615586233437 0.871293275511003 0.635615586233437 2 0 - 12311 N N 3.55128313764676 3.38908332958227 3.38908332958227 15 0 0.218617505005285 N 0.762834821428571 0.743861607142857 N N 5176 11878 ENSG00000141562 ENSG00000198589 - + 17 4 78039430 152156329 upstream intron NARF LRBA 78009349 151405044 + - 0.0608258928571429 78008603 152103821 - - Y - 2.70130698212473 N HCC1954 20 5.57142857142857 2 7 1 N 356 24.628 N LTR,LTR,LTR Other 0.621951219512195 1 1 7 0.585623349113953 0.335662163516534 0.585623349113953 0.335662163516534 3 - 0 3446 N N 3.46869761949767 3.38014703354132 3.38014703354132 0 0 0.728063586278696 N 0 0 Y N 0 9455 ENSG00000209722 ENSG00000160299 - + 21 21 17725836 46690106 upstream coding AP000952.2 PCNT 17725745 46568483 + + 0 17709280 46579049 - + N - 1.40666228734139 N HCC1954 2 1.08333333333333 1 1 2 N 382 16.7655 N LINE - 1 0 1 12 0.842726282871298 1.23552243166724 1.23552243166724 0.842726282871298 1 - 0 638 N N 2.22920401214952 2.04239882705049 2.04239882705049 0 0 0.338204267543343 N 0 0 N N 22864 153581 ENSG00000175274 ENSG00000110092 - + 11 11 44929433 69178422 utr3p utr3p TP53I11 CCND1 44881900 69165054 - + 0 44912478 69176752 + + N - - Y HCC1954 1 1 1 0 1 N - - N Simple_repeat - 0.537190082644628 0 0.537190082644628 4 0.764167053112109 0.442788385915428 0.764167053112109 0.442788385915428 2 - - 44639 Y Y 3.47705127371601 3.6052936758779 3.47705127371601 118 0.674628712871287 0.109587003878017 N 0.792945544554455 0.891542904290429 N Y 14643 15033 ENSG00000187134 ENSG00000151632 - + 10 10 5010445 5050207 coding intron AKR1C1 AKR1C2 4995566 5021966 + - 0 4998106 5050092 - - N 1.33299485969846 203.701156408042 Y HCC1954 36 7.33333333333333 1 3 1 Y - - N - LTR 0 1 1 6 0.657040830713216 0.449930134075354 0.657040830713216 0.449930134075354 4 0 0 26644 Y Y 3.23420410596622 3.69359248957888 3.23420410596622 291 0 0.805254409405498 Y 0 0 N N 0 0 ENSG00000209496 ENSG00000209495 + - 16 16 3161032 3142681 downstream upstream AJ003147.1-1 AC108134.3-1 3160962 3142610 - - 0 3153676 3151306 - + N - - N HCC1954 2 1.5 1 8 4 N - - Y LTR,LTR - 1 0 1 16 0.907002016310634 1.0069864905496 1.0069864905496 0.907002016310634 4 - - 41879 N N 3.54296933622177 3.71617157986699 3.54296933622177 0 0 0.887800339922545 N 0 0 N Y 8537 19339 ENSG00000129292 ENSG00000177570 + - 8 8 133930234 119703365 coding intron PHF20L1 SAMD12 133856786 119270880 + - 0 133886167 119279152 + + N - 2.66256963008135 Y HCC1954 1 1 1 0 1 N 252 7.30508 N - - 0 0 0 223 1.48548361726466 1.39264089118562 1.48548361726466 1.39264089118562 4 - 0 22227 N N 3.28292550416853 3.30062602958175 3.28292550416853 8 0 0.0416683571128895 N 0 0 N N 86447 3798 ENSG00000142949 ENSG00000132635 - - 1 20 43861930 2769836 utr3p intron PTPRF FAM113A 43769134 2763960 + - 0 43818086 2769403 - + Y - 24.9860312247684 N HCC1954 39 29.2 24 5 1 N - - N SINE - 1 0 1 5 0.442788385915428 0.592765097273879 0.592765097273879 0.442788385915428 1 - 0 4184 N Y 3.0725081590115 3.53615261288309 3.0725081590115 174 0 0.554782366816312 Y 0.605727308759413 0.914288545382481 N N 524 0 ENSG00000218609 ENSG00000201515 - - 7 7 65743252 65653116 upstream upstream KCTD7 5S_rRNA 65731380 65652992 + - 0 65694701 65690969 - + N - - N HCC1954 2 1.09090909090909 1 1 5 N - - N - DNA 0 0.840579710144927 0.840579710144927 11 0.657040830713216 0.492780623034912 0.657040830713216 0.492780623034912 1 - - 38965 N N 2.72726988024015 3.47592491799029 2.72726988024015 0 0.475923852183651 0.156962785083496 N 0.510862262038074 0.528331466965285 N N 614 6349 ENSG00000058335 ENSG00000126522 - + 15 7 77169895 65256986 intron intron RASGRF1 CRCP 77041341 65216341 - + 0.528331466965285 77151712 65222584 + + Y 2.10360349777011 0.400269174914543 N HCC1954 16 9.25 4 4 1 N - - N SINE SINE 1 1 1 4 0.278528178237124 0.307095170876829 0.307095170876829 0.278528178237124 2 0 0 41238 Y Y 3.72824693801095 3.67952553980864 3.67952553980864 0 0.32158719027583 0.641709117882325 Y 0.437061711079944 0.971131369798972 N Y 10692 19250 ENSG00000101152 ENSG00000101150 - + 20 20 62035838 61993332 utr5p coding DNAJC5 TPD52L2 61996962 61959531 + + 0.0329008882655448 62030132 61975613 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.421363141435649 0.685607823352921 0.685607823352921 0.421363141435649 4 - - 30238 Y Y 3.3373466175536 3.70822850080258 3.3373466175536 0 0 0.999966574659663 Y 0.128391472868217 0.972329888027562 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62697437 62579737 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LINE 0 1 1 5 0.814159290231593 0.492780623034912 0.814159290231593 0.492780623034912 4 - - 46909 Y Y 3.58424216889964 3.16782203514404 3.16782203514404 231 0.0588863191602919 0.621461901684092 Y 0 0.986360671292178 N N 8 2309 ENSG00000131401 ENSG00000131398 + - 19 19 55539830 55524446 downstream intron NAPSB KCNC3 55528871 55507006 - - 0 55528539 55519152 - + N - 5.76820201606097 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 6 0.435646637755502 0.671324327033068 0.671324327033068 0.435646637755502 1 - 0 22214 N N 3.25256697878875 3.70719543103269 3.25256697878875 0 0 0.0449186997616935 N 0 0 N N 49089 0 ENSG00000117450 ENSG00000166748 - + 1 15 45760196 85332327 coding intron PRDX1 AGBL1 45749295 84486246 - + 0 45757275 85062263 + + Y - 1 N HCC1954 10 7.6 5 5 1 N - - N - SINE 0 1 1 5 0.807017542071667 0.407079645115797 0.807017542071667 0.407079645115797 1 - 0 2690 N Y 3.3712946758864 3.51679652308403 3.3712946758864 3 0 0.126747355832831 N 0.915054667788057 0 N N 8014 1554 ENSG00000149084 ENSG00000124171 - + 11 20 43834736 48806739 utr3p utr3p HSD17B12 PARD6B 43658719 48781488 + + 0 43834013 48801587 - + Y 1.57146936908363 - N HCC1954 74 64 36 5 1 N - - N - SINE 0 1 1 5 0.664182578873142 0.392796148795944 0.664182578873142 0.392796148795944 2 0 - 18528 N Y 3.36145329115156 3.51529944499772 3.36145329115156 306 0 0.160751172977236 Y 0 0.985961520758538 N N 0 8047 ENSG00000216834 ENSG00000186160 + + 1 1 47404179 47356577 upstream intron RP1-18D14.2 CYP4Z1 47402769 47305634 - + 0 47411108 47336679 - + N - 1.24883459697151 N HCC1954 10 3 1 2 1 N - - N LTR,LTR LINE 0.490683229813665 1 1 5 1.05697872766909 0.785592297591888 1.05697872766909 0.785592297591888 4 - 0 2727 N N 3.61464054707278 3.53718568265298 3.53718568265298 0 0 0.62900911613178 N 0 0 N N 0 153581 ENSG00000212451 ENSG00000110092 - + 8 11 127753081 69178422 downstream upstream U11 CCND1 127752949 69165054 + + 0.0233555581549497 128113174 69124235 - + Y - - N HCC1954 1 1 1 0 1 N 107 19.056 N SINE,SINE - 1 0 1 7 0.764167053112109 0.757025304952183 0.764167053112109 0.757025304952183 2 - - 31335 Y Y 3.70360170818306 3.70210463009675 3.70210463009675 229 0 0.0376212934715483 Y 0.965667821111278 0.988555940370426 N N 4 18920 ENSG00000173702 ENSG00000082781 + - 3 3 126136270 126088834 downstream coding MUC13 ITGB5 126106979 125964488 - - 0 126102801 126075066 - + N - 6.77951266824136 N HCC1954 21 12.4545454545455 1 16 1 N - - Y SINE - 1 0 1 22 0.528489363834543 0.671324327033068 0.671324327033068 0.528489363834543 2 - 0 6709 Y Y 3.15791545006551 3.44247137319745 3.15791545006551 135 0 0.139451634539462 Y 0.984888674543847 0.984888674543847 N N 5075 19674 ENSG00000115944 ENSG00000143924 + + 2 2 42449654 42413192 coding downstream COX7A2L EML4 42429982 42249997 - + 0 42433856 42416389 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.982142857142857 0.982142857142857 7 1.02841173502938 0.799875793911741 1.02841173502938 0.799875793911741 4 - - 41723 Y Y 3.21907358120256 3.29334529792665 3.21907358120256 0 0 0.489050155451364 Y 0 0.939571150097466 N N 3478 5969 ENSG00000205268 ENSG00000066855 + + 8 8 66916853 66785339 intron utr3p PDE7A MTFR1 66793537 66719528 - + 0 66800107 66783965 - + N 0.692006714606622 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.307095170876829 0.414221393275723 0.414221393275723 0.307095170876829 2 0 - 28388 N Y 3.59771094201066 3.4267624394105 3.4267624394105 1 0 0.534175682954369 N 0.275814275814276 0.771309771309771 N N 13100 7487 ENSG00000169398 ENSG00000188603 - - 8 16 142080514 28411124 intron coding PTK2 CLN3 141737683 28396101 - - 0 141807943 28408208 + + Y 0.950169615322814 2.3761658886877 N HCC1954 21 20.75 20 4 1 N - - N SINE - 1 0 1 4 0.264244681917271 0.39993789695587 0.39993789695587 0.264244681917271 3 0 0 27364 Y N 3.21336028565066 3.03650460329068 3.03650460329068 0 0.625431034482759 0.108508048553318 Y 0.625431034482759 0.421120689655172 N N 1956 4782 ENSG00000102871 ENSG00000125149 + + 16 16 65751313 65739941 utr5p downstream TRADD C16orf70 65745594 65701416 - + 0.421120689655172 65751264 65741903 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.357087407996313 0.492780623034912 0.492780623034912 0.357087407996313 1 - - 46338 N N 3.36927257903659 3.47117433419139 3.36927257903659 1 0 0.186297148477009 N 0 0 N N 0 21 ENSG00000210765 ENSG00000088053 + - 2 19 15961345 60241444 downstream upstream AC010145.10-1 GP6 15961243 60216885 + - 0.00249999999999984 15975528 60243400 + + Y - - N HCC1954 20 18 12 4 1 N 522 24.6124 N SINE LINE,SINE 1 0.698529411764706 1 4 0.335662163516534 0.721316564152552 0.721316564152552 0.335662163516534 1 - - 33333 N N 3.33936871440342 3.35719722089263 3.33936871440342 0 0 0.689385099835778 N 0 0 Y N 151141 275222 ENSG00000198888 ENSG00000198763 - + MT MT 4264 5512 coding coding MT-ND1 MT-ND2 3308 4471 + + 0 3432 5213 - + N 0.720832612848515 - N HCC1954 2 1.75 1 3 2 N 128 10.5705 N - - 0 0 0 4 0.778450549431962 0.828442786551446 0.828442786551446 0.778450549431962 2 0 - 4827 N N 3.62039369541802 3.10231454779222 3.10231454779222 0 0 0.434392645249627 N 0.815944881889764 0.00393700787401563 Y N 5527 273 ENSG00000146733 ENSG00000214765 - + 7 7 56086762 45771955 coding upstream PSPH AC091439.5-3 56046240 45734299 - - 0 56056417 45774783 + - N - - N HCC1954 5 4 3 10 1 N - - N - - 0 0 0 10 0.34280391167646 0.407079645115797 0.407079645115797 0.34280391167646 1 - - 23659 N N 3.25256697878875 3.60935140704395 3.25256697878875 0 0 0.0728149470336565 N 0 0 N N 49089 33313 ENSG00000117450 ENSG00000179820 - + 1 19 45760196 59071494 coding intron PRDX1 MYADM 45749295 59061423 - + 0 45757275 59070866 + + Y - - N HCC1954 30 18.4285714285714 1 6 1 N - - N - SINE,SINE 0 1 1 7 0.671324327033068 0.328520415356608 0.671324327033068 0.328520415356608 2 - - 10447 Y Y 3.57912086274016 3.67320333000993 3.57912086274016 260 0.0136123680241329 0.446990762026705 Y 0.785143288084464 0.980467571644042 N N 3275 1042 ENSG00000181523 ENSG00000141527 + + 17 17 75808719 75797450 utr3p intron SGSH CARD14 75797685 75766869 - + 0.980467571644042 75797796 75796079 - + N - 1.37492515940005 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.971277749749971 0.614190341753658 0.971277749749971 0.614190341753658 4 - 0 2745 N N 3.23077821698594 3.41423242051993 3.23077821698594 0 0 0.167435915879762 N 0 0.00423728813559321 N N 0 9183 ENSG00000221586 ENSG00000172172 + + 11 8 90242018 121526828 upstream coding hsa-mir-1261 MRPL13 90241937 121477264 - - 0 90965640 121501275 - - Y - - N HCC1954 1 1 1 0 1 N - - N LINE - 1 0 1 5 0.542772860154395 0.807017542071667 0.807017542071667 0.542772860154395 1 - - 35651 N N 3.46551447180198 3.4718366816007 3.46551447180198 1 0 0.109625643973528 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000216315 + - 12 22 6517797 39400402 coding intron GAPDH CTA-229A8.6 6513918 39399439 + - 0 6517409 39399659 + + Y 1.64339537332449 1 N HCC1954 2 1.16666666666667 1 1 1 N - - N - - 0 0 0 6 0.385654400636018 0.278528178237124 0.385654400636018 0.278528178237124 2 0 0 16961 N N 3.54193626645188 3.11827516077098 3.11827516077098 0 0 0.068641540428225 N 0 0 N N 7512 5088 ENSG00000154945 ENSG00000143669 - + 17 1 46140040 234096843 utr3p coding ANKRD40 LYST 46125552 233890964 - - 0 46127491 234060222 + - Y - 0.572008504306488 N HCC1954 37 32.8 25 5 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.407079645115797 0.407079645115797 0.314236919036755 2 - 0 33638 N N 3.26936241550807 3.44247137319745 3.26936241550807 0 0 0.0718376428424587 N 0 0 Y N 336285 339915 ENSG00000198868 ENSG00000198727 - + MT MT 12138 15882 coding coding MT-ND4 MT-CYB 10471 14748 + + 0 10880 15845 - + N - - N HCC1954 2 1.33333333333333 1 3 1 N - - N - - 0 0 0 9 1.0069864905496 1.27123117246687 1.27123117246687 1.0069864905496 1 - - 47608 Y N 3.13846607431061 2.27720743875955 2.27720743875955 0 0.274074074074074 0.0833007914060752 Y 0.406060606060606 0 N N 31124 0 ENSG00000132002 ENSG00000207707 - - 19 19 14490201 14501452 coding upstream DNAJB1 hsa-mir-639 14486582 14501355 - + 0 14489951 14501085 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.435646637755502 0.464213630395207 0.464213630395207 0.435646637755502 2 - - 36401 Y Y 3.68953475841283 3.63552422018169 3.63552422018169 181 0 0.00379751856467636 Y 0.98869914615771 0.98869914615771 N N 792 1026 ENSG00000136010 ENSG00000151131 + + 12 12 104002366 103912635 intron downstream ALDH1L2 C12orf45 103942332 103904228 - + 0.310647915620291 103967523 103913887 - + N 1.10781172869914 - N HCC1954 14 5.16666666666667 1 3 1 N - - Y LTR SINE 1 1 1 6 0.528489363834543 0.599906845433805 0.599906845433805 0.528489363834543 2 0 - 2400 N Y 3.41423242051993 3.65384724021086 3.41423242051993 5 0 0.263206353465735 N 0.943856240893638 0.943856240893638 N N 6632 68 ENSG00000158636 ENSG00000196979 - + 11 9 75940234 131946319 upstream utr3p C11orf30 AL360004.22 75833717 131942710 + - 0 75832968 131943313 - - Y - - N HCC1954 37 30.375 2 32 1 N - - N - SINE 0 0.940298507462687 0.940298507462687 32 1.39264089118562 0.478497126715059 1.39264089118562 0.478497126715059 1 - - 4445 Y Y 2.625 3.63296356710195 2.625 0 0 0.065333974942769 N 0.120274914089347 0.120274914089347 Y N 0 0 ENSG00000207344 ENSG00000207062 - + 7 7 64163945 64168485 downstream downstream SNORA22 SNORA15 64163812 64168351 + + 0.120274914089347 64176521 64168852 - + N - - N HCC1954 4 2.25 1 3 1 N - - N - - 0 0 0 4 0.614190341753658 0.592765097273879 0.614190341753658 0.592765097273879 1 - - 3851 N Y 3.50472116494007 3.52617389950245 3.50472116494007 235 0.780936170212766 0.0106538287172264 N 0.880510638297872 0.880510638297872 N N 4749 0 ENSG00000156162 ENSG00000208307 - + 8 7 95873238 145325416 coding upstream DPY19L4 AC073308.4 95801327 145325354 + + 0.661446808510638 95819780 144911356 - + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.657040830713216 0.45707188223528 0.657040830713216 0.45707188223528 1 - - 39983 Y N 2.92355902877938 3.63552422018169 2.92355902877938 0 0 0.116921909118781 Y 0.218342886920271 0.218342886920271 N N 75 4 ENSG00000166035 ENSG00000103569 - + 15 15 56648365 56265402 upstream downstream LIPC AQP9 56490060 56217700 + + 0.218342886920271 56410753 56337031 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.742741808632331 0.678466075192994 0.742741808632331 0.678466075192994 2 - - 47134 Y Y 3.42576922243396 3.5010341561346 3.42576922243396 288 0 0.090578085576246 Y 0.0532986111111112 0 N N 3492 6250 ENSG00000123815 ENSG00000105245 + - 19 19 45914440 45888396 intron intron ADCK4 NUMBL 45889274 45863650 - - 0 45890690 45882421 - + N 0.896107401382468 3.46045483794144 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.478497126715059 0.521347615674617 0.521347615674617 0.478497126715059 1 0 0 46802 Y Y 3.47548383761281 3.75169126419961 3.47548383761281 274 0 0.0944335324373515 Y 0.961381768799864 0.984552707519946 N N 711 156 ENSG00000198093 ENSG00000161551 + - 19 19 57100059 57083009 coding utr5p ZNF649 ZNF577 57084301 57066367 - - 0 57085898 57075942 - + N 0.2758375214674 4.07552459580323 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 0.971277749749971 1.03555348318931 1.03555348318931 0.971277749749971 4 0 0 27130 N Y 3.15781281653986 3.61360747730288 3.15781281653986 0 0 0.399571226977883 N 0 0.916982323232323 N N 40802 5016 ENSG00000205609 ENSG00000129636 - - 16 16 28322701 46052519 coding intron EIF3CL ITFG1 28298403 45746815 - - 0 28310964 45982013 + + N - 0.997110935680376 Y HCC1954 12 4.5 2 4 1 N - - N - SINE 0 1 1 4 0.407079645115797 0.299953422716903 0.407079645115797 0.299953422716903 3 - 0 4930 N Y 3.58271458558979 3.33680806132368 3.33680806132368 0 0 0.249250138681154 N 0.987847818619031 0.963543455857094 N N 1702 188 ENSG00000170379 ENSG00000159860 + + 7 7 143058435 143146099 upstream intron FAM115C AC099548.6 143028667 143138257 + + 0 143028234 143141806 + + N - 1.14656037452309 Y HCC1954 4 3.33333333333333 2 12 1 Y - - N Simple_repeat - 0.2125 0 0.2125 12 0.5713398527941 1.06412047582901 1.06412047582901 0.5713398527941 1 - 0 18945 Y N 3.54292948342842 3.02788044723418 3.02788044723418 0 0 0.60579541761901 Y 0.117174959871589 0.187800963081862 N N 0 0 ENSG00000223181 ENSG00000217260 + - 1 1 683579 653390 downstream upstream U6 RP11-206L10.1 683476 651474 - - 0.187800963081862 669179 665756 - + N - - N HCC1954 360 281.625 120 8 4 N - - Y DNA - 1 0 1 8 0.435646637755502 0.742741808632331 0.742741808632331 0.435646637755502 1 - - 23910 N N 3.54296933622177 3.15099609320118 3.15099609320118 0 0 0.250495776454929 N 0 0 N N 0 58119 ENSG00000222956 ENSG00000177954 - + 5 1 68810848 152231245 downstream coding SRP_euk_arch RPS27 68810578 152229862 - + 0 68801700 152230268 + + Y - 1.7823186359793 N HCC1954 8 5.46153846153846 4 13 1 N - - N - - 0 0 0 13 0.271386430077198 0.421363141435649 0.421363141435649 0.271386430077198 1 - 0 5668 N N 3.37581458369391 3.71873223294673 3.37581458369391 0 0.0898924731182795 0.0368045176422477 N 0.327311827956989 0.327311827956989 N N 23693 6 ENSG00000152102 ENSG00000206557 - + 2 3 131567474 32908756 coding downstream FAM168B TRIM71 131521919 32834514 - + 0.366881720430108 131545949 32924416 + + Y - - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.407079645115797 0.307095170876829 0.407079645115797 0.307095170876829 1 - - 30279 Y Y 3.59169073442408 3.56761456604966 3.56761456604966 0 0 0.817935615776972 Y 0 0.980116279069767 N N 57 0 ENSG00000177324 ENSG00000218530 + + X X 18148924 17862864 downstream downstream BEND2 RP1-272E8.1 18090974 17861390 - + 0 18032679 17900169 - + N - - N HCC1954 3 1.54545454545455 1 4 3 N - - Y LINE LTR 1 0.832214765100671 1 11 0.728458312312478 1.06412047582901 1.06412047582901 0.728458312312478 1 - - 21879 N N 3.66488952858494 3.40744620240479 3.40744620240479 0 0 0.176114946822183 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000220375 - - 12 1 6517797 558984 coding intron GAPDH RP5-857K21.14 6513918 558778 + + 0 6515961 558959 - - Y - 1 N HCC1954 9 4.25 2 4 1 N - - N - - 0 0 0 4 0.885576771830856 0.471355378555133 0.885576771830856 0.471355378555133 3 - 0 33036 Y Y 3.0824639444532 2.81084861536577 2.81084861536577 359 0.00278551532033411 0.997614780377137 Y 0 0.990680238460938 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.990680238460938 14169 12449 - + N 0.320201474398206 0.802753093676224 N HCC1954 2 1.125 1 1 10 N - - Y - - 0 0 0 8 1.12839620926835 0.585623349113953 1.12839620926835 0.585623349113953 2 0 0 29149 Y Y 3.57912086274016 3.41848849077886 3.41848849077886 324 0 0.00596950327703938 Y 0.986795846619246 0.993397923309623 N N 0 3886 ENSG00000217648 ENSG00000146416 - + 6 6 143706213 143703134 intron coding RP1-95L4.4 AIG1 143705076 143423716 + + 0 143705406 143696276 - + N 1 2.25490798537231 N HCC1954 2 1.22222222222222 1 4 1 N - - Y - - 0 0 0 18 1.24980592798709 1.13553795742827 1.24980592798709 1.13553795742827 1 0 0 44694 Y N 3.13375957610439 3.7527243339695 3.13375957610439 0 0 0.333702352578913 Y 0 0 N N 137 82 ENSG00000184923 ENSG00000214562 - + 10 10 89117109 88984892 upstream downstream FAM22D FAM22A 89107405 88975185 + + 0 89086551 89038235 - + N - - N HCC1954 12 6.14285714285714 3 7 2 N - - Y - SINE 0 0.178571428571429 0.178571428571429 7 0.714174815992626 0.599906845433805 0.714174815992626 0.599906845433805 2 - - 4139 Y Y 3.48167806633553 3.448886868952 3.448886868952 259 0 0.00503303003217548 Y 0.636921300472702 0.99069028975571 N N 2364 3342 ENSG00000106100 ENSG00000180233 + + 7 7 30484833 30373832 downstream downstream NOD1 ZNRF2 30430672 30290448 - + 0 30409051 30397174 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 5 0.978419497909897 0.807017542071667 0.978419497909897 0.807017542071667 1 - - 21732 N N 3.37977631118074 3.73912139251568 3.37977631118074 13 0 0.0412852466444764 N 0.0224278386804787 0 N N 1186 1053 ENSG00000137968 ENSG00000139163 - + 1 12 75849389 22734875 coding downstream SLC44A5 ETNK1 75440404 22669343 - + 0 75538911 23120841 + + Y - - N HCC1954 20 18.4285714285714 9 7 1 N - - N - LINE 0 0.838235294117647 0.838235294117647 7 0.956994253430118 0.485638874874985 0.956994253430118 0.485638874874985 1 - - 11540 N N 3.50165665075055 3.45400817511148 3.45400817511148 0 0 0.379580690473139 N 0.22836941468037 0.697208251330272 N N 1649619 1 ENSG00000141736 ENSG00000069535 - - 17 X 35138441 43626665 upstream intron ERBB2 MAOB 35104766 43510804 + - 0.697208251330272 35104459 43576754 - + Y - 1.03367633302152 N HCC1954 3 1.61538461538462 1 5 1 N - - N - DNA 0 1 1 13 0.785592297591888 0.314236919036755 0.785592297591888 0.314236919036755 2 - 0 47992 N N 3.7297745213208 3.46824295875107 3.46824295875107 0 0 0.999871967493349 N 0 0.0220115021224155 N N 86504 0 ENSG00000104408 ENSG00000182152 + + 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0.0220115021224155 109296012 116871207 - - Y 0.543515163097469 - N HCC1954 2 1.5 1 135 7 N 241 0.00319582 N - DNA 0 0.703030303030303 0.703030303030303 270 0.864151527351077 1.17838844638783 1.17838844638783 0.864151527351077 4 0 - 13110 N Y 3.59425138750382 3.18188898491428 3.18188898491428 8 0 0.496159126033318 N 0.190531716417911 0.900373134328358 N N 3766 20793 ENSG00000132357 ENSG00000141027 - + 5 17 40895948 16059570 utr3p utr5p CARD6 NCOR1 40877043 15875443 + - 0 40890474 16059401 - - Y - 4.35916940862606 N HCC1954 35 26.1212121212121 12 33 1 N - - N SINE Simple_repeat 1 0.647058823529412 1 33 0.528489363834543 0.485638874874985 0.528489363834543 0.485638874874985 4 - 0 764 Y Y 2.99566220883853 3.35719722089263 2.99566220883853 264 0.0120896464646464 0.802991300790061 Y 0.0452967171717173 0.991698232323232 N N 1172 1543 ENSG00000174165 ENSG00000174483 + + 11 11 66070247 66057660 coding intron ZDHHC24 BBS1 66063311 66034666 - + 0 66067754 66045516 - + N - 1.6995032370371 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 13 1.05697872766909 0.807017542071667 1.05697872766909 0.807017542071667 2 - 0 26581 Y Y 3.0667948634596 3.1825606798934 3.0667948634596 336 0 0.0799411243963357 Y 0.873794454490657 0.981069168173599 N N 30723 6267 ENSG00000166747 ENSG00000040199 + - 16 16 70400477 70306205 downstream utr5p AP1G1 PHLPPL 70320404 70232304 - - 0 70315173 70306205 - + N - 60.2919285274184 N HCC1954 1 1 1 0 2 N - - Y Low_complexity,Low_complexity Simple_repeat 0.404907975460123 0.14207650273224 0.404907975460123 40 1.16410495006798 1.27123117246687 1.27123117246687 1.16410495006798 4 - 0 46852 Y Y 2.92758472083715 3.21700744166278 2.92758472083715 200 0 0.0121473280917774 Y 0 0.9801 N N 2718 4583 ENSG00000130299 ENSG00000074855 - - 19 19 17314530 17306638 coding upstream GTPBP3 ANO8 17309379 17295034 + - 0 17309830 17306864 - + N 0.859572877142814 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.243697478991597 0.243697478991597 8 0.835584534711372 0.771308801272036 0.835584534711372 0.771308801272036 2 0 - 42494 Y N 3.43677165801469 3.13636008197748 3.13636008197748 0 0 0.960047254737265 Y 0.394765631574518 0.394765631574518 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 coding downstream AFF1 AC093827.3 88147177 88089842 + - 0.394765631574518 88186356 88075420 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 28 0.914143764470561 0.964136001590045 0.964136001590045 0.914143764470561 2 - - 38832 N N 3.30591516961058 3.40591861909494 3.30591516961058 1 0 0.186988945296873 N 0 0.00310559006211186 N N 1814 5424 ENSG00000178229 ENSG00000033170 + + 19 14 62533956 65279714 utr3p utr5p ZNF543 FUT8 62523689 64947063 + + 0 62532938 65097939 + + Y - - N HCC1954 38 27 23 4 1 N - - N SINE - 1 0 1 4 0.585623349113953 0.635615586233437 0.635615586233437 0.585623349113953 2 - - 7634 N Y 3.63296356710195 3.42680229220385 3.42680229220385 132 0.788499751614506 0.00135472685751448 N 0 0.772230501738698 N N 3790 21810 ENSG00000124120 ENSG00000213699 - + 20 2 42556631 26857603 utr3p utr3p TTPAL C2orf18 42537958 26840646 + + 0.690884252359662 42555888 26855441 - + Y - - N HCC1954 819 648.75 180 4 1 N - - N SINE SINE 1 1 1 4 0.314236919036755 0.271386430077198 0.314236919036755 0.271386430077198 1 - - 37210 N Y 3.50016892023405 3.37295958784206 3.37295958784206 7 0 0.161653527781276 N 0.819602962603205 0.845373967945605 N N 551733 2 ENSG00000204628 ENSG00000133636 - - 5 12 180603512 84800894 coding downstream GNB2L1 NTS 180596536 84792204 - + 0 180601102 84806963 + - Y - - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.764167053112109 0.328520415356608 0.764167053112109 0.328520415356608 1 - - 12021 N N 3.28292550416853 3.30062602958175 3.28292550416853 8 0 0.0387418590521785 N 0.110737314269695 0.0936361087748808 N N 170 3798 ENSG00000181856 ENSG00000132635 + - 17 20 7132090 2769836 utr3p intron SLC2A4 FAM113A 7125778 2763960 + - 0.110737314269695 7131431 2769403 + + Y - 24.9860312247684 N HCC1954 34 26.75 24 4 1 N 416 21.0227 N SINE - 1 0 1 4 0.307095170876829 0.485638874874985 0.485638874874985 0.307095170876829 1 - 0 48207 N N 3.54768941479713 3.65281417044097 3.54768941479713 3 0 0.0517092412582408 N 0 0.251889644746788 N N 3202 78560 ENSG00000164403 ENSG00000112493 - + 5 6 132194489 33390114 utr3p utr3p SHROOM1 TAPBP 132185734 33375449 - - 0.251889644746788 132186230 33376013 + - Y - - N HCC1954 39 37.5714285714286 36 7 1 N - - N SINE DNA 1 0.363636363636364 1 7 0.307095170876829 0.471355378555133 0.471355378555133 0.307095170876829 1 - - 42491 Y Y 3.62145727041145 3.29590595100639 3.29590595100639 0 0 0.999396541947481 Y 0 0.979028967768258 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 coding downstream AFF1 AC093827.3 88147177 88089842 + - 0 88224296 88088747 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 4 0.707033067832699 0.51420586751469 0.707033067832699 0.51420586751469 4 - - 8462 N N 3.75169126419961 3.29020623582363 3.29020623582363 6 0 0.071845483432692 N 0 0.00328947368421062 N N 252027 10501 ENSG00000141738 ENSG00000160967 - - 17 7 35157070 101713969 utr5p intron GRB7 CUX1 35147713 101246012 + + 0.00328947368421062 35147852 101422980 - - Y 0.430618027590555 1.46919168501429 N HCC1954 21 20.125 20 8 1 N - - N - SINE 0 1 1 8 0.778450549431962 0.278528178237124 0.778450549431962 0.278528178237124 2 0 0 4416 N N 3.31592438821476 3.67320333000992 3.31592438821476 4 0 0.179844912228317 Y 0.913798263992817 0.195450463932954 N N 570 0 ENSG00000170356 ENSG00000157680 + - 7 7 143683165 137182149 intron intron OR2A9P DGKI 143578263 136724925 - - 0 143671215 137168552 - + N 5.60090302881915 1 N HCC1954 40 30.5714285714286 15 7 1 N - - N - LTR 0 1 1 7 0.699891319672773 0.521347615674617 0.699891319672773 0.521347615674617 2 0 0 29288 Y Y 3.53871326596283 3.77001428422878 3.53871326596283 266 0 0.0176121180460014 Y 0.991411718952554 0.991411718952554 N N 0 8992 ENSG00000221743 ENSG00000156711 + + 6 6 36216343 36215820 upstream utr3p Z95152.1-2 MAPK13 36216253 36206240 - + 0.991411718952554 36216744 36215361 - + N - 1.39496007727201 N HCC1954 17 3.66666666666667 1 1 1 N - - Y SINE,LINE - 0.698717948717949 0 0.698717948717949 6 1.0069864905496 0.864151527351077 1.0069864905496 0.864151527351077 1 - 0 31007 N N 3.76170048280379 3.63296356710195 3.63296356710195 0 0.0156684118013949 0.393040023997846 N 0.758679997731955 0.76503052410743 N N 10237 100806 ENSG00000182220 ENSG00000163931 - - X 3 40350830 53265078 intron coding ATP6AP2 TKT 40325160 53234715 + - 0 40337319 53244230 - + Y 1.11879726314004 0.944105846321089 N HCC1954 20 10 6 4 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.628473838073511 0.628473838073511 0.271386430077198 3 0 0 26754 Y Y 3.34785034969775 3.69784855983781 3.34785034969775 261 0 0.945159241406254 Y 0.119664973714693 0.768332887819656 N N 1747 10006 ENSG00000157312 ENSG00000132612 + + 16 16 67921999 67916446 downstream downstream COG8 VPS4A 67920025 67895081 - + 0 67919662 67916887 - + N - - N HCC1954 2 1.28571428571429 1 2 4 N - - Y - SINE 0 0.357142857142857 0.357142857142857 7 0.485638874874985 0.585623349113953 0.585623349113953 0.485638874874985 3 - - 46602 N N 3.74913061111987 3.44719145177281 3.44719145177281 0 0 0.119001457374083 N 0.527229532163743 0.755821846282372 N N 73 2111 ENSG00000109743 ENSG00000099308 - + 4 19 15343508 18123499 upstream downstream BST1 MAST3 15313739 18069603 + + 0 15292001 18124242 - + Y - - N HCC1954 26 14.7 13 10 1 N 260 29.3256 N - SINE 0 1 1 10 1.07126222398894 0.257102933757345 1.07126222398894 0.257102933757345 3 - - 36521 Y Y 3.448886868952 3.48593413659447 3.448886868952 321 0 0.140366049080162 Y 0 0.981874822996318 N N 16105 2401 ENSG00000073614 ENSG00000120647 - - 12 12 368881 422065 utr5p intron JARID1A CCDC77 259484 381084 - + 0 368821 384746 + - N - 1.42492339179122 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.428504889595575 0.442788385915428 0.442788385915428 0.428504889595575 2 - 0 9520 Y Y 3.6272104187567 3.51529944499772 3.51529944499772 318 0 0.0496801138332649 Y 0.69715786959637 0.987381577899849 N N 4503 1008 ENSG00000197417 ENSG00000196689 + - 17 17 3486365 3447085 utr3p utr5p CARKL TRPV1 3458305 3415493 - - 0 3458470 3442426 - + N 0.0302710724583488 14.9104306873639 N HCC1954 1 1 1 0 1 N - - Y DNA,DNA - 1 0 1 18 1.09982921662864 1.07840397214886 1.09982921662864 1.07840397214886 4 0 0 5217 N Y 3.6800200533486 3.21063179870157 3.21063179870157 2 0 0.0269591586026967 N 0 0.88605851979346 N N 12076 1702 ENSG00000148219 ENSG00000170379 - + 9 7 119217138 143058435 utr3p utr3p ASTN2 FAM115C 118227328 143028667 - + 0.615447504302926 118415435 143058071 + + Y - - N HCC1954 441 432.6 420 5 1 N - - N LINE LINE 1 1 1 5 0.392796148795944 0.278528178237124 0.392796148795944 0.278528178237124 1 - - 25395 N N 3.72551845106187 3.4267624394105 3.4267624394105 1 0.00378787878787901 0.147802600772161 N 0 0.00378787878787901 N N 0 319 ENSG00000197585 ENSG00000166415 + - 13 15 51726881 51842367 coding intron AL158066.12-1 WDR72 51725879 51593230 - - 0.00378787878787901 51725950 51602812 - + Y - 7.35568168277224 N HCC1954 25 24.125 23 8 1 N - - N LINE Simple_repeat 1 0.0266666666666667 1 8 0.371370904316165 0.535631111994469 0.535631111994469 0.371370904316165 1 - 0 38189 Y Y 3.60930968391471 3.40740634961144 3.40740634961144 291 0 0.00322973155565165 Y 0 0 N N 0 44 ENSG00000214730 ENSG00000221899 - - 14 14 68398995 68332764 upstream upstream AL132986.4-1 C14orf181 68398203 68332264 + - 0.795576702793197 68377494 68364771 - + N - - N HCC1954 20 7.66666666666667 1 3 1 N - - Y SINE LINE,SINE 1 0.694736842105263 1 6 0.735600060472404 0.678466075192994 0.735600060472404 0.678466075192994 1 - - 36781 Y Y 3.43784458057793 3.58064844605001 3.43784458057793 0 0 0.687689448113875 Y 0 0.992215909090909 N N 3257 16989 ENSG00000072609 ENSG00000090615 + - 12 12 131974257 131915361 utr3p upstream CHFR GOLGA3 131927011 131855568 - - 0 131928178 131919897 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 0.342105263157895 0.342105263157895 7 0.892718519990782 0.785592297591888 0.892718519990782 0.785592297591888 1 - - 41643 N N 3.45248059180163 3.72655152083176 3.45248059180163 0 0 0.0721073829574324 Y 0 0 N N 0 0 ENSG00000210582 ENSG00000212407 + - 8 8 32992250 32888658 upstream upstream AC090204.11-5 U6 32992188 32888553 - - 0 33018715 32905303 - + N - - N HCC1954 1 1 1 0 1 N - - N LINE LTR 1 1 1 6 0.442788385915428 0.335662163516534 0.442788385915428 0.335662163516534 1 - - 15269 N N 2.80851194466297 2.89362312503792 2.80851194466297 7 0 0.130065677627208 N 0.481233465608466 0 N N 982 3405 ENSG00000162552 ENSG00000170632 + + 1 7 22342106 102527432 utr3p utr3p WNT4 ARMC10 22316385 102502564 - + 0.066220238095238 22318290 102527276 - + Y - - N HCC1954 990 859.5 720 4 1 N - - N Simple_repeat SINE 0.957446808510638 1 1 4 0.335662163516534 0.542772860154395 0.542772860154395 0.335662163516534 2 - - 7087 Y Y 3.35926336043241 3.41423242051993 3.35926336043241 287 0 0.318813756709391 Y 0.985126631650112 0.992563315825056 N N 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 intron utr3p VAMP5 VAMP8 85665042 85658227 + + 0 85672357 85662508 - + N 0.0482675112884658 2.7382370131711 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 16 0.99270299422975 0.971277749749971 0.99270299422975 0.971277749749971 2 0 0 34366 N Y 3.57336771439491 3.3420972013525 3.3420972013525 336 0.0310613682092554 0.72475620432947 Y 0.311913145539906 0 N N 12832 1085 ENSG00000181090 ENSG00000203993 - - 9 9 139850397 139633086 coding intron EHMT1 C9orf37 139711440 139629606 + - 0 139730899 139631816 - + N 0.208577179203304 1.12406979984539 N HCC1954 1 1 1 0 4 N - - N - SINE,LINE 0 0.921875 0.921875 6 0.964136001590045 0.914143764470561 0.964136001590045 0.914143764470561 4 0 0 17612 Y Y 3.64656650855576 3.57808779297027 3.57808779297027 265 0 0.0570488724699346 Y 0 0 N N 4504 2458 ENSG00000158711 ENSG00000158715 - + 1 1 203868623 203916253 utr5p coding ELK4 SLC45A3 203851860 203893604 - - 0 203859642 203895301 + - N - 1.2205393231485 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 5 0.985561246069823 0.671324327033068 0.985561246069823 0.671324327033068 2 - 0 24448 N Y 3.65384724021086 3.56232542602083 3.56232542602083 0 0 0.348806531702532 N 0 0 N N 497 18703 ENSG00000135205 ENSG00000046604 - + 7 18 76762457 27380754 intron downstream CCDC146 DSG2 76589870 27332170 + + 0 76705921 27381379 - + Y 0.688117577436621 - N HCC1954 31 14 4 6 1 N - - N SINE - 1 0 1 6 0.278528178237124 0.549914608314322 0.549914608314322 0.278528178237124 3 0 - 32991 N N 3.42680229220385 3.6581033104698 3.42680229220385 0 0.0638787646268942 0.99996415371951 N 0.0638787646268942 0.0638787646268942 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0638787646268942 8549 13735 - + N 0.660503713734304 1.04464883352071 N HCC1954 6 2.85714285714286 1 4 10 Y 189 4.09957 N - - 0 0 0 7 1.13553795742827 0.864151527351077 1.13553795742827 0.864151527351077 2 0 0 39810 Y Y 3.32001262460435 3.48656597878024 3.32001262460435 277 0 0.0218227331022153 Y 0.551244247251082 0.992393970292391 N N 10683 490 ENSG00000041357 ENSG00000188266 - + 15 15 76628615 76613067 upstream intron PSMA4 AC027228.16 76619802 76586961 + + 0 76616698 76606961 - + N - 4.18945407464974 N HCC1954 1 1 1 0 2 N - - Y LINE - 0.430656934306569 0 0.430656934306569 35 0.978419497909897 0.907002016310634 0.978419497909897 0.907002016310634 1 - 0 35186 N N 3.58743466416515 3.28126993978269 3.28126993978269 15 0 0.370373181885572 N 0.163992745535714 0.00390625 N N 10552 0 ENSG00000069431 ENSG00000219142 + - 12 7 21985603 17039627 utr3p upstream ABCC9 AC098592.8 21841590 17039238 - - 0.00390625 21843202 17061239 - + Y - - N HCC1954 23 22.25 22 4 1 N - - N LINE LINE 1 0.318181818181818 1 4 0.899860268150708 0.785592297591888 0.899860268150708 0.785592297591888 2 - - 38550 Y Y 3.26191384998362 3.48230056095149 3.26191384998362 0 0 0.266347553104706 Y 0 0 N N 5482 217 ENSG00000012983 ENSG00000100490 + - 14 14 50069126 49952929 coding intron MAP4K5 CDKL1 49954999 49866060 - - 0 49959608 49938415 - + N - 5.58321870701513 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.849868031031224 0.814159290231593 0.849868031031224 0.814159290231593 2 - 0 40080 Y N 3.50848272165904 3.59784511035345 3.50848272165904 0 0.0412893700787402 0.322466094698146 Y 0.115994094488189 0 N N 10683 490 ENSG00000041357 ENSG00000188266 - + 15 15 76628615 76613067 utr5p coding PSMA4 AC027228.16 76619802 76586961 + + 0 76619936 76606912 - + N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 5 0.93556900895034 0.721316564152552 0.93556900895034 0.721316564152552 2 - - 39801 N Y 2.89992840998224 3.20976656280103 2.89992840998224 0 0 0.674765088847904 Y 0.701127819548872 0.980075187969925 N N 6218 5437 ENSG00000215252 ENSG00000175265 + - 15 15 32662353 32487180 upstream upstream GOLGA8B GOLGA8A 32605150 32458557 - - 0 32663009 32487228 - + N - - N HCC1954 2 2 2 36 1 N - - N - - 0 0 0 36 0.471355378555133 0.771308801272036 0.771308801272036 0.471355378555133 4 - - 35130 N Y 3.41103992525442 3.63759035972147 3.41103992525442 0 0.125398550724638 0.655298017732265 N 0.835471014492754 0.835471014492754 N N 34637 0 ENSG00000197111 ENSG00000220595 + - 12 21 52159872 39465902 coding intron PCBP2 AF129408.11 52132161 39464926 + - 0.662282608695652 52142616 39465258 + + Y - 1 N HCC1954 2 1.23076923076923 1 3 2 N - - N - SINE 0 0.210144927536232 0.210144927536232 13 1.25694767614702 0.728458312312478 1.25694767614702 0.728458312312478 2 - 0 13553 N Y 3.5010341561346 3.67167574670007 3.5010341561346 0 0 0.314818655921868 N 0.912848605577689 0.900398406374502 N N 26452 24530 ENSG00000119139 ENSG00000186575 - + 9 22 71059938 28424583 coding utr3p TJP2 NF2 70956382 28329563 + + 0 71017284 28423698 - + Y - - N HCC1954 35 26.25 22 4 1 N - - N - SINE 0 1 1 4 0.499922371194838 0.314236919036755 0.499922371194838 0.314236919036755 3 - - 262 Y Y 3.63825270713077 3.77001428422878 3.63825270713077 278 0 0.0272312463135327 Y 0.379790045514609 0.989832623696961 N N 1873 5896 ENSG00000068971 ENSG00000110046 - - 11 11 64458523 64441298 upstream upstream PPP2R5B ATG2A 64448756 64418595 + - 0 64447054 64441791 - + N - - N HCC1954 4 1.33333333333333 1 1 2 N - - Y SINE SINE 1 0.488235294117647 1 9 0.792734045751814 0.807017542071667 0.807017542071667 0.792734045751814 1 - - 39995 N Y 3.59528445727371 3.5246463161926 3.5246463161926 0 0 0.430238238612043 N 0.874566629990243 0.960389462102182 N N 0 495 ENSG00000221593 ENSG00000187667 - + 15 15 28641387 20759858 upstream utr3p AC026150.7-5 WHAMML1 28641305 20739172 + - 0 28568761 20746156 - - N - - Y HCC1954 12 5.875 3 8 1 N - - N SINE - 1 0 1 8 0.999844742389676 0.928427260790413 0.999844742389676 0.928427260790413 1 - - 43258 N Y 3.57336771439491 3.16725297369057 3.16725297369057 277 0 0.0129588298071602 N 0.916967509025271 0.907741676694745 N N 3077 1260 ENSG00000075790 ENSG00000156398 - + 7 10 107058401 104488930 intron downstream BCAP29 SFXN2 107007946 104464288 + + 0.778580024067389 107056235 104493888 - + Y 20.257048780926 - N HCC1954 2 2 2 20 1 N - - N - Low_complexity 0 1 1 20 0.392796148795944 0.499922371194838 0.499922371194838 0.392796148795944 3 0 - 40694 N N 3.55913293075533 3.37808089400154 3.37808089400154 27 0 0.286100452067796 N 0.87144038756942 0.142935917129466 N N 102780 695 ENSG00000086758 ENSG00000149531 + + X 20 53730398 28265815 intron coding HUWE1 FRG1B 53575782 28225518 - + 0.142935917129466 53621254 28246382 - + Y 1.43353548951387 27.3202787919018 N HCC1954 40 31.25 22 4 1 N - - N Other - 1 0 1 4 0.714174815992626 0.699891319672773 0.714174815992626 0.699891319672773 2 0 0 46634 N Y 3.24575025545007 3.48639814491089 3.24575025545007 0 0.0944055944055943 0.0787501526865536 N 0.676573426573427 0.404895104895105 N N 5 0 ENSG00000169515 ENSG00000216027 + - 19 4 51607907 61212351 upstream downstream CCDC8 AC095061.3 51606291 61212262 - - 0.417832167832168 51625635 60902269 - + Y - - N HCC1954 49 15 2 15 1 N 460 17.2644 N SINE SINE,SINE 1 0.842105263157895 1 15 0.321378667196682 0.271386430077198 0.321378667196682 0.271386430077198 1 - - 47945 N N 3.54296933622177 3.59272380419397 3.54296933622177 0 0 0.999999774318627 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117944553 2608428 - + Y 1.04403290649618 - N HCC1954 2 1.12844036697248 1 14 12 N 282 1.61558 N - LINE 0 0.869565217391304 0.869565217391304 109 0.971277749749971 1.31408166142643 1.31408166142643 0.971277749749971 1 0 - 9543 Y Y 3.14528279764929 3.14471373619582 3.14471373619582 291 0 0.0361774598976002 Y 0 0.919197548063527 N N 70 117 ENSG00000184361 ENSG00000184922 + + 17 17 40695262 40680464 intron downstream C17orf46 FMNL1 40687543 40655075 - + 0 40689686 40681295 - + N 5.67082961641392 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.671324327033068 0.435646637755502 0.671324327033068 0.435646637755502 1 0 - 31193 Y N 3.68577320169385 3.55231620741665 3.55231620741665 8 0.011871386017172 0.442286936320113 Y 0.0262616085509024 0.00227790432801822 N N 13642 763 ENSG00000176945 ENSG00000205814 - + 3 3 196950210 196924416 intron coding MUC20 AC069513.28-3 196933424 196912000 + + 0.00227790432801822 196937085 196920485 - + N 1.58255410711322 3.35091050080189 N HCC1954 2 2 2 4 2 N - - Y - LINE 0 0.225806451612903 0.225806451612903 4 0.328520415356608 0.821301038391519 0.821301038391519 0.328520415356608 1 0 0 38319 N Y 3.3991324009798 3.28296535696188 3.28296535696188 6 0.0283919368119302 0.88175373800114 Y 0.0283919368119302 0 N N 4773 21399 ENSG00000151320 ENSG00000100852 - + 14 14 32372018 31698685 upstream coding AKAP6 ARHGAP5 31868274 31616246 + + 0.00369003690036918 31824918 31656240 - + N - - N HCC1954 2 1.44444444444444 1 4 2 N - - N LTR - 1 0 1 9 0.849868031031224 0.978419497909897 0.978419497909897 0.849868031031224 3 - - 48987 Y Y 3.29127915838687 3.66273010308932 3.29127915838687 259 0 0.072440641048919 Y 0.711643974801869 0.98689290794554 N N 1313 0 ENSG00000133835 ENSG00000202092 - + 5 5 118905923 118809427 intron upstream HSD17B4 5S_rRNA 118816122 118809310 + + 0 118819908 118784406 - + N 0.0421313910700705 - N HCC1954 2 1.14285714285714 1 2 2 N - - Y - LTR,LTR 0 1 1 14 0.45707188223528 1.05697872766909 1.05697872766909 0.45707188223528 1 0 - 36771 N N 3.36613351693357 3.52936639476796 3.36613351693357 2 0 0.797177547223441 N 0.0035460992907802 0 Y N 11392 2251 ENSG00000175203 ENSG00000123297 + + 12 12 56227245 56476784 coding intron DCTN2 TSFM 56210361 56462826 - + 0 56214502 56465662 - + N - 0.881451311801125 N HCC1954 20 2.46153846153846 1 1 3 N 463 0.0544881 N - SINE,DNA 0 0.81021897810219 0.81021897810219 13 0.778450549431962 0.871293275511003 0.871293275511003 0.778450549431962 1 - 0 37795 N N 1.89788596403008 3.22845095762097 1.89788596403008 0 0.0753631961259081 0.200807589573779 N 0.662151937046005 0 N N 0 4006 ENSG00000201027 ENSG00000090565 + + 14 16 89158304 512479 upstream utr3p 7SK RAB11FIP3 89158015 415669 + + 0.0931446731234867 89140352 512042 + + Y - 1.81181970709112 N HCC1954 2 1.6 1 3 1 N - - N Simple_repeat - 0.915254237288136 0 0.915254237288136 5 0.421363141435649 0.807017542071667 0.807017542071667 0.421363141435649 1 - 0 49232 Y N 3.12292497439301 3.35356364524965 3.12292497439301 0 0 0.185134192329854 Y 0 0 N N 25305 7 ENSG00000153113 ENSG00000175426 - - 5 5 96136143 95794708 coding downstream CAST PCSK1 96023533 95751875 + - 0 96037046 95741130 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.692749571512847 0.635615586233437 0.692749571512847 0.635615586233437 3 - - 33897 N Y 3.28871850530713 3.16414437390839 3.16414437390839 317 0 0.995123076230983 Y 0 0.870779296646805 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0.0585348755695759 9225 5379 - + N - - N HCC1954 4 2.46153846153846 2 13 9 N - - N - - 0 0 0 13 0.657040830713216 0.985561246069823 0.985561246069823 0.657040830713216 2 - - 35520 N Y 3.50165665075055 3.12804628055249 3.12804628055249 15 0 0.118950408039954 N 0.868432510885341 0 N N 1641 1649619 ENSG00000166130 ENSG00000141736 - - 12 17 97562863 35138441 utr3p coding AC013283.23-2 ERBB2 97531314 35104766 - + 0 97542855 35122227 + - Y - - N HCC1954 24 11.8571428571429 1 6 1 N 594 21.3156 N SINE - 1 0 1 7 0.264244681917271 0.39993789695587 0.39993789695587 0.264244681917271 2 - - 36562 Y Y 3.43614916339873 3.39015625214551 3.39015625214551 0 0 0.622065105968009 Y 0 0 N N 775 15643 ENSG00000155974 ENSG00000111530 - - 12 12 65359020 65994658 coding upstream GRIP1 CAND1 65029066 65949426 - + 0 65358898 65749099 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 22 1.04983697950916 1.3069399132665 1.3069399132665 1.04983697950916 2 - - 36570 Y Y 3.45976132345673 3.45976132345673 3.45976132345673 288 0 0.71904040295895 Y 0 0.990034722222222 N N 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 utr5p coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6321453 6328155 + - N - 0.93979898501643 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 6 0.942710757110266 0.692749571512847 0.942710757110266 0.692749571512847 1 - 0 9504 Y Y 3.66592259835483 3.46038381807268 3.46038381807268 257 0 0.260088051975292 Y 0.990137535154294 0.990137535154294 N N 830 7432 ENSG00000185158 ENSG00000178691 - + 17 17 27404630 27352162 upstream downstream LRRC37B SUZ12 27372156 27288185 + + 0 27371828 27359263 - + N - - N HCC1954 2 1.0625 1 1 4 N - - Y - Low_complexity 0 0.484076433121019 0.484076433121019 16 0.764167053112109 1.12125446110842 1.12125446110842 0.764167053112109 1 - - 36007 N Y 3.54872248456702 3.47552369040616 3.47552369040616 208 0.755029585798817 0.00486338664416242 N 0.938757396449704 0.908136094674556 N N 5950 0 ENSG00000028203 ENSG00000217548 - + 12 X 94219075 46201578 coding intron VEZT RP11-75A9.3 94135715 46198476 + - 0.387573964497041 94187958 46200790 - - Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.635615586233437 0.364229156156239 0.635615586233437 0.364229156156239 3 - 0 26937 Y Y 3.19334184844229 3.38656252929588 3.19334184844229 0 0 0.467692309708075 Y 0 0.990040322580645 N N 152 36764 ENSG00000196993 ENSG00000184110 - + 16 16 28691577 28654549 upstream utr3p AC145285.2-3 EIF3S8 28677526 28630283 + + 0 28671018 28654406 - + N - - N HCC1954 28 25 20 4 1 N - - Y SINE - 1 0 1 4 0.528489363834543 0.842726282871298 0.842726282871298 0.528489363834543 2 - - 2988 N Y 3.425274708894 3.38080938095063 3.38080938095063 0 0 0.0632343988260785 N 0 0.817714285714286 N N 2335 36582 ENSG00000174951 ENSG00000177600 - - 19 11 53948612 802876 utr3p upstream FUT1 RPLP2 53943080 799936 - + 0 53944263 799396 + - Y - - N HCC1954 35 26.4 23 5 1 N - - N SINE - 1 0 1 5 0.278528178237124 0.407079645115797 0.407079645115797 0.278528178237124 1 - - 44926 Y Y 3.47336426491055 3.56591914887046 3.47336426491055 0 0 0.420888593270119 Y 0.994549712582499 0.994549712582499 N N 2263 1060 ENSG00000155640 ENSG00000196233 - + 10 10 98735572 98708680 upstream coding C10orf12 LCOR 98731031 98582029 + + 0 98730539 98701942 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 74 1.47834186910473 1.37835739486577 1.47834186910473 1.37835739486577 1 - - 43020 N N 2.91088257007367 3.50678730447985 2.91088257007367 0 0.262792452830189 0.543277898250461 N 0.422188679245283 0 N N 2197 551733 ENSG00000184178 ENSG00000204628 + + 4 5 53926865 180603512 intron utr3p SCFD2 GNB2L1 53433910 180596536 - - 0 53614153 180596557 - - Y 0.464350773033795 - N HCC1954 20 8.30434782608696 1 20 1 N - - N SINE,SINE,LINE - 0.711111111111111 0 0.711111111111111 23 0.321378667196682 0.707033067832699 0.707033067832699 0.321378667196682 2 0 - 29172 Y Y 3.68887241100352 3.29703230673212 3.29703230673212 325 0 0.0672038800782008 Y 0 0.988671328671329 N N 446 3909 ENSG00000111837 ENSG00000137210 + + 6 6 10946714 10865200 coding intron MAK TMEM14B 10870942 10856024 - + 0 10878340 10856223 - + N 0.775347417866567 1.40063014543213 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 11 0.785592297591888 0.764167053112109 0.785592297591888 0.764167053112109 3 0 0 19592 N Y 3.73808832274579 3.0066299492991 3.0066299492991 0 0 0.986892485025994 N 0.917028985507246 0.963123993558776 N N 2418 0 ENSG00000142892 ENSG00000206696 + + 1 18 77457720 45272097 intron upstream PIGK SNORD58 77327254 45272032 - - 0.963123993558776 77367374 45272104 - - Y 0.349582486358079 - N HCC1954 6 2.91729323308271 2 133 3 N - - N - - 0 0 0 133 0.664182578873142 0.799875793911741 0.799875793911741 0.664182578873142 4 0 - 526 Y Y 3.27192306858781 3.36034051579497 3.27192306858781 334 0.00299401197604798 0.0199552154104621 Y 0.992978831070254 0.992978831070254 N N 7926 0 ENSG00000011405 ENSG00000213779 - - 11 11 17147930 17172431 utr5p downstream PIK3C2A RPL29P21 17064705 17171612 - + 0 17147928 17185970 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 125 1.36407389854591 1.04983697950916 1.36407389854591 1.04983697950916 1 - - 35010 N Y 3.43511609362884 3.38230645903694 3.38230645903694 0 0 0.567877144070206 N 0.768972176525284 0.993920320434876 N N 13649 0 ENSG00000148110 ENSG00000218062 + + 9 9 96263022 98721421 coding upstream HIATL1 RP11-330M2.3 96176654 98721031 + + 0 96240630 98720930 + + N - - Y HCC1954 4 2.56 2 50 1 N - - N - - 0 0 0 50 1.22838068350732 1.29265641694665 1.29265641694665 1.22838068350732 1 - - 17292 Y Y 3.71823771940677 3.31336373513502 3.31336373513502 0 0 0.984414325664633 Y 0 0 N N 2003 24302 ENSG00000160781 ENSG00000198952 - + 1 1 154484471 154519240 utr5p utr3p PAQR6 SMG5 154479831 154485641 - - 0 154484332 154485987 + - N - 0.500113444715525 N HCC1954 2 1.01098901098901 1 1 4 N - - Y - - 0 0 0 91 1.35693215038599 1.42120788382533 1.42120788382533 1.35693215038599 1 - 0 48010 N N 3.00397601026352 3.23896403733493 3.00397601026352 0 0 0.48220377610578 N 0 0 N N 249 15837 ENSG00000155897 ENSG00000145780 + + 8 5 132123854 114908490 upstream downstream ADCY8 FEM1C 131861736 114884507 - - 0 132526484 114883971 - - Y - - N HCC1954 1 1 1 0 1 N 390 12.8081 N LINE - 1 0 1 32 1.22123893534739 1.24980592798709 1.24980592798709 1.22123893534739 2 - - 359 Y Y 3.41576000382978 3.48958129260659 3.41576000382978 234 0 0.0858729839852197 Y 0.94025641025641 0.96017094017094 N N 0 3207 ENSG00000177236 ENSG00000177225 - - 11 11 770755 767487 downstream upstream AP006621.1 PDDC1 770117 757225 + - 0 773527 768216 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 5 0.785592297591888 0.707033067832699 0.785592297591888 0.707033067832699 1 - - 25888 N Y 3.40631984667906 3.50421730383029 3.40631984667906 0 0 0.0946058287587677 N 0.878872775214238 0.878872775214238 N N 14053 45068 ENSG00000172845 ENSG00000205336 - + 2 16 174538676 56256445 intron upstream SP3 GPR56 174481505 56220023 - + 0 174526733 56211295 + + Y 0.525350375921669 - N HCC1954 20 14.9705882352941 7 34 1 N - - N SINE - 1 0 1 34 0.349945659836387 0.592765097273879 0.592765097273879 0.349945659836387 0 0 - 30349 Y Y 3.76848670091893 3.23061038311659 3.23061038311659 309 0 0.0282104953795705 Y 0 0 N N 62436 145788 ENSG00000102225 ENSG00000130985 - + X X 46974336 46959470 upstream intron PCTK1 UBA1 46962576 46935204 + + 0 46961347 46949691 - + N - 0.849451945576968 N HCC1954 1 1 1 0 1 N - - Y LINE LINE,LINE 1 0.542372881355932 1 13 1.0069864905496 1.26408942430695 1.26408942430695 1.0069864905496 1 - 0 22081 N Y 3.41741556821562 3.5246463161926 3.41741556821562 0 0 0.714373066128845 N 0.973081952920663 0.959622929380994 N N 319 2833 ENSG00000166415 ENSG00000133019 - + 15 1 51842367 238139338 coding utr5p WDR72 CHRM3 51593230 237858996 - + 0 51602811 237859420 + + Y - - N HCC1954 24 22 18 6 2 N - - N - LINE 0 1 1 6 0.407079645115797 0.435646637755502 0.435646637755502 0.407079645115797 4 - - 6568 Y Y 3.59577897081367 3.54569782317086 3.54569782317086 8 0 0.345918597704834 Y 0 0 N N 71 1943 ENSG00000205011 ENSG00000162869 - + 2 2 48612560 48596029 utr5p coding AC073082.6 KLRAQ1 48610026 48521412 + + 0 48610125 48592000 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.5713398527941 0.792734045751814 0.792734045751814 0.5713398527941 1 - - 31364 N Y 3.23321088898968 3.6272104187567 3.23321088898968 346 0 0.00403731351343239 Y 0 0.992502933634665 N N 1246 1246 ENSG00000154743 ENSG00000154743 - + 3 3 12549811 12549811 downstream downstream TSEN2 TSEN2 12500942 12500942 + + 0 12561657 12558521 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.899860268150708 0.985561246069823 0.985561246069823 0.899860268150708 2 - - 18595 Y Y 3.7297745213208 3.40843941938133 3.40843941938133 243 0 0.303382410513598 Y 0.557384545038866 0.975410252502159 N N 0 2210 ENSG00000217453 ENSG00000188290 + - 1 1 933472 925333 intron upstream RP11-54O7.10 HES4 933317 924208 - - 0 933437 926506 - + N 1 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.264244681917271 0.385654400636018 0.385654400636018 0.264244681917271 4 0 - 31436 Y Y 3.38912318237562 3.55826769485478 3.38912318237562 241 0 0.181170594687598 Y 0 0.957921804687044 N N 3393 1246 ENSG00000075975 ENSG00000154743 - + 3 3 12600205 12549811 upstream downstream MKRN2 TSEN2 12573594 12500942 + + 0 12561746 12559728 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.557056356474248 0.471355378555133 0.557056356474248 0.471355378555133 4 - - 48962 Y Y 3.41592783769912 3.28606456627155 3.28606456627155 252 0 0.687083851370822 Y 0 0.989289981225465 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 utr3p utr3p TPPP CEP72 712978 665405 - + 0 716530 706272 - + N 0.799740819289583 3.58331468988003 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 18 1.04269523134923 0.956994253430118 1.04269523134923 0.956994253430118 0 0 0 46265 N Y 3.49272035470961 3.58743466416515 3.49272035470961 22 0.192452830188679 0.0415395688418356 N 0.755857832382624 0.774637999122422 N N 10567 153380 ENSG00000127526 ENSG00000185275 - + 19 Y 16544193 19614093 utr3p utr3p SLC35E1 CD24L4 16522661 19611898 - - 0 16523700 19612795 + - Y - - N HCC1954 39 22.2 5 5 1 N - - N SINE SINE 1 0.539325842696629 1 5 0.307095170876829 0.635615586233437 0.635615586233437 0.307095170876829 1 - - 7963 N N 3.72448538129198 3.62873800206655 3.62873800206655 0 0 0.540035340499229 N 0 0 N N 34197 1 ENSG00000138413 ENSG00000156234 + - 2 4 208828051 78752010 utr3p intron IDH1 CXCL13 208809199 78651930 - + 0 208809462 78688397 - - Y 0.404855183291088 0.941841680129241 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.299953422716903 0.278528178237124 0.299953422716903 0.278528178237124 1 0 0 46806 N N 3.56704550459619 3.23424395875957 3.23424395875957 0 0 0.800290566686355 N 0 0 Y N 10 42203 ENSG00000169169 ENSG00000170889 - + 19 19 54908800 59403327 downstream utr3p CPT1C RPS9 54886205 59396538 + + 0 54914511 59403296 - + N - 0.729311349232969 N HCC1954 2 1.28571428571429 1 4 1 N - - N - - 0 0 0 14 0.22853594111764 0.764167053112109 0.764167053112109 0.22853594111764 3 - 0 46890 Y Y 3.57080706131517 3.53974633573272 3.53974633573272 310 0 0.509765889311653 Y 0 0.992670777988615 N N 1118 889 ENSG00000167744 ENSG00000196337 + - 19 19 54258936 54253929 utr3p utr5p NTF4 CGB7 54256216 54249344 - - 0 54256234 54253416 - + N 0.753944796969624 1.79706875611166 N HCC1954 2 1.57692307692308 1 15 3 N - - Y - - 0 0 0 26 1.01412823870953 1.26408942430695 1.26408942430695 1.01412823870953 1 0 0 16069 N Y 3.4503745994685 3.64503892524591 3.4503745994685 8 0.00411522633744865 0.237848453033081 N 0.912860082304527 0.912860082304527 N N 3826 6406 ENSG00000160072 ENSG00000176407 + + 1 2 1421444 85140106 coding utr3p ATAD3B KCMF1 1397006 85051727 + + 0 1403887 85138987 + + Y - - N HCC1954 42 40 34 4 1 N - - N - SINE 0 1 1 4 0.699891319672773 0.278528178237124 0.699891319672773 0.278528178237124 1 - - 48 Y Y 3.02188845513875 3.30591516961058 3.02188845513875 395 0 0.443123809789151 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream intron TNNI2 SYT8 1816795 1809259 + + 0.978077618583948 1816179 1814954 - + N - 0.728108197200977 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.87843502367093 0.799875793911741 0.87843502367093 0.799875793911741 2 - 0 46714 Y Y 3.28292550416853 3.68953475841283 3.28292550416853 142 0 0.247350157895308 Y 0 0.985137869972173 N N 106 280 ENSG00000213793 ENSG00000183022 - + 19 19 58645397 58637941 upstream utr5p AC022137.6-2 AC022137.6-1 58644449 58627067 + + 0 58642273 58628785 - + N - - N HCC1954 2 2 2 4 3 N - - Y - LTR 0 0.222222222222222 0.222222222222222 4 0.335662163516534 0.257102933757345 0.335662163516534 0.257102933757345 0 - - 34007 N Y 3.46145674063593 3.07147508924161 3.07147508924161 0 0 0.131856201630712 N 0 0.750632911392405 N N 0 38784 ENSG00000200422 ENSG00000164985 - - X 9 86288463 15500989 downstream intron SNORD45 PSIP1 86288392 15454067 + - 0 86292811 15456227 - + Y - 0.157628140434753 N HCC1954 40 16.5714285714286 2 7 1 N - - N SINE SINE 0.182539682539683 0.950617283950617 0.950617283950617 7 0.892718519990782 0.914143764470561 0.914143764470561 0.892718519990782 2 - 0 4491 Y Y 3.5246463161926 3.68697410533309 3.5246463161926 0 0 0.874173092925198 Y 0 0.985853529032503 N N 8842 2897 ENSG00000006453 ENSG00000164713 + + 7 7 97868316 97758775 downstream coding BAIAP2L1 BRI3P1 97760007 97748923 - + 0 97759801 97749701 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.138686131386861 0.138686131386861 6 1.04269523134923 0.849868031031224 1.04269523134923 0.849868031031224 4 - - 34209 N N 3.26356941436947 3.58999531724489 3.26356941436947 0 0 0.0202012473251444 Y 0.953739786297926 0 N N 3461 0 ENSG00000196873 ENSG00000217091 - - 9 9 70104738 67904016 upstream intron CBWD3 RP11-764K9.2 70046662 67903302 + - 0.317661847894406 70036809 67903409 - + N - 1 N HCC1954 12 5.14285714285714 3 7 1 N 90 21.3585 N LTR - 1 0 1 7 0.742741808632331 0.907002016310634 0.907002016310634 0.742741808632331 1 - 0 41595 Y Y 3.33358506083463 3.54040868314203 3.33358506083463 348 0 0.00754265644903718 Y 0 0.96115091804747 N N 434 4746 ENSG00000213865 ENSG00000175073 - - 8 8 67935244 67742036 intron upstream C8orf44 VCPIP1 67751008 67703300 + - 0 67754399 67742450 - + N 1.68246101925237 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.928427260790413 0.771308801272036 0.928427260790413 0.771308801272036 2 0 - 7202 Y Y 3.05740813947137 3.3227106063299 3.05740813947137 333 0 0.0226825356428944 Y 0 0.987537537537537 N N 4489 2 ENSG00000082258 ENSG00000153086 - + 2 2 135431056 135376074 upstream intron CCNT2 ACMSD 135392863 135312587 + + 0 135392453 135351610 - + N - 1.15736505032022 N HCC1954 1 1 1 0 3 N - - Y - LTR,LTR 0 1 1 9 0.757025304952183 0.721316564152552 0.757025304952183 0.721316564152552 2 - 0 36357 Y Y 3.41216628098015 3.32886498225927 3.32886498225927 410 0 0.0205577770314151 Y 0.990074020143186 0.990074020143186 N N 0 4523 ENSG00000210846 ENSG00000070961 - - 12 12 88644930 88573975 upstream upstream AC009522.11 ATP2B1 88644842 88505959 + - 0 88626504 88574015 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 20 1.45691662462496 1.4140661356654 1.45691662462496 1.4140661356654 4 - - 34342 N Y 3.56488607910057 3.81298253408584 3.56488607910057 1 0 0.302254917602315 Y 0.979671868747499 0.969507803121249 N N 30 0 ENSG00000170215 ENSG00000216334 + + 9 9 67384009 46224504 downstream upstream FAM27B RP11-34H11.6 67382750 46224288 - + 0 67381275 46219531 - + N - - N HCC1954 32 20.3333333333333 14 6 1 N 219 17.9253 N Satellite SINE 1 1 1 6 0.964136001590045 0.678466075192994 0.964136001590045 0.678466075192994 4 - - 44598 N N 3.425274708894 3.21279122419719 3.21279122419719 0 0 0.1641148386154 N 0 0 N N 2552 3891 ENSG00000151012 ENSG00000166295 - + 4 10 139382953 73665622 utr3p intron SLC7A11 C10orf104 139304698 73645812 - + 0 139311138 73645955 + + Y - 0.744979490524871 N HCC1954 35 33.5 32 22 1 N - - N SINE - 1 0 1 22 0.28566992639705 0.764167053112109 0.764167053112109 0.28566992639705 1 - 0 32998 N Y 2.87060295437234 3.6491271616355 2.87060295437234 247 0 0.00210940075165711 Y 0 0.982828423844758 N N 339915 151141 ENSG00000198727 ENSG00000198888 - + MT MT 15882 4264 coding coding MT-CYB MT-ND1 14748 3308 + + 0 14764 4135 - + N 0.343791605542793 1.20290576650761 N HCC1954 6 2.16666666666667 1 3 1 N - - N - - 0 0 0 6 1.0069864905496 0.714174815992626 1.0069864905496 0.714174815992626 0 0 0 27415 N Y 3.02030743866642 3.60682125918775 3.02030743866642 0 0 0.940767593249107 Y 0 0.986968826990817 N N 4968 37 ENSG00000104731 ENSG00000154118 + + 16 16 86357056 86289263 coding downstream KLHDC4 JPH3 86298920 86194000 - + 0 86299457 86289569 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 11 1.02126998686945 1.13553795742827 1.13553795742827 1.02126998686945 4 - - 5288 N Y 3.40381262676181 3.79040344379773 3.40381262676181 0 0 0.7065647780029 N 0.437099073414113 0.913399857448325 N N 19481 2 ENSG00000198074 ENSG00000165246 + + 7 Y 133876693 15466924 downstream intron AKR1B10 NLGN4Y 133862884 15144026 + + 0 133884541 15435724 + + Y - 0.977354930020443 N HCC1954 20 18.5555555555556 7 9 1 N - - N LTR LTR 1 1 1 9 0.5713398527941 0.335662163516534 0.5713398527941 0.335662163516534 4 - 0 42427 Y Y 3.39011639935216 3.40319013214585 3.39011639935216 0 0 0.460610316350887 Y 0 0 N N 340 16036 ENSG00000188981 ENSG00000197386 - + 4 4 3243263 3215485 downstream coding C4orf44 HTT 3220565 3046206 + + 0 3249155 3197264 - + N - - N HCC1954 1 1 1 0 2 N - - Y DNA - 1 0 1 4 0.799875793911741 0.771308801272036 0.799875793911741 0.771308801272036 1 - - 39553 N N 3.44040523365767 3.59425138750382 3.44040523365767 5 0 0.0417120986858596 N 0 0 N N 975 1922 ENSG00000198487 ENSG00000180979 + + 6 15 42218335 40628292 coding utr3p AL512274.9 LRRC57 42183124 40622014 - - 0 42204405 40622804 - - Y 0.811586469073095 - N HCC1954 39 35.625 33 8 1 N - - N - SINE 0 1 1 8 0.5713398527941 0.45707188223528 0.5713398527941 0.45707188223528 1 0 - 29377 Y Y 3.45294460011805 3.53039946453785 3.45294460011805 119 0.00401606425702816 0.887340368983211 Y 0.00401606425702816 0.979464248747568 N N 871 5641 ENSG00000171462 ENSG00000124574 + + 6 6 43531764 43526142 intron coding EGFL9 ABCC10 43526068 43503270 - + 0 43527612 43525250 - + N 1.53632437823614 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.742741808632331 0.964136001590045 0.964136001590045 0.742741808632331 4 0 - 39723 N Y 3.43577844103815 3.5816815158199 3.43577844103815 0 0 0.0673833295767152 N 0.0037878787878789 0.889309764309764 N N 27074 2864 ENSG00000137804 ENSG00000165169 - + 15 X 39460535 37591775 coding coding NUSAP1 DYNLT3 39412361 37580954 + - 0 39451128 37581448 - - Y - - N HCC1954 24 22.2 20 10 1 N - - N - SINE 0 1 1 10 1.15696320190805 0.314236919036755 1.15696320190805 0.314236919036755 1 - - 33123 N N 3.14484171727181 3.779528989293 3.14484171727181 1 0 0.817202242324909 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 14052 15834 - + N 1.73382696856726 2.74556537998934 N HCC1954 2 1.16666666666667 1 1 4 N 189 4.09957 N - - 0 0 0 6 0.749883556792257 0.757025304952183 0.757025304952183 0.749883556792257 1 0 0 40767 N Y 3.43887765034782 3.74487454086093 3.43887765034782 9 0.0678312391459803 0.679007366705144 N 0.948922259679232 0.93615282459904 N N 1930 100806 ENSG00000101363 ENSG00000163931 - + 20 3 35379077 53265078 downstream coding MANBAL TKT 35351465 53234715 + - 0 35382246 53249307 - - Y - - N HCC1954 21 20.5 20 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.435646637755502 0.435646637755502 0.321378667196682 4 - - 14369 N Y 3.48081283043499 2.72192809488736 2.72192809488736 0 0.642045454545455 0.0145341566541926 N 0.642045454545455 0.552556818181818 N N 70 24595 ENSG00000170959 ENSG00000116977 - + 11 1 30910027 234779619 utr3p utr5p DCDC5 LGALS8 30841730 234748188 - + 0.642045454545455 30842152 234753881 + + Y - 0.128791315681044 N HCC1954 24 23.25 23 4 1 N - - N SINE - 1 0 1 4 0.378512652476092 0.499922371194838 0.499922371194838 0.378512652476092 1 - 0 34085 N Y 3.44768596531277 3.44040523365767 3.44040523365767 2 0 0.386383496376864 N 0 0.964874753729243 N N 22394 0 ENSG00000107036 ENSG00000216361 + + 9 X 5766555 78228024 coding upstream KIAA1432 RP11-180D15.1 5619120 78227089 + + 0 5703896 78169738 + + Y - - N HCC1954 20 20 20 6 1 N - - N - LINE 0 1 1 6 0.671324327033068 0.371370904316165 0.671324327033068 0.371370904316165 1 - - 659 Y Y 3.21079963257092 3.30591516961058 3.21079963257092 310 0.0248948106591868 0.0303197611640392 Y 0.942215988779804 0.992776998597476 N N 1289 36582 ENSG00000177595 ENSG00000177600 - - 11 11 795245 802876 utr5p upstream LRDD RPLP2 789180 799936 - + 0 795180 799414 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 19 1.20695543902754 0.964136001590045 1.20695543902754 0.964136001590045 2 - - 16472 N Y 3.45976132345673 3.43039601505348 3.43039601505348 40 0.839944379391101 0.318135055048188 N 0.822160421545667 0.839944379391101 N N 3364 52936 ENSG00000115946 ENSG00000179051 + - 2 1 68256593 17638807 utr3p upstream PNO1 RCC2 68238509 17605866 + - 0.839944379391101 68256032 17679096 + + Y 2.01142620673207 - N HCC1954 2 1.125 1 1 1 N - - N SINE SINE 0.426829268292683 1 1 8 0.585623349113953 0.264244681917271 0.585623349113953 0.264244681917271 2 0 - 30383 Y Y 3.18508148017979 3.73080759109069 3.18508148017979 289 0 0.108672902400395 Y 0.200577968744059 0.967147039811399 N N 0 0 ENSG00000188441 ENSG00000182707 - + X X 73168380 73013524 upstream downstream RP13-36G14.2 FXYD8 73168022 73011598 + + 0 73140723 73081224 - + N - - N HCC1954 1 1 1 0 4 N - - Y LINE - 1 0 1 8 0.699891319672773 0.628473838073511 0.699891319672773 0.628473838073511 1 - - 37546 N Y 3.07101108092519 3.63296356710195 3.07101108092519 0 0 0.48951728012968 N 0.632189151176493 0.892348044246778 N N 1649619 9718 ENSG00000141736 ENSG00000156030 - + 17 14 35138441 73323649 coding intron ERBB2 C14orf43 35104766 73251587 + - 0 35125066 73288230 - - Y - 3.20184287604971 N HCC1954 22 20.8260869565217 20 23 1 N - - N - SINE 0 1 1 23 0.742741808632331 0.378512652476092 0.742741808632331 0.378512652476092 1 - 0 34323 Y Y 3.15099609320118 3.58697065584872 3.15099609320118 144 0 0.991001129739305 Y 0 0.982878352490422 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5618853 5583478 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 6 0.628473838073511 0.564198104634174 0.628473838073511 0.564198104634174 2 - - 33117 N Y 3.56911164413597 3.43784458057793 3.43784458057793 402 0 0.000518852518269886 Y 0 0.994884551600969 N N 339915 38150 ENSG00000198727 ENSG00000198840 - + MT MT 15882 10405 coding coding MT-CYB MT-ND3 14748 10060 + + 0 15189 10327 - + N 0.839185107901018 19.3053162017179 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.849868031031224 0.678466075192994 0.849868031031224 0.678466075192994 1 0 0 11654 N N 3.61257440753299 3.48553290901035 3.48553290901035 1 0 0.149976008933811 N 0 0.0886755067825026 N N 79 20793 ENSG00000204118 ENSG00000141027 - - X 17 72264644 16059570 utr3p utr5p NAP1L6 NCOR1 72262601 15875443 - - 0 72263830 16038677 + + Y - - N HCC1954 48 34.4285714285714 21 7 1 N - - N SINE - 1 0 1 7 0.328520415356608 0.742741808632331 0.742741808632331 0.328520415356608 1 - - 45662 N N 3.19442835137467 2.8950896979007 2.8950896979007 0 0.45140995393776 0.0998325857726516 N 0.581339175373554 0.350353892821031 N N 65965 0 ENSG00000108107 ENSG00000217721 + - 19 X 60595261 136234874 utr3p intron RPL28 RP11-332E4.1 60589112 136234797 + - 0.350353892821031 60591520 136234815 + + Y - 1 N HCC1954 2 1.35714285714286 1 5 1 N - - N - Simple_repeat 0 0.0869565217391304 0.0869565217391304 14 0.728458312312478 0.821301038391519 0.821301038391519 0.728458312312478 1 - 0 45350 N N 3.64081336021051 3.39801962562321 3.39801962562321 0 0 0.0525420780565756 N 0 0.00273224043715847 N N 6215 551733 ENSG00000120029 ENSG00000204628 + + 10 5 103805940 180603512 intron coding C10orf76 GNB2L1 103595346 180596536 - - 0.00273224043715847 103756852 180597246 - - Y 0.980519543980865 0.534680688416546 N HCC1954 21 15 1 8 1 N - - N Low_complexity - 0.567567567567568 0 0.567567567567568 9 0.264244681917271 0.5713398527941 0.5713398527941 0.264244681917271 1 0 0 19999 N N 3.54975555433691 3.25935319690388 3.25935319690388 0 0 0.0629781565407459 N 0.151205673758865 0.0583687943262413 N N 1154 45068 ENSG00000180488 ENSG00000205336 - + 1 16 78116667 56256445 intron upstream FAM73A GPR56 78017897 56220023 + + 0.0583687943262413 78046169 56211247 - + Y 1.03972488563582 - N HCC1954 22 20.2222222222222 20 18 1 N - - N SINE - 1 0 1 18 0.328520415356608 0.592765097273879 0.592765097273879 0.328520415356608 2 0 - 9386 Y Y 2.92759830120629 3.50272957331379 2.92759830120629 165 0 0.0964373985764729 Y 0.987418488684311 0.987418488684311 N N 5891 10351 ENSG00000175832 ENSG00000067596 + + 17 17 38979288 38957206 intron coding ETV4 DHX8 38960738 38916860 - + 0 38977055 38955117 - + N 1.69988109296281 1.43529832012655 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 10 0.5713398527941 0.649899082553289 0.649899082553289 0.5713398527941 2 0 0 45730 N Y 3.46977054206091 3.63978029044062 3.46977054206091 1 0 0.412894922444119 N 0 0.883807588075881 N N 1148 6663 ENSG00000198521 ENSG00000163848 + - 19 3 21826670 126576888 utr3p intron ZNF43 ZNF148 21779594 126427205 - - 0 21780138 126515192 - + Y - 0.564982144679114 N HCC1954 21 20.5 19 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.464213630395207 0.464213630395207 0.328520415356608 1 - 0 34879 Y Y 3.40744620240479 3.33424740824393 3.33424740824393 0 0 0.74938427103183 Y 0.991835422693668 0.991835422693668 N Y 86 3018 ENSG00000213213 ENSG00000221865 - + 9 9 138822013 138807589 coding coding AL355987.31-3 KIAA1984 138810623 138805594 + + 0 138813375 138806631 - + N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.764167053112109 0.757025304952183 0.764167053112109 0.757025304952183 4 - - 18375 N Y 3.21079963257092 3.72874145155091 3.21079963257092 355 0 0.00544182132470894 Y 0 0 N N 18522 18522 ENSG00000179403 ENSG00000179403 - + 1 1 1366008 1366008 downstream downstream VWA1 VWA1 1360772 1360772 + + 0 1370370 1368094 - + N - - N HCC1954 2 1.22222222222222 1 2 1 N - - N - - 0 0 0 9 1.29265641694665 1.04983697950916 1.29265641694665 1.04983697950916 1 - - 30627 Y Y 3.67849247003875 3.37655331069169 3.37655331069169 244 0.0814499442941269 0.0820695377480152 Y 0.941986312271208 0.980662104090403 N N 1219 0 ENSG00000169239 ENSG00000200620 - + X X 15715669 15644390 utr5p downstream CA5B SNORA7 15666313 15644252 + + 0 15678015 15649636 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 16 0.99270299422975 0.771308801272036 0.99270299422975 0.771308801272036 4 - - 44372 N N 3.37758638046158 3.5465630590714 3.37758638046158 0 0 0.111579576453558 N 0 0 N N 18316 5424 ENSG00000215136 ENSG00000033170 - + 10 14 45259678 65279714 intron coding AL731567.6 FUT8 45189635 64947063 + + 0 45206607 65205790 - + Y - - N HCC1954 24 23.25 23 4 1 N - - N Other - 1 0 1 4 0.39993789695587 0.392796148795944 0.39993789695587 0.392796148795944 1 - - 15515 N Y 3.74337746277462 3.69106234172268 3.69106234172268 0 0.91461038961039 0.116162898216964 N 0.928841991341991 0.91461038961039 N N 0 179175 ENSG00000169549 ENSG00000163191 - + 7 1 5567212 150276135 intron coding AC006483.5 S100A11 5566900 150271606 + - 0.231493506493506 5567008 150272793 - - Y 1 - N HCC1954 3 1.83333333333333 1 3 1 N - - N - - 0 0 0 6 0.51420586751469 0.964136001590045 0.964136001590045 0.51420586751469 2 0 - 14080 Y Y 3.7297745213208 3.52936639476796 3.52936639476796 123 0 0.225596343518729 Y 0 0.982830459770115 N N 8351 35913 ENSG00000100138 ENSG00000196419 + + 22 22 40416454 40389998 coding downstream NHP2L1 XRCC6 40399886 40347241 - + 0 40401145 40393367 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 4 0.499922371194838 0.499922371194838 0.499922371194838 0.499922371194838 1 - - 46207 N N 3.82080182197087 3.707857778442 3.707857778442 0 0 0.620227012626412 N 0 0.762465932209896 N N 6819 7771 ENSG00000105612 ENSG00000165304 + + 19 9 12853335 36667678 utr3p coding DNASE2 MELK 12847023 36562873 - + 0 12847249 36589481 - + Y - - N HCC1954 27 24.8 21 5 1 N - - N SINE - 1 0 1 5 0.328520415356608 0.528489363834543 0.528489363834543 0.328520415356608 2 - - 31806 N Y 3.60426060610801 3.61041498203738 3.60426060610801 0 0 0.74637813731809 Y 0 0 N N 78 595 ENSG00000114013 ENSG00000145103 - - 3 3 123322672 123223720 coding downstream CD86 ILDR1 123256911 123188861 + - 0 123293138 123181206 - + N - - N HCC1954 7 2.27272727272727 1 3 1 N - - N - LTR 0 1 1 11 1.17838844638783 0.93556900895034 1.17838844638783 0.93556900895034 4 - - 45068 Y Y 3.56228557322748 3.58424216889964 3.56228557322748 101 0.0175862068965515 0.553500687976074 Y 0.0175862068965515 0.973448275862069 N N 13934 2859 ENSG00000067064 ENSG00000047056 - - 10 10 1085061 1168237 coding intron IDI1 WDR37 1075966 1085478 - + 0 1079333 1090108 + - N - 0.045224430150955 N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 4 0.642757334393363 0.428504889595575 0.642757334393363 0.428504889595575 4 - 0 41885 N N 3.54296933622177 3.71617157986699 3.54296933622177 0 0 0.887413678146543 N 0.0025252525252526 0 N Y 8537 19339 ENSG00000129292 ENSG00000177570 + - 8 8 133930234 119703365 coding intron PHF20L1 SAMD12 133856786 119270880 + - 0 133886167 119279152 + + N - 2.66256963008135 Y HCC1954 1 1 1 0 1 N 252 7.30508 N - - 0 0 0 221 1.51405060990437 1.38549914302569 1.51405060990437 1.38549914302569 4 - 0 22274 N N 2.89355276702103 2.56570462970653 2.56570462970653 0 0 0.853610477148688 N 0 0 N N 59828 1673 ENSG00000130702 ENSG00000198799 + + 20 1 60375763 113468865 intron upstream LAMA5 LRIG2 60317516 113417354 - + 0 60341382 113408573 - + Y 1.31407360942352 - N HCC1954 3 2.75 2 4 1 N 40 25.8336 N - Other 0 0.19047619047619 0.19047619047619 4 0.385654400636018 0.299953422716903 0.385654400636018 0.299953422716903 3 0 - 20242 N N 3.43209143223268 3.34103362635907 3.34103362635907 0 0 0.0886235812247573 N 0 0 N N 17725 0 ENSG00000153815 ENSG00000212678 - + 16 1 80302866 560165 downstream intron AC099524.5 RP5-857K21.11 80036395 559619 + + 0 80331739 560032 - + Y - 1 N HCC1954 4 3.66666666666667 2 6 1 N 149 12.7382 N SINE,LTR - 0.692307692307692 0 0.692307692307692 6 0.371370904316165 0.814159290231593 0.814159290231593 0.371370904316165 2 - 0 461 Y Y 3.23640338425519 3.67849247003875 3.23640338425519 0 0 0.194394406937125 Y 0.979919320291304 0.993306440097101 N N 7574 3741 ENSG00000162144 ENSG00000149476 + + 11 11 60886305 60872806 intron coding CYBASC3 DAK 60872856 60857230 - + 0 60876909 60870399 - + N 0.546697517214854 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.22123893534739 0.99270299422975 1.22123893534739 0.99270299422975 2 0 - 35487 N Y 3.54144175291192 3.29549537585246 3.29549537585246 30 0.161048689138577 0.49990875393013 N 0.161048689138577 0.947565543071161 N N 2550 7425 ENSG00000139719 ENSG00000068489 - + 12 17 121317021 54634706 utr3p utr3p VPS33A PRR11 121282049 54587883 - + 0 121282378 54633911 + + Y - 2.28419318010561 N HCC1954 36 33.8333333333333 31 6 1 N - - N SINE - 1 0 1 6 0.392796148795944 0.428504889595575 0.428504889595575 0.392796148795944 2 - 0 33369 N N 3.50848272165904 3.39124275507788 3.39124275507788 5 0 0.99999910388673 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8754 11906 - + N - 1.7738819756246 N HCC1954 6 3.2 2 5 12 N 189 4.09957 N - - 0 0 0 5 0.599906845433805 1.38549914302569 1.38549914302569 0.599906845433805 3 - 0 21402 N N 3.51782959285392 3.57592836747465 3.51782959285392 0 0 0.104033157895185 N 0.816851311953353 0 N N 100806 31125 ENSG00000163931 ENSG00000158769 - + 3 1 53265078 159275358 coding utr3p TKT F11R 53234715 159232609 - - 0 53249308 159233057 + - Y - - N HCC1954 40 29.3 23 10 1 N - - N - SINE 0 1 1 10 1.1426797055882 0.292811674556976 1.1426797055882 0.292811674556976 1 - - 36184 N N 3.31353688881791 3.73552766966605 3.31353688881791 0 0.215807826423867 0.0601197633967241 N 0.249903138318481 0.31809376210771 N N 16017 16989 ENSG00000018236 ENSG00000090615 - + 12 12 39750361 131915361 utr5p intron CNTN1 GOLGA3 39588423 131855568 + - 0.31809376210771 39588491 131908304 - - N 0.240322772101955 2.00781861281297 Y HCC1954 20 14.1428571428571 9 7 1 N 280 26.2126 N - SINE 0 1 1 7 0.528489363834543 0.407079645115797 0.528489363834543 0.407079645115797 2 0 0 3647 N Y 3.36720643949681 3.56591914887046 3.36720643949681 287 0 0.0400653114059628 Y 0 0 N N 83 2636 ENSG00000154645 ENSG00000154642 - - 21 21 18561561 18113574 utr5p upstream CHODL C21orf91 18195451 18083156 + - 0 18211409 18113803 - + N - - N HCC1954 1 1 1 0 2 N - - N LINE,LTR - 0.951219512195122 0 0.951219512195122 7 0.87843502367093 0.799875793911741 0.87843502367093 0.799875793911741 1 - - 41951 Y N 3.46551447180198 3.33370207893424 3.33370207893424 0 0.217769193626267 0.386464993280954 N 0.243843553838725 0.217769193626267 N N 5586 0 ENSG00000185728 ENSG00000221671 + + 8 8 64262863 64284308 coding downstream YTHDF3 AC011978.6-3 64243675 64284220 + + 0.217769193626267 64262836 64284836 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.542772860154395 0.692749571512847 0.692749571512847 0.542772860154395 2 - - 6874 Y Y 3.4780843434859 3.62977107183644 3.4780843434859 299 0 0.0110343870593272 Y 0.978794563438412 0.992931521146137 N N 7635 2458 ENSG00000151694 ENSG00000134330 + + 2 2 9613368 9546201 coding utr3p ADAM17 IAH1 9546864 9532116 - + 0 9552280 9545970 - + N 0.772101319123833 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.821301038391519 1.12125446110842 1.12125446110842 0.821301038391519 2 0 - 18388 Y Y 3.2216342342823 3.76848670091893 3.2216342342823 369 0.00271002710027091 0.00272206303060185 Y 0.988470636151448 0.994235318075724 N N 7607 2409 ENSG00000173171 ENSG00000169231 - - 1 1 153450246 153444314 coding intron MTX1 THBS3 153445114 153432005 + - 0 153445325 153442825 - + N 0.0274637114481205 12.8719813414322 N HCC1954 1 1 1 0 1 N - - Y Low_complexity,Low_complexity - 0.173913043478261 0 0.173913043478261 19 1.4140661356654 1.24266417982717 1.4140661356654 1.24266417982717 1 0 0 4987 Y Y 3.61207989399303 3.52105259334297 3.52105259334297 0 0 0.967018712124498 Y 0 0.981893939393939 N N 8965 4751 ENSG00000127359 ENSG00000006530 + + 7 7 141048422 141000678 coding coding KIAA1147 AGK 141002997 140901712 - + 0 141010441 140999152 - + N - 2.06123740379708 N HCC1954 2 1.3125 1 5 2 N - - Y - - 0 0 0 16 0.707033067832699 0.87843502367093 0.87843502367093 0.707033067832699 4 - 0 27101 N Y 3.56146019012029 3.19503726562149 3.19503726562149 0 0 0.057661034888185 N 0 0.854168437154755 N N 76 0 ENSG00000166676 ENSG00000221151 - - 16 16 10820122 88689322 utr3p upstream FAM18A AC133919.3-4 10768034 88689218 - - 0 10769908 88700673 + + N - - Y HCC1954 160 149.333333333333 140 18 1 N - - N SINE - 1 0 1 18 0.392796148795944 0.5713398527941 0.5713398527941 0.392796148795944 1 - - 6883 Y Y 3.37758638046158 3.24847874239916 3.24847874239916 0 0 0.762578317778476 Y 0.99344075007879 0.986881500157579 N N 5277 307 ENSG00000169756 ENSG00000214184 - - 2 2 108670134 108517107 coding upstream LIMS1 AC012487.12-1 108571199 108492643 + - 0 108642493 108517482 - + N 0.0120959472484257 - N HCC1954 3 2.25316455696203 1 99 1 N - - Y - Simple_repeat 0 0.131428571428571 0.131428571428571 158 1.1426797055882 1.24980592798709 1.24980592798709 1.1426797055882 4 0 - 37092 N N 3.4561676006071 3.57014471390586 3.4561676006071 9 0 0.745438211158454 N 0.143632336655592 0.143632336655592 N N 234233 6175 ENSG00000150991 ENSG00000221983 + + 12 19 123965530 18546960 coding coding UBC UBA52 123962147 18545111 - + 0.143632336655592 123962968 18546681 - + Y 0.702556747683589 - N HCC1954 5 4.14285714285714 1 12 2 N - - N - - 0 0 0 14 0.771308801272036 0.271386430077198 0.771308801272036 0.271386430077198 1 0 - 39790 Y Y 3.76848670091893 3.15103594599453 3.15103594599453 298 0 0.00327077056813518 Y 0 0 N N 64858 468 ENSG00000140575 ENSG00000196391 - + 15 15 88846479 88706833 upstream downstream IQGAP1 ZNF774 88732477 88696481 + + 0 88719733 88706960 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR SINE 1 0.478260869565217 1 5 0.849868031031224 0.492780623034912 0.849868031031224 0.492780623034912 2 - - 3428 N Y 3.36720643949681 3.75847748231475 3.36720643949681 0 0.00334448160535106 0.584617153856949 Y 0.00334448160535106 0 N N 83 2636 ENSG00000154645 ENSG00000154642 - - 21 21 18561561 18113574 utr5p downstream CHODL C21orf91 18195451 18083156 + - 0 18211409 18050978 - + N 0.329893616004435 - N HCC1954 22 6.71428571428571 1 6 2 N - - N LTR SINE,LTR 1 0.510489510489511 1 7 0.949852505270192 1.0069864905496 1.0069864905496 0.949852505270192 1 0 - 43582 N N 3.59169073442408 3.44719145177281 3.44719145177281 1 0 0.354312297747216 N 0 0 N N 0 82714 ENSG00000216879 ENSG00000108518 + + 10 17 104595220 4792570 intron coding RP11-753C18.4 PFN1 104587758 4789697 - - 0 104594916 4790729 - - Y 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.235677689277566 0.45707188223528 0.45707188223528 0.235677689277566 2 0 - 18456 Y Y 3.32527125940964 3.7297745213208 3.32527125940964 296 0 0.0266722603758998 Y 0.970470470470471 0.992617617617618 N N 10984 0 ENSG00000136631 ENSG00000219469 - + 1 1 148384129 148293640 upstream intron VPS45 RP11-458I7.1 148305966 148292470 + + 0 148305653 148293248 - + N - 1 N HCC1954 12 3.42857142857143 1 4 3 N - - Y - SINE 0 0.864661654135338 0.864661654135338 7 0.799875793911741 0.785592297591888 0.799875793911741 0.785592297591888 1 - 0 33105 N N 2.96319769112561 3.11700399217841 2.96319769112561 15 0 0.99930094004897 N 0.0137094747423977 0.0194772555918573 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0.0194772555918573 8593 15716 - + N 0.65879648337433 2.17658419381783 N HCC1954 2 1.66666666666667 1 4 8 N 189 4.09957 N - - 0 0 0 6 1.13553795742827 0.871293275511003 1.13553795742827 0.871293275511003 2 0 0 22409 N Y 3.30640968315054 3.61104682422314 3.30640968315054 0 0 0.119147644571951 N 0.889342403628118 0.875510204081633 N N 86504 5168 ENSG00000104408 ENSG00000121644 + + 8 1 109330135 242938958 coding intron EIF3E PPPDE1 109283149 242883026 - + 0 109316403 242902089 - + Y - 0.58168355207164 N HCC1954 40 11.75 1 2 1 N - - N - SINE 0 1 1 4 0.685607823352921 0.378512652476092 0.685607823352921 0.378512652476092 4 - 0 42963 N N 3.49272035470961 3.21693737543163 3.21693737543163 0 0 0.149288495157681 N 0.00666666666666693 0.00666666666666693 N N 551733 2760 ENSG00000204628 ENSG00000052795 + + 5 4 180603512 160047402 intron intron GNB2L1 FNIP2 180596536 159909632 - + 0.00666666666666693 180597211 160013333 - + Y 0.613203140099103 1.47075163939798 N HCC1954 19 14.875 1 7 1 N - - N - Low_complexity 0 0.638888888888889 0.638888888888889 8 0.542772860154395 0.257102933757345 0.542772860154395 0.257102933757345 3 0 0 19606 N N 3.71873223294673 3.35772223965613 3.35772223965613 0 0 0.445376587626683 N 0.631959003028185 0 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0 109336417 45272185 - - Y - - N HCC1954 6 4.90243902439024 4 41 2 N - - N - - 0 0 0 41 0.485638874874985 0.707033067832699 0.707033067832699 0.485638874874985 1 - - 5327 N N 3.4583056705169 3.31844518850115 3.31844518850115 0 0 0.0461608533319714 N 0.210666666666667 0.26 N N 4653 17694 ENSG00000137364 ENSG00000153827 - + 6 2 18263353 230494912 utr3p upstream TPMT TRIP12 18236526 230340174 - - 0.26 18238382 230494919 + - Y - - N HCC1954 22 21 20 4 1 N - - N SINE Low_complexity 1 0.430769230769231 1 4 0.34280391167646 0.464213630395207 0.464213630395207 0.34280391167646 1 - - 532 Y Y 3.47080361183081 3.30856910864616 3.30856910864616 362 0 0.0126301182244735 Y 0.656507059545734 0.994459791282996 N N 4244 10409 ENSG00000177685 ENSG00000177666 - + 11 11 821985 815216 utr5p downstream EFCAB4A PNPLA2 817618 808902 + + 0.994459791282996 817710 816264 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 396 1.3069399132665 1.37835739486577 1.37835739486577 1.3069399132665 1 - - 28479 N N 3.61360747730288 3.4561676006071 3.4561676006071 0 0 0.046319125764995 N 0 0.0324263038548752 N N 3 45068 ENSG00000163071 ENSG00000205336 - + 4 16 52658212 56256445 upstream upstream SPATA18 GPR56 52612350 56220023 + + 0.0324263038548752 52606644 56211191 - + Y - - N HCC1954 21 20.25 20 4 1 N 614 29.1677 N SINE - 1 0 1 4 0.292811674556976 0.907002016310634 0.907002016310634 0.292811674556976 1 - - 19709 N N 3.0971949539571 2.74296946645728 2.74296946645728 7 0 0.0314973748494344 N 0.182518115942029 0.182518115942029 N N 412 45068 ENSG00000158859 ENSG00000205336 - + 1 16 159435469 56256445 utr3p upstream ADAMTS4 GPR56 159426163 56220023 - + 0.182518115942029 159426804 56211502 + + Y - - N HCC1954 28 22.0833333333333 21 12 1 N - - N SINE - 1 0 1 12 0.407079645115797 0.464213630395207 0.464213630395207 0.407079645115797 1 - - 55 Y Y 3.42680229220385 3.31951811106439 3.31951811106439 371 0 0.0299020817225283 N 0 0.978081217973401 Y N 57665 0 ENSG00000166441 ENSG00000200983 - + 11 11 8667978 8662479 utr5p upstream RPL27A SNORA3 8660571 8662350 + + 0 8660724 8658186 - + N 0.00201727914135246 - N HCC1954 1 1 1 0 1 N - - N - SINE 0 0.819548872180451 0.819548872180451 15 0.678466075192994 1.23552243166724 1.23552243166724 0.678466075192994 4 0 - 41021 Y Y 3.42424163912411 3.59272380419397 3.42424163912411 2 0.00346020761245669 0.510408438042001 Y 0.992334309289326 0.992334309289326 N N 9100 14855 ENSG00000125977 ENSG00000125970 + + 20 20 32163746 32131697 downstream utr3p EIF2S2 RALY 32139776 32045146 - + 0 32136129 32131377 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR - 1 0 1 14 0.964136001590045 1.09982921662864 1.09982921662864 0.964136001590045 3 - - 40299 N Y 3.24255776018456 3.11910063694173 3.11910063694173 124 0 0.15292828169172 N 0.891749821810406 0.913399857448325 N N 5067 0 ENSG00000138767 ENSG00000166466 - + 4 15 78959574 54086651 coding upstream CNOT6L AC039057.8-2 78853565 54085203 - - 0 78916569 54086661 + - Y - - N HCC1954 1 1 1 0 1 N 514 19.5632 N - - 0 0 0 11 0.435646637755502 0.292811674556976 0.435646637755502 0.292811674556976 2 - - 38867 N N 3.30847582269032 3.39020968530799 3.30847582269032 9 0 0.533515255046918 N 0 0 N N 12188 5424 ENSG00000168724 ENSG00000033170 - + 5 14 34994825 65279714 utr3p utr5p DNAJA5 FUT8 34965455 64947063 + + 0.0317113538563389 34991585 64992189 - + Y - - N HCC1954 33 25.75 23 4 1 N - - N SINE - 1 0 1 4 0.614190341753658 0.614190341753658 0.614190341753658 0.614190341753658 4 - - 13640 Y Y 3.35356364524965 3.27658036643087 3.27658036643087 347 0 0.0438129661317943 Y 0 0 N N 51 14981 ENSG00000182057 ENSG00000100207 - - 22 22 41000811 40941389 upstream utr5p Z83851.17 TCF20 40995703 40885963 + - 0 40994264 40941292 - + N - 82.384087295852 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 24 1.35693215038599 1.10697096478857 1.35693215038599 1.10697096478857 1 - 0 8801 N Y 3.58333708020574 3.51104337473878 3.51104337473878 0 0 0.906819299339361 N 0 0.925884844206917 N N 12320 1992 ENSG00000108587 ENSG00000003436 - - 17 2 25877957 188127464 utr3p utr5p GOSR1 TFPI 25828552 188037202 + - 0.925884844206917 25874014 188127365 - + Y - 19.2820371887542 N HCC1954 24 21.6153846153846 15 26 2 N - - N Other - 1 0 1 26 0.685607823352921 0.707033067832699 0.707033067832699 0.685607823352921 3 - 0 34579 Y Y 3.64400585547602 3.44722195699634 3.44722195699634 96 0.125206854214488 0.553955060870334 Y 0.125206854214488 0 N Y 497 13366 ENSG00000198113 ENSG00000188986 - + 9 9 139296913 139287819 utr5p coding C9orf167 COBRA1 139292099 139269580 + + 0 139292926 139286888 - + N 0.115268076815112 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.835584534711372 0.735600060472404 0.835584534711372 0.735600060472404 4 0 - 42476 Y Y 3.68321254861411 3.48271113610543 3.48271113610543 121 0 0.156603984750056 Y 0.970694799658994 0.990231599886331 N N 735 2970 ENSG00000198515 ENSG00000163293 - - 4 4 47678276 47736947 utr5p upstream CNGA1 NPAL1 47632753 47713548 - + 0 47678276 47707570 + - N - - N HCC1954 3 1.26315789473684 1 3 2 N - - Y - LTR 0 1 1 19 1.17124669822791 0.778450549431962 1.17124669822791 0.778450549431962 1 - - 42074 N N 3.28552601004162 3.164599034655 3.164599034655 3 0.00259740259740271 0.750688108846091 N 0.00259740259740271 0.00259740259740271 N N 29840 61 ENSG00000164830 ENSG00000038295 + + 8 4 107834093 167244443 coding upstream OXR1 TLL1 107739270 167013860 + + 0 107827247 166927345 + + Y - - N HCC1954 2 1.2 1 1 4 N - - N - LTR 0 1 1 5 1.01412823870953 0.757025304952183 1.01412823870953 0.757025304952183 0 - - 39844 Y Y 3.47080361183081 3.65657572715995 3.47080361183081 224 0 0.753933237154203 Y 0.990334604715673 0.980669209431345 N N 524 1874 ENSG00000203289 ENSG00000187951 - + 15 15 28848794 28765101 upstream intron AC004460.1-2 ARHGAP11B 28795810 28705695 + + 0 28795715 28738339 - + N - 55.9434610091418 N HCC1954 2 1.8 1 4 3 N - - Y - - 0 0 0 5 0.678466075192994 0.407079645115797 0.678466075192994 0.407079645115797 4 - 0 24356 N Y 3.67423639977982 3.44611852920956 3.44611852920956 0 0 0.52848287042605 N 0 0.853035348360656 N N 1384 3202 ENSG00000124787 ENSG00000172175 - + 6 18 4949270 54568350 coding intron RPP40 MALT1 4940280 54489598 - + 0 4949192 54555385 + + Y 0.373945221181076 1.55790607106224 N HCC1954 4 2.5 1 2 1 N - - N Low_complexity SINE 0.245614035087719 1 1 4 0.407079645115797 0.271386430077198 0.407079645115797 0.271386430077198 3 0 0 45156 N Y 3.05063126892605 3.36079094374226 3.05063126892605 0 0 0.300286957681150 N 0.988685344827586 0.943426724137931 N N 963 0 ENSG00000215033 ENSG00000215065 + + 10 10 47240877 46676017 utr5p intron AL603965.10-2 AL391137.11-1 47216968 46511545 + + 0 47239079 46559999 + + N - 1 Y HCC1954 2 1.875 1 7 2 N - - N - LINE 0 1 1 8 0.614190341753658 0.835584534711372 0.835584534711372 0.614190341753658 1 - 0 18348 N Y 3.65128658713112 3.43887765034782 3.43887765034782 245 0 0.0169834601027257 Y 0 0 N N 97 8 ENSG00000162543 ENSG00000158786 - + 1 1 20395126 20349466 upstream downstream UBXN10 PLA2G2F 20385168 20338406 + + 0 20382300 20353666 - + N - - N HCC1954 10 6.2 1 4 1 N - - N SINE LTR 1 1 1 5 0.557056356474248 0.557056356474248 0.557056356474248 0.557056356474248 1 - - 12109 N Y 3.50575423470996 2.83086705257414 2.83086705257414 10 0 0.0483179870190082 N 0.908391608391608 0.908391608391608 N N 19569 1722 ENSG00000088812 ENSG00000141376 + + 20 17 3579760 56824973 coding intron ATRN BCAS3 3399676 56109998 + + 0.0839160839160837 3532863 56368180 + + Y - 1.28108526101337 N HCC1954 20 19.8 18 10 1 N - - N - LINE 0 1 1 10 0.485638874874985 0.292811674556976 0.485638874874985 0.292811674556976 3 - 0 49000 N N 3.6272104187567 3.41848849077886 3.41848849077886 0 0 0.704374725079138 Y 0 0 N N 0 0 ENSG00000208861 ENSG00000211253 - - 5 5 134287711 93930996 intron intron AC008670.6-1 AC093311.2-1 134287643 93930928 + - 0 134287673 93930981 - + N 1 1 N HCC1954 2 2 2 5 1 N - - N - - 0 0 0 5 0.392796148795944 0.264244681917271 0.392796148795944 0.264244681917271 2 0 0 6969 Y Y 3.41848849077886 3.42001607408871 3.41848849077886 442 0 0.0826517969697923 Y 0 0.994720965309201 N Y 120 38670 ENSG00000163009 ENSG00000171848 - + 2 2 10269307 10188996 intron coding C2orf48 RRM2 10198960 10179906 + + 0 10199432 10186732 - + N 0.165284240996385 2.04382325431415 N HCC1954 2 1.57142857142857 1 12 2 Y - - Y LINE - 1 0 1 21 0.999844742389676 1.07840397214886 1.07840397214886 0.999844742389676 4 0 0 19500 N Y 3.61360747730288 3.41848849077886 3.41848849077886 0 0 0.0453574847194818 N 0 0 Y N 49089 4269 ENSG00000117450 ENSG00000196182 - + 1 1 45760196 36624084 coding intron PRDX1 STK40 45749295 36577812 - - 0 45757256 36595879 + - N - 1.12775303033213 N HCC1954 40 19.5 1 23 1 N - - N - SINE,SINE 0 1 1 24 1.06412047582901 0.428504889595575 1.06412047582901 0.428504889595575 1 - 0 36656 Y Y 3.18143432416767 3.58271458558979 3.18143432416767 0 0 0.858133015044625 Y 0.0946348733233977 0 N N 27079 1803 ENSG00000111341 ENSG00000139055 - + 12 12 14930025 14982750 utr5p downstream MGP ERP27 14925119 14958241 - - 0 14930024 14949361 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 19 1.05697872766909 0.635615586233437 1.05697872766909 0.635615586233437 4 - - 27399 Y Y 3.74913061111987 3.41848849077886 3.41848849077886 2 0.00338983050847463 0.918333688370365 Y 0.00338983050847463 0.989397764154346 N N 1864 6656 ENSG00000154102 ENSG00000131153 + - 16 16 84342190 84280089 coding upstream C16orf74 GINS2 84298624 84268782 - - 0 84326299 84287212 - + N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity,Low_complexity LINE 0.327731092436975 0.841726618705036 0.841726618705036 5 0.864151527351077 0.942710757110266 0.942710757110266 0.864151527351077 2 - - 4434 Y Y 3.56335849579072 3.61360747730288 3.56335849579072 238 0 0.0450500531281179 Y 0.989292491190024 0.989292491190024 N N 0 6389 ENSG00000210544 ENSG00000006451 - + 7 7 39774568 39714240 upstream downstream AC004987.2-1 RALA 39774466 39629687 + + 0 39773526 39740166 - + N - - N HCC1954 4 2.4 1 3 2 N - - Y - LTR 0 1 1 5 0.578481600954027 1.07126222398894 1.07126222398894 0.578481600954027 3 - - 28193 N Y 3.44296588673741 3.51161702706855 3.44296588673741 8 0.112213950923628 0.0261394409621577 N 0.289771160738903 0.847808105872622 N N 13096 5375 ENSG00000166164 ENSG00000119397 + + 16 9 48960346 122979709 utr3p intron BRD7 CEP110 48910442 122876962 - + 0.0868486352357321 48940463 122903924 - + Y - 0.133353547056288 N HCC1954 640 625 620 4 1 N - - N LINE LINE 1 1 1 4 0.292811674556976 0.335662163516534 0.335662163516534 0.292811674556976 3 - 0 13840 Y Y 3.5555392079057 2.47598092998937 2.47598092998937 345 0 0.00544632571970971 Y 0 0.991958859280038 N N 11861 4829 ENSG00000100241 ENSG00000100239 + + 22 22 49260330 49230380 utr3p utr3p SBF1 SAPS2 49232050 49128599 - + 0 49232378 49229848 - + N 0.556049548038659 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.621332089913584 0.307095170876829 0.621332089913584 0.307095170876829 1 0 - 31550 Y N 3.35719722089263 2.96997456167094 2.96997456167094 2 0 0.441592126784446 Y 0 0 N N 13642 763 ENSG00000176945 ENSG00000205814 - + 3 3 196950210 196924416 coding utr3p MUC20 AC069513.28-3 196933424 196912000 + + 0 196937296 196924219 - + N 2.0530091433887 - N HCC1954 2 2 2 7 2 N - - Y - - 0 0 0 7 0.828442786551446 0.735600060472404 0.828442786551446 0.735600060472404 1 0 - 10044 N Y 3.66848325143457 3.64549358599252 3.64549358599252 0 0.00258397932816545 0.987569844921304 Y 0.00258397932816545 0.994549639231302 N Y 18240 62029 ENSG00000062716 ENSG00000141367 - + 17 17 55273235 55129099 coding coding TMEM49 CLTC 55139811 55051832 + + 0 55270438 55115899 - + N - - N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 313 1.3069399132665 1.48548361726466 1.48548361726466 1.3069399132665 4 - - 21564 N Y 3.15319537149015 2.81726411112032 2.81726411112032 151 0.0545263434502693 0.0461689938268857 N 0 0.831165418473262 N N 12076 9363 ENSG00000148219 ENSG00000116288 + + 9 1 119217138 7967928 utr3p upstream ASTN2 PARK7 118227328 7944348 - + 0.898699251083958 118415122 7936217 - + Y - - N HCC1954 441 388.5 42 8 1 N - - N LINE Other,Other,SINE 1 0.762589928057554 1 8 0.45707188223528 0.864151527351077 0.864151527351077 0.45707188223528 2 - - 649 Y Y 3.75016368088976 2.91248470129703 2.91248470129703 253 0.0587808681147334 0.0981192540062698 Y 0.917757551582841 0.981723900351743 N N 175 7069 ENSG00000149489 ENSG00000149499 - - 11 11 62139162 62136813 coding intron ROM1 EML3 62137199 62126267 + - 0 62138306 62136146 - + N - 3.57837221730661 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 0.857009779191151 0.807017542071667 0.857009779191151 0.807017542071667 4 - 0 40222 N Y 3.37808089400154 3.58589773328548 3.37808089400154 0 0 0.179447272962982 N 0.958942961328951 0.948678701661189 N N 695 11928 ENSG00000149531 ENSG00000140350 + - 20 15 28265815 66900277 coding upstream FRG1B ANP32A 28225518 66845404 + - 0 28246382 66940454 + + Y - - N HCC1954 66 44.25 23 4 1 N - - N - Other 0 1 1 4 0.557056356474248 0.492780623034912 0.557056356474248 0.492780623034912 2 - - 24428 N Y 3.60888739872753 3.68953475841283 3.60888739872753 0 0 0.521649068581122 N 0.627763579570809 0.768609792706178 N N 394 18920 ENSG00000141391 ENSG00000082781 + - 18 3 12422234 126088834 intron coding C18orf43 ITGB5 12397928 125964488 + - 0 12412500 126075068 + + Y 0.816758179032298 6.89825995473092 N HCC1954 21 20.25 20 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.499922371194838 0.499922371194838 0.28566992639705 2 0 0 21602 N N 3.37023110089298 3.60682125918775 3.37023110089298 6 0 0.0457622366434451 N 0 0 N N 0 33725 ENSG00000210611 ENSG00000143819 - + 9 1 32059981 224099884 downstream intron AL589825.8 EPHX1 32059823 224064459 + + 0 32154163 224064941 - + Y - 1.40231215390162 N HCC1954 1 1 1 0 1 N - - N LTR - 1 0 1 9 0.292811674556976 0.371370904316165 0.371370904316165 0.292811674556976 1 - 0 41176 Y Y 3.41679307359967 3.36720643949681 3.36720643949681 174 0 0.0774866024263868 Y 0 0.988677685950413 N N 54 16 ENSG00000213714 ENSG00000124103 - + 20 20 54544983 54534605 coding downstream C20orf107 C20orf106 54541709 54532955 + + 0 54541882 54535664 - + N - - N HCC1954 2 1.27272727272727 1 3 1 Y - - Y - LINE 0 1 1 11 0.971277749749971 0.664182578873142 0.971277749749971 0.664182578873142 2 - - 13703 Y Y 3.41741556821562 3.38486711211668 3.38486711211668 225 0 0.423845866387655 Y 0 0.990607966457023 N N 3693 721 ENSG00000198125 ENSG00000100302 + + 22 22 34349347 34279987 downstream downstream MB RASD2 34332757 34267296 - + 0 34306895 34289786 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE - 0.761904761904762 0 0.761904761904762 5 0.749883556792257 0.707033067832699 0.749883556792257 0.707033067832699 2 - - 31494 Y Y 3.46128890676658 3.44143830342756 3.44143830342756 322 0 0.120166082043593 Y 0.987460447673737 0.987460447673737 N N 763 0 ENSG00000205814 ENSG00000207650 - + 3 3 196924416 196911548 utr5p upstream AC069513.28-3 hsa-mir-570 196912000 196911452 + + 0 196913431 196911258 - + N 4.06649424145051 - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 0.168918918918919 0.168918918918919 5 0.614190341753658 0.864151527351077 0.864151527351077 0.614190341753658 4 0 - 29282 Y Y 3.71361092678725 3.56977399154528 3.56977399154528 231 0 0.0956605534928202 Y 0 0.988003963907578 N N 0 4158 ENSG00000208766 ENSG00000111885 - - 6 6 120625246 119712625 upstream upstream AL606830.4 MAN1A1 120625131 119540968 + - 0 120172996 120090889 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 6 0.542772860154395 0.607048593593732 0.607048593593732 0.542772860154395 1 - - 22403 N N 3.67593181695901 3.34681727992786 3.34681727992786 0 0 0.101775335568294 N 0 0 N N 46806 13674 ENSG00000164733 ENSG00000054523 + + 8 1 11763055 10364248 coding intron CTSB KIF1B 11737442 10193418 - + 0 11748353 10226000 - + Y - 0.495535511315607 N HCC1954 2 1.5 1 2 1 N - - N - SINE 0 1 1 4 0.28566992639705 0.221394192957714 0.28566992639705 0.221394192957714 2 - 0 46952 Y Y 3.48639814491089 3.49168728493972 3.48639814491089 335 0 0.0518247966634551 Y 0.0156859017016827 0.980948759387775 N N 1074 610 ENSG00000197608 ENSG00000221897 + - 19 19 57290830 57243918 coding utr5p ZNF841 ZNF432 57259531 57228173 - - 0 57260538 57242125 - + N 0.682733576388045 1.83110976139549 N HCC1954 9 2.42857142857143 1 2 1 N - - Y - - 0 0 0 7 1.12125446110842 1.05697872766909 1.12125446110842 1.05697872766909 4 0 0 1908 N Y 3.54872248456702 3.34103362635907 3.34103362635907 1 0 0.372157605668269 N 0.853058776489404 0 N N 7926 0 ENSG00000011405 ENSG00000221151 - + 11 16 17147930 88689322 utr3p upstream PIK3C2A AC133919.3-4 17064705 88689218 - - 0 17066514 88710197 + - Y - - N HCC1954 190 128.454545454545 88 11 1 N - - N SINE - 1 0 1 11 0.314236919036755 0.821301038391519 0.821301038391519 0.314236919036755 3 - - 41680 N N 3.54872248456702 3.52361324642271 3.52361324642271 0 0 0.117613854000144 N 0 0 Y N 19339 8537 ENSG00000177570 ENSG00000129292 + + 8 8 119703365 133930234 utr3p coding SAMD12 PHF20L1 119270880 133856786 - + 0 119278974 133886099 - + N 2.20452857756743 - N HCC1954 1 1 1 0 1 N 483 13.376 N - - 0 0 0 16 0.857009779191151 0.792734045751814 0.857009779191151 0.792734045751814 1 0 - 34643 N Y 3.22374022661543 3.33830513940999 3.22374022661543 222 0 0.0987740652593326 Y 0.951439244122171 0.987859811030543 N N 2515 13277 ENSG00000137074 ENSG00000086061 - - 9 9 32991626 33029277 utr5p upstream APTX DNAJA1 32962609 33015242 - + 0 32987243 33014805 + - N - - N HCC1954 1 1 1 0 3 N - - N SINE - 0.0933333333333333 0 0.0933333333333333 4 0.778450549431962 0.364229156156239 0.778450549431962 0.364229156156239 1 - - 19523 N Y 3.56761456604966 3.53721618787652 3.53721618787652 303 0.893482478018794 0.00362107880381901 N 0.92391605572771 0.969566422291084 Y N 29204 5570 ENSG00000203832 ENSG00000152042 - + 1 1 146713675 144779602 utr5p utr5p NBPF10 NBPF8 146616873 144743900 - - 0 146713667 144769087 + - N - - N HCC1954 20 12.5 4 4 1 N - - N - LINE 0 0.25503355704698 0.25503355704698 4 0.592765097273879 0.842726282871298 0.842726282871298 0.592765097273879 1 - - 26601 Y Y 3.48167806633553 3.44615838200292 3.44615838200292 283 0 0.152365947389792 Y 0.505457400863761 0.985237534354142 N N 129 59171 ENSG00000157368 ENSG00000189091 - + 16 16 69252085 69163701 upstream downstream IL34 SF3B3 69237969 69115202 + + 0 69237952 69181804 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.9 0.9 19 0.785592297591888 0.771308801272036 0.785592297591888 0.771308801272036 4 - - 33970 N N 3.32995148519165 3.48374420587532 3.32995148519165 2 0 0.300531410181611 N 0 0 Y N 59837 339915 ENSG00000198695 ENSG00000198727 + + MT MT 14674 15882 coding coding MT-ND6 MT-CYB 14150 14748 - + 0 14419 15843 - + N - 2.51112346367471 N HCC1954 3 1.66666666666667 1 2 1 N - - N - - 0 0 0 6 0.892718519990782 1.19981369086761 1.19981369086761 0.892718519990782 1 - 0 19245 N N 3.35000977519337 3.48639814491089 3.35000977519337 0 0 0.0814817698747483 Y 0 0 N N 33725 15504 ENSG00000143819 ENSG00000143742 - + 1 1 224099884 224044788 upstream coding EPHX1 SRP9 224064459 224032154 + + 0 224064256 224043594 - + N - - N HCC1954 2 2 2 6 1 N - - N DNA - 0.514285714285714 0 0.514285714285714 6 0.499922371194838 0.492780623034912 0.499922371194838 0.492780623034912 1 - - 9849 Y Y 3.71720464963688 2.91614120487896 2.91614120487896 0 0 0.96898745824403 Y 0 0 N N 170868 252027 ENSG00000141741 ENSG00000141738 - - 17 17 35140314 35157070 coding upstream C17orf37 GRB7 35138937 35147713 - + 0 35140204 35147420 + - N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 5 0.828442786551446 0.799875793911741 0.828442786551446 0.799875793911741 2 - - 46624 N Y 3.35612429832939 3.44615838200292 3.35612429832939 0 0 0.411462677407351 N 0.527805257207462 0.922731769361221 N N 0 2010 ENSG00000217904 ENSG00000138735 + + 19 4 58968346 120769429 intron downstream AC008753.2 PDE5A 58967572 120635000 - - 0 58968068 120633936 - - Y 1 - N HCC1954 4 3.4 1 4 1 N - - N LTR - 1 0 1 5 0.364229156156239 0.407079645115797 0.407079645115797 0.364229156156239 2 0 - 18083 Y Y 3.44040523365767 3.50637672932591 3.44040523365767 289 0 0.180616250841117 Y 0 0 N N 6613 0 ENSG00000142875 ENSG00000220124 - - 1 1 84476765 84256642 upstream upstream PRKACB RP4-552O12.1 84316329 84254125 + - 0 84302961 84276898 - + N - - N HCC1954 2 1.08333333333333 1 2 2 N - - Y LTR LINE 1 1 1 24 1.02841173502938 1.12839620926835 1.12839620926835 1.02841173502938 2 - - 42276 Y Y 3.38486711211668 3.32423818963975 3.32423818963975 247 0 0.114977581547580 Y 0 0 N N 34599 0 ENSG00000064042 ENSG00000207481 - - 4 4 41395746 41000111 upstream downstream LIMCH1 Y_RNA 41057559 41000011 + - 0 41056180 40999887 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 0.692749571512847 0.671324327033068 0.692749571512847 0.671324327033068 4 - - 42148 Y Y 3.55657227767559 3.66385645881505 3.55657227767559 0 0 0.334649104945112 Y 0.439663461538461 0.989623397435897 N N 2970 735 ENSG00000163293 ENSG00000198515 - - 4 4 47736947 47678276 upstream utr5p NPAL1 CNGA1 47713548 47632753 + - 0 47713256 47678273 - + N - 12.6567844925884 N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.0576923076923077 0.0576923076923077 8 0.99270299422975 0.742741808632331 0.99270299422975 0.742741808632331 1 - 0 39853 Y Y 3.35612429832939 3.58849823915857 3.35612429832939 303 0 0.00219425214965896 Y 0 0.989166307935141 N N 3 3479 ENSG00000169856 ENSG00000047346 + - 15 15 50869501 50709156 downstream upstream ONECUT1 KIAA1370 50836645 50660822 - - 0 50789237 50757705 - + N - - N HCC1954 2 1.14285714285714 1 1 1 N - - Y - - 0 0 0 7 0.685607823352921 0.757025304952183 0.757025304952183 0.685607823352921 1 - - 40156 N Y 3.7061623612628 3.33676820853032 3.33676820853032 270 0.715343915343915 0.0167093470303115 Y 0.987061087061087 0.974122174122174 N N 11478 0 ENSG00000128731 ENSG00000140181 + - 15 15 26240890 20878094 coding intron HERC2 AC091565.10-1 26029781 20833722 - - 0 26124981 20851627 - + N - 1 N HCC1954 3 2.4 2 5 1 N - - N - - 0 0 0 5 0.349945659836387 0.464213630395207 0.464213630395207 0.349945659836387 4 - 0 8668 N Y 3.40587876630159 3.64293293291278 3.40587876630159 112 0 0.689354314189783 N 0.540360873694207 0.904241848686293 N N 5003 0 ENSG00000132478 ENSG00000223330 + - 17 7 71333474 56437356 intron upstream UNK U6 71292532 56437257 + - 0.904241848686293 71300154 56482151 + + Y 1.2255062381494 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.39993789695587 0.378512652476092 0.39993789695587 0.378512652476092 4 0 - 7272 Y Y 3.46977054206092 3.69209541149257 3.46977054206092 191 0 0.0176511758033546 Y 0.184293193717278 0.820942408376963 N N 0 0 ENSG00000199460 ENSG00000211547 + - 2 2 132880901 132755208 downstream upstream U6 AC097532.3-1 132880795 132755117 - - 0 132820601 132812128 - + N - - N HCC1954 2 2 2 4 1 N - - Y - - 0 0 0 4 0.578481600954027 0.407079645115797 0.578481600954027 0.407079645115797 2 - - 30283 N N 3.29127915838687 3.19343513439813 3.19343513439813 18 0 0.344524072994208 N 0.353548480254133 0.388491805645802 Y N 0 13 ENSG00000217035 ENSG00000010671 - - X X 44379422 100527838 downstream intron CHTF8P BTK 44377882 100491091 + - 0.248718504079128 44385725 100493815 - + N - 0.808423737019031 N HCC1954 21 20.25 20 4 1 N 89 22.1154 N SINE SINE 0.65625 1 1 4 0.22853594111764 0.292811674556976 0.292811674556976 0.22853594111764 2 - 0 9593 Y N 3.43717024265986 3.31489131844487 3.31489131844487 0 0 0.914634195241152 Y 0 0 N N 5891 10351 ENSG00000175832 ENSG00000067596 + + 17 17 38979288 38957206 downstream intron ETV4 DHX8 38960738 38916860 - + 0 38959203 38955207 - + N - 1.43571089487821 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.714174815992626 0.578481600954027 0.714174815992626 0.578481600954027 2 - 0 9293 Y Y 3.35935664638825 3.4780843434859 3.35935664638825 379 0 0.0391337644521186 Y 0 0 N N 7525 5 ENSG00000173894 ENSG00000182156 - + 17 17 75375973 75330612 upstream downstream CBX2 ENPP7 75366588 75319276 + + 0 75358293 75347421 - + N - - N HCC1954 22 2.21022727272727 1 30 1 N - - Y LTR LINE,SINE 1 0.649214659685864 1 176 1.46405837278488 1.36407389854591 1.46405837278488 1.36407389854591 4 - - 37512 N Y 3.44785379918211 3.27502227789748 3.27502227789748 295 0.184591679506934 0.0009370602491513 N 0.145762711864407 0.831741140215717 N N 936 1602 ENSG00000151338 ENSG00000175155 - + 14 17 37090214 54833877 downstream intron MIPOL1 YPEL2 36736907 54763835 + + 0.184591679506934 37105946 54827160 - + Y - 1.15083120361765 N HCC1954 20 20 20 11 1 N - - N SINE Other 1 1 1 11 0.692749571512847 0.671324327033068 0.692749571512847 0.671324327033068 1 - 0 8642 N Y 3.54552998930151 3.18188898491428 3.18188898491428 8 0 0.512988995976889 N 0 0.908043287510968 N N 540 20793 ENSG00000198039 ENSG00000141027 - + 7 17 64029390 16059570 utr3p utr5p ZNF273 NCOR1 64001055 15875443 + - 0 64027704 16059401 - - Y - 4.35916940862606 N HCC1954 35 26.5 10 8 1 N - - N SINE Simple_repeat 1 0.745762711864407 1 8 0.314236919036755 0.421363141435649 0.421363141435649 0.314236919036755 3 - 0 4242 Y Y 3.71720464963688 3.7061623612628 3.7061623612628 176 0 0.0771606476235385 Y 0.59984756097561 0.987874168514412 N N 0 0 ENSG00000206634 ENSG00000203448 - - 7 7 64858081 64832435 upstream downstream SNORA22 AC104057.4 64857948 64830585 + - 0 64853296 64829304 - + N - - N HCC1954 8 1.93333333333333 1 3 3 N - - Y - SINE 0 0.38 0.38 15 0.385654400636018 0.714174815992626 0.714174815992626 0.385654400636018 1 - - 47029 Y Y 3.59321831773393 3.36617336972692 3.36617336972692 282 0 0.00622736325643147 Y 0.977691330581137 0.992563776860379 N N 1819 21 ENSG00000160439 ENSG00000088053 + - 19 19 60272709 60241444 downstream upstream RDH13 GP6 60247523 60216885 - - 0 60244504 60242442 - + N - - N HCC1954 1 1 1 0 1 N - - Y DNA LINE,SINE 0.612903225806452 0.9375 0.9375 4 0.87843502367093 0.664182578873142 0.87843502367093 0.664182578873142 3 - - 24929 N Y 3.47233119514066 3.37126417066287 3.37126417066287 163 0 0.0128322944179794 N 0 0.908258612553091 N N 20739 0 ENSG00000143951 ENSG00000220095 - + 2 13 63669355 110390132 utr3p downstream C2orf86 RP11-365P13.2 63202041 110387107 - + 0.908258612553091 63309485 110447336 + + Y - - N HCC1954 640 575 420 4 1 N 396 21.9705 N LINE LINE 1 1 1 4 0.335662163516534 0.371370904316165 0.371370904316165 0.335662163516534 4 - - 47493 Y Y 3.31229081257178 3.38396202342278 3.31229081257178 0 0 0.56743797794927 Y 0.994397715146569 0.994397715146569 N N 3434 1635 ENSG00000130312 ENSG00000127220 - - 19 19 17278652 17275282 utr5p intron MRPL34 ABHD8 17277477 17263941 + - 0 17277641 17264664 - + N - 1.16078744055607 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 35 1.35693215038599 1.31408166142643 1.35693215038599 1.31408166142643 1 - 0 41403 Y Y 3.38552945952599 3.53039946453785 3.38552945952599 325 0 0.0143257491072738 Y 0.978169567658619 0.99272318921954 N N 0 0 ENSG00000221261 ENSG00000221176 - + 8 8 129231616 129130666 upstream downstream hsa-mir-1208 hsa-mir-1207 129231544 129130580 + + 0 129182406 129178080 - + N - - N HCC1954 2 1.04268292682927 1 7 2 N - - Y LTR - 1 0 1 164 1.17124669822791 1.03555348318931 1.17124669822791 1.03555348318931 2 - - 36206 Y Y 3.51104337473878 2.83176698359484 2.83176698359484 132 0 0.0337563398361923 Y 0.899075500770416 0.932717000513611 N N 19299 99057 ENSG00000089159 ENSG00000089157 + - 12 12 119187904 119123397 downstream upstream PXN RPLP0P2 119132637 119118893 - - 0 119132042 119123557 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 76 0.649899082553289 0.621332089913584 0.649899082553289 0.621332089913584 2 - - 36285 Y Y 3.55504469436574 3.53143253430774 3.53143253430774 276 0 0.196047889015612 Y 0.991483958875263 0.982967917750526 N N 98 1664 ENSG00000025423 ENSG00000198056 - - 12 12 55467841 55432413 upstream upstream HSD17B6 PRIM1 55443375 55409326 + - 0 55443249 55432632 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.921285512630487 0.785592297591888 0.921285512630487 0.785592297591888 4 - - 20613 N N 3.49744043328497 3.54400240599166 3.49744043328497 0 0.157747918796553 0.0675076993036083 N 0 0 N N 11860 975 ENSG00000143374 ENSG00000198487 - + 1 6 148746702 42218335 upstream coding TARS2 AL512274.9 148726517 42183124 + - 0 148725238 42183238 - - Y - - N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.521347615674617 0.635615586233437 0.635615586233437 0.521347615674617 2 - - 43432 N Y 3.5963175270436 3.40951234194457 3.40951234194457 6 0 0.230781052616314 N 0 0.7736664162284 N N 2978 3891 ENSG00000021574 ENSG00000166295 + + 2 10 32236209 73665622 utr3p coding SPAST C10orf104 32142184 73645812 + + 0 32234850 73653713 + + Y - - N HCC1954 35 28.71875 21 32 1 N - - N SINE - 1 0 1 32 0.34280391167646 0.471355378555133 0.471355378555133 0.34280391167646 2 - - 30254 Y Y 3.47279520345708 3.61889661733171 3.47279520345708 247 0 0.353393003486687 Y 0.195190774138143 0.989939884676727 N N 57 0 ENSG00000177324 ENSG00000218530 + + X X 18148924 17862864 downstream downstream BEND2 RP1-272E8.1 18090974 17861390 - + 0 18032594 17953528 - + N - - N HCC1954 2 1.4 1 2 3 N - - Y LINE - 1 0 1 5 0.371370904316165 0.542772860154395 0.542772860154395 0.371370904316165 1 - - 28698 N Y 3.15741158895574 3.62398741826765 3.15741158895574 0 0 0.106546495978865 N 0 0.957415832575068 N N 231 321 ENSG00000213971 ENSG00000183196 + + 19 16 23237276 74086783 downstream utr3p AC092329.3-1 CHST6 23234603 74064523 - - 0 23224954 74068182 - - Y - - N HCC1954 27 22.8333333333333 20 6 1 N - - N - SINE 0 1 1 6 0.635615586233437 0.378512652476092 0.635615586233437 0.378512652476092 2 - - 26748 Y Y 3.47080361183081 3.62361669590707 3.47080361183081 307 0 0.801750709493338 Y 0.15408023315618 0.986884964855135 N N 1747 10006 ENSG00000157312 ENSG00000132612 + + 16 16 67921999 67916446 downstream intron COG8 VPS4A 67920025 67895081 - + 0 67919655 67914231 - + N - 1.05622450190527 N HCC1954 1 1 1 0 4 N - - Y - SINE 0 0.129770992366412 0.129770992366412 5 0.735600060472404 0.849868031031224 0.849868031031224 0.735600060472404 2 - 0 30911 N Y 3.58271458558979 3.61360747730288 3.58271458558979 2 0 0.147181597316613 N 0 0.764911014911015 N N 145 0 ENSG00000171121 ENSG00000219023 - - 3 6 180467532 35632019 utr5p intron KCNMB3 RP3-340B19.2 180443259 35631628 - + 0 180452337 35631859 + - Y - 1 N HCC1954 200 146.8 88 10 1 N - - N SINE - 1 0 1 10 0.314236919036755 0.414221393275723 0.414221393275723 0.314236919036755 1 - 0 6989 Y Y 3.3244060235091 3.5514509715161 3.3244060235091 262 0 0.0377949497247241 Y 0 0 N N 0 24774 ENSG00000175194 ENSG00000197756 + + 2 2 217183927 217074428 downstream downstream AC073321.4 RPL37A 217183316 217071765 - + 0 217151887 217106998 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.685607823352921 0.721316564152552 0.721316564152552 0.685607823352921 2 - - 47624 Y Y 3.58743466416515 3.50785087947327 3.50785087947327 0 0.471784511784512 0.830998385515453 Y 0.451851851851852 0.99003367003367 N Y 164 18353 ENSG00000142279 ENSG00000126261 - + 19 19 39683925 39652635 coding coding WTIP UBA2 39664720 39611108 + + 0 39673121 39649759 - + N - 2.67969986613003 N HCC1954 2 1.16666666666667 1 1 1 Y - - Y - - 0 0 0 6 1.12839620926835 0.728458312312478 1.12839620926835 0.728458312312478 4 - 0 13667 Y Y 3.38552945952599 3.3787033886175 3.3787033886175 333 0 0.0304389017728240 N 0.822191618369962 0 Y N 145 30 ENSG00000130487 ENSG00000217442 - - 22 22 49335409 49348200 upstream downstream KLHDC7B C22orf41 49333328 49336407 + - 0.99364970065607 49330084 49328196 - + N - - N HCC1954 1 1 1 0 2 N - - N - LINE 0 0.189024390243902 0.189024390243902 65 1.25694767614702 1.17124669822791 1.25694767614702 1.17124669822791 1 - - 32062 N N 3.51360402781852 3.7297745213208 3.51360402781852 0 0 0.278118524643258 N 0 0 N N 0 47062 ENSG00000221740 ENSG00000047849 - - 7 3 22862830 48105768 downstream intron SNORD93 MAP4 22862757 47867190 + - 0 22863236 47967327 - + Y - 1.20065651885442 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.749883556792257 0.507064119354764 0.749883556792257 0.507064119354764 4 - 0 17506 Y Y 3.53568860456667 3.35872480420248 3.35872480420248 0 0 0.665167080875601 Y 0 0 N Y 132 2752 ENSG00000143653 ENSG00000162852 - + 1 1 244998060 244898484 coding utr5p SCCPDH C1orf71 244954001 244796386 + + 0 244956817 244796588 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 1.02126998686945 1.0069864905496 1.02126998686945 1.0069864905496 4 - - 47165 Y Y 3.3755202409218 3.48167806633553 3.3755202409218 174 0 0.858988924160099 Y 0 0.986697318007663 N N 6 14186 ENSG00000213052 ENSG00000171570 + + 19 19 46048180 46006176 downstream coding CYP2A6 EGLN2 46041284 45996959 - + 0 46024309 46005019 - + N - - N HCC1954 2 1.6875 1 11 3 N - - Y - Low_complexity 0 0.00357142857142857 0.00357142857142857 16 0.971277749749971 1.51405060990437 1.51405060990437 0.971277749749971 4 - - 24920 N N 3.67320333000993 2.8501603616409 2.8501603616409 0 0 0.138636091415738 N 0 0.260390332692891 N N 3752 0 ENSG00000152520 ENSG00000211547 - + 13 2 27767472 132755208 intron downstream PAN3 AC097532.3-1 27611014 132755117 + - 0 27626664 132749166 - - Y 0.608541443172629 - N HCC1954 2 1.75 1 3 1 N 349 17.9298 N SINE - 1 0 1 4 0.278528178237124 0.371370904316165 0.371370904316165 0.278528178237124 3 0 - 19335 N Y 3.58593758607883 3.60000453584907 3.58593758607883 248 0 0.0258331187983839 N 0.803427419354839 0.986895161290323 N N 633 3863 ENSG00000198658 ENSG00000219481 - - 1 1 144791588 146862781 upstream intron FAM108A3 NBPF15 144787932 146827614 + + 0 144785216 146832126 - - N - 1.01507977461503 Y HCC1954 10 6.4 4 5 1 N 406 25.5477 N - SINE 0 1 1 5 0.87843502367093 0.521347615674617 0.87843502367093 0.521347615674617 1 - 0 41776 Y Y 3.51360402781852 3.68105312311849 3.51360402781852 0 0 0.930181104157464 Y 0 0 N N 8687 25855 ENSG00000147813 ENSG00000104529 - + 8 8 144731651 144750726 coding utr3p NAPRT1 EEF1D 144728101 144733041 - - 0 144731256 144733092 + - N - - N HCC1954 3 1.85714285714286 1 4 1 Y - - Y - - 0 0 0 7 0.892718519990782 0.964136001590045 0.964136001590045 0.892718519990782 4 - - 24759 Y Y 3.49640736351508 3.07672437647709 3.07672437647709 273 0 0.00349473786837584 Y 0.989833295955745 0.989833295955745 N N 4155 9396 ENSG00000101745 ENSG00000178127 - + 18 18 9275206 9124343 upstream intron ANKRD12 NDUFV2 9126758 9092725 + + 0 9126361 9123507 - + N - 2.34319100425235 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.607048593593732 0.778450549431962 0.778450549431962 0.607048593593732 1 - 0 47692 Y Y 3.51679652308403 3.63825270713077 3.51679652308403 0 0 0.303335990703192 Y 0 0.987841173054588 N Y 3154 3587 ENSG00000204604 ENSG00000198538 + - 19 19 58119222 58016697 coding intron ZNF468 ZNF28 58033598 57992474 - - 0 58052637 58013096 - + N - 1.19275971756544 N HCC1954 20 5.75 1 1 1 N - - Y - SINE 0 1 1 4 0.314236919036755 0.557056356474248 0.557056356474248 0.314236919036755 4 - 0 46767 N Y 3.28871850530713 3.57800808738356 3.28871850530713 0 0 0.390611448927235 Y 0.00393700787401563 0 N N 5 17943 ENSG00000130287 ENSG00000105141 - + 19 19 19224061 15027900 intron downstream NCAN CASP14 19183782 15024015 + + 0 19219389 15029502 - + N 1.00368909436669 - N HCC1954 20 20 20 22 1 N - - N SINE - 1 0 1 22 0.278528178237124 0.757025304952183 0.757025304952183 0.278528178237124 3 0 - 3969 N Y 3.54292948342842 3.58271458558979 3.54292948342842 7 0.032624962586052 0.188327876142062 N 0.674348997306196 0.990422029332535 N N 1702 16361 ENSG00000170379 ENSG00000198420 - + 7 7 143058435 143230181 utr5p downstream FAM115C FAM115B 143028667 143180984 + - 0 143031009 143164667 - - N 0.134085514995633 - Y HCC1954 2 2 2 6 1 N - - N - Simple_repeat 0 0.478260869565217 0.478260869565217 6 0.749883556792257 0.328520415356608 0.749883556792257 0.328520415356608 1 0 - 4664 N Y 3.48064499656564 3.61513506061274 3.48064499656564 9 0 0.434320829263159 Y 0.0890988740451105 0.978567032330473 N N 327 405 ENSG00000187221 ENSG00000205583 - + 7 7 72081568 72114377 intron intron AC005488.2-4 AC005488.2-6 72076586 72106483 - - 0 72078586 72107034 + - N - 0.764113989424552 N HCC1954 12 7.83333333333333 4 6 1 N - - N - - 0 0 0 6 0.707033067832699 0.557056356474248 0.707033067832699 0.557056356474248 4 - 0 26636 N Y 3.38292895365289 3.61257440753299 3.38292895365289 268 0 0.0087877010400832 Y 0 0 N N 13 13 ENSG00000102970 ENSG00000102970 - + 16 16 56007475 56007475 upstream upstream CCL17 CCL17 55996180 55996180 + + 0.98635248415457 55988077 55986329 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR LTR 1 0.431654676258993 1 4 0.464213630395207 0.971277749749971 0.971277749749971 0.464213630395207 1 - - 45013 Y N 3.54400240599166 3.64450036901598 3.54400240599166 0 0 0.521952423922865 N 0 0 Y N 2456 2746 ENSG00000171813 ENSG00000068383 - + 10 10 134081357 134446974 utr3p intron PWWP2B INPP5A 134060662 134201343 + + 0 134080574 134271452 - + N - 0.343871918957657 N HCC1954 1 1 1 0 2 N 205 11.6558 N - - 0 0 0 10 0.87843502367093 0.349945659836387 0.87843502367093 0.349945659836387 1 - 0 9264 N Y 3.54144175291192 3.87464452633266 3.54144175291192 13 0 0.589311673697289 N 0.891301504251145 0.92753433616743 N N 103 1772 ENSG00000214425 ENSG00000187451 + - 17 17 40951047 42483361 intron downstream AC091132.16-2 AC068152.11-2 40934468 42480430 - + 0.0398299542184435 40941614 42488825 - - N 1.92752095128185 - Y HCC1954 48 11.1666666666667 3 6 1 N - - N - LTR 0 1 1 6 0.592765097273879 0.685607823352921 0.685607823352921 0.592765097273879 4 0 - 440 Y Y 3.46335504630636 3.4780843434859 3.46335504630636 120 0 0.995712596065565 Y 0.991697080291971 0.983394160583942 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 upstream coding C11orf66 C11orf79 61005168 60954173 + + 0 60996793 60962161 - + N - - N HCC1954 1 1 1 0 6 N - - Y LTR - 1 0 1 19 0.899860268150708 1.05697872766909 1.05697872766909 0.899860268150708 4 - - 40336 N N 3.39015625214551 3.6988816296077 3.39015625214551 0 0 0.839119577163605 N 0 0.00414937759336098 N N 60677 24 ENSG00000125740 ENSG00000196645 - + 19 15 50670254 21123747 upstream downstream FOSB AC100756.4-2 50663093 21121113 + - 0.00414937759336098 50644271 21061716 - - Y - - N HCC1954 2 2 2 13 2 N 346 10.2249 N SINE - 1 0 1 13 0.585623349113953 0.778450549431962 0.778450549431962 0.585623349113953 4 - - 33865 N N 3.31485146565152 3.2639799895234 3.2639799895234 0 0.0578932893289329 0.738425708017432 N 0 0.0578932893289329 Y N 59837 336285 ENSG00000198695 ENSG00000198868 - - MT MT 14674 12138 coding coding MT-ND6 MT-ND4 14150 10471 - + 0.0578932893289329 14317 11340 + - N - - N HCC1954 1 1 1 0 2 N 189 4.09957 N - - 0 0 0 4 0.728458312312478 0.749883556792257 0.749883556792257 0.728458312312478 4 - - 13028 N N 3.07101108092519 3.61360747730288 3.07101108092519 0 0 0.178168381459762 N 0.690365772865163 0.782419191743087 N N 1649619 149 ENSG00000141736 ENSG00000184347 - + 17 5 35138441 168660291 coding intron ERBB2 SLIT3 35104766 168025857 + - 0 35125066 168606375 - - Y - 1.44355469360943 N HCC1954 20 20 20 17 1 N - - N - SINE 0 1 1 17 0.635615586233437 0.321378667196682 0.635615586233437 0.321378667196682 1 - 0 1289 N N 3.25984771044384 3.23999710710482 3.23999710710482 0 0.336585365853658 0.166517302855141 N 0.380813008130081 0.226016260162601 N N 86 122511 ENSG00000165495 ENSG00000187514 - + 11 2 124808495 232286495 intron utr3p PKNOX2 PTMA 124539769 232280638 + + 0.226016260162601 124794994 232285829 - + Y 0.890868906823245 - N HCC1954 5 3.75 3 4 1 N - - N SINE,SINE Low_complexity 0.472727272727273 0.0457516339869281 0.472727272727273 4 0.392796148795944 0.928427260790413 0.928427260790413 0.392796148795944 1 0 - 29272 Y Y 3.63655728995158 3.28399842673177 3.28399842673177 293 0 0.101568299545643 Y 0.130796273961354 0 N N 547 2787 ENSG00000189298 ENSG00000197657 - - 6 6 28444527 28429951 intron downstream ZKSCAN3 ZNF323 28425738 28400493 + - 0 28429618 28391962 - + N 0.187918345154444 - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 7 1.04983697950916 0.964136001590045 1.04983697950916 0.964136001590045 4 0 - 39863 Y Y 2.88570297391247 3.19909499678754 2.88570297391247 307 0 0.0059182968244561 Y 0 0.986530504445814 N N 3392 0 ENSG00000140382 ENSG00000186690 - + 15 15 75564998 75358134 upstream downstream HMG20A AC060773.10 75500285 75357862 + + 0 75440601 75365876 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE - 1 0 1 5 0.671324327033068 0.528489363834543 0.671324327033068 0.528489363834543 1 - - 33323 N Y 3.47552369040616 2.9438017485332 2.9438017485332 411 0 0.00755577533878538 Y 0 0.992610615481662 N N 339915 275222 ENSG00000198727 ENSG00000198763 - + MT MT 15882 5512 coding coding MT-CYB MT-ND2 14748 4471 + + 0 15542 5461 - + N 1.27437966361768 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 1.01412823870953 0.749883556792257 1.01412823870953 0.749883556792257 2 0 - 29764 Y Y 3.42254622194492 3.70719543103269 3.42254622194492 0 0 0.989752692801331 Y 0 0.986531233219975 N N 399 1730 ENSG00000221988 ENSG00000168452 - + 6 6 32244040 32239433 utr5p coding EGFL8 PPT2 32240360 32229279 + + 0 32241897 32238653 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 12 0.649899082553289 0.99270299422975 0.99270299422975 0.649899082553289 2 - - 36379 Y Y 3.55504469436574 3.64553343878587 3.55504469436574 0 0 0.866336869662962 Y 0.529222629222629 0.978103378103378 N N 98 1664 ENSG00000025423 ENSG00000198056 - - 12 12 55467841 55432413 upstream utr5p HSD17B6 PRIM1 55443375 55409326 + - 0 55443249 55432369 - + N - 2.6767629456154 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.699891319672773 0.778450549431962 0.778450549431962 0.699891319672773 4 - 0 5548 N Y 3.37614273553776 1.82633368241897 1.82633368241897 0 0.0777630219861294 0.435438010949174 N 0.649549948354729 0.631105208794452 N N 4157 2859 ENSG00000124313 ENSG00000152056 + - X 2 53367247 224410563 coding upstream IQSEC2 AP1S3 53278784 224325785 - - 0 53325471 224410721 - + Y - - N HCC1954 1 1 1 0 1 N - - N - Low_complexity 0 0.605263157894737 0.605263157894737 5 0.799875793911741 0.271386430077198 0.799875793911741 0.271386430077198 4 - - 32986 N N 2.91783662205815 3.14484171727181 2.91783662205815 0 0 0.999985927920076 N 0 0 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0 8407 14090 - + N 0.984947018030751 2.12300180977667 N HCC1954 2 1.25 1 2 10 Y 189 4.09957 N - - 0 0 0 8 1.23552243166724 1.07840397214886 1.23552243166724 1.07840397214886 1 0 0 37825 N N 3.49744043328497 3.54400240599166 3.49744043328497 0 0 0.0794459309911282 N 0 0 N N 0 975 ENSG00000214392 ENSG00000198487 + + 14 6 18483783 42218335 upstream coding CR383656.1 AL512274.9 18481432 42183124 - - 0 18518184 42183238 - - Y - - N HCC1954 23 21.1818181818182 20 11 1 N - - N SINE - 1 0 1 11 0.292811674556976 0.585623349113953 0.585623349113953 0.292811674556976 2 - - 474 Y Y 3.52783881145811 3.448886868952 3.448886868952 84 0 0.0858851925451124 Y 0 0.984783377988979 N N 11081 9875 ENSG00000166801 ENSG00000189057 - + 11 11 58679083 58651443 upstream utr5p FAM111A FAM111B 58668828 58631286 + + 0 58667169 58633670 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE,LINE 0 0.267543859649123 0.267543859649123 4 0.849868031031224 0.985561246069823 0.985561246069823 0.849868031031224 1 - - 47484 Y Y 3.44719145177281 3.47705127371601 3.44719145177281 250 0.387076923076923 0.00383656622387685 Y 0.387076923076923 0 N N 32890 3483 ENSG00000160877 ENSG00000104907 - - 19 19 13112955 13088563 utr5p upstream NACC1 TRMT1 13090109 13076721 + - 0 13107014 13088699 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity SINE 0.0153061224489796 0.508196721311475 0.508196721311475 11 1.12125446110842 0.871293275511003 1.12125446110842 0.871293275511003 2 - - 27863 N Y 3.55504469436573 3.21848159181014 3.21848159181014 1 0 0.0341956747971464 N 0 0 N N 1990 0 ENSG00000182504 ENSG00000221151 - - 3 16 102972095 88689322 utr3p upstream CEP97 AC133919.3-4 102926177 88689218 + - 0 102971599 88700561 - + Y - - N HCC1954 148 110.47619047619 29 21 1 N - - N SINE - 1 0 1 21 0.328520415356608 0.585623349113953 0.585623349113953 0.328520415356608 1 - - 13641 Y Y 3.81079260336669 3.27039548527796 3.27039548527796 325 0 0.00710862431338244 Y 0 0 N N 34911 126 ENSG00000100280 ENSG00000100276 + - 22 22 28114569 28041748 downstream upstream AP1B1 RASL10A 28053669 28038922 - - 0 28052439 28046532 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE,SINE 0 0.594117647058824 0.594117647058824 10 0.971277749749971 1.21409718718746 1.21409718718746 0.971277749749971 3 - - 36363 Y Y 3.47402661231985 3.24099032408136 3.24099032408136 198 0 0.0975109290126829 Y 0 0.989185331576636 N N 878 42060 ENSG00000111077 ENSG00000063046 - + 12 12 51744430 51722259 intron utr3p TENC1 EIF4B 51727077 51686329 + + 0 51733446 51720313 - + N 0.195728072265403 3.00415363152468 N HCC1954 4 4 4 4 2 N - - Y - - 0 0 0 4 0.621332089913584 0.542772860154395 0.621332089913584 0.542772860154395 1 0 0 563 N Y 3.72146071989581 3.2044774227722 3.2044774227722 0 0 0.0933051484504996 Y 0 0.985948400684481 N N 9074 2102 ENSG00000166444 ENSG00000166452 - - 11 11 8817478 8898202 utr5p upstream ST5 C11orf17 8671478 8889277 - + 0 8817433 8888314 + - N - - N HCC1954 20 5.4 1 2 1 N - - N - SINE 0 0.772727272727273 0.772727272727273 5 1.03555348318931 0.628473838073511 1.03555348318931 0.628473838073511 1 - - 33164 N Y 3.00919060237884 2.9438017485332 2.9438017485332 279 0 0.00590055944202561 Y 0 0.992451395677202 N N 38150 275222 ENSG00000198840 ENSG00000198763 - + MT MT 10405 5512 coding coding MT-ND3 MT-ND2 10060 4471 + + 0 10184 5460 - + N 1.46591097877407 2.03304001294344 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.51420586751469 0.785592297591888 0.785592297591888 0.51420586751469 2 0 0 30289 Y N 3.02495296932827 3.81401560385573 3.02495296932827 0 0 0.994301352761064 Y 0 0 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62697234 62565587 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 4 0.499922371194838 0.357087407996313 0.499922371194838 0.357087407996313 1 - - 30886 N N 3.49744043328497 3.54400240599166 3.49744043328497 3 0 0.239258793396561 N 0 0 N N 439 975 ENSG00000187715 ENSG00000198487 - + 3 6 129189204 42218335 utr3p coding KLHDC6 AL512274.9 129116765 42183124 + - 0 129188138 42183238 - - Y - - N HCC1954 33 27.7837837837838 21 37 2 N - - N SINE - 1 0 1 37 0.328520415356608 0.821301038391519 0.821301038391519 0.328520415356608 2 - - 32795 N Y 3.28399842673177 3.33784113109357 3.28399842673177 0 0 0.0465538688877148 N 0.932983682983683 0.952131202131202 N N 45909 2906 ENSG00000073578 ENSG00000214135 - + 5 3 309794 196895854 downstream coding SDHA AC069513.28-1 271439 196874647 + + 0 316442 196893717 - + Y - - N HCC1954 8 4.52941176470588 1 16 1 Y - - N LINE - 0.46969696969697 0 0.46969696969697 17 0.849868031031224 1.03555348318931 1.03555348318931 0.849868031031224 2 - - 48787 N Y 2.96595182135875 3.48908677906663 2.96595182135875 256 0 0.107345145578100 N 0.927556818181818 0.954723011363636 N N 45909 1157 ENSG00000073578 ENSG00000185986 - + 5 5 309794 1646257 downstream utr3p SDHA AC091849.2 271439 1625243 + - 0 316424 1625297 - - N - 0.494896883439215 Y HCC1954 8 4.3 1 18 1 Y 615 7.90522 N LINE - 0.752212389380531 0 0.752212389380531 20 0.807017542071667 0.785592297591888 0.807017542071667 0.785592297591888 4 - 0 27522 N N 3.44615838200292 3.21808036422602 3.21808036422602 0 0 0.0711787023714 N 0.00636942675159236 0 N N 5747 45068 ENSG00000096060 ENSG00000205336 + + 6 16 35804336 56256445 intron upstream FKBP5 GPR56 35649345 56220023 - + 0 35694537 56211249 - + Y 0.385756989237151 - N HCC1954 21 20.25 20 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.649899082553289 0.649899082553289 0.328520415356608 2 0 - 21033 N N 3.03276290964348 3.56129235625094 3.03276290964348 0 0 0.275811832959324 N 0 0 N N 53009 2 ENSG00000131236 ENSG00000185008 + + 1 3 40310908 77779351 coding intron CAP1 ROBO2 40278492 76069335 + + 0 40308069 76566633 + + Y 0.931275344664774 0.970242214532872 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.314236919036755 0.28566992639705 0.314236919036755 0.28566992639705 2 0 0 46838 Y N 3.38552945952599 3.09508724929961 3.09508724929961 0 0 0.442847755707351 N 0.0375732375732376 0 Y N 9856 2494 ENSG00000105443 ENSG00000142235 - - 19 19 53674457 53708258 downstream downstream CYTH2 LMTK3 53664420 53680340 + - 0 53676864 53679077 - + N - - N HCC1954 1 1 1 0 1 N 319 23.9964 N SINE,LTR - 0.717241379310345 0 0.717241379310345 10 1.03555348318931 0.942710757110266 1.03555348318931 0.942710757110266 2 - - 36374 Y Y 3.45078517462244 3.42936294528359 3.42936294528359 288 0 0.362190213106524 Y 0 0.991482668566002 N N 37 351 ENSG00000139194 ENSG00000205885 + + 12 12 7172754 7165701 intron intron RBP5 AC018653.29-1 7167557 7152443 - + 0 7172052 7164498 - + N 1.00814598354028 15.5779209940653 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.949852505270192 0.857009779191151 0.949852505270192 0.857009779191151 1 0 0 29597 N Y 3.26936241550807 3.29127915838687 3.26936241550807 17 0 0.739365034831163 Y 0.979247416020672 0.979247416020672 N Y 2351 3656 ENSG00000111801 ENSG00000186470 - + 6 6 26561629 26486527 coding utr5p BTN3A3 BTN3A2 26548742 26473377 + + 0 26552164 26476257 - + N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 11 0.364229156156239 0.928427260790413 0.928427260790413 0.364229156156239 4 - - 68 N N 3.62977107183644 3.46145674063593 3.46145674063593 0 0.269382875011496 0.446779322050157 Y 0.269382875011496 0.27699347006346 N N 0 951 ENSG00000223269 ENSG00000172818 - + 11 11 98496430 65321259 upstream intron 7SK OVOL1 98496116 65311105 + + 0.27699347006346 98343332 65311521 - + N - 1.19929972162419 N HCC1954 1 1 1 0 2 N 108 7.42619 N LTR,LTR - 0.638297872340426 0 0.638297872340426 28 1.0069864905496 1.26408942430695 1.26408942430695 1.0069864905496 1 - 0 44435 N Y 3.40016547074969 2.76175649480287 2.76175649480287 0 0 0.0306619213614999 N 0.777417682136375 0.777417682136375 N N 3891 0 ENSG00000166295 ENSG00000218856 - - 10 20 73665622 4942370 intron upstream C10orf104 RP5-1116H23.1 73645812 4942166 + - 0 73653649 4966519 - + Y 0.744979490524871 - N HCC1954 21 20.1666666666667 20 6 1 N - - N - SINE,SINE 0 0.527272727272727 0.527272727272727 6 0.628473838073511 0.578481600954027 0.628473838073511 0.578481600954027 1 0 - 18229 N Y 3.60000453584907 3.57167229721571 3.57167229721571 0 0 0.878882047456854 Y 0.984662576687117 0.969325153374233 N N 3863 2251 ENSG00000219481 ENSG00000186275 - + 1 1 146862781 143541658 intron upstream NBPF15 NBPF8 146827614 143326471 + + 0 146832127 143310137 - + N 1.01507977461503 - N HCC1954 20 5.88888888888889 3 9 2 N - - N SINE - 1 0 1 9 0.614190341753658 0.928427260790413 0.928427260790413 0.614190341753658 4 0 - 10215 N Y 3.51104337473878 3.43097865687609 3.43097865687609 236 0 0.168477930375306 N 0 0.990947611710324 N N 1620 0 ENSG00000176681 ENSG00000213330 - - 17 17 41770918 41020078 utr5p upstream LRRC37A AC126544.5-1 41726926 41019020 + + 0.302966101694915 41727882 41017719 - - N - - Y HCC1954 5 3 1 2 2 N 461 16.1917 N SINE,SINE - 0.138461538461538 0 0.138461538461538 4 0.692749571512847 0.599906845433805 0.692749571512847 0.599906845433805 1 - - 7209 Y Y 3.10078696448237 3.17208745297279 3.10078696448237 249 0 0.366504132775867 Y 0.541847389558233 0.99004016064257 N N 4489 2 ENSG00000082258 ENSG00000153086 - + 2 2 135431056 135376074 upstream intron CCNT2 ACMSD 135392863 135312587 + + 0 135392605 135343083 - + N - 1.09857317847745 N HCC1954 1 1 1 0 3 N - - Y - SINE 0 1 1 10 1.02126998686945 0.671324327033068 1.02126998686945 0.671324327033068 3 - 0 5961 N Y 3.60256518892881 3.63655728995158 3.60256518892881 236 0.751059322033899 0.262461041841606 N 0 0.893311138014528 N N 355 9 ENSG00000106066 ENSG00000178568 - + 7 2 29201417 213111810 coding downstream CPVL ERBB4 29001772 211948691 - - 0 29098843 211722426 + - Y - - N HCC1954 20 5.85714285714286 1 5 2 N - - N - SINE 0 1 1 7 0.428504889595575 0.299953422716903 0.428504889595575 0.299953422716903 4 - - 3807 N N 2.99040357403324 3.23892418454158 2.99040357403324 7 0 0.195243405242108 N 0 0 N N 0 4749 ENSG00000208307 ENSG00000156162 - + 7 8 145325416 95873238 upstream coding AC073308.4 DPY19L4 145325354 95801327 + + 0.0139155324137513 144911115 95801404 - + Y - 0.604608522256063 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 14 0.478497126715059 0.692749571512847 0.692749571512847 0.478497126715059 1 - 0 24609 N Y 3.6272104187567 3.77030327419823 3.6272104187567 0 0 0.0249571145752105 N 0.843668577384054 0.843668577384054 N N 2054 2530 ENSG00000154889 ENSG00000138744 - + 18 4 11898641 77081190 utr3p coding MPPE1 NAAA 11873470 77050833 - - 0 11873918 77060124 + - Y - - N HCC1954 32 25.8 23 5 1 N - - N SINE - 1 0 1 5 0.464213630395207 0.714174815992626 0.714174815992626 0.464213630395207 1 - - 13727 N Y 3.61530289448208 2.8088570237395 2.8088570237395 275 0.140392156862745 0.0999334238251725 Y 0.960926916221034 0.980463458110517 N N 94 94 ENSG00000197182 ENSG00000197182 - + 22 22 44884554 44884554 intron utr5p RP4-695O20__B.10 RP4-695O20__B.10 44828413 44828413 + + 0 44831391 44828464 - + N 0.560355592214547 0.551417899680993 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.785592297591888 0.692749571512847 0.785592297591888 0.692749571512847 4 0 0 49177 N N 3.51001030496889 3.57848902055439 3.51001030496889 0 0 0.276483806289943 N 0 0 N N 9006 8224 ENSG00000112893 ENSG00000171444 - + 5 5 109231328 112852010 intron coding MAN2A1 MCC 109053055 112385695 + - 0 109076954 112486391 - - N 0.432961545437724 - Y HCC1954 1 1 1 0 1 Y 570 7.73351 N - - 0 0 0 4 0.771308801272036 0.849868031031224 0.849868031031224 0.771308801272036 2 0 - 10265 Y Y 3.57485544491141 3.72448538129198 3.57485544491141 0 0 0.92560209832882 Y 0 0 N N 9 93323 ENSG00000182676 ENSG00000185624 - + 17 17 77386215 77411833 coding coding DYSFIP1 P4HB 77384657 77394323 - - 0 77385998 77406307 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.757025304952183 0.742741808632331 0.757025304952183 0.742741808632331 4 - - 41733 Y Y 3.44615838200292 3.71145150129163 3.44615838200292 1 0 0.265715112550541 Y 0.0199190787426081 0 N N 12 3873 ENSG00000214954 ENSG00000155100 - + 8 8 92300522 92168499 coding coding LRRC69 OTUD6B 92184049 92151600 + + 0 92184092 92166238 - + N 2.42550398499766 - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 5 0.771308801272036 0.807017542071667 0.807017542071667 0.771308801272036 2 0 - 33906 N N 2.92867122376953 3.73912139251568 2.92867122376953 11 0 0.101148488878158 N 0 0.301130271229939 Y N 1291380 544065 ENSG00000198804 ENSG00000198744 - + MT MT 7446 9988 coding coding MT-CO1 MT-CO3 5905 8367 + + 0 6400 8603 - + N - 0.640385512776686 N HCC1954 4 2.75 1 3 1 Y 563 8.20203 N - - 0 0 0 4 0.757025304952183 0.549914608314322 0.757025304952183 0.549914608314322 2 - 0 36442 Y Y 3.57696143724454 3.27767621693306 3.27767621693306 0 0 0.422542167391558 Y 0.992672413793103 0.97801724137931 N N 22666 1823 ENSG00000111684 ENSG00000126749 + + 12 12 6996103 6955232 intron coding LPCAT3 EMG1 6955608 6950348 - + 0 6962424 6954801 - + N 1.21742472556179 - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.581560283687943 0 0.581560283687943 7 0.949852505270192 0.949852505270192 0.949852505270192 0.949852505270192 4 0 - 29509 N Y 3.43677165801469 3.47336426491055 3.43677165801469 342 0.792554652851368 0.00184142840088430 N 0.839397150594607 0.785862867459476 N N 95833 736 ENSG00000204525 ENSG00000204622 - + 6 6 31432935 30085708 utr3p utr3p HLA-C HLA-J 31344505 30082339 - + 0.424506456297343 31429788 30085555 + + N - - Y HCC1954 2 1.6 1 3 1 N - - N - - 0 0 0 5 0.635615586233437 0.728458312312478 0.728458312312478 0.635615586233437 1 - - 25396 N N 3.57233464462502 3.65657572715995 3.57233464462502 2 0 0.0453362015401577 N 0 0 N N 2873 1906 ENSG00000136146 ENSG00000069974 + + 13 15 47567268 53369293 coding utr3p MED4 RAB27A 47548093 53283094 - - 0 47549385 53283175 - - Y - - N HCC1954 36 32.2857142857143 27 7 1 N - - N - SINE,SINE 0 1 1 7 1.04269523134923 0.299953422716903 1.04269523134923 0.299953422716903 1 - - 45113 N Y 3.2965682984157 3.7527243339695 3.2965682984157 0 0 0.208163821534653 N 0.740186586868509 0.97113184298539 N N 0 82 ENSG00000219443 ENSG00000214562 + + 10 10 81435395 88984892 upstream downstream RP11-773D16.3 FAM22A 81433020 88975185 + + 0 81420936 89038235 + + N - - Y HCC1954 16 11.3846153846154 4 13 1 N 534 16.3728 N - SINE 0 0.597014925373134 0.597014925373134 13 0.414221393275723 0.956994253430118 0.956994253430118 0.414221393275723 1 - - 28377 N Y 3.37336081542618 3.50421730383029 3.37336081542618 0 0 0.0689243218573865 N 0.848687747421925 0.785640975514393 N N 17 45068 ENSG00000165061 ENSG00000205336 - + 8 16 40874500 56256445 intron upstream ZMAT4 GPR56 40507270 56220023 - + 0 40786711 56211295 + + Y 1.20544829232941 - N HCC1954 16 13.1739130434783 12 23 1 N - - N SINE,SINE - 1 0 1 23 0.292811674556976 0.707033067832699 0.707033067832699 0.292811674556976 0 0 - 10451 Y Y 3.60888739872753 3.35247714231727 3.35247714231727 92 0 0.565621072966459 Y 0.585754720361148 0.982372541291964 N N 256 0 ENSG00000167524 ENSG00000203459 + + 17 17 23965338 23958792 coding upstream AC005726.6 AC005726.1-3 23959109 23958639 - + 0 23962712 23956360 - + N - - N HCC1954 21 5.875 1 2 2 N - - Y - Other 0 1 1 8 0.807017542071667 0.757025304952183 0.807017542071667 0.757025304952183 4 - - 33213 N N 3.1986844216336 2.8616666583314 2.8616666583314 0 0 0.78310470425355 N 0 0 Y N 171855 247001 ENSG00000198886 ENSG00000198786 - + MT MT 12138 14149 coding coding MT-ND4 MT-ND5 10761 12338 + + 0 11236 14084 - + N 0.822758636538603 - N HCC1954 1 1 1 0 3 Y 189 4.09957 N - - 0 0 0 7 1.47834186910473 1.09268746846872 1.47834186910473 1.09268746846872 1 0 - 20860 N Y 3.50529022639353 3.18040125439778 3.18040125439778 6 0 0.161712404037795 N 0.381302907618697 0.894368789105631 N N 86 10428 ENSG00000117400 ENSG00000114346 - + 1 3 43592722 174021957 utr3p intron MPL ECT2 43576062 173951207 + + 0.894368789105631 43591770 173951361 - + Y - 0.443838089061747 N HCC1954 36 27.5789473684211 22 19 1 N - - N SINE - 1 0 1 19 0.392796148795944 0.557056356474248 0.557056356474248 0.392796148795944 1 - 0 4276 N Y 3.76426113588353 3.38296880644625 3.38296880644625 228 0 0.436643111689976 Y 0.949203365556749 0.969522019334049 N N 0 0 ENSG00000201959 ENSG00000186704 - + 7 7 76509001 76483049 upstream downstream Y_RNA PMS2L11 76508900 76469431 + + 0 76507204 76486250 - + N - - N HCC1954 24 8.08333333333333 2 12 2 N - - N - LTR,LTR 0 1 1 12 0.849868031031224 0.5713398527941 0.849868031031224 0.5713398527941 4 - - 158 N Y 3.5816815158199 3.22010665097245 3.22010665097245 192 0 0.00560247142442682 Y 0 0 N N 0 34 ENSG00000196447 ENSG00000180475 - - 11 11 57812436 57752923 intron upstream AP000435.5-2 OR10Q1 57808145 57751964 + - 0 57810387 57758683 - + N 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 0.549914608314322 0.678466075192994 0.678466075192994 0.549914608314322 1 0 - 35011 N Y 3.43511609362884 3.33255199106474 3.33255199106474 0 0 0.762749519055581 N 0.97410638896707 0.993526597241767 N N 13649 111 ENSG00000148110 ENSG00000188152 + + 9 9 96263022 98744393 coding downstream HIATL1 FAM22G 96176654 98721960 + + 0 96240630 98744856 + + N - - Y HCC1954 4 3.94444444444444 2 36 2 N 261 23.4476 N - - 0 0 0 36 1.24266417982717 1.16410495006798 1.24266417982717 1.16410495006798 1 - - 21386 N N 3.64231043829683 3.18188898491428 3.18188898491428 7 0 0.153453961051893 N 0 0.111375111375111 N N 11670 310 ENSG00000117360 ENSG00000053524 - + 1 3 148592292 184628549 coding utr3p PRPF3 MCF2L2 148560642 184378525 + - 0.111375111375111 148572098 184378705 - - Y 1.15468725769604 - N HCC1954 35 34.8 34 5 1 N - - N - SINE 0 1 1 5 0.464213630395207 0.278528178237124 0.464213630395207 0.278528178237124 2 0 - 20577 N N 3.28036485108879 3.54400240599166 3.28036485108879 1 0 0.181306142570456 N 0 0 N N 0 568998 ENSG00000212679 ENSG00000156508 - + 1 6 559619 74288344 intron intron RP5-857K21.10 EEF1A1 558939 74282194 + - 0 559616 74284797 - - Y 1 0.258130970250347 N HCC1954 14 10 6 9 1 N - - N - - 0 0 0 9 0.964136001590045 1.02841173502938 1.02841173502938 0.964136001590045 2 0 0 3832 N N 3.4178566485931 3.39065076568547 3.39065076568547 37 0 0.295097050406498 N 0.581114058355438 0.122334217506631 N N 5969 879 ENSG00000066855 ENSG00000152926 - + 8 7 66785339 64088849 utr5p downstream MTFR1 ZNF117 66719528 64072265 + - 0.132307692307692 66744662 64066158 - - Y 2.90956936496812 - N HCC1954 20 20 20 4 1 N - - N - Other 0 1 1 4 0.585623349113953 0.771308801272036 0.771308801272036 0.585623349113953 4 0 - 41741 Y N 3.07990329137346 3.11704384497176 3.07990329137346 14 0.0300361570247935 0.954494949394782 Y 0.746177685950413 0 N N 9799 0 ENSG00000076554 ENSG00000222697 - - 8 8 81155565 81279688 coding upstream TPD52 SRP_euk_arch 81109662 81279396 - + 0 81139320 81246263 + - N - - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.00581395348837209 0.00581395348837209 1086 2.12824095165802 1.22838068350732 2.12824095165802 1.22838068350732 1 - - 16676 N N 3.39483647792751 3.53784803006229 3.39483647792751 14 0 0.0682419274673449 N 0 0.123907103825136 N N 252027 9945 ENSG00000141738 ENSG00000159363 - - 17 1 35157070 17211010 utr5p intron GRB7 ATP13A2 35147713 17185040 + - 0.123907103825136 35147875 17194747 - + Y 0.410465831783318 1.32932403448828 N HCC1954 21 20.2 20 5 1 N - - N - SINE,SINE 0 1 1 5 0.471355378555133 0.321378667196682 0.471355378555133 0.321378667196682 2 0 0 13793 N Y 3.61041498203738 3.13656776864017 3.13656776864017 267 0 0.0121062080950892 Y 0 0 N N 24800 34 ENSG00000186716 ENSG00000100218 - - 22 22 21990224 21817208 upstream intron BCR RTDR1 21852552 21731594 + - 0 21852151 21812720 - + N - 2.57421287285878 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.614190341753658 0.657040830713216 0.657040830713216 0.614190341753658 2 - 0 36 Y Y 3.18655563032715 3.59590695188967 3.18655563032715 308 0 0.0533573768198804 Y 0.859517998779744 0.986620761788547 N N 3722 2427 ENSG00000110080 ENSG00000110063 - + 11 11 125815743 125720853 upstream intron ST3GAL4 DCPS 125730789 125678857 + + 0 125730547 125717427 - + N - 0.91159771214403 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 58 0.949852505270192 1.1141127129485 1.1141127129485 0.949852505270192 4 - 0 38405 N Y 3.63296356710195 3.46807512488172 3.46807512488172 0 0 0.319016120614327 Y 0.978488496331648 0.978488496331648 N N 11716 1311 ENSG00000213741 ENSG00000165501 - - 14 14 49122844 49151705 coding upstream RPS29 PPIL5 49113809 49135165 - + 0 49122517 49134868 + - N - - N HCC1954 3 2 1 2 1 N - - N - - 0 0 0 4 0.721316564152552 0.599906845433805 0.721316564152552 0.599906845433805 4 - - 27058 Y Y 3.65401507408021 3.0667948634596 3.0667948634596 0 0.00254452926208648 0.62781188970862 Y 0.558817772558231 0.993606054674757 N N 6267 30723 ENSG00000040199 ENSG00000166747 - + 16 16 70306205 70400477 coding downstream PHLPPL AP1G1 70232304 70320404 - - 0 70294134 70315172 + - N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.214285714285714 0.214285714285714 6 1.13553795742827 0.499922371194838 1.13553795742827 0.499922371194838 1 - - 21529 N Y 3.22332965146149 3.5465630590714 3.22332965146149 0 0 0.208391621790073 N 0.42212144116906 0 N N 5170 124 ENSG00000116918 ENSG00000099139 + + 1 9 229768890 78163658 upstream intron TSNAX PCSK5 229731022 77695406 + + 0 229725009 78120508 + + Y - 2.37752054094933 N HCC1954 26 21.75 13 4 1 N - - N LTR SINE 1 1 1 4 0.549914608314322 0.385654400636018 0.549914608314322 0.385654400636018 2 - 0 18205 Y Y 3.59784511035345 3.4780843434859 3.4780843434859 264 0 0.0073219813780917 Y 0.913303049967554 0.985550508327925 N N 0 0 ENSG00000218833 ENSG00000220261 - - 1 1 222257979 222242479 upstream intron RP11-504P24.3 RP11-504P24.2 222250220 222237079 + - 0 222246660 222240965 - + N - 1 N HCC1954 10 9.5 9 4 2 N - - Y - - 0 0 0 4 0.421363141435649 0.364229156156239 0.421363141435649 0.364229156156239 2 - 0 748 Y Y 3.53039946453785 2.82085783396995 2.82085783396995 1 0 0.99189691930077 Y 0.994489268203077 0.994489268203077 N Y 103869 1594 ENSG00000117984 ENSG00000188082 + - 11 11 1741798 1728397 coding coding CTSD AC068580.3 1730561 1710216 - - 0 1731609 1725925 - + N - 7.79243224517708 N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 90 1.52833410622422 1.38549914302569 1.52833410622422 1.38549914302569 4 - 0 1368 N Y 3.67849247003875 3.64081336021051 3.64081336021051 0 0 0.741367647011032 N 0 0.901810865191147 N N 3301 3780 ENSG00000070081 ENSG00000115020 - + 11 2 17309646 208931720 coding utr3p NUCB2 PIP5K3 17254860 208839236 + + 0 17273447 208929440 - + Y - - N HCC1954 38 33.25 25 4 1 N - - N - SINE 0 1 1 4 0.357087407996313 0.321378667196682 0.357087407996313 0.321378667196682 2 - - 34219 N Y 3.36976709257655 2.79313874238274 2.79313874238274 280 0 0.870942769384935 Y 0 0.990687583444593 N N 12832 1085 ENSG00000181090 ENSG00000203993 - - 9 9 139850397 139633086 utr5p upstream EHMT1 C9orf37 139711440 139629606 + - 0 139725238 139633320 - + N 0.0556685809233559 - N HCC1954 1 1 1 0 4 N - - N - Simple_repeat 0 0.770491803278688 0.770491803278688 5 0.928427260790413 0.821301038391519 0.928427260790413 0.821301038391519 3 0 - 10101 N N 3.46807512488172 3.40744620240479 3.40744620240479 3 0 0.68758006249429 N 0.993122188905547 0 Y Y 1572 8390 ENSG00000136447 ENSG00000120071 - + 17 17 42012364 41625943 coding coding ARL17P1 KIAA1267 41949797 41463181 - - 0 42003551 41527743 + - N - - N HCC1954 6 2.18518518518519 2 54 1 Y 498 1.79514 N LTR - 0.502304147465438 0 0.502304147465438 54 1.42834963198525 1.07126222398894 1.42834963198525 1.07126222398894 4 - - 16825 N N 3.09508724929961 3.28871850530713 3.09508724929961 5 0 0.124382708496996 N 0 0.0169343065693431 N N 443941 0 ENSG00000172057 ENSG00000212678 - - 17 1 35337380 560165 utr3p intron ORMDL3 RP5-857K21.11 35330822 559619 - + 0.0169343065693431 35331580 559638 + - Y - 1 N HCC1954 2 2 2 4 1 N 506 15.0412 N - - 0 0 0 4 0.857009779191151 1.12839620926835 1.12839620926835 0.857009779191151 1 - 0 2769 N Y 3.13904871613321 3.58849823915857 3.13904871613321 0 0.872857265914377 0.403723358617406 N 0.915238177276251 0.915238177276251 N N 4153 36780 ENSG00000120533 ENSG00000156599 - + 8 11 110425074 57225235 coding upstream ENY2 ZDHHC5 110415764 57191944 + + 0 110417535 57189364 - + Y - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 76 1.29265641694665 0.378512652476092 1.29265641694665 0.378512652476092 2 - - 49124 Y Y 3.51576345331414 3.31063524818594 3.31063524818594 322 0 0.00213142715639048 Y 0 0.992560489478076 N N 6 40405 ENSG00000204661 ENSG00000169045 + - 5 5 179004614 178984276 downstream utr5p AC136604.2-1 HNRNPH1 179001166 178973785 - - 0 178993628 178982799 - + N - 36.8216418667958 N HCC1954 2 2 2 4 1 N - - Y LTR - 0.530612244897959 0 0.530612244897959 4 0.628473838073511 0.664182578873142 0.664182578873142 0.628473838073511 2 - 0 31374 Y N 2.90825913626163 3.37295958784206 2.90825913626163 0 0 0.0848911658751055 Y 0.00507614213197982 0 N N 26070 6477 ENSG00000132182 ENSG00000144711 + - 3 3 13436809 12983960 downstream intron NUP210 IQSEC1 13332737 12914374 - - 0 13299214 12958366 - + N - 5.34385936588847 N HCC1954 1 1 1 0 1 N - - Y Low_complexity - 0.44578313253012 0 0.44578313253012 15 0.592765097273879 0.707033067832699 0.707033067832699 0.592765097273879 1 - 0 26548 N Y 3.54975555433691 3.70512929149291 3.54975555433691 73 0 0.0978783421826996 N 0 0.853973799126638 N N 105 6304 ENSG00000196796 ENSG00000196696 - + 16 16 28577452 68657352 upstream intron AC145285.2-1 PDXDC2 28563412 68567713 + - 0 28563397 68584217 - - N - 0.415584680567614 Y HCC1954 48 27 18 4 1 N - - N - SINE 0 0.14792899408284 0.14792899408284 4 0.414221393275723 0.635615586233437 0.635615586233437 0.414221393275723 2 - 0 32935 N Y 3.33784113109357 3.65231965690101 3.33784113109357 144 0.87889566395664 0.00293159769806350 N 0.87889566395664 0.87889566395664 N N 2906 1157 ENSG00000214135 ENSG00000185986 + - 3 5 196895854 1646257 coding coding AC069513.28-1 AC091849.2 196874647 1625243 + - 0 196895804 1625397 + + Y - 0.420092449948565 N HCC1954 2 1.75 1 3 1 Y 373 21.2183 N - - 0 0 0 4 0.28566992639705 0.628473838073511 0.628473838073511 0.28566992639705 1 - 0 40937 N Y 3.64400585547602 3.18342591579394 3.18342591579394 172 0 0.0124928615589596 Y 0.0058139534883721 0 N N 1 9050 ENSG00000124092 ENSG00000132819 + + 20 20 55534041 55417795 downstream downstream CTCFL RBM38 55505630 55399870 - + 0 55503670 55443523 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.492780623034912 0.899860268150708 0.899860268150708 0.492780623034912 2 - - 31348 Y Y 3.4210491438586 3.31695745798465 3.31695745798465 0 0 0.764933195871352 Y 0.973076923076923 0.982051282051282 N N 1844 1031 ENSG00000179021 ENSG00000175105 - + 3 3 88289801 88276504 upstream intron C3orf38 ZNF654 88281583 88270952 + + 0 88281551 88272918 - + N - 2.30081462380602 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 0.749883556792257 0.821301038391519 0.821301038391519 0.749883556792257 4 - 0 38197 Y N 3.03586211895315 3.6491271616355 3.03586211895315 0 0 0.0935742872311174 Y 0.218164188752424 0.42792501616031 N N 8613 1102 ENSG00000071537 ENSG00000140022 + - 14 14 81069886 80934680 downstream upstream SEL1L STON2 81007646 80806662 - - 0.42792501616031 80972516 80963269 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.376811594202899 0.376811594202899 5 0.657040830713216 0.492780623034912 0.657040830713216 0.492780623034912 2 - - 40964 Y Y 3.3739528048186 3.55657227767559 3.3739528048186 303 0 0.0124066778633081 Y 0.99331074047002 0.98662148094004 N N 0 0 ENSG00000218697 ENSG00000218860 + - 20 20 22894700 22814706 upstream upstream RP11-189G24.2 CYB5P4 22889171 22814308 - - 0 22895302 22845620 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE LINE 0.916083916083916 1 1 10 1.02126998686945 1.0069864905496 1.02126998686945 1.0069864905496 4 - - 38108 Y Y 3.37548038812845 3.79362644428678 3.37548038812845 346 0 0.0152936258179921 Y 0.992928299102201 0.985856598204403 N N 4802 4944 ENSG00000027075 ENSG00000182107 - - 14 14 61087443 60817712 upstream upstream PRKCH TMEM30B 60858186 60814159 + - 0 60843539 60834987 - + N - - N HCC1954 8 1.53846153846154 1 1 1 N - - Y SINE - 0.647887323943662 0 0.647887323943662 13 1.01412823870953 1.3069399132665 1.3069399132665 1.01412823870953 4 - - 36333 Y Y 3.41741556821562 3.47233119514066 3.41741556821562 254 0 0.802491615802636 Y 0 0.983803853786569 N N 37 351 ENSG00000139194 ENSG00000205885 + + 12 12 7172754 7165701 intron coding RBP5 AC018653.29-1 7167557 7152443 - + 0 7171451 7164497 - + N 1.00814598354028 15.3479964663511 N HCC1954 1 1 1 0 3 N - - Y DNA,LINE - 0.730769230769231 0 0.730769230769231 8 0.742741808632331 0.828442786551446 0.828442786551446 0.742741808632331 4 0 0 9765 Y Y 3.43784458057793 3.38080938095063 3.38080938095063 6 0 0.977918475655641 Y 0 0.987151120944739 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron utr3p C17orf76 C17orf45 16286053 16283081 - + 0 16306711 16285119 - + N 3.43189971253672 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 7 0.649899082553289 0.464213630395207 0.649899082553289 0.464213630395207 2 0 - 2279 N Y 3.56591914887046 3.39128260787123 3.39128260787123 0 0 0.117731108395480 N 0.828818044354839 0.844380040322581 N N 238 12271 ENSG00000076706 ENSG00000177479 - - 11 3 118693050 48997971 utr5p intron MCAM ARIH2 118684444 48931285 - + 0 118689462 48939897 + - Y - 0.963247002497696 N HCC1954 32 25.6 1 4 1 N - - N SINE Simple_repeat 1 0.0972222222222222 1 5 0.271386430077198 0.51420586751469 0.51420586751469 0.271386430077198 1 - 0 20596 N Y 3.60256518892881 3.67849247003875 3.60256518892881 0 0 0.42025234618195 N 0.774465898245357 0.755671389765803 N N 0 7 ENSG00000207623 ENSG00000124721 - + 1 6 207672210 39106545 upstream intron hsa-mir-205 DNAH8 207672101 38792313 + + 0.755671389765803 207669147 38803812 - + Y - 1.13701473697666 N HCC1954 2 1.13636363636364 1 3 1 N - - N SINE SINE 0.188679245283019 1 1 22 0.757025304952183 0.28566992639705 0.757025304952183 0.28566992639705 1 - 0 5696 N Y 3.40528677690917 3.30232144676095 3.30232144676095 9 0 0.0723499732228982 N 0 0.892598480833775 N N 2706 0 ENSG00000132326 ENSG00000213113 - + 2 3 238861946 199332046 utr3p downstream PER2 AC073135.3-1 238817418 199330983 - + 0 238818358 199368867 + + Y - - N HCC1954 156 142.909090909091 108 11 1 N 378 24.4915 N SINE - 1 0 1 11 0.335662163516534 0.621332089913584 0.621332089913584 0.335662163516534 2 - - 27284 N Y 3.5507886241068 3.20079041396673 3.20079041396673 0 0 0.216821028589644 N 0.905023547880691 0.928767660910518 Y N 18192 3423 ENSG00000157106 ENSG00000169246 + - 16 16 18844887 21365985 coding intron SMG1 AC008740.7-1 18723677 21321106 - - 0 18777033 21344199 - + N - 6.37633175960702 N HCC1954 21 8.14814814814815 3 27 1 N 338 25.8583 N - SINE,SINE 0 0.56969696969697 0.56969696969697 27 0.664182578873142 1.17124669822791 1.17124669822791 0.664182578873142 1 - 0 36315 Y Y 3.18399497724741 3.42424163912411 3.18399497724741 335 0 0.00474039261178127 Y 0 0.988922056384743 N N 0 0 ENSG00000198923 ENSG00000210725 - - 12 12 74645047 74638176 downstream downstream AC011611.26-2 AC011611.26-1 74644079 74637880 + - 0 74663846 74636574 - + N - - N HCC1954 3 1.28571428571429 1 1 1 N - - Y LINE LINE,DNA 1 0.919540229885057 1 7 0.914143764470561 0.621332089913584 0.914143764470561 0.621332089913584 4 - - 33011 N N 3.28552601004162 3.17932833183454 3.17932833183454 0 0 0.99999775359902 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8381 11284 - + N 0.20081558422945 0.887000711039733 N HCC1954 6 3.2 2 5 12 Y 189 4.09957 N - - 0 0 0 5 1.21409718718746 0.699891319672773 1.21409718718746 0.699891319672773 2 0 0 7922 N N 3.44040523365767 3.44143830342756 3.44040523365767 2 0 0.0574857733360038 N 0.20337552742616 0.433171048360922 N N 307 0 ENSG00000214184 ENSG00000213430 + + 2 4 108517107 145987949 utr3p downstream AC012487.12-1 AC109811.4 108492643 145987174 - + 0 108493134 146006712 - + Y - - N HCC1954 580 545 440 4 1 N - - N SINE LINE 1 1 1 4 0.292811674556976 0.278528178237124 0.292811674556976 0.278528178237124 1 - - 21484 N N 2.09044429747436 2.97699410973283 2.09044429747436 34 0 0.0523531591362542 N 0.559374085990056 0.406112898508336 N N 982 11502 ENSG00000162552 ENSG00000159921 - + 1 9 22342106 36248450 utr3p utr3p WNT4 GNE 22316385 36204430 - - 0 22318286 36206333 + - Y - - N HCC1954 748 712.25 682 4 1 N 218 25.5901 N Simple_repeat SINE 1 1 1 4 0.257102933757345 0.442788385915428 0.442788385915428 0.257102933757345 1 - - 16163 N N 3.60103760561896 3.53039946453785 3.53039946453785 0 0 0.687098680444535 N 0 0 N N 14038 30525 ENSG00000115183 ENSG00000134202 - + 2 1 159797412 110085183 intron coding TANC1 GSTM3 159533392 110078077 + - 0 159621514 110082480 - - Y 0.680008452721304 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.257102933757345 0.535631111994469 0.535631111994469 0.257102933757345 2 0 - 29638 N Y 3.28399842673177 3.25992225835735 3.25992225835735 157 0 0.278352831233053 Y 0 0.970339385873182 N N 7010 6367 ENSG00000146457 ENSG00000112096 - - 6 6 160097339 160034343 utr5p coding WTAP SOD2 160068142 160020141 + - 0 160068290 160033791 - + N - 0.911862082616161 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 12 0.699891319672773 0.799875793911741 0.799875793911741 0.699891319672773 2 - 0 21788 N Y 3.42254622194492 3.64553343878587 3.42254622194492 286 0.901110340041638 0.00171588378155119 N 0.901110340041638 0.80982757700315 N N 712661 0 ENSG00000111640 ENSG00000219966 + - 12 1 6517797 119840987 coding intron GAPDH RP5-920G3.2 6513918 119839985 + - 0.80982757700315 6515960 119840917 + + Y - 1 N HCC1954 4 1.8 1 2 1 N - - N - - 0 0 0 5 0.5713398527941 0.649899082553289 0.649899082553289 0.5713398527941 1 - 0 33001 N Y 3.38383404234679 3.34040178417331 3.34040178417331 358 0.0745921787709498 0.00229646811681372 Y 0.0745921787709498 0.880335195530726 N N 247001 151141 ENSG00000198786 ENSG00000198888 - + MT MT 14149 4264 coding coding MT-ND5 MT-ND1 12338 3308 + + 0 13720 4231 - + N 1.04101289839273 1.7871488758144 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.614190341753658 0.99270299422975 0.99270299422975 0.614190341753658 3 0 0 31392 Y Y 3.04214963363171 3.76848670091893 3.04214963363171 309 0 0.145000212982322 Y 0.456310679611651 0.977346278317152 N N 2481 3 ENSG00000158092 ENSG00000168917 - + 3 3 138150657 138057422 upstream intron NCK1 TMEM22 138063763 138020551 + + 0 138063279 138048118 - + N - 0.87027027027027 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 1.19981369086761 0.692749571512847 1.19981369086761 0.692749571512847 4 - 0 36591 Y Y 3.59681204058356 3.46551447180198 3.46551447180198 0 0 0.562115961827994 Y 0.862538118695754 0.965634529673938 N N 16989 3257 ENSG00000090615 ENSG00000072609 - + 12 12 131915361 131974257 utr5p utr3p GOLGA3 CHFR 131855568 131927011 - - 0 131914989 131928191 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.778450549431962 0.807017542071667 0.807017542071667 0.778450549431962 2 - - 36748 Y Y 3.42572936964061 3.59169073442408 3.42572936964061 323 0 0.686442020362929 Y 0 0.993609589584822 N N 55227 23800 ENSG00000111319 ENSG00000067182 + - 12 12 6354976 6321522 coding intron SCNN1A TNFRSF1A 6326276 6308185 - - 0 6327500 6313673 - + N - 0.932309771787885 N HCC1954 1 1 1 0 4 Y - - Y Low_complexity - 0.0338983050847458 0 0.0338983050847458 27 1.26408942430695 1.12125446110842 1.26408942430695 1.12125446110842 2 - 0 18267 Y Y 3.57696143724454 3.33528047801382 3.33528047801382 275 0 0.116178652922305 Y 0.991627196333079 0.991627196333079 N N 0 33 ENSG00000209354 ENSG00000177757 + + 1 1 798820 745077 downstream downstream AL669831.13-2 FAM87B 798710 742614 - + 0 777168 753016 - + N - - N HCC1954 6 3 1 5 3 N - - Y - - 0 0 0 6 0.999844742389676 1.16410495006798 1.16410495006798 0.999844742389676 2 - - 7279 N Y 3.52936639476796 3.55657227767559 3.52936639476796 287 0 0.00594388666258527 Y 0.760836236933798 0.99202787456446 N N 8605 6570 ENSG00000196975 ENSG00000115977 - - 2 2 69907095 69724353 upstream upstream ANXA4 AAK1 69822610 69542036 + - 0 69801412 69733920 - + N - - N HCC1954 1 1 1 0 1 N - - N DNA DNA 0.392592592592593 0.2734375 0.392592592592593 6 0.964136001590045 0.914143764470561 0.964136001590045 0.914143764470561 1 - - 5417 N Y 3.47233119514066 3.37126417066287 3.37126417066287 2 0 0.134670102504082 N 0 0.91228680821441 N N 20739 0 ENSG00000143951 ENSG00000199932 - - 2 6 63669355 122574656 utr3p downstream C2orf86 U1 63202041 122574493 - + 0.897667942916812 63309485 122592901 + - Y - - N HCC1954 580 451.428571428571 400 7 1 N - - N LINE LINE 1 1 1 7 0.442788385915428 0.392796148795944 0.442788385915428 0.392796148795944 4 - - 38243 Y Y 3.45297510534159 3.27677112823916 3.27677112823916 288 0 0.182651300746456 Y 0 0 N N 1620 8813 ENSG00000126775 ENSG00000178974 + + 14 14 54948329 54890080 coding downstream KIAA0831 FBXO34 54902863 54807832 - + 0 54906332 54891693 - + N 0.720420502919363 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.08554572030879 0.799875793911741 1.08554572030879 0.799875793911741 4 0 - 35909 N N 2.52863513635247 3.26936241550807 2.52863513635247 0 0.0375 0.228435920731924 N 0.535344827586207 0.103879310344827 N N 5293 78560 ENSG00000102189 ENSG00000112493 + - 12 6 91847238 33390114 intron utr3p EEA1 TAPBP 91690417 33375449 - - 0.103879310344827 91731947 33376426 - + Y 0.448288732240583 0.848618951972173 N HCC1954 168 46.5384615384615 3 13 1 N - - N SINE SINE 0.972972972972973 1 1 13 0.264244681917271 0.449930134075354 0.449930134075354 0.264244681917271 2 0 0 35103 N N 3.5295342286373 3.58743466416515 3.5295342286373 8 0 0.310041464493932 N 0 0.701083032490975 N N 0 0 ENSG00000222476 ENSG00000184565 - + 9 Y 9432367 19698690 intron intron SRP_euk_arch TTTY14 9432060 19553973 + - 0 9432089 19612795 - - Y 1 1 N HCC1954 7 5.25 4 4 1 N - - N srpRNA SINE 1 0.866071428571429 1 4 0.742741808632331 0.628473838073511 0.742741808632331 0.628473838073511 1 0 0 28814 N Y 3.34152813989903 3.76273355257368 3.34152813989903 23 0.0689876578440465 0.375155012209574 N 0.851038025255047 0.841727901833488 N N 5408 0 ENSG00000171466 ENSG00000210272 + + 19 16 9646734 51926076 utr3p downstream ZNF562 AC079416.4-1 9620363 51925975 - + 0.0689876578440465 9620681 51970017 - + Y - - N HCC1954 22 21.2105263157895 20 19 1 N - - N LTR - 1 0 1 19 0.485638874874985 0.692749571512847 0.692749571512847 0.485638874874985 4 - - 16363 N Y 3.41679307359967 3.6052936758779 3.41679307359967 1 0 0.110272827013838 N 0.864986237867594 0.864986237867594 N N 49089 2363 ENSG00000117450 ENSG00000135900 - + 1 2 45760196 224540668 utr5p intron PRDX1 MRPL44 45749295 224530378 - + 0 45760088 224539180 + + Y - 2.04499594176697 N HCC1954 6 3.44444444444444 1 7 1 N - - N - SINE 0 1 1 9 0.628473838073511 0.299953422716903 0.628473838073511 0.299953422716903 1 - 0 17526 Y Y 3.29383981146661 3.48639814491089 3.29383981146661 0 0 0.079188919308508 Y 0.00296735905044498 0 N N 6231 1659 ENSG00000156875 ENSG00000117620 - + 1 1 100321515 100261594 coding coding HIAT1 SLC35A3 100276377 100208128 + + 0 100288106 100260573 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.864151527351077 0.842726282871298 0.864151527351077 0.842726282871298 1 - - 8306 N N 2.46144997190271 3.7297745213208 2.46144997190271 0 0 0.862205276764185 N 0 0.0170755968169762 N N 0 51 ENSG00000182152 ENSG00000115290 + - 5 2 117142614 165186606 downstream intron AC114322.2 GRB14 117142420 165057579 - - 0.0170755968169762 116890300 165138554 - + Y - 1.67260042593817 N HCC1954 2 2 2 24 3 N - - N LINE - 1 0 1 24 1.06412047582901 0.428504889595575 1.06412047582901 0.428504889595575 2 - 0 44920 N Y 3.41489476792923 3.09400074636723 3.09400074636723 166 0 0.0079953449670741 Y 0 0 N N 5901 0 ENSG00000182022 ENSG00000219465 + + 10 10 125841898 125742175 coding upstream RP11-47G11.1 RP11-47G11.3 125757210 125741416 - + 0 125761901 125711566 - + N 0.644086848050091 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.499922371194838 0.699891319672773 0.699891319672773 0.499922371194838 1 0 - 38067 Y Y 3.66385645881505 3.3244060235091 3.3244060235091 240 0 0.0818787623277385 Y 0.705579710144927 0.991340579710145 N N 2 3765 ENSG00000178107 ENSG00000165804 - - 14 14 20654701 20636639 upstream intron AL161668.6-2 ZNF219 20646042 20628076 + - 0 20642511 20631674 - + N - 15.9152742610745 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.557056356474248 0.828442786551446 0.828442786551446 0.557056356474248 1 - 0 21209 N N 3.49061436237648 3.71823771940677 3.49061436237648 0 0 0.0829437562197074 N 0 0 N N 50281 457 ENSG00000135862 ENSG00000168038 - + 1 3 181381350 41978664 intron intron LAMC1 ULK4 181259218 41263097 + - 0 181365985 41541361 - - Y 1.28372031756573 0.951672304265325 N HCC1954 20 14.5714285714286 10 7 1 N - - N - SINE 0 1 1 7 0.45707188223528 0.321378667196682 0.45707188223528 0.321378667196682 2 0 0 22755 N N 3.39487633072086 3.46448140203209 3.39487633072086 1 0 0.259672793355451 N 0 0 N N 0 2752 ENSG00000202536 ENSG00000162852 + - 4 1 113896522 244898484 upstream intron Y_RNA C1orf71 113896421 244796386 - + 0 113928700 244862163 - - Y - 1.2443699952896 N HCC1954 11 4.15217391304348 3 46 1 N - - N - - 0 0 0 46 0.599906845433805 0.271386430077198 0.599906845433805 0.271386430077198 1 - 0 7412 Y Y 3.37758638046158 3.24847874239916 3.24847874239916 0 0 0.793890803452005 Y 0.994168613223332 0.988337226446664 N N 5277 307 ENSG00000169756 ENSG00000214184 - - 2 2 108670134 108517107 coding upstream LIMS1 AC012487.12-1 108571199 108492643 + - 0 108642493 108517482 - + N - - N HCC1954 3 2.21019108280255 1 95 1 N - - Y - Simple_repeat 0 0.116751269035533 0.116751269035533 157 1.22838068350732 1.40692438750547 1.40692438750547 1.22838068350732 4 - - 3780 N N 3.00935843624818 3.39640391403071 3.00935843624818 0 0 0.160722490544894 N 0 0 N N 0 0 ENSG00000217620 ENSG00000209860 - + 8 21 103888783 32832266 upstream upstream AP003356.2 AP000272.2-1 103888246 32832200 + + 0 103838036 32822632 - + Y - - N HCC1954 20 17.0961538461538 15 52 1 N 354 18.0397 N - SINE 0 1 1 52 0.857009779191151 0.28566992639705 0.857009779191151 0.28566992639705 2 - - 40867 N Y 3.53146303953127 3.52617389950245 3.52617389950245 225 0.130464135021097 0.0226961336176447 N 0.0422503516174404 0.873980309423348 N N 1618 261 ENSG00000148200 ENSG00000125966 - - 9 20 126573410 33328218 utr3p intron NR6A1 MMP24 126319380 33278095 - + 0.0926582278481014 126321974 33323223 + - Y - 0.210873212770377 N HCC1954 39 27.5 23 4 1 N - - N SINE - 1 0 1 4 0.385654400636018 0.521347615674617 0.521347615674617 0.385654400636018 3 - 0 32884 N Y 3.44785379918211 3.48809356209009 3.44785379918211 2 0 0.109708974409116 N 0 0.938801529961751 N N 3772 11413 ENSG00000151576 ENSG00000112877 - + 3 5 115289954 706664 utr3p intron QTRTD1 CEP72 115258301 665405 + + 0 115289013 665560 - + Y - 0.779055593662006 N HCC1954 38 32 21 7 1 N - - N SINE - 1 0 1 7 0.307095170876829 0.421363141435649 0.421363141435649 0.307095170876829 2 - 0 30216 N Y 3.32895826821511 3.20487865035633 3.20487865035633 0 0.549138638228056 0.478845004071723 N 0.605496308449549 0.643068088597211 N N 10598 153380 ENSG00000112062 ENSG00000185275 - + 6 Y 36186513 19614093 intron utr3p MAPK14 CD24L4 36103551 19611898 + - 0.643068088597211 36123460 19612783 - - Y 0.689186772774346 - N HCC1954 1 1 1 0 1 N - - N SINE SINE 1 0.506024096385542 1 4 0.328520415356608 0.592765097273879 0.592765097273879 0.328520415356608 3 0 - 10891 N Y 3.57229479183167 3.12804628055249 3.12804628055249 0 0 0.248361143079735 N 0 0.957268170426065 N N 0 1649619 ENSG00000180518 ENSG00000141736 + - 6 17 51383062 35138441 downstream intron AL158050.8 ERBB2 51382838 35104766 - + 0 51258284 35125062 - - Y - 0.991162890469566 N HCC1954 22 22 22 10 1 N 409 22.0258 N SINE - 1 0 1 10 0.328520415356608 0.449930134075354 0.449930134075354 0.328520415356608 2 - 0 8098 N N 2.16621732508409 2.38809629360432 2.16621732508409 6 0 0.196970739975407 N 0.557496360989811 0 N N 5996 11 ENSG00000187678 ENSG00000179915 - + 5 2 141684750 51113178 utr3p utr3p SPRY4 NRXN1 141670189 50000992 - - 0.0928675400291122 141671705 50001369 + - Y - - N HCC1954 39 36.2 34 5 1 N - - N - Simple_repeat 0 1 1 5 0.392796148795944 0.328520415356608 0.392796148795944 0.328520415356608 1 - - 5240 N N 3.37973645838739 3.2222168761049 3.2222168761049 0 0.288220551378446 0.130025338692948 N 0.448370927318296 0.288220551378446 N N 1266 0 ENSG00000170260 ENSG00000147974 - + 7 9 148583619 33666649 utr5p upstream ZNF212 AL356489.14-3 148567675 33665438 + - 0 148567708 33667015 - - Y - - N HCC1954 16 6 1 2 1 N 320 7.24429 N - Simple_repeat 0 0.682926829268293 0.682926829268293 4 0.592765097273879 0.292811674556976 0.592765097273879 0.292811674556976 1 - - 3409 N N 3.60256518892881 3.35719722089263 3.35719722089263 0 0 0.161201297040992 Y 0 0 N N 15240 0 ENSG00000157540 ENSG00000215353 - - 21 21 37809550 20054277 downstream upstream DYRK1A AP000568.2 37661749 20053544 + - 0 37822410 20181406 - + N - - N HCC1954 1 1 1 0 1 N 217 8.10543 N - - 0 0 0 5 0.471355378555133 0.485638874874985 0.485638874874985 0.471355378555133 2 - - 5419 N N 3.45976132345673 2.96369639456219 2.96369639456219 2 0 0.139266657929949 N 0.636049382716049 0 N N 35 0 ENSG00000213963 ENSG00000204789 - + 2 6 177965661 27447283 utr5p upstream AC079305.6-3 ZNF204 177856484 27433584 - - 0 177884005 27450967 + - Y - - N HCC1954 21 20.5 20 6 1 N - - N LTR - 1 0 1 6 0.328520415356608 0.314236919036755 0.328520415356608 0.314236919036755 3 - - 29356 N N 3.34256120966892 3.47701142092266 3.34256120966892 0 0 0.798204705882397 N 0 0 Y Y 28710 1905 ENSG00000111912 ENSG00000066651 - + 6 6 126293949 126402115 intron coding ESNA1 TRMT11 126144000 126349269 + + 0 126241102 126361523 - + N 0.15021654509283 - N HCC1954 1 1 1 0 1 N 117 3.97072 N - - 0 0 0 7 0.735600060472404 0.757025304952183 0.757025304952183 0.735600060472404 4 0 - 44406 N Y 3.44615838200292 2.24878080211111 2.24878080211111 0 0 0.113017500311400 N 0 0.687622493592643 N N 18564 0 ENSG00000140319 ENSG00000095713 + + 15 10 38118657 99780575 intron upstream SRP14P1 CRTAC1 38115535 99614748 - - 0.687622493592643 38116639 99794243 - - Y 0.606640286692737 - N HCC1954 2 1.2 1 1 1 N - - N - LINE 0 1 1 5 0.407079645115797 0.364229156156239 0.407079645115797 0.364229156156239 2 0 - 41585 Y Y 3.60256518892881 3.57080706131517 3.57080706131517 127 0 0.299041747912094 Y 0.892160219103047 0.978432043820609 N N 0 0 ENSG00000222501 ENSG00000207110 + + 8 8 129092039 129080722 downstream upstream U4 U1 129091912 129080559 - + 0 129091743 129070696 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 7 0.51420586751469 0.371370904316165 0.51420586751469 0.371370904316165 1 - - 4579 Y Y 3.38593068711011 3.43784458057793 3.38593068711011 103 0.00409836065573776 0.957732458329179 Y 0.236475409836066 0.988934426229508 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 upstream coding CRCP ASL 65216341 65178207 + + 0 65212756 65195078 - + N - - N HCC1954 4 1.6 1 1 6 N - - Y LTR - 1 0 1 5 0.757025304952183 1.01412823870953 1.01412823870953 0.757025304952183 1 - - 33536 N N 3.30232144676095 3.39483647792751 3.30232144676095 0 0 0.18141194991559 N 0 0 Y N 247001 0 ENSG00000198786 ENSG00000210194 - - MT MT 14149 14743 coding intron MT-ND5 AF347015.1-22 12338 14675 + - 0 12428 14717 - + N - 1 N HCC1954 3 1.61538461538462 1 7 1 N 189 4.09957 N - - 0 0 0 13 0.978419497909897 1.05697872766909 1.05697872766909 0.978419497909897 3 - 0 2125 N Y 3.49272035470961 3.41526549028982 3.41526549028982 249 0.631622379930682 0.00485408409537835 N 0.727127688837542 0.740771304395665 N N 6060 0 ENSG00000079482 ENSG00000211200 - - X 11 67570372 115003112 utr3p upstream OPHN1 AP000997.1 67179440 115003012 - - 0.849920228860648 67179584 115242018 + + Y - - N HCC1954 60 55.6666666666667 50 6 1 N - - N LINE LINE 1 1 1 6 0.521347615674617 0.271386430077198 0.521347615674617 0.271386430077198 2 - - 44781 N Y 3.23317103619633 3.22332965146149 3.22332965146149 0 0 0.254347734064104 N 0.968450036330261 0.968450036330261 Y N 603 1726 ENSG00000204176 ENSG00000165874 + + 10 10 46390818 88941200 intron downstream SYT15 FAM35A 46372768 88844933 - + 0 46386482 88953717 - + N 0.772112907211746 - N HCC1954 2 1.97142857142857 1 34 1 N - - N - LTR 0 0.2 0.2 35 1.21409718718746 1.09268746846872 1.21409718718746 1.09268746846872 0 0 - 31985 N Y 3.53296011761759 3.42779550918039 3.42779550918039 361 0 0.0040159716724254 N 0.331402669352808 0.943339209267187 N N 0 0 ENSG00000222792 ENSG00000212450 - + 3 7 199408117 45795812 downstream downstream U6 U6 199408014 45795709 + + 0 199419524 45797968 - + Y - - N HCC1954 150 131.2 120 5 1 N 347 25.9331 N SINE - 1 0 1 5 0.664182578873142 0.535631111994469 0.664182578873142 0.535631111994469 2 - - 34870 Y Y 3.15099609320118 3.3755202409218 3.15099609320118 0 0 0.960876257855815 Y 0.993442206803182 0.993442206803182 N Y 364 1351 ENSG00000137070 ENSG00000213930 - + 9 9 34651883 34640571 utr5p coding IL11RA GALT 34643932 34636635 + + 0 34645215 34639561 - + N - 1.73202769854472 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 7 1.05697872766909 1.03555348318931 1.05697872766909 1.03555348318931 4 - 0 49140 N N 3.20015857178097 3.70889084821189 3.20015857178097 0 0.044761744239243 0.54792867943896 Y 0.120175290746671 0 N N 0 21549 ENSG00000201910 ENSG00000063438 - + 5 5 103462638 491392 downstream coding U1 PDCD6 103462474 324736 + + 0 103467775 357292 - + N - - N HCC1954 20 2.46153846153846 1 12 2 N 312 11.8566 N LINE,LTR - 0.610687022900763 0 0.610687022900763 26 0.93556900895034 1.62831858046319 1.62831858046319 0.93556900895034 1 - - 27188 Y Y 3.51679652308403 3.5816815158199 3.51679652308403 0 0 0.872988532052173 Y 0.980064935064935 0.993354978354978 N Y 188 4224 ENSG00000131152 ENSG00000103264 - + 16 16 85908523 85974877 coding intron AC010531.8-2 FBXO31 85893924 85920445 - - 0 85906930 85924993 + - N - 0.912752329035427 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 12 1.01412823870953 1.07840397214886 1.07840397214886 1.01412823870953 4 - 0 38920 N N 3.32316526707651 3.57912086274016 3.32316526707651 0 0.19863670252423 0.204725578069849 N 0.222920438811375 0.0772180210885075 N N 5437 850768 ENSG00000175265 ENSG00000075624 + + 15 7 32487180 5536758 downstream utr3p GOLGA8A ACTB 32458557 5533313 - - 0.0772180210885075 32452959 5533869 - - Y - - N HCC1954 16 5.29411764705882 1 14 1 N 232 23.5936 N - - 0 0 0 17 0.264244681917271 0.921285512630487 0.921285512630487 0.264244681917271 1 - - 38802 N N 3.02382661360254 3.2802368700128 3.02382661360254 0 0 0.48015743415735 N 0 0.146489104116223 N N 2963 3492 ENSG00000133983 ENSG00000123815 - + 14 19 69896147 45914440 coding intron COX16 ADCK4 69680762 45889274 - - 0.146489104116223 69865706 45907401 + - Y - 1.83039323569056 N HCC1954 3 1.8 1 2 1 N - - N - SINE 0 1 1 5 0.478497126715059 0.307095170876829 0.478497126715059 0.307095170876829 3 - 0 9450 Y Y 3.42680229220385 3.68527868815389 3.42680229220385 265 0 0.0343523055760279 Y 0.551698113207547 0.991698113207547 N N 0 275 ENSG00000199961 ENSG00000204303 - + 17 17 72068869 72068110 downstream utr5p snoR38 SNORD1C 72068786 72065446 + + 0.360754716981132 72068964 72065533 - + N - 3.57579743403654 N HCC1954 2 1.7037037037037 1 19 1 N - - Y - - 0 0 0 27 1.01412823870953 0.985561246069823 1.01412823870953 0.985561246069823 1 - 0 26139 N N 3.39487633072086 3.49528100778935 3.39487633072086 0 0 0.0446831429111542 N 0 0 N N 882 7525 ENSG00000167971 ENSG00000173894 + - 16 17 2186466 75375973 intron upstream CASKIN1 CBX2 2167185 75366588 - + 0 2183268 75358159 - - Y 12.6725314183124 - N HCC1954 21 20.25 20 4 1 N - - N SINE LTR 1 1 1 4 0.292811674556976 0.292811674556976 0.292811674556976 0.292811674556976 1 0 - 38104 Y Y 3.22948402739086 3.62192127872787 3.22948402739086 268 0 0.0782070048472543 Y 0.947564807541241 0.989512961508248 N N 2447 4331 ENSG00000157379 ENSG00000100949 + - 14 14 23838770 23810643 intron utr5p DHRS1 RABGGTA 23829646 23804661 - - 0 23837658 23810354 - + N 1.7936746240795 3.80639939049814 N HCC1954 6 1.07766990291262 1 2 3 N - - Y SINE,DNA - 0.685483870967742 0 0.685483870967742 103 0.885576771830856 0.757025304952183 0.885576771830856 0.757025304952183 3 0 0 38245 Y Y 3.34888341946764 3.61786354756182 3.34888341946764 351 0 0.0281034642396438 Y 0 0.583970113771438 N N 182 8277 ENSG00000183484 ENSG00000170779 + - 14 14 104602799 104558538 upstream upstream GPR132 CDCA4 104586773 104547326 - - 0 104608594 104570570 - + N - - N HCC1954 6 1.44444444444444 1 3 2 N - - Y SINE LTR 1 1 1 18 1.34264865406614 1.13553795742827 1.34264865406614 1.13553795742827 2 - - 14146 N Y 3.54296933622177 3.56488607910057 3.54296933622177 1 0 0.609601331283573 N 0.00273972602739736 0.86703196347032 N N 3693 1612 ENSG00000198125 ENSG00000214367 - + 22 4 34349347 2213658 utr5p utr3p MB C4orf15 34332757 2199894 - - 0 34349184 2203000 + - Y - - N HCC1954 34 30.8333333333333 22 6 1 N - - N - SINE 0 1 1 6 1.32122340958636 0.471355378555133 1.32122340958636 0.471355378555133 2 - - 319 Y Y 3.66848325143457 3.78208964237274 3.66848325143457 262 0 0.0512984674647571 Y 0 0.974012612014603 N N 28586 4055 ENSG00000214753 ENSG00000168000 + - 11 11 62251397 62233562 downstream utr5p HNRNPUL2 BSCL2 62238798 62214323 - - 0 62236419 62231342 - + N - 12.1591289077988 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.485638874874985 0.792734045751814 0.792734045751814 0.485638874874985 2 - 0 44569 N Y 3.12023634023727 3.48639814491089 3.12023634023727 232 0 0.00489096405613354 N 0.297160243407708 0.140973630831643 N N 34 0 ENSG00000107611 ENSG00000216027 + - 10 4 17211822 61212351 intron downstream CUBN AC095061.3 16905971 61212262 - - 0.765720081135903 16966125 60902269 - + Y 1.51241768025223 - N HCC1954 154 33 2 16 1 N 342 25.1675 N SINE SINE,SINE 1 0.853658536585366 1 16 0.371370904316165 0.292811674556976 0.371370904316165 0.292811674556976 1 0 - 16417 N Y 3.50678730447985 3.2965682984157 3.2965682984157 0 0 0.480137072651036 N 0.766506109022557 0.75093984962406 N N 213 19744 ENSG00000185495 ENSG00000068878 - - 1 2 222264932 54051481 intron upstream AC138393.2-1 PSME4 222263052 53944708 + - 0 222264886 54051962 - + Y - - N HCC1954 21 20.25 19 4 1 N 523 24.6671 N LTR - 1 0 1 4 0.307095170876829 0.635615586233437 0.635615586233437 0.307095170876829 4 - - 34887 N Y 3.42576922243396 3.30016202126533 3.30016202126533 0 0 0.303662584886049 Y 0 0 N N 5530 271 ENSG00000148154 ENSG00000165181 - - 9 9 113735168 113597044 coding upstream UGCG C9orf84 113698867 113488274 + - 0 113716757 113597285 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.28566992639705 0.314236919036755 0.314236919036755 0.28566992639705 2 - - 47649 Y N 2.06887716220512 3.131238775818 2.06887716220512 0 0 0.142528634573631 N 0 0 N N 746 8022 ENSG00000126460 ENSG00000126464 + + 19 19 54785999 54821507 downstream upstream PRRG2 PRR12 54778280 54790591 + + 0 54786895 54788482 + + N - - Y HCC1954 1 1 1 0 1 N 288 23.6231 N Simple_repeat - 0.0352941176470588 0 0.0352941176470588 7 0.5713398527941 0.771308801272036 0.771308801272036 0.5713398527941 3 - - 20584 N Y 3.38656252929588 3.41679307359967 3.38656252929588 0 0 0.50624052262255 N 0.986727272727273 0.973454545454546 N N 0 8888 ENSG00000201692 ENSG00000112159 + + 1 6 172100669 90586163 downstream intron snosnR60_Z15 MDN1 172100588 90409952 - - 0.973454545454546 172100437 90488018 - - Y - 1.96227421382155 N HCC1954 3 1.625 1 3 2 N - - N - SINE 0 0.25 0.25 8 0.792734045751814 0.885576771830856 0.885576771830856 0.792734045751814 1 - 0 42145 Y Y 3.47233119514066 3.41525614272 3.41525614272 316 0 0.172002775210185 Y 0.950158227848101 0.985759493670886 N N 4707 0 ENSG00000125386 ENSG00000206738 - - 4 4 2704097 2586749 upstream downstream C4orf8 Y_RNA 2596957 2586649 + - 0 2596787 2567854 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 67 1.04269523134923 1.22123893534739 1.22123893534739 1.04269523134923 4 - - 48917 Y Y 2.98734840741354 3.64400585547602 2.98734840741354 184 0 0.0248805183519742 Y 0 0.974821133736929 N N 39039 25 ENSG00000145623 ENSG00000205785 - + 5 5 38970159 38859954 upstream intron OSMR AC091435.3-1 38881893 38848753 + + 0 38881569 38849559 - + N - 0.382180539273154 N HCC1954 3 1.5 1 3 2 N - - Y - SINE 0 1 1 8 0.592765097273879 0.792734045751814 0.792734045751814 0.592765097273879 1 - 0 10201 Y Y 3.54144175291192 3.44508545943967 3.44508545943967 0 0 0.325610914656257 Y 0 0.791135283820955 N N 1244 0 ENSG00000108666 ENSG00000207928 - - 17 17 27693302 27701334 coding upstream C17orf75 hsa-mir-632 27682505 27701241 - + 0 27693145 27700977 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.385654400636018 0.621332089913584 0.621332089913584 0.385654400636018 1 - - 48700 N N 3.42630777866389 3.49384671043534 3.42630777866389 2 0 0.186588515056712 N 0 0 N N 0 45208 ENSG00000152931 ENSG00000119335 - + 5 9 59819923 130498488 upstream coding AC109486.2-2 SET 59819516 130485996 + + 0 59791562 130495903 - + Y - - N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.361111111111111 0 0.361111111111111 4 0.257102933757345 0.292811674556976 0.292811674556976 0.257102933757345 2 - - 9657 Y Y 3.58424216889964 3.16217152032444 3.16217152032444 201 0 0.730726572935479 Y 0 0.976023496972967 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron intron C17orf76 C17orf45 16286053 16283081 - + 0 16314339 16283464 - + N 3.43189971253672 0.402833229639786 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 6 0.578481600954027 0.578481600954027 0.578481600954027 0.578481600954027 1 0 0 42313 Y Y 3.29652844562235 3.61616813038263 3.29652844562235 267 0 0.0627371235591938 Y 0.824190350297422 0.980465594477491 N N 0 0 ENSG00000223208 ENSG00000209291 + - 4 4 120574711 120574710 downstream downstream U6 AC093752.2-3 120574608 120574608 - - 0 120570023 120563177 - + N - - N HCC1954 224 150.875 16 8 1 N - - Y LTR,SINE,SINE SINE 0.754716981132076 1 1 8 0.707033067832699 0.592765097273879 0.707033067832699 0.592765097273879 4 - - 39114 N Y 3.41741556821562 3.60103760561896 3.41741556821562 0 0 0.390762276214066 N 0.985362517099863 0.970725034199726 N N 319 0 ENSG00000166415 ENSG00000222591 - + 15 2 51842367 66320290 coding downstream WDR72 AC118345.1 51593230 66320136 - - 0 51602811 66287300 + - Y - - N HCC1954 25 22.6 20 5 1 N - - N - LINE 0 1 1 5 0.649899082553289 0.392796148795944 0.649899082553289 0.392796148795944 4 - - 41983 N N 3.54400240599166 3.43937216388778 3.43937216388778 19 0.123643651945539 0.574659412957314 N 0.123643651945539 0.00314465408805009 N N 159165 0 ENSG00000164754 ENSG00000219931 + + 8 X 117956182 99944702 coding intron RAD21 RP3-347M6.2 117927355 99942822 - + 0 117944561 99943115 - + Y - 1 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.321378667196682 0.257102933757345 0.321378667196682 0.257102933757345 1 - 0 31423 Y Y 3.36551102231762 3.34934742778406 3.34934742778406 337 0 0.00721954944726744 Y 0 0 N N 5 1833 ENSG00000198685 ENSG00000179348 + - 3 3 129777619 129694718 downstream intron C3orf27 GATA2 129773533 129680962 - - 0 129739542 129691599 - + N - 35.096657582219 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.728458312312478 1.04269523134923 1.04269523134923 0.728458312312478 1 - 0 9713 Y Y 3.34735583615779 3.55657227767559 3.34735583615779 118 0 0.420271342944922 Y 0.480930884184309 0.986340286425903 N N 2256 34343 ENSG00000011258 ENSG00000011052 + + 17 17 46692426 46604104 intron coding MBTD1 NME1-NME2 46609785 46585919 - + 0 46613404 46602409 - + N 0.635653353038152 - N HCC1954 40 5.61290322580645 1 15 2 N - - Y SINE - 1 0 1 31 1.04983697950916 1.4426331283051 1.4426331283051 1.04983697950916 4 0 - 21771 N N 2.93279931295247 3.39384326095097 2.93279931295247 0 0 0.316327908843995 N 0.204081632653061 0.204081632653061 N N 25366 183 ENSG00000139644 ENSG00000203666 + + 12 1 48460589 243352916 intron intron TMBIM6 EFCAB2 48421630 243199794 + + 0.204081632653061 48444771 243250539 + + Y 42.7119851007888 1.20620859078389 N HCC1954 1 1 1 0 1 N - - N - DNA,SINE 0 0.604651162790698 0.604651162790698 13 0.707033067832699 0.307095170876829 0.707033067832699 0.307095170876829 2 0 0 19507 N N 3.5074097990958 3.47076375903745 3.47076375903745 11 0 0.907520102173082 Y 0.0034129692832765 0 N Y 13137 1725 ENSG00000163486 ENSG00000196369 - + 1 1 204704406 142805834 coding coding SRGAP2 SRGAP2P2 204582820 142627547 + + 0 204623992 142627649 - + N - - N HCC1954 6 5.17777777777778 1 133 1 Y - - N - - 0 0 0 135 1.09268746846872 0.792734045751814 1.09268746846872 0.792734045751814 4 - - 18517 N N 3.67849247003875 3.53615261288309 3.53615261288309 2 0 0.694643438013684 N 0.957314974182444 0 Y N 11287 0 ENSG00000178104 ENSG00000213223 + + 1 1 143787552 147820286 intron downstream PDE4DIP AL451058.16-1 143562784 147819627 - + 0 143716138 147844284 - + N 63.3121857012565 - N HCC1954 30 10 5 13 2 N 225 28.4156 N SINE - 0.796116504854369 0 0.796116504854369 13 0.735600060472404 0.414221393275723 0.735600060472404 0.414221393275723 1 0 - 26571 Y Y 3.38552945952599 3.18867520302942 3.18867520302942 448 0 0.0938675298385238 Y 0.827202214684757 0.988851755786113 N N 8642 3792 ENSG00000099381 ENSG00000175938 - + 16 16 30903482 30873757 upstream coding SETD1A ORAI3 30876116 30867916 + + 0 30875022 30872282 - + N - 1.67921748788182 N HCC1954 1 1 1 0 3 N - - Y SINE - 0.456989247311828 0 0.456989247311828 99 1.32836515774628 1.94969724765987 1.94969724765987 1.32836515774628 4 - 0 31768 N Y 3.42729680574381 3.15199091029045 3.15199091029045 193 0.573649148778682 0.0321737235000424 Y 0.28941524796447 0.810510732790526 N N 298 7313 ENSG00000182983 ENSG00000181061 - - 3 3 42933958 42820986 coding upstream ZNF662 HIGD1D 42922406 42800797 + - 0 42925298 42825959 - + N - - N HCC1954 1 1 1 0 3 N - - N - LTR 0 1 1 18 1.34979040222606 0.649899082553289 1.34979040222606 0.649899082553289 1 - - 14613 N Y 2.70587329418536 3.14232091698542 2.70587329418536 6 0 0.0179894948666681 N 0.976014148336465 0.00458715596330261 N N 0 8014 ENSG00000219853 ENSG00000149084 - + 1 11 192954989 43834736 downstream utr3p RP11-489C13.1 HSD17B12 192954548 43658719 + + 0.00458715596330261 193231090 43834024 - + Y - - N HCC1954 20 12.2857142857143 5 7 1 N - - N SINE - 1 0 1 7 0.464213630395207 0.821301038391519 0.821301038391519 0.464213630395207 1 - - 41482 N Y 3.6344911504118 3.53399318738748 3.53399318738748 348 0 0.566611139106917 Y 0.978323338330835 0.992774446110278 N N 0 4 ENSG00000207110 ENSG00000184090 - - 8 8 129080722 129029462 upstream downstream U1 TMEM75 129080559 129029046 + - 0 129070588 128972424 - + N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 35 0.999844742389676 1.42834963198525 1.42834963198525 0.999844742389676 1 - - 49359 Y Y 3.3446273492087 3.56591914887046 3.3446273492087 112 0.00317460317460316 0.88485602029971 Y 0.00317460317460316 0 N N 46607 3556 ENSG00000146063 ENSG00000146054 - - 5 5 180595414 180564783 coding upstream TRIM41 TRIM7 180582912 180553531 + - 0 180584416 180567015 - + N - - N HCC1954 26 3.68181818181818 1 9 3 N - - Y - SINE 0 0.848684210526316 0.848684210526316 22 0.99270299422975 1.08554572030879 1.08554572030879 0.99270299422975 3 - - 36507 Y Y 3.20331121425312 3.66488952858494 3.20331121425312 150 0 0.228874364986796 Y 0.00222222222222235 0.994060846560846 N N 112 2428 ENSG00000053702 ENSG00000111203 + + 12 12 2814451 2804367 intron utr3p NRIP2 ITFG2 2804773 2792124 - + 0 2809639 2803663 - + N 2.9561335424364 - N HCC1954 2 1.25 1 3 2 N - - Y LINE - 0.713414634146341 0 0.713414634146341 12 1.0069864905496 1.34979040222606 1.34979040222606 1.0069864905496 1 0 - 21661 N Y 3.41376841220351 3.57489529770476 3.41376841220351 53 0 0.0150697623952142 N 0.631653511434932 0.742157458004453 N N 49089 0 ENSG00000117450 ENSG00000214121 + - 1 9 45760196 12963437 upstream intron PRDX1 AL161449.7 45749295 12962842 - - 0 45761046 12963379 - + Y - 1 N HCC1954 40 2.75187969924812 2 133 1 N - - N SINE - 1 0 1 133 0.99270299422975 0.607048593593732 0.99270299422975 0.607048593593732 1 - 0 33271 N N 3.53768019619294 2.85847416306589 2.85847416306589 0 0 0.100210746752749 N 0 0 Y N 151141 171855 ENSG00000198888 ENSG00000198886 - + MT MT 4264 12138 coding coding MT-ND1 MT-ND4 3308 10761 + + 0 3664 12055 - + N 0.795446544768818 - N HCC1954 4 1.75 1 1 1 N 168 10.2917 N - - 0 0 0 4 0.721316564152552 0.821301038391519 0.821301038391519 0.721316564152552 2 0 - 47923 N N 3.40319013214585 2.96319769112561 2.96319769112561 0 0 0.976466980363546 N 0 0 N Y 10798 29840 ENSG00000113761 ENSG00000164830 - + 5 8 176426349 107834093 coding utr5p ZNF346 OXR1 176382303 107739270 + + 0 176421665 107739589 - + Y 1.50280302095311 1.03199430721578 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 9 0.742741808632331 1.18553019454776 1.18553019454776 0.742741808632331 4 0 0 40542 N Y 2.42680847320244 2.62977000554364 2.42680847320244 0 0.449915110356536 0.151686222556038 N 0.476109628910987 0 N N 5996 1007 ENSG00000187678 ENSG00000128891 - + 5 15 141684750 38644544 utr3p utr3p SPRY4 C15orf57 141670189 38632592 - - 0.449915110356536 141671703 38633440 + - Y - - N HCC1954 39 36.625 34 8 1 N - - N - Simple_repeat 0 0.984126984126984 0.984126984126984 8 0.435646637755502 0.449930134075354 0.449930134075354 0.435646637755502 1 - - 33548 N N 2.91676369949491 3.29383981146661 2.91676369949491 5 0 0.893458039090502 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 13650 15406 - + N - 1.06845627074886 N HCC1954 1 1 1 0 4 N 189 4.09957 N - - 0 0 0 4 0.842726282871298 0.735600060472404 0.842726282871298 0.735600060472404 2 - 0 32915 N N 3.09555125761603 2.86109759687793 2.86109759687793 0 0.350872879272191 0.114019678944532 N 0.371158101794935 0 N N 551733 0 ENSG00000204628 ENSG00000179170 + + 5 3 180603512 126949420 utr3p downstream GNB2L1 AF186996.5-3 180596536 126946642 - + 0 180596545 126958351 - + Y - - N HCC1954 9 3.25 1 2 2 N - - N - LINE 0 1 1 4 0.785592297591888 0.364229156156239 0.785592297591888 0.364229156156239 2 - - 34149 Y Y 3.63552422018169 3.19806192701765 3.19806192701765 207 0.106899541682151 0.59811078639376 Y 0.987241422024031 0.974482844048061 N N 0 11502 ENSG00000222760 ENSG00000159921 - - 9 9 36257919 36248450 downstream utr5p U4 GNE 36257780 36204430 + - 0 36266891 36239394 - + N - 135.879330455301 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.578481600954027 0.949852505270192 0.949852505270192 0.578481600954027 4 - 0 1575 N Y 3.41423242051993 3.68577320169385 3.41423242051993 0 0 0.203281048958272 N 0.853575050709939 0.853575050709939 N N 6632 1298 ENSG00000158636 ENSG00000154035 - + 11 17 75940234 21097315 upstream utr3p C11orf30 C17orf103 75833717 21082780 + - 0 75832968 21083421 - - Y - - N HCC1954 37 34.7058823529412 4 17 1 N - - N - SINE 0 1 1 17 0.828442786551446 0.364229156156239 0.828442786551446 0.364229156156239 1 - - 5152 Y Y 3.34528969661801 2.91403521254583 2.91403521254583 355 0 0.00132216837494070 Y 0 0 N N 74 239 ENSG00000178459 ENSG00000146530 + - 7 7 12410056 12376543 utr3p upstream AC013470.10-2 VWDE 12383715 12337036 - - 0 12383961 12377148 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.585623349113953 0.857009779191151 0.857009779191151 0.585623349113953 2 - - 37248 N N 2.16780768912624 1.50141938708673 1.50141938708673 0 0 0.0861984072516906 N 0 0 N N 25305 0 ENSG00000153113 ENSG00000213470 + - 5 12 96136143 52313202 utr5p downstream CAST AC073594.31 96023533 52312835 + - 0 96023799 52312250 + + Y 0.0278427559323116 - N HCC1954 20 15.8333333333333 8 6 1 N - - N - Simple_repeat 0 1 1 6 0.771308801272036 0.371370904316165 0.771308801272036 0.371370904316165 1 0 - 41191 Y Y 3.43801241444727 3.3524907226864 3.3524907226864 285 0 0.0186274609569649 Y 0 0.992830998359207 N N 28646 2106 ENSG00000125835 ENSG00000088876 - + 20 20 2399499 2453165 coding coding SNRPB ZNF343 2390281 2410463 - - 0 2396391 2412175 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.685607823352921 0.607048593593732 0.685607823352921 0.607048593593732 1 - - 20600 N N 3.26037691910396 3.4503745994685 3.26037691910396 10 0 0.100471143842484 N 0 0 N N 10 67499 ENSG00000143603 ENSG00000124614 + - 1 6 153109378 34501814 intron intron KCNN3 RPS10 152946541 34493209 - - 0 153022073 34493345 - + Y 1.45566647093365 1.05874787194176 N HCC1954 54 16 3 4 1 N 2 20.9254 N SINE - 1 0 1 4 0.349945659836387 0.28566992639705 0.349945659836387 0.28566992639705 2 0 0 36262 Y Y 3.59102838701478 3.28193228719199 3.28193228719199 316 0 0.00157138988391703 Y 0 0.982813182016587 N N 234233 0 ENSG00000150991 ENSG00000209201 + + 12 12 123965530 123952075 intron upstream UBC AC126309.8 123962147 123952011 - + 0 123964905 123941265 - + N 4.29170405212757 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.364229156156239 0.435646637755502 0.435646637755502 0.364229156156239 1 0 - 4460 Y Y 3.21228736308742 3.52101274054962 3.21228736308742 251 0 0.239183326728261 Y 0 0.974461129839616 N N 0 0 ENSG00000223022 ENSG00000209951 + - 7 7 86961 86960 downstream downstream U6 AC097646.2-1 86858 86858 - - 0 82428 72083 - + N - - N HCC1954 120 62.6 8 5 3 N - - Y LTR,SINE - 0.619354838709677 0 0.619354838709677 5 1.10697096478857 0.51420586751469 1.10697096478857 0.51420586751469 4 - - 47337 Y Y 3.63825270713077 3.33416770265723 3.33416770265723 333 0 0.169904531888848 Y 0 0.993920750018311 N N 16146 7111 ENSG00000167491 ENSG00000129933 - + 19 19 19480736 19339989 utr5p downstream GATAD2A KIAA0892 19399336 19292614 + + 0 19399366 19357946 - + N - - N HCC1954 37 13.1 1 7 3 N - - Y SINE Simple_repeat 1 0.252941176470588 1 10 0.971277749749971 1.09982921662864 1.09982921662864 0.971277749749971 1 - - 36692 Y Y 3.48081283043499 3.59169073442408 3.48081283043499 104 0.00338983050847441 0.223291524849242 Y 0.990508474576271 0.971525423728814 N N 889 15151 ENSG00000002016 ENSG00000082805 - - 12 12 929124 1475360 utr5p upstream RAD52 ERC1 891516 970665 - + 0 912503 969236 + - N - - N HCC1954 2 1.125 1 1 1 N - - Y - SINE 0 0.190909090909091 0.190909090909091 8 1.1426797055882 0.785592297591888 1.1426797055882 0.785592297591888 4 - - 5561 N Y 3.28036485108879 3.8333716936548 3.28036485108879 0 0 0.721636696947973 N 0.29329194223242 0.957169208620147 N N 0 3966 ENSG00000217835 ENSG00000175772 + + X 2 65093763 110111006 downstream upstream AL034397.1 AC013268.5-1 65092856 110103138 - + 0.303999640077383 65076057 110102056 - + Y - - N HCC1954 60 45 40 4 1 N 466 26.9668 N LINE - 1 0 1 4 0.328520415356608 0.428504889595575 0.428504889595575 0.328520415356608 3 - - 6658 N N 2.62802896936265 2.70990445569631 2.62802896936265 0 0.451067083305631 0.0577818701362209 N 0.462269795891231 0.495877933648029 N N 122511 131026 ENSG00000187514 ENSG00000115053 + - 2 2 232286495 232037449 coding coding PTMA NCL 232280638 232027706 + - 0.395053520377634 232285421 232033718 + + N - 0.500147375781468 Y HCC1954 6 3.42857142857143 1 6 2 Y - - N Low_complexity Simple_repeat 0.174825174825175 0.75 0.75 7 1.52119235806429 0.828442786551446 1.52119235806429 0.828442786551446 0 - 0 26984 Y Y 3.49424793801946 3.29078464484691 3.29078464484691 255 0 0.213853067753488 Y 0 0 N Y 16564 3216 ENSG00000185883 ENSG00000162065 - + 16 16 2510219 2493487 coding coding ATP6V0C TBC1D24 2503954 2465148 + + 0 2509220 2487115 - + N 0.667831255677257 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.435646637755502 0.578481600954027 0.578481600954027 0.435646637755502 4 0 - 6806 N Y 3.2802368700128 3.31894904961092 3.2802368700128 229 0.790393013100437 0.0158396060884659 Y 0.930131004366812 0.930131004366812 N N 126 3186 ENSG00000186281 ENSG00000115042 + + 2 2 96064454 95442605 downstream coding AC013272.5-2 FAHD2A 96051422 95432203 - + 0.930131004366812 96050876 95442184 - + N - - N HCC1954 2 2 2 11 2 N - - N - - 0 0 0 11 0.371370904316165 0.749883556792257 0.749883556792257 0.371370904316165 1 - - 47549 Y Y 3.46704205511183 3.53974633573272 3.46704205511183 110 0 0.0532336157648468 Y 0 0.995565280816922 N N 3991 6767 ENSG00000104872 ENSG00000161618 - - 19 19 54646879 54665657 utr5p utr5p PIH1D1 ALDH16A1 54641368 54648325 - + 0 54646662 54648341 + - N - 0.204060410926721 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 1.12839620926835 0.899860268150708 1.12839620926835 0.899860268150708 1 - 0 47973 N N 2.88048419190053 3.09555125761603 2.88048419190053 0 0.257198317696538 0.0573883043609029 N 0.311549660304109 0 N N 9 551733 ENSG00000177400 ENSG00000204628 + + 8 5 12588894 180603512 downstream utr3p OR7E8P GNB2L1 12586149 180596536 - - 0 12577481 180596545 - - Y - - N HCC1954 10 5.06666666666667 1 10 1 N - - N LINE - 1 0 1 15 0.257102933757345 0.942710757110266 0.942710757110266 0.257102933757345 2 - - 40107 Y Y 3.62361669590707 3.49640736351508 3.49640736351508 0 0 0.994480691958518 Y 0 0.992451106812809 N Y 856 4995 ENSG00000129007 ENSG00000128973 - + 15 15 66285502 66309079 coding coding CALML4 CLN6 66270098 66286386 - - 0 66273504 66297928 + - N - - N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 4 0.778450549431962 0.699891319672773 0.778450549431962 0.699891319672773 4 - - 34138 Y Y 3.55976477294109 3.31894904961092 3.31894904961092 299 0 0.00778081535996611 Y 0 0.987992102188016 N N 2119 4646 ENSG00000165264 ENSG00000197579 + - 9 9 32563182 32542601 intron utr5p NDUFB6 TOPORS 32543523 32530545 - - 0 32555436 32542538 - + N 0.143828198744892 1.5496605064919 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.792734045751814 0.671324327033068 0.792734045751814 0.671324327033068 2 0 0 31228 Y Y 3.61464054707278 3.24784690021339 3.24784690021339 342 0 0.00283602174298836 Y 0 0.928780284043442 N N 458 1603 ENSG00000206567 ENSG00000180385 + + 3 3 10027779 10021928 utr3p intron AC022007.5-2 AC022007.5-1 10023102 10003595 - + 0 10023515 10004084 - + N 2.4877373733344 1.10422918263263 N HCC1954 60 32.6 1 4 1 N - - Y - SINE 0 0.767123287671233 0.767123287671233 5 0.39993789695587 0.842726282871298 0.842726282871298 0.39993789695587 3 0 0 29252 Y Y 3.41529599551336 2.88636532132177 2.88636532132177 248 0 0.111002958867234 Y 0 0.981029185867896 N N 17344 417 ENSG00000204267 ENSG00000204273 + - 6 6 32914525 32892803 coding utr5p TAP2 HLA-DOB 32897588 32888530 - - 0 32905155 32892707 - + N 0.361196915539242 2.69194701746975 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.607048593593732 0.621332089913584 0.621332089913584 0.607048593593732 4 0 0 42497 N Y 3.62361669590707 3.21075977977757 3.21075977977757 2 0.0114685314685316 0.922872240569664 Y 0.0114685314685316 0.904335664335664 N N 1192 1975 ENSG00000109265 ENSG00000174799 - + 4 4 56891647 56594283 utr5p downstream KIAA1211 CEP135 56731118 56509794 + + 0 56740207 56610222 - + N - - N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.266666666666667 0.266666666666667 9 0.93556900895034 0.964136001590045 0.964136001590045 0.93556900895034 4 - - 32989 N N 2.72660753283084 3.73080759109069 2.72660753283084 0 0 0.999932005440788 N 0 0 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0 8477 12877 - + N 0.671136416302083 0.795000684085075 N HCC1954 1 1 1 0 10 N 189 4.09957 N - - 0 0 0 4 0.585623349113953 0.985561246069823 0.985561246069823 0.585623349113953 1 0 0 8496 N N 3.22167408707565 3.52361324642271 3.22167408707565 0 0.0818477553675991 0.0269454782652303 N 0.868835393623943 0.156798959011061 N N 1772 282 ENSG00000187451 ENSG00000179869 - + 17 7 42483361 48657637 downstream intron AC068152.11-2 ABCA13 42480430 48208389 + + 0.156798959011061 42499833 48212170 - + Y - 0.942065272661236 N HCC1954 20 9.96875 2 32 1 N - - N - LTR 0 1 1 32 0.707033067832699 0.607048593593732 0.707033067832699 0.607048593593732 2 - 0 16523 N Y 3.60256518892881 3.51207644450867 3.51207644450867 0 0 0.44149895524873 N 0.870890971292578 0.815558530417968 N N 0 45264 ENSG00000207623 ENSG00000131473 - - 1 17 207672210 37328798 upstream intron hsa-mir-205 ACLY 207672101 37276696 + - 0 207669147 37289590 - + Y - 0.680179639036654 N HCC1954 9 4.8 1 4 1 N - - N - SINE 0 1 1 5 0.292811674556976 0.278528178237124 0.292811674556976 0.278528178237124 1 - 0 29268 N Y 3.10910076590736 2.88107618129295 2.88107618129295 290 0 0.00548912559185954 Y 0 0 N N 3861 8888 ENSG00000118412 ENSG00000112159 - - 6 6 90637843 90586163 upstream intron CASP8AP2 MDN1 90596379 90409952 + - 0 90596014 90570060 - + N - 5.53338799824619 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.442788385915428 0.642757334393363 0.642757334393363 0.442788385915428 1 - 0 47183 N N 3.57952209032428 3.11175470494294 3.11175470494294 0 0 0.997944019974804 N 0 0 Y N 8665 5583 ENSG00000079313 ENSG00000104885 + + 19 19 1799452 2181007 coding coding REXO1 DOT1L 1766245 2115148 - + 0 1767101 2159974 - + N 0.694459313640286 - N HCC1954 1 1 1 0 5 N 279 3.37031 N - - 0 0 0 7 0.692749571512847 0.592765097273879 0.692749571512847 0.592765097273879 1 0 - 46659 N Y 3.55703628599201 3.66745018166468 3.55703628599201 0 0 0.107597841377196 N 0.878909477162752 0.878909477162752 N N 389 2530 ENSG00000104953 ENSG00000138744 - + 19 4 2946176 77081190 intron coding TLE6 NAAA 2927853 77050833 + - 0 2943920 77058954 - - Y 1.02742587625229 - N HCC1954 20 20 20 6 1 N - - N SINE - 1 0 1 6 0.335662163516534 0.499922371194838 0.499922371194838 0.335662163516534 2 0 - 9332 Y Y 3.18512133297314 3.42783536197374 3.18512133297314 233 0.0335773794496339 0.999996601370235 Y 0.0335773794496339 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p intron ORMDL3 GSDMB 35330822 35314374 - - 0 35331927 35327748 - + N 2.88148042838036 9.44764878355004 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 10 0.964136001590045 0.771308801272036 0.964136001590045 0.771308801272036 2 0 0 26404 N Y 3.55128313764676 3.06460493274045 3.06460493274045 0 0 0.349456837926535 N 0 0.891064257028112 N N 5016 0 ENSG00000129636 ENSG00000169575 + + 16 22 46052519 20929926 intron downstream ITFG1 VPREB1 45746815 20929192 - + 0.035140562248996 45942253 20952111 - + Y 0.921589444081448 - N HCC1954 240 228 200 5 1 N - - N LINE - 1 0 1 5 0.371370904316165 0.499922371194838 0.499922371194838 0.371370904316165 3 0 - 2253 N Y 3.49744043328497 3.64234094352036 3.49744043328497 12 0 0.346521137222069 N 0 0.798811156835848 N N 100806 4335 ENSG00000163931 ENSG00000166483 - + 3 11 53265078 9567874 coding downstream TKT WEE1 53234715 9550916 - + 0.0644718792866941 53244121 9582806 + + Y - - N HCC1954 35 23.75 20 4 1 N - - N - SINE 0 1 1 4 0.664182578873142 0.292811674556976 0.664182578873142 0.292811674556976 1 - - 43511 N Y 3.45976132345673 3.63296356710195 3.45976132345673 231 0.745786128764852 0.00361819951703579 N 0.777562862669246 0.809339596573639 N N 4691 249 ENSG00000152253 ENSG00000150076 - + 2 10 169455190 33211797 utr3p intron SPC25 C10orf68 169435648 32896657 - + 0.788155107304044 169435798 33113488 + + Y - 13.7178929359707 N HCC1954 32 27.2222222222222 23 18 1 N - - N LINE LINE 1 1 1 18 0.764167053112109 0.264244681917271 0.764167053112109 0.264244681917271 0 - 0 20799 N Y 3.25256697878875 3.7061623612628 3.25256697878875 0 0 0.0728345928422613 N 0 0 N N 49089 6 ENSG00000117450 ENSG00000086717 - - 1 X 45760196 18756097 coding intron PRDX1 PPEF1 45749295 18618967 - + 0 45757275 18702196 + - Y - 1.18555775295312 N HCC1954 40 22.25 3 4 1 N - - N - SINE 0 1 1 4 0.499922371194838 0.435646637755502 0.499922371194838 0.435646637755502 2 - 0 31761 Y Y 3.36551102231762 3.63655728995158 3.36551102231762 0 0 0.941796939981568 Y 0 0.992393386022172 N N 6749 46 ENSG00000118855 ENSG00000214217 - + 3 3 160030198 159943998 coding utr5p MFSD1 AC080013.17 160002606 159940900 + + 0 160004803 159942615 - + N - - N HCC1954 2 1.2 1 1 3 N - - Y - SINE,SINE 0 0.263736263736264 0.263736263736264 5 0.899860268150708 1.12839620926835 1.12839620926835 0.899860268150708 2 - - 19007 Y Y 3.54872248456702 3.57167229721571 3.54872248456702 392 0 0.000468719011867513 Y 0 0.976251214771623 N N 0 521 ENSG00000212230 ENSG00000215799 + - 1 1 241311184 241285412 downstream upstream U6 AL606534.15-1 241311081 241283859 - - 0.0144254130223519 241299469 241287349 - + N - - N HCC1954 260 232.25 208 4 1 N - - Y SINE DNA 1 0.62962962962963 1 4 0.528489363834543 0.578481600954027 0.578481600954027 0.528489363834543 2 - - 6404 N Y 3.18974812559266 3.8333716936548 3.18974812559266 0 0 0.707985648867765 N 0.230936708860759 0.949569620253164 N N 0 3966 ENSG00000220644 ENSG00000175772 - + Y 2 12876163 110111006 upstream upstream AC004772.1 AC013268.5-1 12875458 110103138 + + 0 12769266 110102056 - + Y - - N HCC1954 40 40 40 18 1 N 8 27.7988 N LINE - 1 0 1 18 0.364229156156239 0.692749571512847 0.692749571512847 0.364229156156239 3 - - 21105 N Y 3.69784855983781 3.40951234194457 3.40951234194457 0 0 0.0802609531432634 N 0.865577227200843 0.865577227200843 N N 12271 13757 ENSG00000177479 ENSG00000135823 + - 3 1 48997971 179258669 utr5p intron ARIH2 STX6 48931285 179208801 + - 0.0115972588297312 48935246 179225253 + + Y - 0.4508918927804 N HCC1954 28 23.75 20 4 1 N - - N - SINE 0 1 1 4 0.621332089913584 0.28566992639705 0.621332089913584 0.28566992639705 1 - 0 31459 N Y 3.31526204080546 3.4780843434859 3.31526204080546 322 0 0.0464079882600631 Y 0 0.987219302436694 N N 298 6473 ENSG00000182983 ENSG00000144648 - + 3 3 42933958 42883778 upstream coding ZNF662 CCBP2 42922406 42836115 + + 0 42913534 42881355 - + N - 0.696517877287547 N HCC1954 1 1 1 0 1 N - - N LTR - 1 0 1 6 1.06412047582901 1.16410495006798 1.16410495006798 1.06412047582901 4 - 0 33358 N N 2.96319769112561 3.49272035470961 2.96319769112561 0 0 0.999428501907653 N 0 0.00308641975308643 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0.00308641975308643 8593 14908 - + N - 0.647784255393754 N HCC1954 9 4.70588235294118 1 16 8 N 189 4.09957 N - - 0 0 0 17 0.692749571512847 0.864151527351077 0.864151527351077 0.692749571512847 2 - 0 7073 Y Y 3.25525561294448 3.20334171947666 3.20334171947666 419 0 0.00673941654367138 Y 0.98175097502765 0.993916991675883 N N 126 0 ENSG00000186281 ENSG00000222119 + - 2 2 96064454 96034328 downstream upstream AC013272.5-2 SRP_euk_arch 96051422 96034040 - - 0 96048771 96040204 - + N - - N HCC1954 2 2 2 4 3 N - - Y - - 0 0 0 4 0.349945659836387 0.542772860154395 0.542772860154395 0.349945659836387 1 - - 35724 N N 3.53871326596283 3.16104516459872 3.16104516459872 0 0 0.291322912217072 N 0 0 N N 871 0 ENSG00000084453 ENSG00000210456 + - 12 13 21439638 105605840 utr5p upstream SLCO1A2 AL161617.12-1 21311651 105605751 - - 0 21439547 105641082 - + Y - - N HCC1954 25 21.2222222222222 20 9 1 N - - N LINE - 1 0 1 9 0.599906845433805 0.857009779191151 0.857009779191151 0.599906845433805 3 - - 13670 Y Y 3.60785432895764 3.2980560289322 3.2980560289322 264 0 0.0407315336994727 Y 0.203030303030303 0 N N 28 140 ENSG00000128298 ENSG00000100156 + - 22 22 36836622 36809116 intron upstream BAIAP2L2 SLC16A8 36810843 36804093 - - 0 36813419 36809142 - + N 1.60505401507644 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.771308801272036 0.807017542071667 0.807017542071667 0.771308801272036 1 0 - 32908 N N 3.12747721909902 2.51941318816285 2.51941318816285 0 0.321759259259259 0.0439190702712036 N 0.0587679516250943 0 N N 551733 0 ENSG00000204628 ENSG00000209700 + - 5 3 180603512 1082559 utr3p downstream GNB2L1 AC087430.3-1 180596536 1082264 - - 0 180596544 1016523 - + Y - - N HCC1954 22 17.3333333333333 1 11 1 N - - N - LINE 0 1 1 12 0.542772860154395 0.264244681917271 0.542772860154395 0.264244681917271 2 - - 39884 Y Y 3.59681204058356 3.14061615223641 3.14061615223641 0 0 0.231106481711924 Y 0 0.86870603996874 N N 5454 5834 ENSG00000166716 ENSG00000140612 - - 15 15 83150663 83060678 upstream upstream ZNF592 SEC11A 83126889 83013781 + - 0 83109008 83092835 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat 0 0.979865771812081 0.979865771812081 14 0.642757334393363 0.921285512630487 0.921285512630487 0.642757334393363 1 - - 46219 N N 2.61150406380635 3.65488030998075 2.61150406380635 0 0.316816816816817 0.647235932932299 N 0.453453453453453 0.316816816816817 N N 1525 2321 ENSG00000135049 ENSG00000127226 + + 9 19 87546709 18168552 intron utr3p AGTPBP1 AC068499.1 87351275 18165040 - + 0.316816816816817 87383183 18168520 - + Y 0.526736687569713 30.1570961790202 N HCC1954 2 1.8 1 4 1 N - - N SINE SINE 0.432432432432432 0.488888888888889 0.488888888888889 5 0.264244681917271 0.642757334393363 0.642757334393363 0.264244681917271 3 0 0 41541 Y Y 3.60256518892881 3.21484801616716 3.21484801616716 259 0 0.594648927693475 Y 0.475716317821581 0.979028652712863 N N 3685 2650 ENSG00000164695 ENSG00000104231 - - 8 8 82834305 82796090 upstream coding CHMP4C ZFAND1 82807243 82776513 + - 0 82806989 82793014 - + N - 0.676017761086529 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 1.04269523134923 0.642757334393363 1.04269523134923 0.642757334393363 4 - 0 31567 Y Y 3.04843199063708 3.70719543103269 3.04843199063708 6 0 0.368111173432332 Y 0 0.989613526570049 N N 95 2906 ENSG00000215837 ENSG00000214135 - + 3 3 196900773 196895854 coding coding AC069513.28-2 AC069513.28-1 196900191 196874647 + + 0 196900440 196895825 - + N 0.578597697123594 - N HCC1954 8 3.06818181818182 1 42 2 N - - Y LINE - 0.413461538461538 0 0.413461538461538 44 0.742741808632331 0.907002016310634 0.907002016310634 0.742741808632331 2 0 - 2730 N N 3.65231965690101 3.54144175291192 3.54144175291192 0 0 0.734499573088933 N 0.178481258496796 0.493105457370363 N N 0 2 ENSG00000222048 ENSG00000169946 + + 11 8 10836196 106885939 intron upstream ZBED5 ZFPM2 10830827 106400323 - + 0.493105457370363 10836154 106345892 - + Y 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.371370904316165 0.371370904316165 0.371370904316165 0.371370904316165 2 0 - 30330 Y Y 3.56695221864035 3.51679652308403 3.51679652308403 263 0 0.112772201088171 Y 0 0 N N 3149 438 ENSG00000123595 ENSG00000176896 - + X X 13637681 13593449 upstream downstream RAB9A TCEANC 13617262 13581146 + + 0 13608529 13596423 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 11 0.714174815992626 0.735600060472404 0.735600060472404 0.714174815992626 4 - - 33251 N N 2.91783662205815 3.39483647792751 2.91783662205815 21 0.157141601476663 0.99999857984683 N 0.202179836512262 0.022026896369869 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.022026896369869 8407 12084 - + N 0.984947018030751 - N HCC1954 4 1.66666666666667 1 14 12 Y 189 4.09957 N - - 0 0 0 27 1.17838844638783 1.67831081758267 1.67831081758267 1.17838844638783 1 0 - 38146 Y Y 3.43821530293851 3.68850168864294 3.43821530293851 344 0 0.0559719871172908 Y 0 0.994029383094277 N N 182 8277 ENSG00000183484 ENSG00000170779 + - 14 14 104602799 104558538 coding upstream GPR132 CDCA4 104586773 104547326 - - 0 104592788 104570569 - + N 0.580808520801203 - N HCC1954 4 1.12 1 1 2 N - - Y LINE LTR 1 1 1 25 1.2783729206268 1.24980592798709 1.2783729206268 1.24980592798709 2 0 - 42327 Y Y 3.50575423470996 3.30484224704734 3.30484224704734 286 0 0.240607678561919 Y 0.992275166693771 0.976825500081314 N N 10761 25208 ENSG00000138768 ENSG00000138757 - - 4 4 76954388 76817629 upstream upstream USO1 G3BP2 76869028 76786991 + - 0 76868484 76839137 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 15 1.1426797055882 0.971277749749971 1.1426797055882 0.971277749749971 4 - - 38439 Y Y 3.50425715662364 3.08251737761569 3.08251737761569 137 0 0.410032694823113 Y 0 0.989834279576492 N Y 7845 837 ENSG00000012963 ENSG00000153485 - + 14 14 92765306 92723180 coding utr5p UBR7 C14orf109 92743154 92721082 + + 0 92745923 92721130 - + N - 2.6544644490068 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.228571428571429 0.228571428571429 4 0.749883556792257 0.642757334393363 0.749883556792257 0.642757334393363 4 - 0 5193 N Y 3.42100929106525 3.66745018166468 3.42100929106525 230 0 0.0177486383183134 N 0.908295194508009 0.895194508009153 N N 32979 4 ENSG00000106105 ENSG00000148408 - + 7 9 30640168 140138897 upstream intron GARS CACNA1B 30600706 139892062 + + 0 30591471 139961209 - + Y - 0.969237342448195 N HCC1954 3 2.5 1 3 1 N - - N SINE LTR 1 0.555555555555556 1 4 0.657040830713216 0.321378667196682 0.657040830713216 0.321378667196682 3 - 0 31437 N N 3.50848272165904 3.52833332499807 3.50848272165904 0 0 0.149396139772428 N 0 0 Y N 2906 13642 ENSG00000214135 ENSG00000176945 - + 3 3 196895854 196950210 upstream intron AC069513.28-1 MUC20 196874647 196933424 + + 0 196833509 196933701 - + N - 1.58255410711322 N HCC1954 4 3 2 4 1 N - - N - - 0 0 0 4 0.542772860154395 0.478497126715059 0.542772860154395 0.478497126715059 2 - 0 27640 N N 3.33464863582806 2.31748924548137 2.31748924548137 0 0.0907928388746805 0.346219271777125 N 0.581476068688345 0 N N 4006 4713 ENSG00000090565 ENSG00000114541 - - 16 3 512479 69518120 utr3p intron RAB11FIP3 FRMD4B 415669 69301836 + - 0.0907928388746805 512036 69485512 - + Y 1.81209539239338 55.7953400870633 N HCC1954 3 2 1 5 1 N 555 5.24923 N - Simple_repeat 0 0.869565217391304 0.869565217391304 6 0.557056356474248 0.328520415356608 0.557056356474248 0.328520415356608 1 0 0 5191 N N 3.67849247003875 3.1416492220063 3.1416492220063 1 0 0.627643082405081 N 0 0 N N 850768 0 ENSG00000075624 ENSG00000219293 + + 7 9 5536758 102534442 coding intron ACTB RP11-394D2.1 5533313 102533343 - + 0 5534452 102534139 - + Y 1.19960355278068 1 N HCC1954 4 4 4 6 1 N 14 21.9233 N - - 0 0 0 6 0.335662163516534 0.22853594111764 0.335662163516534 0.22853594111764 1 0 0 4610 Y Y 3.20344435300231 3.57848902055439 3.20344435300231 126 0.0218924916371344 0.531200798582264 Y 0.0310336833040772 0.981717616666115 N N 3355 2500 ENSG00000146826 ENSG00000188186 + + 7 7 99594244 99589769 intron coding C7orf43 C7orf59 99589983 99584466 - + 0 99591135 99589076 - + N 0.849811615574015 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.728458312312478 0.828442786551446 0.828442786551446 0.728458312312478 4 0 - 34189 Y Y 3.17151839151932 3.58999531724489 3.17151839151932 261 0 0.401133925759062 Y 0.907024265644955 0.960153256704981 N N 0 0 ENSG00000218062 ENSG00000215364 - + 9 9 98721421 98713998 upstream upstream RP11-330M2.3 RP11-330M2.4 98721031 98713138 + + 0 98720746 98700230 - + N - - N HCC1954 2 1.16666666666667 1 1 2 N - - Y - - 0 0 0 6 0.449930134075354 0.414221393275723 0.449930134075354 0.414221393275723 4 - - 33131 N Y 3.34785034969775 3.6581033104698 3.34785034969775 535 0 0.000508562367393495 Y 0 0.984933874096279 N N 336285 539404 ENSG00000198868 ENSG00000198712 - + MT MT 12138 8270 coding coding MT-ND4 MT-CO2 10471 7587 + + 0 10753 7988 - + N 0.853896908130666 1.64143967000864 N HCC1954 6 2.6 1 4 1 N - - N - - 0 0 0 5 0.949852505270192 1.16410495006798 1.16410495006798 0.949852505270192 4 0 0 33115 N Y 3.50016892023405 3.49164743214637 3.49164743214637 234 0 0.689861541535173 Y 0 0.980475951064186 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0 9303 7280 - + N 0.785527554095222 1.55045835641748 N HCC1954 4 2 1 2 5 Y - - N - - 0 0 0 4 0.721316564152552 0.828442786551446 0.828442786551446 0.721316564152552 2 0 0 13335 N Y 3.36870351758313 3.42208221362849 3.36870351758313 7 0 0.0576167598963327 N 0 0.706454918032787 N N 417 3693 ENSG00000172986 ENSG00000198125 - + 3 22 73107077 34349347 intron coding GLT8D4 MB 73020075 34332757 + - 0 73043972 34343239 - - Y 0.597299285419338 - N HCC1954 16 3.76470588235294 1 15 1 N - - N SINE SINE 1 0.618556701030928 1 17 0.278528178237124 0.692749571512847 0.692749571512847 0.278528178237124 1 0 - 36319 Y Y 3.69528790675807 3.58320909912975 3.58320909912975 134 0 0.0594031287478339 Y 0.133499170812604 0.98424543946932 N N 2025 1204 ENSG00000176894 ENSG00000176876 - + 12 12 131805819 131791649 upstream downstream PGAM5 PXMP2 131797509 131774265 + + 0 131797232 131791809 - + N - - N HCC1954 11 5.6 1 4 2 N - - Y - SINE 0 1 1 5 0.607048593593732 0.371370904316165 0.607048593593732 0.371370904316165 1 - - 47674 Y Y 3.69209541149257 3.64450036901598 3.64450036901598 0 0 0.818851546892043 Y 0 0.943455396342934 N N 31369 1953 ENSG00000105281 ENSG00000181027 + + 19 19 51983691 51953581 coding downstream SLC1A5 FKRP 51969982 51941143 - + 0 51972072 51955492 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.868613138686131 0.868613138686131 8 0.849868031031224 0.799875793911741 0.849868031031224 0.799875793911741 4 - - 45328 N Y 3.49847350305486 3.63296356710195 3.49847350305486 237 0.741097046413502 0.0025675831852664 N 0.761012658227848 0.810801687763713 N N 5622 249 ENSG00000158985 ENSG00000150076 - + 5 10 130758279 33211797 intron intron CDC42SE2 C10orf68 130627601 32896657 + + 0.780928270042194 130670986 33113488 - + Y 0.578314102338253 13.7178929359707 N HCC1954 25 21.25 20 4 1 N - - N LINE LINE 1 1 1 4 0.39993789695587 0.264244681917271 0.39993789695587 0.264244681917271 0 0 0 18212 Y Y 3.54975555433691 3.56331864299737 3.54975555433691 273 0 0.0471512452673049 Y 0 0.991965024223089 N N 0 0 ENSG00000212094 ENSG00000200033 - - 1 1 220253055 220077402 upstream upstream AC092765.2 U6 220252972 220077299 + - 0 220209254 220158676 - + N - - N HCC1954 140 11.2666666666667 1 3 1 N - - Y LTR,LTR SINE 0.775193798449612 1 1 15 0.921285512630487 0.792734045751814 0.921285512630487 0.792734045751814 1 - - 41548 Y Y 3.4748918482204 2.98992264086242 2.98992264086242 251 0 0.00254015886300951 Y 0 0.970705413639559 N N 24621 0 ENSG00000083307 ENSG00000222841 - - 8 8 102750995 102479337 upstream upstream GRHL2 SRP_euk_arch 102574162 102479039 + - 0 102533616 102499198 - + N - - N HCC1954 6 2 1 4 1 N - - Y - SINE 0 1 1 20 1.10697096478857 1.06412047582901 1.10697096478857 1.06412047582901 1 - - 29129 Y Y 3.20075056117338 3.35616415112274 3.20075056117338 243 0 0.471896824698524 Y 0 0 N N 0 61 ENSG00000183239 ENSG00000181577 + + 6 6 44165423 44080864 downstream downstream AL109615.42-1 C6orf223 44164963 44076317 - + 0 44122971 44119399 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE SINE 1 0.61 1 11 0.757025304952183 0.714174815992626 0.757025304952183 0.714174815992626 1 - - 10243 N Y 3.66641711189479 2.5911894521509 2.5911894521509 270 0 0.259590016779230 Y 0.124466891133558 0.969809203142536 N N 1834 0 ENSG00000178607 ENSG00000221462 - - 17 17 59529654 59577563 coding upstream ERN1 SNORA76 59474122 59577431 - + 0 59529333 59561068 + - N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.364229156156239 0.464213630395207 0.464213630395207 0.364229156156239 4 - - 33798 N N 2.79058743687281 3.45140766923839 2.79058743687281 0 0 0.996137737976702 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8444 11807 - + N - - N HCC1954 3 1.6 1 5 7 Y 189 4.09957 N - - 0 0 0 10 1.04269523134923 1.18553019454776 1.18553019454776 1.04269523134923 1 - - 30900 N Y 3.18974812559266 3.4331380823717 3.18974812559266 0 0 0.606963699058566 N 0.347290640394089 0.88548958603405 N N 18437 14 ENSG00000163932 ENSG00000164691 - - 3 6 53201771 159386172 utr5p intron PRKCD TAGAP 53170263 159376017 + - 0 53174267 159378333 - + Y - 1.09627214031362 N HCC1954 21 20.25 20 4 1 N - - N - SINE 0 1 1 4 0.578481600954027 0.28566992639705 0.578481600954027 0.28566992639705 2 - 0 41431 N N 3.4722913423473 3.41319935075004 3.41319935075004 0 0 0.98924581056664 Y 0 0 N N 8783 0 ENSG00000147697 ENSG00000221261 + + 8 8 130868316 129231616 intron upstream GSDMC hsa-mir-1208 130829625 129231544 - + 0.0205406911928649 130843210 129181152 - + N 0.654695145605657 - N HCC1954 1 1 1 0 4 N 195 7.32662 N - LINE 0 0.959016393442623 0.959016393442623 11 1.28551466878673 0.785592297591888 1.28551466878673 0.785592297591888 2 0 - 34720 Y Y 3.50525037360018 3.6272104187567 3.50525037360018 143 0 0.131772637508524 Y 0.985608594304247 0.985608594304247 N N 329 1173 ENSG00000218011 ENSG00000182150 - + 9 9 97774767 97770942 coding utr3p AL159167.23-1 C9orf102 97772706 97677721 + + 0 97774051 97769666 - + N - 15.3936498869151 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.93556900895034 0.835584534711372 0.93556900895034 0.835584534711372 2 - 0 39935 Y Y 3.72655152083176 3.43039601505348 3.43039601505348 0 0 0.961475000171281 Y 0.916975308641975 0.979243827160494 N N 0 0 ENSG00000180987 ENSG00000215302 + - 15 15 30678304 30608228 downstream upstream AC123768.8-1 AC135983.4-1 30677791 30606298 - - 0 30655410 30616499 - + N - - N HCC1954 8 3.57142857142857 1 4 3 N - - Y DNA - 1 0 1 7 0.528489363834543 1.15696320190805 1.15696320190805 0.528489363834543 4 - - 2463 N Y 3.6491271616355 3.353603498043 3.353603498043 2 0 0.197953933779905 N 0.932721182721183 0.932721182721183 N N 1555 3567 ENSG00000148153 ENSG00000177951 - - 9 11 114520250 197428 utr3p coding C9orf80 BET1L 114488618 157784 - - 0 114488739 195611 + + Y - - N HCC1954 180 142.571428571429 105 14 1 N - - N SINE,SINE - 1 0 1 14 0.407079645115797 1.17124669822791 1.17124669822791 0.407079645115797 3 - - 41913 N N 2.96319769112561 3.51952501003312 2.96319769112561 20 0.199960338445267 0.984172023543304 N 0.199960338445267 0 N N 29840 30 ENSG00000164830 ENSG00000212993 + + 8 8 107834093 128498621 utr5p upstream OXR1 POU5F1P1 107739270 128497039 + + 0 107739589 128184810 + + N - - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - - 0 0 0 4 0.842726282871298 0.649899082553289 0.842726282871298 0.649899082553289 4 - - 39403 N Y 3.33105491297843 3.56232542602083 3.33105491297843 0 0 0.179448369924101 N 0 0.902401829965688 N N 7566 4 ENSG00000188064 ENSG00000103569 - + 22 15 44751395 56265402 intron downstream WNT7B AQP9 44696323 56217700 - + 0.170415554708349 44731539 56339667 + + Y 13.7502301556359 - N HCC1954 20 20 20 10 1 N - - N SINE LTR 1 1 1 10 0.34280391167646 0.471355378555133 0.471355378555133 0.34280391167646 3 0 - 27965 N N 2.90087335146949 3.38486711211668 2.90087335146949 17 0 0.0734016131856344 N 0.325356953992597 0.164727657324167 N N 0 10339 ENSG00000217035 ENSG00000177200 - + X 16 44379422 51918914 downstream intron CHTF8P CHD9 44377882 51646446 + + 0.164727657324167 44385720 51784865 - + Y - 1.27613943306093 N HCC1954 21 20.25 20 4 1 N - - N SINE SINE 0.65625 1 1 4 0.22853594111764 0.28566992639705 0.28566992639705 0.22853594111764 0 - 0 14930 N Y 3.41679307359967 3.54400240599166 3.41679307359967 0 0 0.072149732785047 N 0.853097721950181 0 N N 49089 3838 ENSG00000117450 ENSG00000154710 - + 1 7 45760196 65913881 utr5p downstream PRDX1 RABGEF1 45749295 65843078 - + 0 45760088 65937875 + + Y - - N HCC1954 6 3.57142857142857 1 5 1 N - - N - SINE 0 1 1 7 0.742741808632331 0.264244681917271 0.742741808632331 0.264244681917271 1 - - 49332 Y Y 3.59528445727371 2.75021969288884 2.75021969288884 21 0.0643737508327781 0.532800375847808 Y 0.108094603597601 0.973767488341106 N N 12950 29911 ENSG00000171421 ENSG00000145494 - - 5 5 1852946 1869161 utr5p upstream MRPL36 NDUFS6 1851499 1854509 - + 0.0381412391738841 1852928 1854397 + - N - - N HCC1954 2 1.11111111111111 1 3 2 N - - Y - - 0 0 0 27 0.921285512630487 1.06412047582901 1.06412047582901 0.921285512630487 2 - - 33073 N Y 3.14168907479965 2.929112304147 2.929112304147 363 0 0.264266672933916 Y 0 0.966758494031221 N N 339915 544065 ENSG00000198727 ENSG00000198744 - + MT MT 15882 9988 coding coding MT-CYB MT-CO3 14748 8367 + + 0 14767 8692 - + N 0.562987042701105 0.557408083470372 N HCC1954 3 1.8 1 2 5 N - - N - - 0 0 0 5 0.914143764470561 0.764167053112109 0.914143764470561 0.764167053112109 2 0 0 40068 Y Y 3.41103992525442 2.99926951205729 2.99926951205729 0 0 0.568424953134474 Y 0.993883454006153 0.96330072403692 N Y 4948 2587 ENSG00000157823 ENSG00000214446 - + 15 15 88238206 88257163 coding coding AP3S2 C15orf38 88177793 88244836 - - 0 88233376 88247452 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 31 1.15696320190805 1.1426797055882 1.15696320190805 1.1426797055882 4 - - 36412 Y Y 3.69784855983781 3.55657227767559 3.55657227767559 0 0 0.231106634145011 Y 0.990865576386119 0.990865576386119 N N 9 30465 ENSG00000139209 ENSG00000134294 + - 12 12 45506006 45060677 downstream upstream SLC38A4 SLC38A2 45444813 45038239 - - 0 45332439 45150311 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR 0.871794871794872 1 1 7 0.835584534711372 0.564198104634174 0.835584534711372 0.564198104634174 1 - - 48865 Y Y 3.68105312311849 3.52361324642271 3.52361324642271 269 0 0.977242296854659 Y 0 0.992509153925706 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 downstream downstream TPPP CEP72 712978 665405 - + 0.992509153925706 710675 708698 - + N - - N HCC1954 1 1 1 0 6 N - - Y LINE - 0.0517241379310345 0 0.0517241379310345 13 0.828442786551446 0.956994253430118 0.956994253430118 0.828442786551446 1 - - 17868 Y N 2.31441296411064 3.06788136639198 2.31441296411064 0 0 0.196359241998220 N 0 0.0945896209054103 N N 582 0 ENSG00000153363 ENSG00000220338 + + 1 1 209638102 209657899 coding downstream C1orf97 RP11-318L16.4 209622768 209656990 + + 0.0945896209054103 209636822 209666294 + + N - - Y HCC1954 1 1 1 0 1 N 188 26.6138 N - - 0 0 0 4 0.678466075192994 0.328520415356608 0.678466075192994 0.328520415356608 2 - - 42245 N Y 3.34728128824428 3.70512929149291 3.34728128824428 297 0 0.00783841900091542 Y 0.958760013932428 0.993126668988738 N N 12 8729 ENSG00000109163 ENSG00000033178 + - 4 4 68304399 68249484 downstream upstream GNRHR UBA6 68285701 68164077 - - 0 68276854 68249798 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR,LINE - 0.312101910828025 0 0.312101910828025 39 1.12125446110842 1.10697096478857 1.12125446110842 1.10697096478857 1 - - 47177 N N 3.5529387020326 3.4342508577283 3.4342508577283 0 0 0.171545384468103 N 0.0736206896551723 0 Y N 1744 10721 ENSG00000007255 ENSG00000007047 + + 19 19 50373325 50500381 upstream coding TRAPPC6A MARK4 50358027 50446390 - + 0 50382685 50446708 - + N - - N HCC1954 1 1 1 0 1 N 446 7.40245 N DNA Low_complexity 0.405172413793103 0.218390804597701 0.405172413793103 6 0.828442786551446 0.621332089913584 0.828442786551446 0.621332089913584 2 - - 33161 N N 3.04950491320032 3.04168562531529 3.04168562531529 0 0 0.0622425806652617 N 0 0 Y N 275222 339915 ENSG00000198763 ENSG00000198727 - + MT MT 5512 15882 coding coding MT-ND2 MT-CYB 4471 14748 + + 0 5303 14805 - + N 1.09100182653801 1.33925469588148 N HCC1954 4 2.25 1 2 1 Y 106 8.09281 N - - 0 0 0 4 0.635615586233437 0.757025304952183 0.757025304952183 0.635615586233437 1 0 0 7241 Y Y 3.47080361183081 2.71510123614034 2.71510123614034 362 0 0.00245461403383584 Y 0.23795997081205 0 N N 6338 0 ENSG00000187605 ENSG00000201876 - - 2 2 74188811 74048832 upstream upstream TET3 5S_rRNA 74083348 74048741 + - 0.981184196810174 74066612 74065130 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.607048593593732 0.771308801272036 0.771308801272036 0.607048593593732 2 - - 5517 N N 3.22167408707565 3.45976132345673 3.22167408707565 13 0 0.178541596008691 N 0 0.764068825910931 N N 1994 4140 ENSG00000171365 ENSG00000152117 - - X 2 49750632 131995615 utr3p utr5p CLCN5 AC093838.3-2 49573965 131967133 + + 0.0475371120107964 49747789 131975549 - - Y - - N HCC1954 40 25.75 21 4 1 N 18 21.7341 N SINE - 1 0 1 4 0.28566992639705 0.385654400636018 0.385654400636018 0.28566992639705 1 - - 30603 Y Y 3.33680806132368 3.41741556821562 3.33680806132368 0 0 0.927553978093604 Y 0.835852936931736 0.98784095829124 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 coding intron STS HDHD1A 7147472 6976961 + - 0 7147726 7075641 - + N - 0.638327297478365 N HCC1954 1 1 1 0 5 N - - Y - DNA 0 0.637837837837838 0.637837837837838 14 1.18553019454776 1.02126998686945 1.18553019454776 1.02126998686945 1 - 0 11246 N N 3.07101108092519 3.68680627146374 3.07101108092519 0 0 0.309578560593665 N 0.596488128886376 0.690927077444884 N N 1649619 0 ENSG00000141736 ENSG00000176243 - + 17 3 35138441 97979221 coding downstream ERBB2 AC109782.7 35104766 97978469 + + 0 35125066 97993401 - + Y - - N HCC1954 23 21 20 15 1 N - - N - SINE 0 1 1 15 0.657040830713216 0.357087407996313 0.657040830713216 0.357087407996313 1 - - 7527 Y Y 3.48912663185998 3.61464054707278 3.48912663185998 221 0 0.00391704320834974 Y 0 0 N N 24726 3 ENSG00000136699 ENSG00000152086 - + 2 2 130656793 130672510 utr5p upstream SMPD4 TUBA3E 130625450 130665790 - - 0 130656722 130676351 + - N - - N HCC1954 4 3.25925925925926 2 27 1 N - - Y - - 0 0 0 27 1.03555348318931 0.899860268150708 1.03555348318931 0.899860268150708 1 - - 47723 Y Y 3.68680627146374 3.26001554431319 3.26001554431319 5 0.00901230462254732 0.577286184750257 Y 0.993565014965082 0.993565014965082 N N 2047 5583 ENSG00000104886 ENSG00000104885 + + 19 19 2187319 2181007 coding downstream PLEKHJ1 DOT1L 2184155 2115148 - + 0 2184999 2181613 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 1.50690886174444 1.05697872766909 1.50690886174444 1.05697872766909 3 - - 46965 Y Y 3.05744799226472 3.35981130713485 3.05744799226472 224 0 0.00943449543301622 Y 0 0 N N 949 579 ENSG00000174586 ENSG00000121410 + - 19 19 63565932 63556669 intron intron ZNF497 A1BG 63557537 63548356 - - 0 63561271 63551077 - + N 5.17112058463346 8.86378735953658 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 0.635615586233437 0.578481600954027 0.635615586233437 0.578481600954027 2 0 0 38921 N N 3.45976132345673 3.57912086274016 3.45976132345673 13 0.00387596899224807 0.290923163254787 N 0.00387596899224807 0.00387596899224807 N N 357 850768 ENSG00000171877 ENSG00000075624 + + 15 7 42274700 5536758 intron utr3p FRMD5 ACTB 41950257 5533313 - - 0.00387596899224807 42068477 5533869 - - Y 1.60869433467783 - N HCC1954 2 1.46153846153846 1 6 1 N - - N Simple_repeat - 0.14 0 0.14 13 0.357087407996313 1.17124669822791 1.17124669822791 0.357087407996313 1 0 - 22184 N Y 3.58424216889964 3.63402714209538 3.58424216889964 0 0 0.382298614583477 N 0.705612077453233 0.879225467673121 N N 27074 1435 ENSG00000137804 ENSG00000132879 - + 15 1 39460535 11645971 coding utr3p NUSAP1 FBXO44 39412361 11637019 + + 0 39451018 11645744 - + Y 1.63156942559928 - N HCC1954 35 29.4583333333333 22 24 1 N - - N - SINE,SINE 0 1 1 24 0.914143764470561 0.34280391167646 0.914143764470561 0.34280391167646 1 0 - 7951 N Y 3.68953475841283 3.0008369481605 3.0008369481605 229 0 0.0484218616123843 N 0.629077832006165 0.902388903159517 N N 0 10665 ENSG00000221415 ENSG00000115233 - + 4 2 48895063 161976474 downstream upstream AC118282.4-1 PSMD14 48894981 161872795 + + 0.902388903159517 49011270 161845428 - + Y - - N HCC1954 5 1.6 1 3 1 N 317 9.53442 N - - 0 0 0 10 0.371370904316165 0.557056356474248 0.557056356474248 0.371370904316165 1 - - 38309 Y Y 3.52208566311286 3.53296011761759 3.52208566311286 116 0 0.201287563522195 Y 0.902288674667191 0.980457734933438 N Y 259 1147 ENSG00000100739 ENSG00000168398 - + 14 14 95800851 95780536 utr5p coding BDKRB1 BDKRB2 95792300 95740950 + + 0 95798742 95773271 - + N 0.231291505600159 - N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 11 0.757025304952183 1.31408166142643 1.31408166142643 0.757025304952183 4 0 - 38655 N Y 3.55976477294109 3.29400764533596 3.29400764533596 28 0 0.817894611286958 N 0.234028683181226 0.712760756192959 N N 10321 0 ENSG00000125772 ENSG00000222136 - - 20 14 5539672 49390382 upstream intron RP5-1022P6.2 SRP_euk_arch 5473081 49390086 - - 0.329775097783572 5575070 49390338 + + Y - 1 N HCC1954 8 4.4 1 4 1 N - - N SINE,SINE srpRNA,srpRNA 0.568181818181818 1 1 5 0.314236919036755 0.585623349113953 0.585623349113953 0.314236919036755 3 - 0 36286 Y Y 3.54144175291192 3.24740581983591 3.24740581983591 215 0 0.172459744036753 Y 0 0.987073391724555 N N 756 0 ENSG00000139132 ENSG00000207176 - - 12 12 32684940 32440348 upstream upstream FGD4 Y_RNA 32546361 32440251 + - 0 32517621 32444187 - + N - - N HCC1954 20 3.11764705882353 1 7 3 N - - Y LTR - 1 0 1 17 1.02126998686945 0.599906845433805 1.02126998686945 0.599906845433805 3 - - 20299 N Y 3.65016023140539 3.33168675516419 3.33168675516419 3 0 0.0253987661065783 N 0.931308155446086 0.942756796205072 N N 4626 0 ENSG00000133059 ENSG00000221151 - + 1 16 203447322 88689322 utr3p upstream DSTYK AC133919.3-4 203378255 88689218 - - 0 203382455 88710196 + - Y - - N HCC1954 190 155.575757575758 70 33 1 N - - N SINE - 1 0 1 33 0.485638874874985 1.1426797055882 1.1426797055882 0.485638874874985 0 - - 16960 N N 3.70256863841317 3.2948728812365 3.2948728812365 0 0 0.163113092617326 N 0 0 N N 42814 0 ENSG00000170315 ENSG00000212678 - - 17 1 16226779 560165 utr5p intron UBB RP5-857K21.11 16225092 559619 + + 0 16225941 559627 - - Y - 1 N HCC1954 10 4 2 4 1 N 5 21.1711 N - - 0 0 0 4 0.742741808632331 0.278528178237124 0.742741808632331 0.278528178237124 2 - 0 29208 N Y 3.55760534744548 3.30488209984069 3.30488209984069 343 0.00291545189504394 0.0804086564258616 Y 0.00291545189504394 0.993845157110463 N N 0 9273 ENSG00000223286 ENSG00000213079 - + 6 6 155244196 155196882 downstream utr3p AL121952.18-2 RBM16 155244108 155096204 + + 0 155270554 155196233 - + N - 5.7665494602103 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 22 1.22123893534739 1.24266417982717 1.24266417982717 1.22123893534739 3 - 0 16074 N N 2.77555883775188 3.42849770938305 2.77555883775188 0 0 0.105868187112188 N 0 0 N N 4363 3748 ENSG00000173436 ENSG00000168887 + + 1 2 19839759 85692666 utr5p utr3p C1orf151 C2orf68 19796054 85687290 + - 0.0358961920931357 19796110 85691451 + - Y - - N HCC1954 37 34.5 32 6 1 N - - N - SINE 0 1 1 6 0.707033067832699 0.449930134075354 0.707033067832699 0.449930134075354 2 - - 10064 Y Y 3.67952553980864 3.54292948342842 3.54292948342842 2 0 0.999987056936062 N 0 0.992151549238163 Y N 1482 317991 ENSG00000171345 ENSG00000171346 - + 17 17 36938167 36932191 coding upstream KRT19 KRT15 36933396 36923523 - - 0 36937606 36946877 + - N - - N HCC1954 2 1.12121212121212 1 4 8 N - - N - LINE 0 0.0359712230215827 0.0359712230215827 33 1.1426797055882 0.964136001590045 1.1426797055882 0.964136001590045 2 - - 2800 N Y 3.33168675516419 3.70144228268744 3.33168675516419 2 0 0.153940434850763 N 0.905135387488329 0.920946156240274 N N 3567 0 ENSG00000177951 ENSG00000211029 - + 11 8 197428 55495806 intron upstream BET1L AC027250.8-1 157784 55495581 - + 0 170406 55452749 + + Y 2.87394543524002 - N HCC1954 84 70 28 4 1 N - - N - SINE 0 1 1 4 0.364229156156239 0.328520415356608 0.364229156156239 0.328520415356608 2 0 - 41037 Y Y 3.33528047801382 3.41844863798551 3.33528047801382 0 0 0.180045731631693 Y 0.991103202846975 0.991103202846975 N N 60 2529 ENSG00000124251 ENSG00000198641 + + 20 20 43440447 43431263 intron coding C20orf10 SYS1 43435942 43423991 - + 0 43436347 43427739 - + N 0.308328587075575 - N HCC1954 5 1.33333333333333 1 2 1 N - - Y SINE - 1 0 1 15 0.93556900895034 0.792734045751814 0.93556900895034 0.792734045751814 2 0 - 42190 Y Y 3.26100876128973 3.34566041897859 3.26100876128973 163 0 0.296585100371556 Y 0 0.985801928133217 N N 95 7918 ENSG00000168993 ENSG00000185619 + + 4 4 809945 754428 downstream downstream CPLX1 PCGF3 768746 689573 - + 0 765580 761141 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LINE,LINE 0 1 1 5 0.357087407996313 0.749883556792257 0.749883556792257 0.357087407996313 3 - - 10053 Y Y 3.66488952858494 3.31229081257178 3.31229081257178 0 0 0.879647098136726 Y 0 0 N N 19270 0 ENSG00000170921 ENSG00000207552 - + 17 17 58858799 58375405 utr5p downstream TANC2 hsa-mir-633 58440630 58375308 + + 0 58440630 58397842 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.140625 0.140625 136 1.55690109886392 1.37121564670584 1.55690109886392 1.37121564670584 4 - - 17237 N Y 3.25616070163838 3.53974633573272 3.25616070163838 0 0 0.151037881244648 N 0.0958345613518026 0.816877885843403 N N 0 12495 ENSG00000217829 ENSG00000100320 - + 1 22 153470740 34754419 intron intron RP11-263K19.9 RBM9 153467390 34464730 + - 0 153468734 34738852 - - Y 1 3.48440322463009 N HCC1954 2 1.4 1 2 1 N - - N - SINE 0 1 1 5 0.742741808632331 0.564198104634174 0.742741808632331 0.564198104634174 1 0 0 47950 N N 3.68527868815389 3.6491271616355 3.6491271616355 18 0 0.725528449392151 N 0 0.146279491833031 N N 86504 0 ENSG00000104408 ENSG00000182152 + - 8 5 109330135 117142614 intron downstream EIF3E AC114322.2 109283149 117142420 - - 0.146279491833031 109296009 116871253 - + Y 0.54481186694143 - N HCC1954 2 1.66666666666667 1 8 3 N - - N - DNA 0 0.478723404255319 0.478723404255319 12 0.564198104634174 0.671324327033068 0.671324327033068 0.564198104634174 3 0 - 4618 N Y 3.60103760561896 3.77208042376856 3.60103760561896 288 0.0034722222222221 0.554433208480598 Y 0.925073099415205 0.99250730994152 N N 3729 0 ENSG00000178234 ENSG00000208257 - - 7 7 151450178 151353493 utr5p upstream GALNT11 AC006017.2-1 151407293 151353212 + - 0 151422209 151355737 - + N - - N HCC1954 20 3.76 1 8 4 N - - N - LTR,LTR 0 0.58273381294964 0.58273381294964 25 1.07126222398894 0.99270299422975 1.07126222398894 0.99270299422975 1 - - 42135 N N 3.59528445727371 3.34000055658918 3.34000055658918 0 0 0.248428509000711 N 0.199015217437443 0.112634505592461 N N 306 201827 ENSG00000205940 ENSG00000096384 + + 4 6 12949024 44329598 coding coding AC006226.4 HSP90AB1 12944136 44322802 + + 0.112634505592461 12948145 44326250 + + Y - 1.27090008820874 N HCC1954 1 1 1 0 1 Y - - N Low_complexity Low_complexity 1 0.310160427807487 1 4 0.321378667196682 0.535631111994469 0.535631111994469 0.321378667196682 1 - 0 34329 Y Y 3.60256518892881 3.51889316784735 3.51889316784735 293 0 0.983708593961416 Y 0.060129304364716 0.991897666416937 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5598943 5567513 - + N - - N HCC1954 1 1 1 0 7 N - - Y LTR,SINE LTR 0.5625 1 1 9 0.914143764470561 1.1141127129485 1.1141127129485 0.914143764470561 1 - - 14851 N Y 3.41679307359967 3.54400240599166 3.41679307359967 0 0 0.179247709597799 N 0.869401193497497 0.869401193497497 N N 49089 1976 ENSG00000117450 ENSG00000166471 - + 1 11 45760196 9292872 utr5p upstream PRDX1 TMEM41B 45749295 9258780 - - 0 45759868 9313357 + - Y - - N HCC1954 6 3.77777777777778 2 9 1 N 445 17.6977 N - SINE 0 1 1 9 0.799875793911741 0.264244681917271 0.799875793911741 0.264244681917271 2 - - 31 Y Y 3.4033579660152 3.21551971114628 3.21551971114628 146 0 0.0577859978045275 Y 0 0.981261307831481 N N 2006 9059 ENSG00000134824 ENSG00000168496 - + 11 11 61391401 61321284 coding utr5p FADS2 FEN1 61340325 61316726 + + 0 61361884 61317033 - + N 0.0895042128416844 0.369483847370317 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 117 0.842726282871298 0.785592297591888 0.842726282871298 0.785592297591888 1 0 0 36429 Y Y 3.56232542602083 2.98061562246089 2.98061562246089 316 0 0.0258673265781293 Y 0 0.992723828882934 N N 349 0 ENSG00000180806 ENSG00000207924 - + 12 12 52683383 52671898 coding downstream HOXC9 hsa-mir-196a-2 52680144 52671789 + + 0 52680362 52675688 - + N 0.868965517241379 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.828442786551446 0.635615586233437 0.828442786551446 0.635615586233437 3 0 - 29236 N Y 3.4006201314963 3.57485544491141 3.4006201314963 260 0.873216783216783 0.0129646674984736 Y 0.873216783216783 0.963776223776224 N N 0 95833 ENSG00000219108 ENSG00000204525 + - 6 6 31458044 31432935 downstream utr3p HLA-S HLA-C 31457830 31344505 - - 0 31457734 31429951 - + N - 1.17270319597108 N HCC1954 2 1.6 1 3 1 N - - N - - 0 0 0 5 0.335662163516534 0.364229156156239 0.364229156156239 0.335662163516534 2 - 0 4717 Y Y 3.54144175291192 3.64400585547602 3.54144175291192 0 0 0.71704641343337 Y 0.245757385292269 0.99326569094011 N N 1760 2548 ENSG00000189077 ENSG00000127952 - + 7 7 75461913 75515257 utr5p coding TMEM120A STYXL1 75454238 75463592 - - 0 75461744 75463700 + - N - 0.321211767936372 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 1.1426797055882 0.978419497909897 1.1426797055882 0.978419497909897 1 - 0 4093 Y Y 3.79362644428678 3.31229081257178 3.31229081257178 287 0 0.196858099753473 Y 0 0.988412608378576 N N 32979 386 ENSG00000106105 ENSG00000196295 - - 7 7 30640168 30570758 upstream upstream GARS AC005154.1 30600706 30566129 + - 0.119358236771736 30591355 30584232 - + N - - N HCC1954 9 1.92857142857143 1 3 4 N - - Y SINE LTR 1 1 1 14 0.614190341753658 0.599906845433805 0.614190341753658 0.599906845433805 2 - - 41922 N N 3.6784526172454 3.41423242051993 3.41423242051993 0 0 0.940783231233652 Y 0 0 N N 38251 0 ENSG00000156802 ENSG00000206719 + + 8 8 124477868 115032403 coding upstream ATAD2 Y_RNA 124401922 115032291 - + 0 124437810 114885171 - + N - - N HCC1954 1 1 1 0 2 N 405 1.47521 N - - 0 0 0 10 1.24266417982717 1.06412047582901 1.24266417982717 1.06412047582901 4 - - 19478 Y Y 3.36357286385383 3.44871903508266 3.36357286385383 0 0 0.320876211053638 Y 0 0.989507749957418 N N 10809 3 ENSG00000090273 ENSG00000131910 - - 1 1 27145475 27113047 coding downstream NUDC NR0B2 27120811 27110566 + - 0 27123225 27110412 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.785592297591888 0.849868031031224 0.849868031031224 0.785592297591888 3 - - 47463 Y Y 3.45553575842133 3.2493439782997 3.2493439782997 210 0 0.633925245789236 Y 0 0.994549180327869 N N 2309 8 ENSG00000131398 ENSG00000131401 - + 19 19 55524446 55539830 coding downstream KCNC3 NAPSB 55507006 55528871 - - 0 55518044 55528259 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 10 1.32122340958636 1.27123117246687 1.32122340958636 1.27123117246687 1 - - 28659 N N 3.26407327547924 3.31894904961092 3.26407327547924 4 0 0.408897616418357 N 0.597731370192308 0 N N 14989 9809 ENSG00000142230 ENSG00000072864 - + 19 16 52405287 15727711 intron intron SAE1 NDE1 52326028 15644625 + + 0 52388748 15701996 - + Y 1.16202894239963 0.824712173930072 N HCC1954 9 2.6 1 1 1 N - - N SINE SINE 1 1 1 5 0.349945659836387 0.328520415356608 0.349945659836387 0.328520415356608 2 0 0 44227 N N 3.54193626645188 3.33528047801382 3.33528047801382 2 0 0.0648217509549123 N 0.601476014760147 0 N N 4516 3891 ENSG00000144645 ENSG00000166295 + + 3 10 31998242 73665622 utr3p utr5p OSBPL10 C10orf104 31674407 73645812 - + 0 31676115 73645839 - + Y - 0.9337793124204 N HCC1954 25 24.125 23 8 1 N - - N SINE - 1 0 1 8 0.271386430077198 0.692749571512847 0.692749571512847 0.271386430077198 1 - 0 13676 N Y 3.33784113109356 3.684245618384 3.33784113109356 306 0 0.0361925043849473 Y 0.766893316466371 0.99196183849884 N N 480 0 ENSG00000159496 ENSG00000218145 - - 22 22 22371363 22312612 upstream intron RGL4 AP000347.4 22360329 22310865 + - 0 22355910 22311127 - + N - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.657040830713216 0.792734045751814 0.792734045751814 0.657040830713216 2 - 0 5973 N Y 3.47911741325579 3.28655907981151 3.28655907981151 188 0.85790273556231 0.00252178267288683 N 0.893427051671733 0.810536980749747 N N 266 850768 ENSG00000204434 ENSG00000075624 - + 2 7 132101558 5536758 coding coding ACTBL3 ACTB 132065738 5533313 + - 0.810536980749747 132101106 5534337 - - Y - - N HCC1954 4 2.8 2 5 1 Y - - N - - 0 0 0 5 0.51420586751469 0.899860268150708 0.899860268150708 0.51420586751469 2 - - 18831 Y Y 3.6272104187567 3.75016368088976 3.6272104187567 409 0.00947002307241984 0.000491587548020589 Y 0.00947002307241984 0.985949929405282 N N 6809 7035 ENSG00000143222 ENSG00000158796 - - 1 1 159395269 159369102 utr5p upstream UFC1 DEDD 159390173 159357391 + - 0 159390216 159369181 - + N 0.140713660221546 - N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.189189189189189 0.189189189189189 4 0.621332089913584 0.707033067832699 0.707033067832699 0.621332089913584 1 0 - 21722 N N 3.60632674564779 3.38908332958226 3.38908332958226 0 0 0.0586350453983716 N 0 0 N N 3709 0 ENSG00000152022 ENSG00000219468 - + 1 9 144213026 140250262 utr3p upstream LIX1L RP11-885N19.5 144188516 140249980 + + 0 144211302 140231669 - + Y - - N HCC1954 148 126.5 96 14 1 N 254 22.866 N SINE - 1 0 1 14 0.314236919036755 0.564198104634174 0.564198104634174 0.314236919036755 2 - - 33174 N Y 3.47961192679575 3.12332620197713 3.12332620197713 320 0 0.0220291149333707 Y 0 0.992560634328358 N N 0 544065 ENSG00000210191 ENSG00000198744 - + MT MT 12337 9988 intron coding AF347015.1-21 MT-CO3 12267 8367 + + 0 12284 8670 - + N 1 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.821301038391519 1.19267194270768 1.19267194270768 0.821301038391519 1 0 - 34014 N N 3.44359772892318 3.6344911504118 3.44359772892318 0 0 0.774686331874016 N 0.0322497420020639 0 N N 0 115137 ENSG00000216739 ENSG00000147403 + + 9 X 118983195 153283874 intron coding RPL10P3 RPL10 118982728 153278689 - + 0 118982800 153282376 - + Y 1 5.91322130254683 N HCC1954 10 6 1 4 1 N - - N - - 0 0 0 5 0.664182578873142 0.978419497909897 0.978419497909897 0.664182578873142 2 0 0 19742 N N 3.34359427943881 2.8459975773378 2.8459975773378 0 0.219381369569104 0.0334455565030665 N 0.261576971214018 0.0716967638119077 N N 7144 0 ENSG00000116984 ENSG00000216095 - + 1 16 235130585 2261842 utr3p downstream MTR hsa-mir-940 235025341 2261749 + + 0.219381369569104 235128448 2261856 - + Y - - N HCC1954 21 21 21 4 1 N 315 25.6201 N SINE - 1 0 1 4 0.257102933757345 0.299953422716903 0.299953422716903 0.257102933757345 1 - - 24990 N N 3.49528100778935 3.39487633072086 3.39487633072086 0 0 0.045018154126877 N 0 0 N N 7525 0 ENSG00000173894 ENSG00000214051 - - 17 13 75375973 100207314 upstream upstream CBX2 AL356732.10 75366588 100206806 + - 0 75358159 100217221 - + Y - - N HCC1954 22 17.7142857142857 2 7 1 N 262 21.0874 N LTR SINE 1 1 1 7 0.507064119354764 0.328520415356608 0.507064119354764 0.328520415356608 1 - - 36068 N N 3.02235246345518 3.23999710710482 3.02235246345518 0 0.0312613595056345 0.045336537321941 N 0.0548891312250093 0 N N 38048 41507 ENSG00000111676 ENSG00000188846 - + 12 3 6921743 40478862 coding coding ATN1 RPL14 6903887 40473834 + + 0.00763358778625967 6916205 40478438 - + Y 0.92804087966065 - N HCC1954 44 26.8 3 5 1 N 229 25.5958 N Simple_repeat - 0.529411764705882 0 0.529411764705882 5 0.5713398527941 0.614190341753658 0.614190341753658 0.5713398527941 1 0 - 10955 N Y 3.13073491470822 3.11080976345569 3.11080976345569 103 0 0.48192649684452 N 0.950133333333333 0.956366666666667 N N 4310 2906 ENSG00000183011 ENSG00000079819 - - 17 6 7701897 131426017 coding downstream LSMD1 EPB41L2 7700730 131202180 - - 0 7701243 131164594 + + Y - - N HCC1954 4 2.97647058823529 2 85 2 N - - N - - 0 0 0 85 1.17838844638783 1.26408942430695 1.26408942430695 1.17838844638783 2 - - 36294 Y Y 3.4576553311236 3.38127338926705 3.38127338926705 271 0 0.0067647348159795 Y 0.99189991899919 0.99189991899919 N N 1619 191 ENSG00000075089 ENSG00000120853 - - 12 12 99142332 99091202 upstream upstream ACTR6 GOLGA2L1 99117996 99074348 + - 0 99116755 99098627 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 6 0.864151527351077 0.914143764470561 0.914143764470561 0.864151527351077 2 - - 21427 N Y 3.22526780992528 3.48908677906663 3.22526780992528 6 0 0.384394904507987 N 0.963553742001298 0.963553742001298 N N 11670 2513 ENSG00000117360 ENSG00000113838 - + 1 3 148592292 187767806 coding utr3p PRPF3 TBCCD1 148560642 187746824 + - 0 148567548 187747191 - - Y - - N HCC1954 35 32.2 28 5 1 N - - N - SINE 0 1 1 5 0.407079645115797 0.385654400636018 0.407079645115797 0.385654400636018 2 - - 12572 N N 3.52208566311286 3.16463888744835 3.16463888744835 0 0 0.199909741555519 N 0 0 N N 14 313916 ENSG00000118160 ENSG00000131748 - + 19 17 52666934 35073248 downstream intron SLC8A2 STARD3 52623735 35046938 - + 0 52620211 35047101 + + Y - 1.09830374749134 N HCC1954 22 17.8571428571429 11 7 1 N 306 23.8266 N SINE - 1 0 1 7 0.292811674556976 0.499922371194838 0.499922371194838 0.292811674556976 4 - 0 36936 N N 3.54872248456702 3.44934152969861 3.44934152969861 0 0.0422175480769231 0.942935499082752 N 0.0422175480769231 0 N N 1977 16017 ENSG00000196074 ENSG00000018236 + + 20 12 57942105 39750361 downstream coding SYCP2 CNTN1 57872016 39588423 - + 0 57869894 39619554 - + Y - - N HCC1954 1 1 1 0 3 N 470 0.598344 N LINE - 1 0 1 22 0.499922371194838 1.13553795742827 1.13553795742827 0.499922371194838 4 - - 19660 N N 3.58593758607883 3.31804396091703 3.31804396091703 7 0 0.0402435759114685 N 0 0 N N 1061 23303 ENSG00000143156 ENSG00000136149 + + 1 13 167603810 53913472 intron upstream NME7 RPL13AP20 167368399 53912798 - - 0 167493413 54053779 - - Y 0.953801057647253 - N HCC1954 23 22.25 22 4 1 N - - N LINE LTR 1 1 1 4 0.428504889595575 0.599906845433805 0.599906845433805 0.428504889595575 1 0 - 13014 N Y 3.64231043829683 3.49168728493972 3.49168728493972 233 0.810341303903536 0.00464245856043599 N 0 0.747121738538047 N N 0 5961 ENSG00000204458 ENSG00000113456 - + 17 5 17086925 34954139 upstream coding AC055811.5 RAD1 17086049 34938268 + - 0 17084460 34944659 - - Y - - N HCC1954 24 14.25 9 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.699891319672773 0.699891319672773 0.321378667196682 3 - - 33301 N Y 3.07933422991999 3.42357929171481 3.07933422991999 388 0 0.151857419969954 Y 0 0.994300441826215 N N 339915 544065 ENSG00000198727 ENSG00000198744 - + MT MT 15882 9988 coding coding MT-CYB MT-CO3 14748 8367 + + 0 15521 8567 - + N 1.1965108104896 - N HCC1954 2 1.25 1 1 5 Y - - N - - 0 0 0 4 0.871293275511003 0.749883556792257 0.871293275511003 0.749883556792257 1 0 - 43047 N N 3.57696143724454 3.51679652308403 3.51679652308403 0 0 0.537676780011297 N 0 0 N N 9848 0 ENSG00000164134 ENSG00000220996 - + 4 5 140531972 115406857 intron upstream NARG1 AC034236.5-1 140442126 115406767 + - 0 140443022 115417608 - - Y 1.36681297140778 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 42 0.999844742389676 1.12125446110842 1.12125446110842 0.999844742389676 2 0 - 33121 N N 2.95952426268928 3.08152416063915 2.95952426268928 0 0 0.120484822102388 N 0 0 Y N 59837 0 ENSG00000198695 ENSG00000210196 + - MT MT 14674 16024 coding intron MT-ND6 AF347015.1-24 14150 15956 - - 0 14321 15969 - + N 0.879271926564333 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.792734045751814 0.928427260790413 0.928427260790413 0.792734045751814 2 0 0 20646 N Y 3.53871326596283 3.65488030998075 3.53871326596283 1 0 0.223381793604820 N 0.569151569151569 0.973071973071973 N N 1186 0 ENSG00000137968 ENSG00000218439 - - 1 X 75849389 77662339 coding downstream SLC44A5 RP1-198G23.1 75440404 77661746 - - 0 75634856 77614198 + + Y - - N HCC1954 21 16.25 1 7 1 N - - N - LINE 0 1 1 8 1.14982145374813 0.485638874874985 1.14982145374813 0.485638874874985 2 - - 35440 N Y 3.12804628055249 3.4503745994685 3.12804628055249 0 0 0.560157325572151 N 0.889295889295889 0.889295889295889 N N 1649619 1123 ENSG00000141736 ENSG00000111785 - + 17 12 35138441 105807215 coding downstream ERBB2 RIC8B 35104766 105692529 + + 0 35122227 105834249 - + Y - - N HCC1954 23 2.68333333333333 1 15 2 N - - N - SINE 0 1 1 60 1.28551466878673 0.414221393275723 1.28551466878673 0.414221393275723 2 - - 30377 N Y 3.37655331069169 3.47486134299686 3.37655331069169 367 0 0.273080659300564 Y 0 0.984170234851434 N N 0 18 ENSG00000207820 ENSG00000215107 + + X X 73423769 73353624 downstream intron hsa-mir-545 AC004386.1-2 73423664 73334464 - + 0 73410902 73340513 - + N - 0.179897201599086 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 21 0.99270299422975 1.59260983966356 1.59260983966356 0.99270299422975 4 - 0 6137 N N 3.05950478423469 3.09462324098319 3.05950478423469 0 0 0.442865584537154 N 0 0 N N 29655 122511 ENSG00000136938 ENSG00000187514 - + 9 2 99818046 232286495 coding coding ANP32B PTMA 99785310 232280638 + + 0 99807215 232284908 - + Y - - N HCC1954 4 2 1 2 1 Y - - N Low_complexity,Low_complexity Low_complexity 0.461111111111111 0.378787878787879 0.461111111111111 4 0.885576771830856 0.921285512630487 0.921285512630487 0.885576771830856 3 - - 29165 Y Y 3.79209886097693 3.59784511035345 3.59784511035345 290 0 0.401737991004241 Y 0.992334217506631 0.984668435013263 N N 154 27657 ENSG00000124743 ENSG00000001084 + - 6 6 53638465 53517790 downstream upstream KLHL31 GCLC 53620658 53470098 - - 0 53589643 53542362 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR - 1 0 1 13 0.785592297591888 1.08554572030879 1.08554572030879 0.785592297591888 4 - - 662 N Y 3.48809356209009 3.56761456604966 3.48809356209009 0 0 0.139767413989368 Y 0 0.981552162849873 N N 87534 10477 ENSG00000198561 ENSG00000213593 - + 11 11 57353279 57265020 coding coding CTNND1 TMX2 57285810 57236618 + + 0 57315721 57263271 - + N - - N HCC1954 2 1.25 1 1 1 Y - - N LINE - 0.293706293706294 0 0.293706293706294 4 0.849868031031224 0.93556900895034 0.93556900895034 0.849868031031224 1 - - 33034 Y Y 2.95952426268928 3.64656650855576 2.95952426268928 263 0 0.998972567350297 Y 0 0.987851247333766 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.987851247333766 14321 12519 - + N 0.879271926564333 0.80034286630944 N HCC1954 1 1 1 0 10 N - - Y - - 0 0 0 13 1.34264865406614 0.828442786551446 1.34264865406614 0.828442786551446 1 0 0 42013 N N 3.10812112929996 3.72824693801095 3.10812112929996 0 0 0.0446564363142511 N 0 0 N N 1618 86504 ENSG00000148200 ENSG00000104408 - + 9 8 126573410 109330135 utr3p coding NR6A1 EIF3E 126319380 109283149 - - 0 126321853 109330074 + - Y - 0.800702901203512 N HCC1954 38 33.375 30 8 1 N - - N SINE - 1 0 1 8 0.428504889595575 0.349945659836387 0.428504889595575 0.349945659836387 1 - 0 30004 N N 3.24255776018456 2.8225133983558 2.8225133983558 9 0 0.201603932396652 N 0 0 N N 568998 86 ENSG00000156508 ENSG00000196511 + + 6 7 74288344 144164079 coding intron EEF1A1 TPK1 74282194 143779976 - - 0 74286334 143976448 - - Y 1.54863708447361 0.560376212542264 N HCC1954 6 4.8 4 5 1 N - - N - - 0 0 0 5 0.442788385915428 0.257102933757345 0.442788385915428 0.257102933757345 1 0 0 1518 N Y 3.26824964015148 3.41679307359967 3.26824964015148 0 0 0.592960332375098 N 0.931307073735859 0.828267684339648 N N 8014 1892 ENSG00000149084 ENSG00000108306 - + 11 17 43834736 34811424 utr3p intron HSD17B12 FBXL20 43658719 34670374 + - 0 43834016 34671580 - - Y 1.56799368003871 0.845593914619183 N HCC1954 20 4.53333333333333 1 8 1 N 259 22.3731 N - SINE 0 0.680851063829787 0.680851063829787 15 0.864151527351077 0.335662163516534 0.864151527351077 0.335662163516534 2 0 0 16195 N N 3.23999710710482 3.4780843434859 3.23999710710482 0 0.0996811418159732 0.184990777035946 N 0.932812025508655 0.0996811418159732 N N 892 0 ENSG00000185304 ENSG00000212679 + + 2 1 87906586 559619 intron intron RGPD2 RP5-857K21.10 87836589 558939 - + 0.0996811418159732 87905580 559309 - + Y 2.62981467744803 1 N HCC1954 2 2 2 4 1 N 501 23.6442 N - - 0 0 0 4 0.499922371194838 0.51420586751469 0.51420586751469 0.499922371194838 2 0 0 178 Y N 3.67718745321157 3.72874145155091 3.67718745321157 0 0 0.359221668104042 Y 0 0 N N 1873 5896 ENSG00000068971 ENSG00000110046 - - 11 11 64458523 64441298 upstream upstream PPP2R5B ATG2A 64448756 64418595 + - 0 64448278 64441667 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.535631111994469 0.392796148795944 0.535631111994469 0.392796148795944 2 - - 33037 Y Y 2.95952426268928 3.86682523844763 2.95952426268928 363 0 0.99814900867245 Y 0 0.992825574251343 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.992825574251343 14322 12785 - + N 0.882650788732857 0.780251842054878 N HCC1954 2 1.18181818181818 1 2 10 N - - Y - - 0 0 0 11 1.19981369086761 1.4426331283051 1.4426331283051 1.19981369086761 0 0 0 8007 N N 3.27192306858781 3.52936639476796 3.27192306858781 0 0 0.771089778473358 N 0.211185889997679 0.017567881178928 N Y 3699 8425 ENSG00000115947 ENSG00000109586 - + 2 4 148495606 174481692 coding coding ORC4L GALNT7 148408202 174326479 - + 0.017567881178928 148432905 174461844 + + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 77 1.04983697950916 1.21409718718746 1.21409718718746 1.04983697950916 4 - - 3992 N Y 3.65488030998075 3.34359427943881 3.34359427943881 395 0 0.213967379723778 Y 0.994489125113644 0.994489125113644 N N 3729 0 ENSG00000178234 ENSG00000208257 - - 7 7 151450178 151353493 intron upstream GALNT11 AC006017.2-1 151407293 151353212 + - 0.189901391705714 151422207 151353901 - + N 0.0792694063926941 - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 132 1.52119235806429 1.37121564670584 1.52119235806429 1.37121564670584 1 0 - 38167 Y Y 3.38552945952599 3.48337348351473 3.38552945952599 260 0 0.0083735901223655 Y 0.989835164835165 0.989835164835165 N N 8985 8764 ENSG00000100603 ENSG00000119705 + + 14 14 77297249 77253690 intron coding SNW1 C14orf156 77253699 77244188 - + 0 77256610 77251973 - + N 0.509362371887365 0.748856806826888 N HCC1954 2 1.25 1 1 1 N - - Y - - 0 0 0 4 0.771308801272036 0.678466075192994 0.771308801272036 0.678466075192994 1 0 0 32490 N N 3.13959243003634 3.29809588172555 3.13959243003634 0 0.0169324417009603 0.0433513250225458 N 0.0169324417009603 0 N N 7272 0 ENSG00000157500 ENSG00000212451 + + 3 8 57282539 127753081 utr3p downstream APPL U11 57236805 127752949 + + 0.0307784636488342 57282070 128107294 + + Y - - N HCC1954 37 30.5 25 4 1 N - - N SINE LTR 1 1 1 4 0.607048593593732 0.435646637755502 0.607048593593732 0.435646637755502 1 - - 45289 N N 3.57800808738356 3.40847927217468 3.40847927217468 0 0 0.400989254937647 N 0.00404858299595157 0 N N 17943 1285 ENSG00000105141 ENSG00000183049 + + 19 10 15027900 12911741 downstream intron CASP14 CAMK1D 15024015 12431738 + + 0.00404858299595157 15029502 12826900 + + Y - 1.04728572126965 N HCC1954 20 16.1111111111111 3 9 1 N - - N - SINE 0 1 1 9 0.478497126715059 0.278528178237124 0.478497126715059 0.278528178237124 3 - 0 41608 N Y 3.59375687396386 3.44615838200292 3.44615838200292 334 0 0.688844744348491 Y 0.993957539466522 0.987915078933043 N N 0 4 ENSG00000207110 ENSG00000184090 - - 8 8 129080722 129029462 upstream downstream U1 TMEM75 129080559 129029046 + - 0 129065332 129021104 - + N - - N HCC1954 20 3.07142857142857 1 3 5 N - - N SINE SINE 1 0.245614035087719 1 14 1.09982921662864 1.22123893534739 1.22123893534739 1.09982921662864 4 - - 17606 Y Y 3.19702885724776 2.54916136176366 2.54916136176366 0 0.204324324324324 0.316088488325825 Y 0.204324324324324 0.204324324324324 N N 15448 81453 ENSG00000143294 ENSG00000143321 - - 1 1 155037226 154988864 coding intron PRCC HDGF 155003898 154978526 + - 0 155004582 154987004 - + N - 7.77358128564457 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.499922371194838 0.435646637755502 0.499922371194838 0.435646637755502 1 - 0 36232 Y Y 3.41529599551336 3.70463477795295 3.41529599551336 258 0 0.036217316981199 Y 0.989053582076838 0.978107164153676 N N 124 8011 ENSG00000174456 ENSG00000076513 + + 12 12 108989883 108961614 intron coding AC007546.6-1 ANKRD13A 108963366 108921618 - + 0 108970551 108950777 - + N 8.34876281104222 1.07494897614632 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 0.449930134075354 0.635615586233437 0.635615586233437 0.449930134075354 4 0 0 26827 Y Y 3.48912663185998 3.23102095827053 3.23102095827053 341 0 0.00352110407878914 Y 0 0.989825842360405 N N 1567 1495 ENSG00000167186 ENSG00000170537 - + 16 16 18998851 18982000 upstream utr3p COQ7 TMC7 18986428 18902828 + + 0 18986243 18981693 - + N - 4.27987870721147 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.578481600954027 0.678466075192994 0.678466075192994 0.578481600954027 3 - 0 44741 N Y 3.39657174790006 3.09087103183403 3.09087103183403 304 0 0.00119140857922562 Y 0 0.988925438596491 N N 3891 3891 ENSG00000166295 ENSG00000166295 - + 10 10 73665622 73665622 intron intron C10orf104 C10orf104 73645812 73645812 + + 0 73649891 73645953 - + N 0.744979490524871 0.744979490524871 N HCC1954 19 14.5 3 4 1 N - - N SINE - 1 0 1 4 0.449930134075354 0.278528178237124 0.449930134075354 0.278528178237124 1 0 0 21235 N Y 3.52511032450902 3.42680229220385 3.42680229220385 245 0.675747508305648 0.0130356190706503 N 0.675747508305648 0.675747508305648 N N 0 0 ENSG00000218918 ENSG00000201398 + + 1 3 31354056 155207981 intron upstream RP11-490K7.1 U8 31353582 155207846 - - 0.745230185097295 31353948 155224425 - - Y 1 - N HCC1954 42 42 42 7 1 N - - N - - 0 0 0 7 0.278528178237124 0.271386430077198 0.278528178237124 0.271386430077198 1 0 - 34052 N N 3.6800200533486 3.38912318237562 3.38912318237562 0 0 0.738124513744518 N 0 0 N N 0 0 ENSG00000196205 ENSG00000217946 + + 9 X 134886082 97532574 intron intron AL593851.6-1 RP11-390F10.1 134884659 97531164 + + 0 134885585 97532107 + + Y 1 1 N HCC1954 11 7.91304347826087 3 46 1 N - - N - - 0 0 0 46 0.814159290231593 0.278528178237124 0.814159290231593 0.278528178237124 3 0 0 24712 Y Y 3.03334131866677 3.53312795148693 3.03334131866677 259 0 0.0951038636882113 Y 0 0.992094134951278 N N 0 0 ENSG00000141650 ENSG00000202159 - + 18 18 53657194 53573730 upstream downstream AC022724.8-1 U6 53656706 53573624 + + 0 53621231 53580172 - + N - - N HCC1954 21 12 1 3 1 N - - Y Low_complexity SINE 0.551020408163265 1 1 4 0.349945659836387 0.385654400636018 0.385654400636018 0.349945659836387 2 - - 35398 N Y 3.12804628055249 3.40910176679063 3.12804628055249 0 0 0.584126665469369 N 0 0.882736156351791 N N 1649619 1123 ENSG00000141736 ENSG00000111785 - + 17 12 35138441 105807215 intron downstream ERBB2 RIC8B 35104766 105692529 + + 0 35125062 105834247 - + Y 0.991162890469566 - N HCC1954 20 2.31428571428571 1 7 2 N - - N - SINE 0 1 1 35 0.692749571512847 0.407079645115797 0.692749571512847 0.407079645115797 2 0 - 30307 N N 3.50575423470996 3.36191729946799 3.36191729946799 0 0 0.0651144913946826 Y 0 0 N N 0 75117 ENSG00000130224 ENSG00000205542 + + X X 114374891 12905267 intron utr3p LRCH2 TMSB4X 114251441 12903150 - + 0 114273998 12905137 - + N 1 0.794151537114978 N HCC1954 4 3 2 5 1 N - - N - - 0 0 0 5 0.264244681917271 0.657040830713216 0.657040830713216 0.264244681917271 1 0 0 38560 Y Y 3.2948728812365 3.70463477795295 3.2948728812365 181 0.0236504427511083 0.0296410213525684 Y 0.967988539106594 0.994664756517766 N N 2078 2999 ENSG00000080823 ENSG00000140153 + + 14 14 101841284 101759760 coding downstream RAGE WDR20 101762375 101675965 - + 0 101768627 101760886 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 21 1.77115354366171 1.36407389854591 1.77115354366171 1.36407389854591 1 - - 31362 N Y 3.6623288755052 3.39743698380061 3.39743698380061 186 0 0.368414640875624 Y 0.055737035524704 0.987409827140329 N N 763 95 ENSG00000205814 ENSG00000215837 - + 3 3 196924416 196900773 coding downstream AC069513.28-3 AC069513.28-2 196912000 196900191 + + 0 196920310 196901489 - + N 3.37484639304147 - N HCC1954 2 1.28571428571429 1 2 4 N - - N - - 0 0 0 7 0.771308801272036 0.785592297591888 0.785592297591888 0.771308801272036 1 0 - 9872 Y N 3.36657459731105 3.528871881228 3.36657459731105 0 0.170124481327801 0.413759286404477 N 0.170124481327801 0.170124481327801 N N 1649619 109916 ENSG00000141736 ENSG00000161395 - + 17 17 35138441 35097836 utr5p upstream ERBB2 PERLD1 35104766 35080902 + - 0 35104878 35098533 - - N - - Y HCC1954 1 1 1 0 2 N 298 9.39526 N - LINE 0 0.685714285714286 0.685714285714286 5 0.707033067832699 0.499922371194838 0.707033067832699 0.499922371194838 1 - - 18121 Y Y 2.2857009512806 3.22804973003685 2.2857009512806 374 0 0.000536657016420139 Y 0 0.991688948306595 N N 22021 0 ENSG00000117632 ENSG00000207302 + + 1 1 26105955 26076683 downstream downstream STMN1 Y_RNA 26099196 26076574 - + 0 26091448 26084898 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.401785714285714 0 0.401785714285714 6 0.799875793911741 0.785592297591888 0.799875793911741 0.785592297591888 1 - - 29324 Y Y 3.53296011761759 3.42104914385861 3.42104914385861 267 0 0.0178363921235909 Y 0.335830212234707 0.992277095491101 N N 0 9273 ENSG00000218757 ENSG00000213079 + + 6 6 155208446 155196882 upstream utr3p RP3-472M2.2 RBM16 155207900 155096204 - + 0 155223566 155196237 - + N - 5.79982639190538 N HCC1954 1 1 1 0 1 N - - Y DNA - 0.153284671532847 0 0.153284671532847 5 0.735600060472404 0.857009779191151 0.857009779191151 0.735600060472404 1 - 0 49458 N N 3.34831435801417 3.74337746277462 3.34831435801417 0 0.00261096605744116 0.97019847426824 N 0.00261096605744116 0 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 coding intron TICAM2 AC034236.1 114942238 115326170 - + 0 114984131 115388478 - + N - 0.493778452200303 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 52 0.971277749749971 0.778450549431962 0.971277749749971 0.778450549431962 2 - 0 31907 N Y 3.25099954268554 3.58015393251005 3.25099954268554 0 0 0.606167033363212 Y 0.956654700172849 0.993807814310407 N N 7179 30872 ENSG00000175792 ENSG00000058262 + + 3 3 129325332 129273215 coding intron RUVBL1 SEC61A1 129282493 129253902 - + 0 129284018 129266755 - + N - 1.65832413471081 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 9 1.02126998686945 0.971277749749971 1.02126998686945 0.971277749749971 2 - 0 25405 N Y 3.43101850966944 3.71976530271662 3.43101850966944 0 0 0.0666644023087195 N 0 0.928771508603442 N N 894 4 ENSG00000132950 ENSG00000103569 + + 13 15 19335773 56265402 utr3p downstream ZMYM5 AQP9 19295622 56217700 - + 0 19296067 56339885 - + Y - - N HCC1954 34 30.8 25 5 1 N 321 16.6238 N SINE LTR 1 1 1 5 0.357087407996313 0.378512652476092 0.378512652476092 0.357087407996313 1 - - 33222 N N 2.91783662205815 3.39483647792751 2.91783662205815 21 0.155161997479848 0.998457556698292 N 0.199627155507224 0.0217665233977179 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0.0217665233977179 8407 12084 - + N 0.984947018030751 - N HCC1954 4 1.6 1 13 7 Y 189 4.09957 N - - 0 0 0 25 1.19267194270768 1.67831081758267 1.67831081758267 1.19267194270768 1 0 - 14158 N Y 3.6289058359359 3.28615785222739 3.28615785222739 0 0 0.183612326083448 N 0.304057044504549 0.832013769363167 N N 1 0 ENSG00000163116 ENSG00000218995 - + 4 22 99283414 22601761 intron upstream C4orf37 AP000350.6 98699050 22599087 - + 0.352053110400787 99124453 22591713 + + Y 0.907096774193548 - N HCC1954 80 21.9375 4 16 1 N 203 28.4648 N LINE,SINE SINE 0.871794871794872 1 1 16 0.278528178237124 0.335662163516534 0.335662163516534 0.278528178237124 1 0 - 44010 N N 3.49272035470961 3.61464054707278 3.49272035470961 5 0 0.0264124904867724 N 0.850454227812718 0.10272536687631 N N 975 2471 ENSG00000198487 ENSG00000151474 + - 6 10 42218335 14412889 coding intron AL512274.9 FRMD4A 42183124 13725712 - - 0.0840321453529 42204419 14117936 - + Y 0.84799579943379 26.6372942315673 N HCC1954 33 26.25 6 4 1 N 120 22.0151 N - SINE 0 1 1 4 0.357087407996313 0.278528178237124 0.357087407996313 0.278528178237124 2 0 0 36274 Y Y 3.56591914887046 3.36720643949681 3.36720643949681 287 0 0.0556938707976011 Y 0 0.991764333227748 N N 1888 482 ENSG00000139291 ENSG00000173451 - + 12 12 70384107 70360684 upstream intron TMEM19 THAP2 70366145 70344051 + + 0 70365970 70351830 - + N - 5.53314642113364 N HCC1954 1 1 1 0 1 N - - Y - DNA 0 1 1 14 0.585623349113953 0.657040830713216 0.657040830713216 0.585623349113953 1 - 0 3895 N N 3.6272104187567 3.2965682984157 3.2965682984157 0 0 0.751627510665934 N 0 0 N N 0 850768 ENSG00000217920 ENSG00000075624 + + X 7 46033507 5536758 intron coding RP1-30G7.1 ACTB 46032395 5533313 - - 0 46032527 5534175 - - Y 1 - N HCC1954 4 2.57142857142857 1 5 2 N - - N - - 0 0 0 7 0.87843502367093 0.814159290231593 0.87843502367093 0.814159290231593 2 0 - 30124 N N 3.29699245393877 3.49487978020523 3.29699245393877 9 0 0.196696064182634 N 0 0 N N 85100 0 ENSG00000148303 ENSG00000220370 + + 9 6 135208102 95111401 coding intron RPL7A RP3-399J4.2 135204890 95111176 + + 0 135208034 95111331 + + Y - 1 N HCC1954 10 5.5 3 4 1 N - - N - - 0 0 0 4 0.664182578873142 0.271386430077198 0.664182578873142 0.271386430077198 2 - 0 26794 Y Y 3.35719722089263 3.28296535696188 3.28296535696188 331 0 0.00147640423144824 Y 0 0.990128922257785 N N 2901 15670 ENSG00000196470 ENSG00000102910 + + 16 16 46976730 46944908 utr3p downstream SIAH1 LONP2 46951943 46835712 - + 0 46952812 46948115 - + N 0.98328397906957 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.778450549431962 0.764167053112109 0.778450549431962 0.764167053112109 1 0 - 38413 Y Y 3.37295958784206 3.18036140160443 3.18036140160443 110 0 0.486659945029323 Y 0.982677983717305 0.974016975575957 N N 2273 516 ENSG00000187097 ENSG00000119636 - - 14 14 73552387 73602546 utr5p upstream ENTPD5 C14orf45 73502946 73555873 - + 0 73552386 73554930 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.821301038391519 0.635615586233437 0.821301038391519 0.635615586233437 4 - - 12700 N N 3.57063922744582 3.41167176744019 3.41167176744019 0 0 0.261482244669530 N 0 0 N N 0 7525 ENSG00000105255 ENSG00000173894 - - 19 17 4274833 75375973 intron upstream FSD1 CBX2 4255668 75366588 + + 0 4257649 75358294 - - Y 1 - N HCC1954 20 15.4285714285714 4 7 1 N - - N SINE LTR 1 1 1 7 0.335662163516534 0.45707188223528 0.45707188223528 0.335662163516534 1 0 - 43628 N N 3.36447795254773 3.40691183607148 3.36447795254773 0 0 0.145492467337672 N 0 0 N N 1649619 5901 ENSG00000141736 ENSG00000182022 - + 17 10 35138441 125841898 coding intron ERBB2 RP11-47G11.1 35104766 125757210 + - 0 35122202 125802456 - - Y - 37.9887065186533 N HCC1954 21 18.4 8 5 1 N - - N - SINE 0 1 1 5 0.464213630395207 0.264244681917271 0.464213630395207 0.264244681917271 2 - 0 25897 N N 3.39545897254347 3.50272957331379 3.39545897254347 4 0 0.607984310150398 N 0.342724482568663 0.527583221846227 N N 8194 16390 ENSG00000144036 ENSG00000140950 - - 2 16 72906685 83095794 intron intron EXOC6B KIAA1609 72256621 83068608 - - 0 72698310 83089223 + + Y 0.464323603265729 1.98970794067006 N HCC1954 13 3.15 1 7 2 N - - N SINE - 1 0 1 20 0.292811674556976 0.614190341753658 0.614190341753658 0.292811674556976 2 0 0 16354 N Y 3.25256697878875 3.66592259835483 3.25256697878875 0 0 0.073438481766053 N 0 0 N N 49089 860 ENSG00000117450 ENSG00000178074 - - 1 2 45760196 200500276 coding intron PRDX1 C2orf69 45749295 200484268 - + 0 45757275 200488542 + - Y - 1.05853047260083 N HCC1954 17 12.6 6 10 1 N - - N - SINE 0 1 1 10 0.5713398527941 0.264244681917271 0.5713398527941 0.264244681917271 2 - 0 34630 Y Y 3.19806192701765 3.63552422018169 3.19806192701765 210 0.103057025279248 0.465742751102749 Y 0.987713109935332 0.975426219870664 N N 11502 0 ENSG00000159921 ENSG00000222760 - - 9 9 36248450 36257919 utr5p downstream GNE U4 36204430 36257780 - + 0 36239394 36266891 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.999844742389676 0.621332089913584 0.999844742389676 0.621332089913584 4 - - 29508 N Y 3.61464054707278 3.42886843174363 3.42886843174363 208 0.827844982078853 0.0332163165417381 N 0.827844982078853 0.869399641577061 N N 95833 99 ENSG00000204525 ENSG00000204623 - - 6 6 31432935 30136900 coding intron HLA-C C6orf12 31344505 30076768 - - 0.869399641577061 31432477 30082792 + + N - 0.455072933993676 Y HCC1954 2 1.16666666666667 1 1 1 N - - N - - 0 0 0 6 0.871293275511003 0.728458312312478 0.871293275511003 0.728458312312478 1 - 0 30880 N N 3.27870928670295 3.0302421093571 3.0302421093571 0 0.0446996612410145 0.520736134459501 N 0.532512600181773 0.0446996612410145 N N 78560 1272 ENSG00000112493 ENSG00000157388 - - 6 3 33390114 53821001 utr3p intron TAPBP CACNA1D 33375449 53504116 - + 0.268280591588862 33376424 53566571 + - Y - 0.658239688161162 N HCC1954 132 48 3 9 1 N - - N SINE SINE,LINE 1 0.804878048780488 1 9 0.842726282871298 0.292811674556976 0.842726282871298 0.292811674556976 2 - 0 16939 N N 3.7061623612628 3.25256697878875 3.25256697878875 1 0 0.0715696685275462 N 0 0 N N 838 49089 ENSG00000182534 ENSG00000117450 - - 17 1 72218682 45760196 utr5p coding MXRA7 PRDX1 72183404 45749295 - - 0 72197638 45757275 + + Y - - N HCC1954 42 22.25 1 15 1 N 476 24.198 N SINE - 1 0 1 16 0.385654400636018 0.942710757110266 0.942710757110266 0.385654400636018 2 - - 38031 N Y 3.6727393216935 3.4780843434859 3.4780843434859 0 0 0.107933665531671 N 0.552407316940781 0 N N 8350 147 ENSG00000179364 ENSG00000179082 - + 14 9 104935529 131127005 utr3p downstream PACS2 C9orf106 104852126 131123116 + + 0 104934084 131144169 - + Y - - N HCC1954 36 32.5652173913044 29 23 1 N - - N SINE - 1 0 1 23 0.364229156156239 0.735600060472404 0.735600060472404 0.364229156156239 2 - - 18210 Y Y 3.0349223351391 3.39950312334039 3.0349223351391 269 0 0.00555367190527101 Y 0 0.987850213074621 N N 698 6891 ENSG00000126091 ENSG00000066135 - + 1 1 44169417 43943775 upstream utr3p ST3GAL3 JMJD2A 43945805 43888384 + + 0 43945288 43942702 - + N - 1.34392546711515 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.449930134075354 0.542772860154395 0.542772860154395 0.449930134075354 1 - 0 7021 Y Y 3.51207644450867 3.58999531724489 3.51207644450867 293 0 0.0694997446949666 Y 0 0.99256278335286 N N 0 0 ENSG00000216921 ENSG00000188011 + + 2 2 242493375 242464155 downstream downstream AC131097.4 C2orf85 242484809 242460559 - + 0 242478569 242473460 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR LINE 1 0.295302013422819 1 4 0.785592297591888 0.778450549431962 0.785592297591888 0.778450549431962 1 - - 17398 N N 3.27398920812759 3.19612376855386 3.19612376855386 0 0 0.0676860884747689 N 0 0 N N 2252 2251 ENSG00000181873 ENSG00000186275 - - 1 1 226436581 143541658 utr3p upstream C1orf69 NBPF8 226420139 143326471 + + 0 226432862 143309731 - - N - - Y HCC1954 48 44 40 13 1 N 206 29.0663 N SINE LINE 1 0.0357142857142857 1 13 0.299953422716903 0.799875793911741 0.799875793911741 0.299953422716903 2 - - 42369 Y Y 3.77104735399867 3.31745197152461 3.31745197152461 410 0 0.0051791332973653 Y 0 0.994636768948335 N N 73 5741 ENSG00000109743 ENSG00000118564 - - 4 4 15343508 15266111 upstream upstream BST1 FBXL5 15313739 15215252 + - 0 15291996 15279385 - + N - - N HCC1954 1 1 1 0 3 N - - Y - DNA 0 1 1 4 0.564198104634174 0.257102933757345 0.564198104634174 0.257102933757345 1 - - 46929 Y Y 2.85175072568305 3.52361324642271 2.85175072568305 254 0 0.153137523602538 Y 0 0.98722996163941 N N 4980 0 ENSG00000063169 ENSG00000223326 - + 19 19 52898291 52776388 upstream downstream GLTSCR1 SRP_euk_arch 52874031 52776092 + + 0 52868538 52804237 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 19 0.39993789695587 0.485638874874985 0.485638874874985 0.39993789695587 3 - - 47675 N N 3.64127736852694 3.5010341561346 3.5010341561346 0 0 0.121933166204204 Y 0 0 N N 294 40617 ENSG00000197497 ENSG00000130164 + + 19 19 58388431 11105490 utr3p utr3p ZNF665 LDLR 58358364 11061132 - + 0 58359454 11104135 - + N - 2.27267372255859 N HCC1954 40 33.5 21 4 1 N - - N SINE SINE 1 0.0222222222222222 1 4 0.321378667196682 0.321378667196682 0.321378667196682 0.321378667196682 3 - 0 41356 N N 3.58064844605001 3.39801962562321 3.39801962562321 0 0 0.0466635680240078 N 0 0.0276202128053979 N N 3 551733 ENSG00000179242 ENSG00000204628 - + 20 5 59945671 180603512 intron coding CDH4 GNB2L1 59260965 180596536 + - 0.0276202128053979 59292403 180597246 - - Y 0.929733246584255 0.534680688416546 N HCC1954 19 8.83333333333333 1 5 1 N - - N SINE - 1 0 1 6 0.264244681917271 0.464213630395207 0.464213630395207 0.264244681917271 1 0 0 18290 Y Y 3.48271113610543 3.74081680969488 3.48271113610543 250 0 0.143034139230273 Y 0 0 N N 548 3 ENSG00000162654 ENSG00000213512 + - 1 1 89437150 89414311 downstream coding GBP4 GBP7 89420044 89370022 - - 0 89417590 89387817 - + N - 0.901378575297468 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 8 0.442788385915428 0.885576771830856 0.885576771830856 0.442788385915428 4 - 0 45089 Y Y 3.51633251476761 3.25468655149101 3.25468655149101 0 0 0.181973062932843 Y 0.994026652577199 0.994026652577199 N N 3115 1401 ENSG00000107796 ENSG00000026103 - - 10 10 90702509 90765521 utr5p intron ACTA2 FAS 90684814 90739206 - + 0 90702469 90740678 + - N - 0.508855205514608 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 1.13553795742827 1.56404284702385 1.56404284702385 1.13553795742827 1 - 0 9558 Y Y 3.44359772892318 3.26953024937741 3.26953024937741 195 0 0.00816799423251302 Y 0.0761904761904761 0 N N 2648 2257 ENSG00000218884 ENSG00000125458 + - 17 17 70662207 70639472 intron intron AC022211.5-2 NT5C 70643489 70637919 - - 0 70656179 70638836 - + N 0.684312077541507 1.60879701743562 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.214814814814815 0 0.214814814814815 7 0.949852505270192 0.821301038391519 0.949852505270192 0.821301038391519 2 0 0 47999 N N 3.42424163912411 2.93975336493696 2.93975336493696 0 0 0.208379365277983 N 0 0.00384615384615383 N N 0 14754 ENSG00000208693 ENSG00000113504 + + 8 5 112016351 1165172 upstream intron AC104946.4-4 SLC12A7 112016284 1103491 - - 0.00384615384615383 112599304 1134428 - - Y - 1.06497208853964 N HCC1954 1 1 1 0 1 N 76 0.498376 N - SINE 0 1 1 9 0.814159290231593 0.978419497909897 0.978419497909897 0.814159290231593 2 - 0 33116 N Y 2.93548794710821 3.61257440753299 2.93548794710821 399 0.0189484700762895 0.00075528169920247 Y 0.0353906744884189 0.945192651959569 N N 339915 539404 ENSG00000198727 ENSG00000198712 - + MT MT 15882 8270 coding coding MT-CYB MT-CO2 14748 7587 + + 0.0408714092924618 14765 8109 - + N 0.420492310719871 1.85257889519219 N HCC1954 4 1.8 1 2 1 N - - N - - 0 0 0 5 0.771308801272036 0.671324327033068 0.771308801272036 0.671324327033068 2 0 0 34564 N N 3.63345808064191 3.39640391403072 3.39640391403072 0 0.199819168173598 0.45743815163173 N 0.18203737191079 0.18203737191079 N N 0 82252 ENSG00000218778 ENSG00000137154 + + 9 9 19191044 19385742 intron coding RP11-146N23.1 RPS6 19190333 19366254 - - 0.18203737191079 19190838 19368866 - - N 1 - Y HCC1954 2 1.16666666666667 1 1 1 N - - N - - 0 0 0 6 0.278528178237124 0.357087407996313 0.357087407996313 0.278528178237124 1 0 - 34234 Y Y 3.43718223316862 3.23533046169195 3.23533046169195 330 0 0.191184462729741 Y 0.938458660680883 0.987691732136176 N N 333 14753 ENSG00000214654 ENSG00000119402 - - 9 9 122601666 122595561 intron upstream AL161911.17 FBXW2 122600367 122559075 + - 0 122600674 122596021 - + N 0.0469635433514239 - N HCC1954 1 1 1 0 2 N - - Y - SINE,SINE,LINE 0 0.976608187134503 0.976608187134503 28 1.19267194270768 1.22123893534739 1.22123893534739 1.19267194270768 4 0 - 24600 N Y 3.47080361183081 3.45612774781375 3.45612774781375 0 0 0.447530371291095 N 0 0.936786410470621 N N 0 13271 ENSG00000221499 ENSG00000081923 + - 4 18 178702712 53550037 downstream upstream AC078881.5-1 ATP8B1 178702625 53464656 - - 0.936786410470621 178683766 53550060 - + Y - - N HCC1954 6 4.6 4 5 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.378512652476092 0.378512652476092 0.299953422716903 1 - - 7624 N N 3.24575025545007 3.1474422231449 3.1474422231449 0 0.228752208858234 0.120226125389812 N 0.88713446958901 0.00302114803625375 N N 2078 3 ENSG00000182621 ENSG00000222017 - + 20 2 8813547 198347792 coding coding PLCB1 AC011997.1 8061296 198266075 + + 0 8078973 198266130 - + Y - - N HCC1954 25 22.0909090909091 7 33 1 Y - - N - LINE,LINE 0 0.990825688073395 0.990825688073395 33 2.00683123293928 0.778450549431962 2.00683123293928 0.778450549431962 3 - - 26888 Y Y 3.6035982586987 3.60935140704395 3.6035982586987 0 0 0.71224092560721 Y 0 0.993690007266052 N N 95267 76996 ENSG00000039068 ENSG00000062038 - + 16 16 67426943 67290440 upstream coding CDH1 CDH3 67328696 67236240 + + 0 67313827 67287325 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 31 1.14982145374813 1.24266417982717 1.24266417982717 1.14982145374813 2 - - 31637 Y Y 3.15575602456989 3.52680574168822 3.15575602456989 89 0.0198814091384724 0.402434304806789 Y 0.0443843739100105 0.991832345076154 N N 139 298 ENSG00000206552 ENSG00000182983 - + 3 3 42959283 42933958 utr5p intron C3orf41 ZNF662 42952856 42922406 + + 0 42955346 42929832 - + N - 0.609585909077787 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.757025304952183 0.592765097273879 0.757025304952183 0.592765097273879 2 - 0 6908 Y Y 3.8333716936548 3.60785432895764 3.60785432895764 365 0 0.332071504143451 Y 0.0210942095974452 0 N N 0 52 ENSG00000183846 ENSG00000214164 + - 2 2 110575338 110569923 upstream downstream AC112229.4-1 AC112229.4-2 110574935 110569013 - - 0 110576428 110566855 - + N - - N HCC1954 22 6.56140350877193 4 57 4 N - - Y - - 0 0 0 57 1.45691662462496 1.22123893534739 1.45691662462496 1.22123893534739 1 - - 48827 Y Y 3.56761456604966 3.65760879692984 3.56761456604966 350 0 0.111563232848209 Y 0.603620230700976 0.993806566104703 N N 2506 38037 ENSG00000214302 ENSG00000131446 + - 5 5 180210585 180175147 downstream upstream AC022413.4-2 MGAT1 180208398 180150147 - - 0 180193919 180191413 - + N - - N HCC1954 22 2.59285714285714 1 33 3 N - - Y SINE,SINE,LTR,LTR - 0.570588235294118 0 0.570588235294118 140 1.21409718718746 1.31408166142643 1.31408166142643 1.21409718718746 1 - - 41404 Y Y 3.38552945952599 3.53039946453785 3.38552945952599 306 0 0.0122860023867274 Y 0.957585871227924 0.992930978537987 N N 0 0 ENSG00000221261 ENSG00000221176 - + 8 8 129231616 129130666 upstream downstream hsa-mir-1208 hsa-mir-1207 129231544 129130580 + + 0 129182406 129178080 - + N - - N HCC1954 4 1.77777777777778 1 8 2 N - - Y LTR - 1 0 1 18 0.892718519990782 1.0069864905496 1.0069864905496 0.892718519990782 2 - - 34649 N Y 3.48912663185998 3.4780843434859 3.4780843434859 0 0 0.97064932723742 Y 0 0 N N 22735 8003 ENSG00000119314 ENSG00000119471 - - 9 9 114135768 114274511 coding upstream ROD1 HSDL2 114020536 114182038 - + 0 114100017 114180801 + - N - - N HCC1954 1 1 1 0 2 N - - N - DNA 0 0.236842105263158 0.236842105263158 8 0.978419497909897 1.08554572030879 1.08554572030879 0.978419497909897 4 - - 41671 Y Y 3.38705704283584 3.66592259835483 3.38705704283584 269 0 0.00606910334926025 Y 0.991104620286776 0.991104620286776 N N 159165 5870 ENSG00000164754 ENSG00000147679 + + 8 8 117956182 117867997 intron downstream RAD21 UTP23 117927355 117847923 - + 0 117930307 117868068 - + N 0.445106285889818 - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 5 0.721316564152552 0.87843502367093 0.87843502367093 0.721316564152552 1 0 - 9835 Y Y 3.33424740824393 3.6272104187567 3.33424740824393 0 0 0.998978103956422 Y 0.125989720794555 0 N N 252027 170868 ENSG00000141738 ENSG00000141741 - - 17 17 35157070 35140314 utr5p intron GRB7 C17orf37 35147713 35138937 + - 0 35147806 35140073 - + N - 1.69054296358442 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 16 1.17124669822791 1.15696320190805 1.17124669822791 1.15696320190805 2 - 0 20458 N Y 3.2778440508024 3.46717003618782 3.2778440508024 91 0 0.176147216306116 N 0.970899279708993 0.970899279708993 N N 0 8888 ENSG00000208313 ENSG00000112159 - - 1 6 172102129 90586163 downstream intron SNORD77 MDN1 172102062 90409952 - - 0.970899279708993 172101963 90487771 + + Y - 1.96227421382155 N HCC1954 2 1.38461538461538 1 5 1 N - - N - - 0 0 0 13 0.928427260790413 0.821301038391519 0.928427260790413 0.821301038391519 2 - 0 46406 N N 3.51104337473878 3.58333708020574 3.51104337473878 7 0 0.434647112559821 N 0 0.0392260148897318 N N 1992 0 ENSG00000003436 ENSG00000174677 - - 2 19 188127464 58462730 utr5p upstream TFPI VN1R4 188037202 58461825 - - 0.0392260148897318 188127365 58465698 + + Y - - N HCC1954 21 20.7142857142857 20 7 1 N - - N - Other 0 1 1 7 0.785592297591888 0.557056356474248 0.785592297591888 0.557056356474248 3 - - 4030 N N 3.29231222815676 3.45872825368684 3.29231222815676 0 0 0.82609201477892 Y 0 0.0372770729913587 N N 28646 9342 ENSG00000164880 ENSG00000164818 + + 7 7 1510772 795716 coding intron INTS1 HEATR2 1476439 732864 - + 0.0372770729913587 1499959 742216 - + N 0.708695348786148 0.730643023203145 N HCC1954 7 1.78378378378378 1 12 1 N 22 4.15045 N - LINE 0 1 1 37 1.09982921662864 1.06412047582901 1.09982921662864 1.06412047582901 3 0 0 26001 N N 3.64553343878587 3.48809356209009 3.48809356209009 0 0 0.0923142034141669 N 0 0.00364963503649651 N N 297 45068 ENSG00000157851 ENSG00000205336 - + 2 16 27024572 56256445 upstream upstream DPYSL5 GPR56 26924467 56220023 + + 0.00364963503649651 26920507 56211646 - + Y - - N HCC1954 21 18.9230769230769 4 13 1 N 469 17.2343 N SINE - 1 0 1 13 0.34280391167646 0.657040830713216 0.657040830713216 0.34280391167646 1 - - 46807 Y Y 3.36870351758313 2.8282436187621 2.8282436187621 298 0 0.51912725956868 Y 0 0 N N 675 793 ENSG00000179922 ENSG00000171443 + + 19 19 60827753 60806316 downstream downstream ZNF784 ZNF524 60823919 60803542 - + 0 60816770 60808909 - + N - - N HCC1954 1 1 1 0 4 N - - Y Simple_repeat Simple_repeat 0.326797385620915 0.0442477876106195 0.326797385620915 67 1.09268746846872 0.807017542071667 1.09268746846872 0.807017542071667 1 - - 30107 N N 3.51104337473878 3.11192253881228 3.11192253881228 15 0 0.0644673418393676 N 0 0 N N 0 78560 ENSG00000222476 ENSG00000112493 + - 9 6 9432367 33390114 intron utr3p SRP_euk_arch TAPBP 9432060 33375449 + - 0 9432332 33376428 + + Y 1 0.848737848600813 N HCC1954 81 27.6666666666667 5 6 1 N - - N srpRNA SINE 1 1 1 6 0.985561246069823 0.835584534711372 0.985561246069823 0.835584534711372 2 0 0 32344 N Y 3.40666674327076 3.41526549028982 3.40666674327076 0 0 0.0631011066164232 N 0.197946859903381 0 N N 10229 22539 ENSG00000114450 ENSG00000187210 - + 3 9 180652065 78312150 utr3p utr5p GNB4 GCNT1 180596570 78263888 - + 0 180598420 78305652 + + Y - - N HCC1954 34 30.4 27 5 1 N 435 25.3683 N SINE - 1 0 1 5 0.321378667196682 0.821301038391519 0.821301038391519 0.321378667196682 2 - - 36642 Y Y 3.28871850530713 3.38590018188657 3.28871850530713 14 0.0177375565610861 0.878982492318514 Y 0.157013574660634 0.985339366515837 N N 6867 635 ENSG00000166987 ENSG00000175197 - - 12 12 56210198 56200567 utr5p upstream MBD6 DDIT3 56202926 56196640 + - 0 56204079 56200797 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.857009779191151 0.842726282871298 0.857009779191151 0.842726282871298 4 - - 33265 N N 2.79058743687281 3.45140766923839 2.79058743687281 0 0 0.99999599722073 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8444 11807 - + N 0.872163740421758 - N HCC1954 3 2 1 6 12 N 189 4.09957 N - - 0 0 0 8 1.27123117246687 0.892718519990782 1.27123117246687 0.892718519990782 1 0 - 39982 Y Y 3.28808666312136 3.47125827257741 3.28808666312136 245 0 0.069950335200252 Y 0.991700680272109 0.983401360544218 N N 1922 3186 ENSG00000180979 ENSG00000092531 + + 15 15 40628292 40612548 coding downstream LRRC57 SNAP23 40622014 40575127 - + 0 40624567 40619101 - + N 1.04545448343649 - N HCC1954 2 1.2 1 1 1 N - - Y - SINE 0 0.984848484848485 0.984848484848485 5 0.728458312312478 0.471355378555133 0.728458312312478 0.471355378555133 4 0 - 10392 N N 3.64549358599252 3.33996070379583 3.33996070379583 0 0 0.315698245351193 N 0 0 N N 62029 18240 ENSG00000141367 ENSG00000062716 + + 17 17 55129099 55273235 coding coding CLTC TMEM49 55051832 55139811 + + 0 55115898 55270538 + + N - 0.586153570503566 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.914143764470561 0.764167053112109 0.914143764470561 0.764167053112109 2 - 0 42332 Y Y 3.65488030998075 2.84234107375587 2.84234107375587 257 0 0.0605281634475738 Y 0.627827425492795 0.989053747808612 N N 0 12369 ENSG00000206738 ENSG00000063978 + + 4 4 2586749 2487382 downstream downstream Y_RNA RNF4 2586649 2440605 - + 0 2567607 2508693 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.74 0.74 27 0.821301038391519 0.714174815992626 0.821301038391519 0.714174815992626 2 - - 37059 N N 3.26616992024256 3.21808036422602 3.21808036422602 5 0.0180894953982862 0.355307509630861 N 0.0180894953982862 0.0180894953982862 N N 712661 3629 ENSG00000111640 ENSG00000145332 + - 12 4 6517797 88360698 utr3p intron GAPDH KLHL8 6513918 88301238 + - 0.0180894953982862 6517673 88348366 + + Y - 1.543351600084 N HCC1954 20 7.71428571428571 1 10 1 N - - N - - 0 0 0 14 0.471355378555133 0.364229156156239 0.471355378555133 0.364229156156239 3 - 0 26617 Y Y 3.49760826715431 3.084614022379 3.084614022379 239 0 0.0132617131975792 Y 0.356362894172875 0.987855903663639 N N 68 321 ENSG00000135702 ENSG00000183196 + - 16 16 74126569 74086783 downstream upstream CHST5 CHST6 74119931 74064523 - - 0 74108615 74096682 - + N - - N HCC1954 2 2 2 4 1 N - - Y - - 0 0 0 4 0.614190341753658 0.771308801272036 0.771308801272036 0.614190341753658 2 - - 38800 N Y 2.39788152983156 3.10447397328784 2.39788152983156 0 0 0.06756313327334 N 0 0.895972722593927 N N 0 4657 ENSG00000182225 ENSG00000198252 + + 19 14 5527949 52311409 downstream utr3p AC011533.6 STYX 5527671 52266675 - + 0 5518621 52310012 - + Y - - N HCC1954 38 24.1034482758621 21 29 1 N - - N Low_complexity SINE 0.0176991150442478 1 1 29 0.807017542071667 0.414221393275723 0.807017542071667 0.414221393275723 1 - - 32997 N N 2.95079565331103 2.89575204531 2.89575204531 22 0.0469285853901238 0.999960701451104 N 0.0154592462284771 0.150327842635535 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.150327842635535 8400 13783 - + N 0.831765520441717 1.04914904086967 N HCC1954 3 1.55555555555556 1 4 10 Y 189 4.09957 N - - 0 0 0 9 0.99270299422975 1.28551466878673 1.28551466878673 0.99270299422975 2 0 0 29157 Y Y 3.72551845106187 3.01972902964314 3.01972902964314 0 0 0.97848308528109 Y 0 0.983667499542934 N N 11566 0 ENSG00000130338 ENSG00000188451 - - 6 6 158852842 158583817 upstream downstream TULP4 RP1-274L14.2 158653680 158578356 + - 0 158623283 158573323 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Simple_repeat 0 0.484662576687117 0.484662576687117 38 0.93556900895034 1.16410495006798 1.16410495006798 0.93556900895034 4 - - 34239 Y Y 2.88461647098009 3.60888739872753 2.88461647098009 0 0 0.889373866683417 Y 0.0599400152200188 0.97761761941 N N 7771 4429 ENSG00000165304 ENSG00000137075 - - 9 9 36667678 36391195 upstream coding MELK RNF38 36562873 36326401 + - 0 36477308 36366122 - + N - 3.82938281180514 N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.0707070707070707 0 0.0707070707070707 15 0.707033067832699 1.20695543902754 1.20695543902754 0.707033067832699 2 - 0 3476 N N 3.39401109482032 3.4780843434859 3.39401109482032 0 0 0.974796441449554 N 0 0 N N 5889 7284 ENSG00000198862 ENSG00000156299 + + 21 21 29287141 31853161 intron coding RNF160 TIAM1 29222337 31412607 - - 0 29276830 31517594 - - N 0.514303670861949 - Y HCC1954 1 1 1 0 4 N 566 1.62267 N LTR,LTR - 0.632075471698113 0 0.632075471698113 6 0.749883556792257 0.707033067832699 0.749883556792257 0.707033067832699 1 0 - 34176 Y Y 3.3463227663879 3.03656431915581 3.03656431915581 405 0 0.00091650389993525 Y 0.711060025542784 0.993120476798638 N N 0 551 ENSG00000199437 ENSG00000165716 + + 9 9 138740512 138738323 upstream downstream SNORA43 FAM69B 138740377 138726851 - + 0.993120476798638 138740587 138739386 - + N - - N HCC1954 2 1.60194174757282 1 62 1 N - - Y - - 0 0 0 103 1.08554572030879 1.61403508414333 1.61403508414333 1.08554572030879 1 - - 19609 N Y 3.53039946453785 3.75913982972405 3.53039946453785 9 0 0.0918013332016712 N 0.134708249496982 0.943259557344064 N N 323 13271 ENSG00000183347 ENSG00000081923 - - 1 18 89626307 53550037 utr3p coding GBP6 ATP8B1 89602024 53464656 + - 0.0921529175050303 89625984 53549994 - + Y - 1.91652705132396 N HCC1954 25 19.4285714285714 4 7 1 N - - N SINE - 1 0 1 7 0.357087407996313 0.93556900895034 0.93556900895034 0.357087407996313 2 - 0 2231 N Y 3.18974812559266 3.5074097990958 3.18974812559266 0 0 0.447297211753909 N 0.533889140823944 0.872047999441867 N N 18437 2195 ENSG00000163932 ENSG00000177030 - + 3 11 53201771 685740 utr5p intron PRKCD DEAF1 53170263 634225 + - 0 53174267 642534 - - Y - 0.765249722334855 N HCC1954 20 20 20 7 1 N 599 22.5468 N - SINE 0 1 1 7 0.678466075192994 0.299953422716903 0.678466075192994 0.299953422716903 2 - 0 36594 Y Y 3.68680627146374 3.46720988898117 3.46720988898117 0 0 0.98241546139686 Y 0 0.994168899674739 N N 756 0 ENSG00000139132 ENSG00000207176 - - 12 12 32684940 32440348 utr5p upstream FGD4 Y_RNA 32546361 32440251 + - 0 32546539 32444159 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 41 1.23552243166724 1.2783729206268 1.2783729206268 1.23552243166724 2 - - 38068 Y Y 3.81145495077599 3.44611852920956 3.44611852920956 0 0 0.740539347779067 Y 0 0.328799526907155 N N 0 3324 ENSG00000199739 ENSG00000129534 + - 14 14 44813409 44792146 upstream upstream U6 C14orf106 44813312 44742144 - - 0 44905098 44800897 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE SINE 1 1 1 6 0.649899082553289 0.949852505270192 0.949852505270192 0.649899082553289 4 - - 14361 N Y 3.56335849579072 3.49168728493972 3.49168728493972 0 0 0.599065920638153 N 0.589422937509062 0 N N 498 14402 ENSG00000168243 ENSG00000156689 - + 1 11 233880677 58368833 utr3p utr5p GNG4 GLYATL2 233777610 58358118 - - 0 233781459 58368484 + - Y - 0.956449640258661 N HCC1954 39 33.5 14 6 1 N - - N SINE - 1 0 1 6 0.507064119354764 0.742741808632331 0.742741808632331 0.507064119354764 2 - 0 18376 Y Y 3.38809011260573 3.29959295981186 3.29959295981186 211 0 0.226117413881751 Y 0.987712831314727 0.975425662629454 N N 0 1472 ENSG00000212577 ENSG00000117543 - - 1 1 101371483 101263950 upstream upstream SCARNA16 DPH5 101371297 101227773 + - 0 101321605 101315652 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.607048593593732 0.914143764470561 0.914143764470561 0.607048593593732 4 - - 11576 N N 3.62398741826765 3.24575025545007 3.24575025545007 0 0.439798263534218 0.0165217439585432 N 0.439798263534218 0.00284090909090917 N N 1649619 6060 ENSG00000141736 ENSG00000079482 - + 17 X 35138441 67570372 coding intron ERBB2 OPHN1 35104766 67179440 + - 0.00284090909090917 35116918 67238622 - - Y - 1.37757076718904 N HCC1954 20 20 20 4 1 N - - N - snRNA,snRNA 0 1 1 4 0.778450549431962 0.264244681917271 0.778450549431962 0.264244681917271 1 - 0 4828 N Y 3.36291051644453 3.56125250345759 3.36291051644453 2 0 0.0816820293901531 Y 0.632315751445087 0.968840317919075 N N 12112 101 ENSG00000106290 ENSG00000214309 - - 7 7 99554915 99564056 utr5p utr5p TAF6 AC073842.5 99542638 99562253 - + 0 99554447 99562586 + - N - 0.550287789515864 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.93556900895034 0.964136001590045 0.964136001590045 0.93556900895034 2 - 0 329 Y Y 3.29383981146661 3.56890511773614 3.29383981146661 7 0 0.327600635275904 Y 0.147331154684096 0.972494553376906 N N 0 1856 ENSG00000197188 ENSG00000149231 + - 11 11 95762591 95757574 downstream coding AP003781.3-1 CCDC82 95762258 95725589 - - 0 95762182 95757520 - + N - 1.10888187947592 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.357087407996313 0.542772860154395 0.542772860154395 0.357087407996313 1 - 0 48296 N N 2.93388581588485 3.51935717616377 2.93388581588485 0 0.27370406824147 0.519468814780121 N 0.398211942257218 0 N N 0 551733 ENSG00000216395 ENSG00000204628 - + X 5 61916521 180603512 upstream utr3p RP11-3D23.1 GNB2L1 61915445 180596536 + - 0 61731141 180596558 - - Y - - N HCC1954 15 11 6 4 1 N - - N SINE - 0.842105263157895 0 0.842105263157895 4 0.271386430077198 0.385654400636018 0.385654400636018 0.271386430077198 2 - - 525 Y Y 3.59065766465419 3.22696322710447 3.22696322710447 110 0 0.951356122018082 Y 0.00257069408740351 0.987686057951696 N Y 4055 28586 ENSG00000168000 ENSG00000214753 - + 11 11 62233562 62251397 utr5p coding BSCL2 HNRNPUL2 62214323 62238798 - - 0 62231372 62239548 + - N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 23 1.24980592798709 1.39264089118562 1.39264089118562 1.24980592798709 4 - - 34615 Y Y 3.15311566590345 3.75169126419961 3.15311566590345 0 0 0.369898879567196 Y 0 0 N N 71 0 ENSG00000160339 ENSG00000219785 - + 9 9 136919745 136900142 utr5p upstream FCN2 RP11-263F14.3 136912475 136899686 + + 0 136912475 136896223 - + N - - N HCC1954 2 1.4 1 2 2 N - - Y - - 0 0 0 5 0.871293275511003 0.492780623034912 0.871293275511003 0.492780623034912 2 - - 36358 Y Y 3.72551845106187 3.48167806633553 3.48167806633553 205 0 0.168835920174078 Y 0.228780487804878 0.975121951219512 N N 3495 30837 ENSG00000144785 ENSG00000062485 + - 12 12 54996387 54980442 intron coding CNPY2 CS 54990484 54951750 - - 0 54994580 54980238 - + N 1.70162180839779 2.6483323699041 N HCC1954 2 1.11111111111111 1 1 2 N - - Y - - 0 0 0 9 0.857009779191151 0.799875793911741 0.857009779191151 0.799875793911741 4 0 0 27 Y Y 3.36034051579497 3.27192306858781 3.27192306858781 317 0.0031545741324922 0.0244824660756802 Y 0.992979961789666 0.992979961789666 N N 0 7926 ENSG00000213779 ENSG00000011405 - - 11 11 17172431 17147930 downstream utr5p RPL29P21 PIK3C2A 17171612 17064705 + - 0 17185970 17147928 - + N - 77.701279884086 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 131 0.814159290231593 1.27123117246687 1.27123117246687 0.814159290231593 1 - 0 20451 N Y 3.65488030998075 3.31336373513502 3.31336373513502 0 0 0.749490576114971 N 0.958132719279883 0.958132719279883 N N 0 8888 ENSG00000202394 ENSG00000112159 - - 1 6 172100206 90586163 upstream intron SNORD47 MDN1 172100130 90409952 - - 0.958132719279883 172100263 90487999 + + Y - 1.96227421382155 N HCC1954 3 2.375 1 6 2 N - - N - - 0 0 0 8 1.09982921662864 0.778450549431962 1.09982921662864 0.778450549431962 2 - 0 3459 Y Y 3.67952553980864 3.29024608861698 3.29024608861698 0 0 0.417063771132261 Y 0.953028381163786 0.990605676232757 N N 0 0 ENSG00000198618 ENSG00000154646 - - 21 21 19152671 18697844 upstream upstream PPIAL3 PRSS7 19151924 18563561 + - 0 19032114 18906483 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 7 0.714174815992626 0.821301038391519 0.821301038391519 0.714174815992626 1 - - 2115 N Y 3.40847927217468 3.40951234194457 3.40847927217468 251 0 0.0225316001037654 N 0.458050152331849 0.956058120459339 N N 0 2134 ENSG00000218210 ENSG00000150779 - + X 11 133128628 111462679 intron intron AC002407.1 TIMM8B 133128378 111461083 + - 0.956058120459339 133128465 111462570 - - Y 1 1.07896589586194 N HCC1954 2 2 2 11 1 N - - N - - 0 0 0 11 0.507064119354764 0.321378667196682 0.507064119354764 0.321378667196682 1 0 0 47559 Y Y 3.32845440710533 2.62842748160167 2.62842748160167 0 0 0.0364946901226366 Y 0.911486169714018 0.988935771214252 N N 157 6985 ENSG00000105737 ENSG00000105732 - - 19 19 47261797 47277557 coding intron GRIK5 ZNF574 47194317 47264704 - + 0 47261741 47265288 + - N - 0.00604855092266314 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.14622641509434 0.14622641509434 6 0.956994253430118 0.985561246069823 0.985561246069823 0.956994253430118 1 - 0 10291 N Y 3.8097595335968 3.77001428422878 3.77001428422878 14 0 0.131555328660668 N 0.958057305425727 0.968542979069295 N N 1772 477 ENSG00000187451 ENSG00000214176 + - 17 17 42483361 60263719 downstream intron AC068152.11-2 AC103810.5-2 42480430 60247480 + - 0 42489120 60256493 + + N - 1.18022311805381 Y HCC1954 63 35.2857142857143 1 6 1 N - - N LTR - 1 0 1 7 0.842726282871298 0.728458312312478 0.842726282871298 0.728458312312478 1 - 0 4234 Y Y 3.54144175291192 3.66658494576413 3.54144175291192 465 0 0.0253927114212302 Y 0 0.995464320625611 N N 32979 386 ENSG00000106105 ENSG00000196295 - - 7 7 30640168 30570758 upstream upstream GARS AC005154.1 30600706 30566129 + - 0 30590709 30585413 - + N - - N HCC1954 7 2.83333333333333 1 2 4 N - - Y LTR LTR,LTR 1 0.776061776061776 1 6 0.649899082553289 0.821301038391519 0.821301038391519 0.649899082553289 2 - - 46469 N Y 3.38912318237562 3.30272267434507 3.30272267434507 0 0 0.271828838401247 N 0 0.886097794822627 N N 13294 243 ENSG00000132549 ENSG00000119559 - + 8 19 100958983 1430198 intron coding VPS13B C19orf25 100094670 1425814 + - 0 100330945 1426041 - - Y 2.32746190856807 - N HCC1954 23 18.25 10 4 1 N - - N SINE - 1 0 1 4 0.385654400636018 0.607048593593732 0.607048593593732 0.385654400636018 3 0 - 28328 N N 3.40422320191574 3.16828604346046 3.16828604346046 0 0 0.0711093070720906 N 0 0 N N 17406 75177 ENSG00000078668 ENSG00000125107 - + 8 16 42382568 57221251 upstream intron VDAC3 CNOT1 42368547 57111359 + - 0 42365357 57220949 - - Y - 2.02597604330693 N HCC1954 35 20.75 20 20 1 N - - N SINE - 1 0 1 20 0.357087407996313 0.664182578873142 0.664182578873142 0.357087407996313 2 - 0 30476 Y Y 3.3984700535705 3.49744043328497 3.3984700535705 157 0 0.0598712041121289 Y 0 0 N N 0 0 ENSG00000217920 ENSG00000214009 + - X X 46033507 45803461 downstream upstream RP1-30G7.1 AL034410.9 46032395 45803125 - - 0 45946028 45911301 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.649899082553289 0.449930134075354 0.649899082553289 0.449930134075354 2 - - 39936 Y Y 2.844945834375 2.65181837462783 2.65181837462783 0 0 0.0703600613566666 Y 0 0 N N 15652 2047 ENSG00000180357 ENSG00000103671 - + 15 15 62765320 62534530 upstream downstream ZNF609 TRIP4 62578672 62467073 + + 0.319001729676304 62578624 62539972 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat,Low_complexity 0 0.41869918699187 0.41869918699187 7 0.728458312312478 0.956994253430118 0.956994253430118 0.728458312312478 1 - - 41939 N N 3.24425317736376 3.6769648867289 3.24425317736376 0 0 0.672263241537038 N 0 0 Y N 354 2 ENSG00000104313 ENSG00000169946 + + 8 8 72437021 106885939 coding intron EYA1 ZFPM2 72272222 106400323 - + 0 72319392 106667237 - + N - 0.966628041714948 N HCC1954 1 1 1 0 1 N 33 8.84783 N - SINE 0 0.727272727272727 0.727272727272727 9 0.999844742389676 0.864151527351077 0.999844742389676 0.864151527351077 4 - 0 31803 Y Y 3.59887818012334 3.38552945952599 3.38552945952599 0 0 0.469481016960073 Y 0.992979684963363 0.992979684963363 N N 3385 8254 ENSG00000075914 ENSG00000163812 - - 3 3 45027966 44992618 coding intron EXOSC7 ZDHHC3 44992768 44941663 + - 0 45005637 44991973 - + N - 2.92028372115872 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.01412823870953 1.1426797055882 1.1426797055882 1.01412823870953 1 - 0 14888 N N 3.11129069662652 3.29006956921008 3.11129069662652 2 0 0.118969134993246 N 0 0 N N 0 5 ENSG00000220337 ENSG00000183844 - + 1 21 142087113 41651524 downstream intron BX571672.7 FAM3B 142086687 41610526 + + 0 142121774 41632350 - + Y - 0.768768578837518 N HCC1954 13 8.5 2 6 1 N - - N Satellite - 1 0 1 6 0.328520415356608 0.507064119354764 0.507064119354764 0.328520415356608 3 - 0 16391 N N 3.69255941980899 3.16203838157526 3.16203838157526 0 0 0.106367230540347 N 0 0 N N 12708 0 ENSG00000138069 ENSG00000212679 - - 2 1 65210744 559619 utr5p intron RAB1A RP5-857K21.10 65167493 558939 - + 0 65210684 559061 + - Y - 1 N HCC1954 2 2 2 4 1 N - - N Simple_repeat - 0.243243243243243 0 0.243243243243243 4 0.535631111994469 0.614190341753658 0.614190341753658 0.535631111994469 1 - 0 46266 N Y 3.54400240599166 3.38383404234679 3.38383404234679 16 0.227239797150447 0.0163153343569401 N 0.227239797150447 0.227239797150447 N N 215 0 ENSG00000214189 ENSG00000172297 - - 19 Y 12071475 26015710 coding upstream AC022415.5-4 GOLGA2LY1 12064151 26012510 + + 0.227239797150447 12069859 26010141 - - Y - - N HCC1954 252 225 144 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.371370904316165 0.371370904316165 0.321378667196682 1 - - 24470 N Y 3.45612774781375 3.57063922744582 3.45612774781375 0 0 0.52867869064242 N 0.00456621004566204 0.84952745035574 N N 13271 0 ENSG00000081923 ENSG00000211323 - - 18 7 53550037 68504225 upstream downstream ATP8B1 AC092100.5-9 53464656 68504124 - - 0 53550062 68490876 + + Y - - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.528489363834543 0.299953422716903 0.528489363834543 0.299953422716903 3 - - 19105 Y Y 3.81401560385573 3.6491271616355 3.6491271616355 261 0 0.489184003006538 Y 0 0.969813073261349 N N 0 2967 ENSG00000209804 ENSG00000120656 - - 1 1 28847832 28842172 upstream upstream U11 TAF12 28847699 28802200 + - 0 28847292 28842307 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.428504889595575 0.34280391167646 0.428504889595575 0.34280391167646 4 - - 34341 N Y 3.8333716936548 3.56488607910057 3.56488607910057 304 0 0.0171734273449383 Y 0.99133295194508 0.98266590389016 N N 0 0 ENSG00000202152 ENSG00000220068 + + 9 9 44959899 44934987 upstream upstream Y_RNA RP11-374M1.6 44959788 44934285 - + 0 44993616 44932962 - + N - - N HCC1954 32 13 2 10 1 N - - N SINE Satellite 1 1 1 10 0.842726282871298 1.22123893534739 1.22123893534739 0.842726282871298 4 - - 33331 N Y 3.14168907479965 2.8925595500445 2.8925595500445 348 0 0.0278635598434431 Y 0 0.993956809474051 N N 339915 275222 ENSG00000198727 ENSG00000198763 - + MT MT 15882 5512 coding coding MT-CYB MT-ND2 14748 4471 + + 0 14767 5433 - + N 0.562987042701105 - N HCC1954 3 1.30769230769231 1 3 2 N - - N - - 0 0 0 13 1.24980592798709 1.15696320190805 1.24980592798709 1.15696320190805 2 0 - 22673 N Y 3.45716081758364 3.51679652308403 3.45716081758364 0 0 0.688718678503705 N 0 0 N N 24548 2325 ENSG00000134369 ENSG00000137460 - + 1 4 200062720 154120298 upstream utr3p NAV1 FHDC1 199859224 154083585 + + 0 199858600 154118348 - + Y - - N HCC1954 28 23 21 6 1 N - - N - SINE 0 1 1 6 0.742741808632331 0.328520415356608 0.742741808632331 0.328520415356608 2 - - 37820 N N 2.97532648243206 3.48383749183115 2.97532648243206 255 0.778649237472767 0.00930543873866796 N 0.944662309368192 0.35439360929557 N N 32016 78560 ENSG00000092148 ENSG00000112493 + + 14 6 30746440 33390114 intron utr3p HECTD1 TAPBP 30639075 33375449 - - 0.169934640522876 30675780 33376425 - - Y 1.4639885942594 - N HCC1954 20 6.14285714285714 1 6 1 N - - N SINE SINE 0.805555555555556 1 1 7 0.257102933757345 0.499922371194838 0.499922371194838 0.257102933757345 2 0 - 45756 N Y 3.40488554932505 3.19872427442695 3.19872427442695 261 0.94140184809556 0.0395660867708162 N 0.94140184809556 0.94140184809556 N N 6657 9146 ENSG00000163428 ENSG00000104960 + + 3 19 121550876 55055802 downstream utr3p LRRC58 PTOV1 121526266 55045950 - + 0.94140184809556 121509546 55055402 - + Y - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 21 0.492780623034912 1.13553795742827 1.13553795742827 0.492780623034912 2 - - 33064 N Y 2.7459636226299 3.56335849579072 2.7459636226299 0 0.364404616013072 0.989757417835149 Y 0.374183006535948 0.960886437908497 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding coding MT-CO3 MT-ND1 8367 3308 + + 0 8474 3893 - + N 0.683366249773457 0.89011333354872 N HCC1954 2 1.5 1 2 6 Y - - N - - 0 0 0 4 0.649899082553289 0.842726282871298 0.842726282871298 0.649899082553289 2 0 0 8070 N N 2.71758641493553 3.09248674342652 2.71758641493553 60 0.227172906015167 0.0633898252045497 N 0.398912260234019 0.471571217788148 N N 131026 57426 ENSG00000115053 ENSG00000181163 - + 2 5 232037449 170770492 coding coding NCL NPM1 232027706 170747403 - + 0.471571217788148 232034538 170752563 + + Y - - N HCC1954 14 6.8 2 5 1 Y - - N Simple_repeat,Simple_repeat Simple_repeat 0.310160427807487 0.0698689956331878 0.310160427807487 5 0.928427260790413 1.09982921662864 1.09982921662864 0.928427260790413 0 - - 47949 N N 3.54296933622177 3.61464054707278 3.54296933622177 0 0 0.999999802051616 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 intron downstream RAD21 IRX2 117927355 2798959 - - 0.00316455696202533 117944549 2596253 - + Y 1.0363918474073 - N HCC1954 2 1.2 1 9 12 N 282 1.61558 N - - 0 0 0 45 0.978419497909897 1.42120788382533 1.42120788382533 0.978419497909897 1 0 - 60 Y N 2.76473201800662 3.22076899838175 2.76473201800662 0 0.227053140096618 0.827669560356812 Y 0.227053140096618 0.227053140096618 N N 1289 3448 ENSG00000177595 ENSG00000177542 + - 11 11 795245 786221 downstream utr5p LRDD SLC25A22 789180 780478 - - 0.227053140096618 787996 785056 - + N - 6.67584016835744 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 7 0.621332089913584 0.842726282871298 0.842726282871298 0.621332089913584 2 - 0 1245 N N 3.23121929736341 3.10081746970591 3.10081746970591 0 0 0.98015161492123 N 0 0.157331810828813 N N 3570 15620 ENSG00000155352 ENSG00000149218 - + 2 11 114073079 94505463 intron coding FAM39B ENDOD1 114058161 94462665 + + 0.157331810828813 114069107 94463039 - + Y 0.58949852430692 - N HCC1954 6 5.85714285714286 5 7 2 N 181 4.74815 N - Low_complexity 0 0.174863387978142 0.174863387978142 7 0.892718519990782 0.914143764470561 0.914143764470561 0.892718519990782 4 0 - 691 N N 3.5514509715161 3.59016315111423 3.5514509715161 0 0 0.893767081008659 N 0 0 Y Y 5365 138744 ENSG00000166670 ENSG00000152558 - + 11 11 102156569 101828985 coding coding MMP10 TMEM123 102146455 101772268 - - 0 102155302 101824753 + - N - 1.06295412494166 N HCC1954 2 1.75 1 3 2 N - - N - - 0 0 0 4 0.721316564152552 0.378512652476092 0.721316564152552 0.378512652476092 4 - 0 47464 Y Y 3.14846594534498 3.18445898556383 3.14846594534498 335 0 0.81092494291338 Y 0 0.986617249323851 N N 2309 8 ENSG00000131398 ENSG00000131401 - + 19 19 55524446 55539830 coding downstream KCNC3 NAPSB 55507006 55528871 - - 0 55519151 55528258 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 15 1.07126222398894 1.12125446110842 1.12125446110842 1.07126222398894 4 - - 34640 N Y 3.6533527266709 3.47129812537077 3.47129812537077 99 0.0190697674418605 0.334724312388993 Y 0.787906976744186 0.92046511627907 N N 2515 13277 ENSG00000137074 ENSG00000086061 - - 9 9 32991626 33029277 coding upstream APTX DNAJA1 32962609 33015242 - + 0 32979847 33015054 + - N - - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 51 0.792734045751814 0.842726282871298 0.842726282871298 0.792734045751814 3 - - 10664 N Y 3.07101108092519 3.54296933622177 3.07101108092519 2 0 0.306290608075024 N 0.796844660194175 0.903259361997226 N N 1649619 1021 ENSG00000141736 ENSG00000101695 - + 17 18 35138441 27907152 coding utr3p ERBB2 RNF125 35104766 27852443 + + 0 35125066 27904809 - + Y - - N HCC1954 28 23.632183908046 1 86 1 N - - N - SINE 0 1 1 87 1.19981369086761 0.39993789695587 1.19981369086761 0.39993789695587 1 - - 43949 N Y 3.46910819465161 3.62617734898681 3.46910819465161 0 0.00389105058365768 0.580729286866816 N 0.598061301112704 0.80776844835825 N N 6328 0 ENSG00000167508 ENSG00000218641 - + 16 10 87257019 28766013 coding upstream MVD RP11-351M16.1 87245849 28765136 - + 0.80776844835825 87250213 28761641 + + Y - - N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 6 0.649899082553289 0.314236919036755 0.649899082553289 0.314236919036755 2 - - 40754 N Y 3.39128260787123 3.50206722590449 3.39128260787123 0 0 0.104520667996696 N 0.927836911419809 0.927836911419809 N N 12271 20796 ENSG00000177479 ENSG00000124209 - + 3 20 48997971 56375966 intron utr3p ARIH2 RAB22A 48931285 56318177 + + 0 48939897 56373337 - + Y 0.963247002497696 - N HCC1954 56 29.3684210526316 26 19 1 N - - N - SINE 0 1 1 19 0.557056356474248 0.378512652476092 0.557056356474248 0.378512652476092 1 0 - 31618 Y Y 3.29693902077628 3.47076375903745 3.29693902077628 144 0 0.570267007113971 Y 0 0.982878352490422 N N 46598 46 ENSG00000118849 ENSG00000214217 - - 3 3 159932969 159943998 utr5p upstream RARRES1 AC080013.17 159897597 159940900 - + 0 159932907 159940873 + - N - - N HCC1954 1 1 1 0 3 N - - Y - SINE 0 0.903614457831325 0.903614457831325 7 0.699891319672773 0.592765097273879 0.699891319672773 0.592765097273879 1 - - 49316 Y Y 3.16783138271386 3.18312982294665 3.16783138271386 0 0.194896449704142 0.17252995164427 Y 0.194896449704142 0.194896449704142 N N 19352 5810 ENSG00000170561 ENSG00000186493 - - 5 5 2804774 2808511 coding coding IRX2 C5orf38 2798959 2805258 - + 0.194896449704142 2804404 2805840 + - N - 1.19836006059226 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.628473838073511 0.549914608314322 0.628473838073511 0.549914608314322 1 - 0 36301 Y Y 3.69359248957888 3.5246463161926 3.5246463161926 357 0.00280112044817926 0.215790033668613 Y 0.00280112044817926 0.993648414779925 N N 3074 122756 ENSG00000135477 ENSG00000135480 + + 12 12 50938438 50928976 downstream coding AC021066.37 KRT7 50932079 50913221 - + 0 50931827 50925682 - + N - 1.79042218814237 N HCC1954 6 1.66666666666667 1 16 3 N - - Y DNA - 0.94578313253012 0 0.94578313253012 36 1.18553019454776 1.42120788382533 1.42120788382533 1.18553019454776 1 - 0 48373 N Y 3.44975210485255 3.40744620240479 3.40744620240479 0 0 0.0207064090343018 N 0 0.953400735294118 N N 6060 1013 ENSG00000079482 ENSG00000039139 + - X 5 67570372 13997589 utr3p intron OPHN1 DNAH5 67179440 13745039 - - 0.953400735294118 67179530 13848602 - + Y - 0.409352795354892 N HCC1954 620 620 620 4 1 N 246 21.4525 N LINE LINE 1 1 1 4 0.307095170876829 0.335662163516534 0.335662163516534 0.307095170876829 1 - 0 9684 Y Y 3.1923087786724 3.16935896602371 3.16935896602371 342 0 0.213209097490885 Y 0.902724290400799 0.99392026815005 N N 18893 6556 ENSG00000141551 ENSG00000141526 + + 17 17 77824862 77790658 intron coding CSNK1D SLC16A3 77795535 77779582 - + 0 77812062 77789056 - + N 1.53392144218755 - N HCC1954 1 1 1 0 3 N - - Y SINE - 0.8 0 0.8 34 1.03555348318931 1.26408942430695 1.26408942430695 1.03555348318931 3 0 - 4635 Y Y 3.08615095325867 3.1703920357936 3.08615095325867 0 0 0.116315291718005 Y 0.960763379153877 0.992152675830775 N N 2897 1806 ENSG00000164713 ENSG00000205356 - - 7 7 97758775 97719404 coding upstream BRI3P1 TECPR1 97748923 97683993 + - 0 97749600 97719777 - + N - - N HCC1954 2 1.04347826086957 1 1 1 N - - Y - - 0 0 0 23 0.892718519990782 0.942710757110266 0.942710757110266 0.892718519990782 1 - - 34311 Y Y 3.24165267149067 3.26352956157612 3.24165267149067 215 0 0.183208004734776 Y 0 0.980858676207513 N N 7118 0 ENSG00000137145 ENSG00000218778 - - 9 9 19364139 19191044 upstream upstream DENND4C RP11-146N23.1 19280749 19190333 + - 0 19266156 19220831 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.521347615674617 0.692749571512847 0.692749571512847 0.521347615674617 4 - - 45611 N N 3.43780472778458 3.53615261288309 3.43780472778458 0 0.237260861791525 0.754650403379821 N 0.237260861791525 0.237260861791525 N N 0 36093 ENSG00000152467 ENSG00000005893 - + 19 X 63257811 119487189 upstream utr3p ZSCAN1 LAMP2 63237212 119446367 + - 0.237260861791525 63224367 119455966 - - Y - 0.186536257449212 N HCC1954 1 1 1 0 1 N - - N SINE,SINE - 0.583333333333333 0 0.583333333333333 8 0.34280391167646 0.607048593593732 0.607048593593732 0.34280391167646 3 - 0 38177 N Y 3.13383928169109 3.5587317031712 3.13383928169109 277 0 0.145332949196221 Y 0.992335462371563 0.992335462371563 N N 681 25285 ENSG00000089775 ENSG00000100714 + + 14 14 64041055 63996474 coding intron ZBTB25 MTHFD1 64023310 63924821 - + 0 64026834 63986111 - + N 2.16912589773636 1.49735544871697 N HCC1954 2 1.08333333333333 1 1 2 N - - N - - 0 0 0 12 0.93556900895034 1.02126998686945 1.02126998686945 0.93556900895034 2 0 0 69 Y N 3.42783536197374 3.33784113109357 3.33784113109357 0 0 0.0448693536282767 Y 0.889489489489489 0.447447447447447 N N 0 10312 ENSG00000197882 ENSG00000150687 + + 11 11 86221791 86199923 downstream utr5p AP000654.4 PRSS23 86221278 86189139 - + 0.447447447447447 86212145 86189312 - + N - 0.818549569439628 N HCC1954 1 1 1 0 1 N - - Y LINE - 0.461538461538462 0 0.461538461538462 50 1.1141127129485 0.87843502367093 1.1141127129485 0.87843502367093 2 - 0 49066 Y Y 3.48652612598689 3.64400585547602 3.48652612598689 329 0 0.0134475699296212 Y 0.992149917430534 0.992149917430534 N N 1390 1 ENSG00000131732 ENSG00000131730 - + 5 5 80644872 80597970 upstream intron ZCCHC9 CKMT2 80633178 80564895 + + 0 80632864 80570937 - + N - 0.951677852348993 N HCC1954 1 1 1 0 2 N - - Y LINE,LINE,LINE - 0.52803738317757 0 0.52803738317757 9 1.13553795742827 0.942710757110266 1.13553795742827 0.942710757110266 1 - 0 10845 N N 3.54400240599166 3.49744043328497 3.49744043328497 0 0 0.0825454528308814 N 0 0 N N 975 1 ENSG00000198487 ENSG00000176160 + - 6 17 42218335 53920758 coding intron AL512274.9 HSF5 42183124 53852528 - - 0 42183238 53883350 - + Y - 0.962441314553991 N HCC1954 33 22.3333333333333 21 9 1 N - - N - SINE 0 1 1 9 0.528489363834543 0.371370904316165 0.528489363834543 0.371370904316165 2 - 0 47459 Y Y 3.50848272165904 3.15575602456989 3.15575602456989 169 0.0110157367668097 0.0206289777107109 Y 0.0243204577968527 0.982260371959943 N N 46239 1 ENSG00000167642 ENSG00000167641 - - 19 19 43474948 43439071 coding downstream SPINT2 PPP1R14A 43447042 43433717 + - 0 43466122 43426740 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.565217391304348 0.565217391304348 5 0.885576771830856 0.492780623034912 0.885576771830856 0.492780623034912 2 - - 42908 N N 3.74234439300473 3.67849247003875 3.67849247003875 0 0 0.998240993761332 N 0 0 N N 11640 21519 ENSG00000137038 ENSG00000164111 + + 9 4 7789799 122837585 downstream coding C9orf123 ANXA5 7786490 122808598 - - 0 7747089 122837186 - - Y - - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 32 1.05697872766909 1.17838844638783 1.17838844638783 1.05697872766909 4 - - 16835 N Y 3.61360747730288 3.18615440274303 3.18615440274303 5 0 0.0613309609231215 N 0 0.788418445571412 N N 49089 1 ENSG00000117450 ENSG00000176160 - - 1 17 45760196 53920758 coding intron PRDX1 HSF5 45749295 53852528 - - 0.218775799032905 45757256 53918050 + + Y - 0.903614457831325 N HCC1954 5 4.66666666666667 3 6 1 N 350 21.8203 N - SINE 0 1 1 6 0.392796148795944 0.257102933757345 0.392796148795944 0.257102933757345 1 - 0 24432 N N 3.59528445727371 3.61464054707278 3.59528445727371 1 0.199356368563686 0.224928417949557 N 0.18555216802168 0.627286585365854 N N 7 0 ENSG00000144847 ENSG00000215401 + - 3 18 120347588 1353874 utr5p upstream IGSF11 AP005119.2 120102173 1352441 - - 0 120314213 1504367 - + Y - - N HCC1954 24 22.1875 21 32 2 N - - N LINE - 1 0 1 32 0.392796148795944 0.799875793911741 0.799875793911741 0.392796148795944 2 - - 13725 Y Y 3.56232542602083 3.62295434849776 3.56232542602083 285 0.5417595082597 0.00938860186549828 Y 0.963631707004738 0.992726341400948 N N 2726 0 ENSG00000177663 ENSG00000215568 - - 22 22 15971387 15869112 upstream upstream IL17RA GAB4 15945849 15822826 + - 0 15908216 15905892 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.985561246069823 0.864151527351077 0.985561246069823 0.864151527351077 1 - - 3402 Y Y 3.55297855482595 3.53768019619294 3.53768019619294 231 0 0.0277423010335232 Y 0 0.986544986544987 N N 0 0 ENSG00000214889 ENSG00000179408 - + 21 21 36427200 36426078 intron intron AP000689.1-2 AP000689.1-1 36426618 36424539 + + 0.986544986544987 36426772 36425280 - + N 1 1 N HCC1954 3 1.66666666666667 1 2 1 N - - Y - - 0 0 0 6 0.621332089913584 0.528489363834543 0.621332089913584 0.528489363834543 1 0 0 9364 N N 2.96059718525252 3.21063179870157 2.96059718525252 12 0.00342465753424659 0.984757097587541 Y 0 0 N N 3927 0 ENSG00000176155 ENSG00000211264 + + 17 17 77763978 67836854 coding downstream CCDC57 AC005243.1 77652635 67836654 - + 0 77752838 67938961 - + N 0.778382604290656 - N HCC1954 1 1 1 0 4 N 449 0.607786 N - - 0 0 0 31 1.38549914302569 0.814159290231593 1.38549914302569 0.814159290231593 1 0 - 18123 Y N 3.58593758607883 3.42886843174363 3.42886843174363 0 0 0.786226269284892 N 0 0.123859072654253 Y N 9 34977 ENSG00000163564 ENSG00000163565 - + 1 1 157213468 157291569 upstream intron PYHIN1 IFI16 157167966 157236382 + + 0.123859072654253 157167131 157242455 - + N - 0.0576118814096263 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 10 0.335662163516534 0.328520415356608 0.335662163516534 0.328520415356608 4 - 0 47240 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 0 0 0.756781886535775 Y 0 0.989390454284071 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - 0.874038927123448 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 121 1.26408942430695 0.742741808632331 1.26408942430695 0.742741808632331 4 - 0 17558 N N 3.70144228268745 3.42680229220385 3.42680229220385 0 0 0.070263512280426 N 0 0 N N 42298 17904 ENSG00000078369 ENSG00000180198 - + 1 1 1812355 28738194 utr5p utr5p GNB1 RCC1 1706590 28705083 - + 0 1760491 28705172 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.642757334393363 0.28566992639705 0.642757334393363 0.28566992639705 1 - - 32126 N N 3.09616017186285 3.28552601004162 3.09616017186285 0 0 0.287274046298099 N 0.808904109589041 0 N N 5448 6858 ENSG00000131374 ENSG00000164715 - + 3 7 17757403 97673537 utr5p intron TBC1D5 LMTK2 17174903 97574133 - + 0 17640409 97648278 + + Y - 0.728085935442038 N HCC1954 3 1.625 1 4 1 N - - N - Low_complexity 0 0.206185567010309 0.206185567010309 8 0.628473838073511 0.692749571512847 0.692749571512847 0.628473838073511 2 - 0 3423 N N 3.14999610749143 3.35253057547976 3.14999610749143 0 0 0.368229595579382 N 0 0 Y N 0 9455 ENSG00000209722 ENSG00000160299 - + 21 21 17725836 46690106 upstream coding AP000952.2 PCNT 17725745 46568483 + + 0 17662812 46579110 - + N - 1.42897890447035 N HCC1954 1 1 1 0 2 N 382 16.7655 N - - 0 0 0 5 0.5713398527941 0.549914608314322 0.5713398527941 0.549914608314322 2 - 0 42895 N Y 3.24471718568018 3.48639814491089 3.24471718568018 238 0 0.00488909910922841 N 0.573229291716687 0.0753301320528211 N N 224 0 ENSG00000205337 ENSG00000216027 + - 7 4 99073480 61212351 utr5p downstream AC005020.5-2 AC095061.3 99070839 61212262 + - 0.146458583433374 99071483 60902269 + + Y - - N HCC1954 168 87.5 6 4 1 N - - N SINE SINE,SINE 1 0.864864864864865 1 4 0.271386430077198 0.264244681917271 0.271386430077198 0.264244681917271 1 - - 35020 N Y 3.52783881145811 3.36551102231762 3.36551102231762 12 0.0058139534883721 0.0326287456462247 N 0.620639534883721 0.843023255813953 Y N 1555 0 ENSG00000148153 ENSG00000219468 + + 9 9 114520250 140250262 utr3p upstream C9orf80 RP11-885N19.5 114488618 140249980 - + 0 114488664 140231534 - + N - - N HCC1954 160 137.45 105 20 1 N - - N SINE,SINE - 1 0 1 20 0.364229156156239 0.899860268150708 0.899860268150708 0.364229156156239 2 - - 24728 Y Y 3.65909652744634 3.32523140661629 3.32523140661629 285 0 0.0387707962496529 Y 0.766255144032922 0.987697639159627 N N 2239 504 ENSG00000215421 ENSG00000206029 - - 18 18 70906616 70416040 utr5p upstream ZNF407 AC116904.7 70471907 70411054 + - 0 70471907 70416149 - + N 0.0447931731119526 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 62 1.49976711358451 0.592765097273879 1.49976711358451 0.592765097273879 2 0 - 34143 Y Y 3.55231620741665 3.58999531724489 3.55231620741665 356 0 0.210745226068836 Y 0.994334141981614 0.988668283963228 N N 1727 0 ENSG00000147905 ENSG00000216536 - + 9 9 37348143 37037234 upstream downstream ZCCHC7 RP11-297B17.2 37110469 37036832 + + 0 37076665 37070533 - + N - - N HCC1954 2 1.42622950819672 1 52 3 N - - Y - - 0 0 0 122 1.29265641694665 1.32836515774628 1.32836515774628 1.29265641694665 4 - - 279 Y Y 3.61360747730288 3.54975555433691 3.54975555433691 215 0 0.0576932639152106 Y 0.672120383036936 0.988290013679891 N N 0 0 ENSG00000222225 ENSG00000209356 + - 11 11 143102 143101 downstream downstream U6 AC069287.7-1 142999 142999 - - 0 140838 138614 - + N - - N HCC1954 195 116.6 75 5 2 N - - Y - LTR,SINE 0 0.932291666666667 0.932291666666667 5 0.549914608314322 0.792734045751814 0.792734045751814 0.549914608314322 2 - - 48864 Y Y 3.47705127371601 3.56232542602083 3.47705127371601 326 0 0.781539281908852 Y 0 0.98696820241389 N N 1658 551733 ENSG00000183718 ENSG00000204628 + - 5 5 180620725 180603512 upstream upstream TRIM52 GNB2L1 180615994 180596536 - - 0 180623235 180606992 - + N - - N HCC1954 1 1 1 0 3 N - - Y DNA,LINE - 0.380368098159509 0 0.380368098159509 4 0.807017542071667 1.09982921662864 1.09982921662864 0.807017542071667 4 - - 48386 N Y 3.32895826821511 3.16783138271386 3.16783138271386 0 0 0.297579027252083 N 0 0.987399572279059 N N 951 0 ENSG00000152348 ENSG00000220344 + + 5 X 81586524 70099865 coding downstream ATG10 RP11-320L13.2 81303630 70099539 + + 0 81510087 70099874 + + Y - - N HCC1954 2 2 2 10 1 N - - N - - 0 0 0 10 0.742741808632331 0.728458312312478 0.742741808632331 0.728458312312478 3 - - 16244 N N 3.22543564379462 2.8357178275706 2.8357178275706 11 0.0565488147850541 0.132211317087814 N 0.13263358778626 0.147850542386501 N N 131026 0 ENSG00000115053 ENSG00000216685 - + 2 1 232037449 27406874 coding intron NCL RP11-40H20.2 232027706 27406008 - + 0.368496384089996 232034515 27406404 + + Y - 1 N HCC1954 14 10 3 5 1 N - - N Simple_repeat,Simple_repeat - 0.311320754716981 0 0.311320754716981 5 0.814159290231593 0.735600060472404 0.814159290231593 0.735600060472404 1 - 0 498 Y Y 3.37820887507754 3.38552945952599 3.37820887507754 312 0 0.602784316128728 Y 0 0.991895976652074 N N 95337 3156 ENSG00000172757 ENSG00000172732 - - 11 11 65382380 65390485 coding intron CFL1 MUS81 65378884 65384801 - + 0 65382144 65385007 + - N - 0.358136684251868 N HCC1954 2 1.2 1 1 3 N - - Y - - 0 0 0 5 0.821301038391519 0.792734045751814 0.821301038391519 0.792734045751814 3 - 0 483 Y Y 3.53871326596283 3.71297908460148 3.53871326596283 313 0 0.0378027200100374 Y 0.00319488817891378 0 N Y 1764 9180 ENSG00000149798 ENSG00000014138 - + 11 11 64846475 64821663 utr5p coding CDC42EP2 POLA2 64838907 64786006 + + 0 64844591 64820037 - + N - 2.93733249168729 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 24 1.22838068350732 0.914143764470561 1.22838068350732 0.914143764470561 4 - 0 47694 N N 3.61360747730289 3.64400585547602 3.61360747730289 9 0.146153846153846 0.0405537187383231 Y 0.330769230769231 0.146153846153846 N N 8826 0 ENSG00000167747 ENSG00000221233 + + 19 19 55999786 55981968 utr5p upstream C19orf48 AC010325.7-3 55992774 55981899 - + 0 55997302 55981044 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.599906845433805 0.335662163516534 0.599906845433805 0.335662163516534 1 - - 1487 N N 3.58593758607883 3.29590595100639 3.29590595100639 10 0 0.119267606210419 N 0.0181884765625 0.0259806315104165 N N 0 2667 ENSG00000189343 ENSG00000197149 + + 17 11 19290757 17207311 intron coding AC004448.3-1 AC107956.8-2 19289875 17206368 - + 0.0259806315104165 19290078 17207090 - + Y 1 6.48774421156616 N HCC1954 11 6.25 2 4 1 N 410 24.9601 N - - 0 0 0 4 0.799875793911741 0.278528178237124 0.799875793911741 0.278528178237124 1 0 0 34781 Y Y 3.56232542602083 3.192891420495 3.192891420495 0 0 0.99231693139031 Y 0 0.976811399381637 N N 4263 0 ENSG00000187764 ENSG00000218102 - - 9 9 91260688 91277427 utr5p downstream SEMA4D RP13-93L13.1 91181972 91276972 - + 0 91260688 91280220 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 9 1.48548361726466 0.542772860154395 1.48548361726466 0.542772860154395 4 - - 20471 N Y 3.35823029066252 3.6272104187567 3.35823029066252 0 0 0.313082283977957 N 0.745421862712055 0.745421862712055 N N 0 8888 ENSG00000208310 ENSG00000112159 - - 1 6 172102699 90586163 upstream intron SNORD75 MDN1 172102640 90409952 - - 0.745421862712055 172102801 90487627 + + Y - 1.96227421382155 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.785592297591888 0.357087407996313 0.785592297591888 0.357087407996313 0 - 0 10142 N Y 3.66695566812472 3.84271856484967 3.66695566812472 1 0 0.1103137431053 Y 0.905481298438728 0.982814781534314 N N 1246 1772 ENSG00000185829 ENSG00000187451 - - 17 17 41794865 42483361 coding downstream ARL17 AC068152.11-2 41719640 42480430 - + 0 41744393 42488813 + - N - - N HCC1954 108 17.5 2 8 1 N - - N - LTR 0 1 1 8 1.35693215038599 0.757025304952183 1.35693215038599 0.757025304952183 1 - - 46968 Y Y 3.44615838200292 3.4959035024053 3.44615838200292 364 0 0.00220111937742873 Y 0.992773530817009 0.992773530817009 N N 1180 1746 ENSG00000196085 ENSG00000105085 + - 19 19 16631941 16600015 coding upstream AC024075.4 MED26 16618405 16546718 - - 0 16618930 16603534 - + N 0.441421823030384 - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.893162393162393 0.893162393162393 42 1.15696320190805 1.66402732126282 1.66402732126282 1.15696320190805 1 0 - 33489 N N 2.85799322989507 3.02548217798839 2.85799322989507 31 0.0721555084634905 0.0866151575231667 N 0.0721555084634905 0.0614289825497736 Y N 240508 247001 ENSG00000198899 ENSG00000198786 - + MT MT 9208 14149 coding coding MT-ATP6 MT-ND5 8528 12338 + + 0.0614289825497736 8656 14088 - + N - - N HCC1954 2 1.5 1 2 1 N 189 4.09957 N - - 0 0 0 4 0.707033067832699 0.799875793911741 0.799875793911741 0.707033067832699 2 - - 26845 Y Y 3.26294691975351 3.32679884271949 3.26294691975351 286 0 0.100400102425486 Y 0.0554879902705989 0.991334752204317 N N 6938 516 ENSG00000198211 ENSG00000182289 - + 16 16 88530006 88510383 upstream upstream TUBB3 AC092143.4-2 88513168 88508026 + + 0 88511821 88507558 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.985561246069823 0.99270299422975 0.99270299422975 0.985561246069823 3 - - 14401 N N 3.3233729537392 3.61360747730289 3.3233729537392 2 0 0.0206235490935672 N 0.614079728583545 0 N N 31 49089 ENSG00000186642 ENSG00000117450 - - 11 1 72063113 45760196 downstream coding PDE2A PRDX1 71964834 45749295 - - 0 71940390 45757256 + + Y - 3.16366837851847 N HCC1954 7 4.14285714285714 2 7 1 N 74 26.8608 N SINE - 1 0 1 7 0.357087407996313 0.442788385915428 0.442788385915428 0.357087407996313 1 - 0 37497 N Y 3.2216342342823 3.51104337473878 3.2216342342823 132 0 0.290480956323128 N 0.906915887850467 0.869682242990654 N N 89 64575 ENSG00000204253 ENSG00000092199 + - 2 14 190497187 20807478 upstream intron AC019178.7-3 HNRNPC 190496307 20747135 + - 0 190496270 20801828 + + Y - 0.38955189038318 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.328520415356608 0.485638874874985 0.485638874874985 0.328520415356608 3 - 0 41419 Y Y 3.32320511986986 3.63655728995158 3.32320511986986 368 0 0.00063410037293743 Y 0.993805698082636 0.993805698082636 N N 4 0 ENSG00000184090 ENSG00000221315 + + 8 8 129029462 128877456 downstream intron TMEM75 hsa-mir-1204 129029046 128877390 - + 0 128972018 128877437 - + N - 1 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 50 1.57118459518378 1.65688557310289 1.65688557310289 1.57118459518378 1 - 0 40914 Y Y 3.70889084821189 3.49847350305486 3.49847350305486 212 0 0.0530292323988368 Y 0 0 N N 1 1149 ENSG00000124092 ENSG00000124097 + - 20 20 55534041 55497489 downstream upstream CTCFL HMGB1L1 55505630 55496854 - - 0 55503666 55497676 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 4 0.885576771830856 0.414221393275723 0.885576771830856 0.414221393275723 1 - - 40959 Y Y 3.54759612884129 2.79574859582564 2.79574859582564 0 0 0.496390501669502 Y 0.862622905414762 0.982827863176845 N N 0 549 ENSG00000125822 ENSG00000185052 + + 20 20 19752587 19651540 downstream downstream AL132821.17 SLC24A3 19752090 19141487 - + 0 19728266 19686971 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.372549019607843 0.372549019607843 7 0.87843502367093 0.728458312312478 0.87843502367093 0.728458312312478 4 - - 4446 Y Y 3.28808666312136 3.09715338883939 3.09715338883939 250 0 0.760596394467373 Y 0 0.989173913043478 N N 0 524 ENSG00000203446 ENSG00000218609 + + 7 7 65814279 65743252 downstream downstream AC027644.9 KCTD7 65814003 65731380 - + 0 65783844 65757046 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 4 0.507064119354764 0.521347615674617 0.521347615674617 0.507064119354764 3 - - 47689 Y Y 3.39590940049075 3.21547985835293 3.21547985835293 319 0 0.473445285066427 Y 0.973938164607536 0.986969082303768 N N 4775 0 ENSG00000127527 ENSG00000219228 + - 19 19 16443762 16330138 coding downstream EPS15L1 AC020917.4-2 16333408 16329998 - - 0 16333590 16327662 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 38 1.13553795742827 1.17124669822791 1.17124669822791 1.13553795742827 4 - - 4448 Y Y 3.18557599371975 2.96526383066539 2.96526383066539 268 0 0.041055035375017 Y 0 0 N N 243 291 ENSG00000127388 ENSG00000197558 - + 7 7 149162001 149127103 upstream downstream SSPO AC004877.1-2 149150127 149114241 + + 0.991336794289423 149138718 149137554 - + N - - N HCC1954 1 1 1 0 1 N - - Y Unknown - 0.471910112359551 0 0.471910112359551 4 0.635615586233437 0.657040830713216 0.657040830713216 0.635615586233437 1 - - 1122 N N 2.98892942388588 3.40377277396846 2.98892942388588 0 0 0.218599365099015 N 0.0366385684708666 0.158754806270334 N N 81 3301 ENSG00000214248 ENSG00000070081 + + 7 11 100913300 17309646 coding utr5p AC004965.2 NUCB2 100906891 17254860 + + 0 100911814 17261039 + + Y - - N HCC1954 27 25.1666666666667 21 6 1 N 171 23.4075 N SINE SINE 1 0.4 1 6 0.357087407996313 0.942710757110266 0.942710757110266 0.357087407996313 1 - - 3551 N N 3.45976132345673 3.64231043829683 3.45976132345673 0 0 0.35647121155106 N 0 0 Y N 64 3005 ENSG00000197934 ENSG00000159113 - + 21 21 26863442 33591390 utr5p coding AP001597.1 IL10RB 26700133 33560542 + + 0 26797833 33570922 - + N 2.53968545059041 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 0.699891319672773 0.714174815992626 0.714174815992626 0.699891319672773 2 0 - 30333 Y Y 3.49640736351508 2.62886856197914 2.62886856197914 317 0 0.00919577890522749 Y 0.993568739187952 0.993568739187952 N N 0 2000 ENSG00000197180 ENSG00000102125 + + X X 153309989 153303259 downstream downstream BX936347.3 TAZ 153309731 153293071 - + 0 153309670 153306164 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,SINE LTR 0.470238095238095 1 1 35 1.19981369086761 1.19267194270768 1.19981369086761 1.19267194270768 2 - - 29399 Y Y 3.24272559405391 3.49164743214637 3.24272559405391 0 0 0.99884792789651 Y 0.729427670121676 0.985759351059036 N N 399 1730 ENSG00000221988 ENSG00000168452 - + 6 6 32244040 32239433 upstream coding EGFL8 PPT2 32240360 32229279 + + 0 32240334 32238377 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 10 0.885576771830856 1.19267194270768 1.19267194270768 0.885576771830856 4 - - 6045 N Y 3.8333716936548 3.25463311832853 3.25463311832853 0 0 0.741813248855357 N 0.253012048192771 0.958500669344043 N N 0 0 ENSG00000183846 ENSG00000213875 + - 2 7 110575338 13878666 upstream upstream AC112229.4-1 AC005019.1 110574935 13878006 - + 0 110576429 13815991 - - Y - - N HCC1954 40 39.0833333333333 26 24 1 N 598 20.5894 N - LINE 0 1 1 24 0.728458312312478 0.428504889595575 0.728458312312478 0.428504889595575 3 - - 47160 Y Y 3.31319590126568 3.64553343878587 3.31319590126568 3 0 0.819322805838042 Y 0.985341709499334 0.985341709499334 N N 1092 8931 ENSG00000222015 ENSG00000099622 - + 19 19 1230227 1224169 upstream coding C19orf24 CIRBP 1226438 1220336 + + 0 1225306 1223050 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 31 1.01412823870953 1.09268746846872 1.09268746846872 1.01412823870953 4 - - 14979 N N 3.53871326596283 3.65488030998075 3.53871326596283 0 0 0.184645670824018 N 0.817350746268657 0 N N 1186 0 ENSG00000137968 ENSG00000214035 - + 1 7 75849389 144339029 coding downstream SLC44A5 AC073310.7 75440404 144333895 - + 0 75634856 144746792 + + Y - - N HCC1954 6 2.25 1 3 1 N - - N - LINE 0 1 1 8 0.592765097273879 0.278528178237124 0.592765097273879 0.278528178237124 2 - - 49470 Y Y 3.32679884271949 3.43681151080804 3.32679884271949 0 0 0.967755001105327 Y 0 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883894 140816150 - + N - 0.194212665568841 N HCC1954 4 1.41176470588235 1 3 2 N - - Y - LTR 0 1 1 17 1.04983697950916 1.31408166142643 1.31408166142643 1.04983697950916 4 - 0 17444 Y Y 3.52361324642271 3.55334927718654 3.52361324642271 3 0 0.766592051852871 Y 0.993483107528726 0.993483107528726 N N 251 0 ENSG00000142583 ENSG00000212602 - - 1 1 9052257 9065525 utr5p downstream SLC2A5 SCARNA16 9019594 9065342 - + 0 9052241 9067661 + - N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 0.136363636363636 0.136363636363636 28 1.34979040222606 1.09982921662864 1.34979040222606 1.09982921662864 1 - - 3852 N N 2.90616249149831 3.59105889223831 2.90616249149831 0 0 0.0582172245882456 N 0 0 N N 0 165508 ENSG00000167910 ENSG00000196262 - + 8 7 59575275 44807754 upstream utr3p CYP7A1 PPIA 59565292 44802805 - + 0 59579550 44807593 + + Y - 1.46297363886808 N HCC1954 18 5 2 21 1 N - - N - - 0 0 0 21 0.278528178237124 0.949852505270192 0.949852505270192 0.278528178237124 1 - 0 36875 N Y 1.72125183600447 3.250006325709 1.72125183600447 0 0.543647363872083 0.0440449890859387 N 0.543647363872083 0.543647363872083 N N 12659 34637 ENSG00000182979 ENSG00000197111 + + 14 12 105008111 52159872 utr3p utr3p MTA1 PCBP2 104957202 52132161 + + 0.543647363872083 105008089 52159635 + + Y - - N HCC1954 56 33.75 21 4 1 N - - N - - 0 0 0 4 0.371370904316165 0.507064119354764 0.507064119354764 0.371370904316165 2 - - 33775 N N 2.77892265388278 3.07933422991999 2.77892265388278 0 0 0.998998123211964 N 0 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8476 15561 - + N - 1.35512665870557 N HCC1954 2 1.3 1 3 8 N 189 4.09957 N - - 0 0 0 10 1.1141127129485 1.19267194270768 1.19267194270768 1.1141127129485 1 - 0 20469 N Y 3.51104337473878 3.64656650855576 3.51104337473878 198 0.221343873517787 0.00434892843121248 N 0.711608842043625 0.88464353681745 N N 0 0 ENSG00000155816 ENSG00000174556 + - 1 6 238711086 66604668 intron intron FMN2 AL391500.13 238321604 66603565 + - 0.88464353681745 238400180 66604580 + + Y 1 1 N HCC1954 2 2 2 6 1 N - - N - - 0 0 0 6 0.364229156156239 0.478497126715059 0.478497126715059 0.364229156156239 1 0 0 33918 Y N 3.54296933622177 3.02122610772945 3.02122610772945 0 0 0.240413504576378 N 0 0 N N 247001 59837 ENSG00000198786 ENSG00000198695 + - MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 13505 14674 + + N 0.961537921090628 8726.77946768061 Y HCC1954 6 2.71428571428571 1 6 2 N 24 8.70278 N - - 0 0 0 7 0.914143764470561 1.21409718718746 1.21409718718746 0.914143764470561 1 0 0 41443 Y Y 3.41588798490577 3.19297112608171 3.19297112608171 372 0 0.473424590087562 Y 0 0.989276216903688 N N 0 9799 ENSG00000222697 ENSG00000076554 - - 8 8 81279688 81155565 upstream upstream SRP_euk_arch TPD52 81279396 81109662 + - 0 81246080 81184704 - + N - - N HCC1954 1 1 1 0 6 N - - Y - LTR 0 1 1 11 0.985561246069823 0.671324327033068 0.985561246069823 0.671324327033068 2 - - 32990 N N 2.76022891149302 2.86791432021661 2.76022891149302 0 0 0.999980677776876 N 0.00502512562814073 0.196366447622729 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.196366447622729 8492 12426 - + N 0.619501286280727 0.907957619037389 N HCC1954 3 1.4 1 1 10 N 189 4.09957 N - - 0 0 0 5 0.87843502367093 0.607048593593732 0.87843502367093 0.607048593593732 3 0 0 34221 Y Y 3.40591861909494 3.63552422018169 3.40591861909494 275 0 0.0112102110415172 Y 0 0 N N 147 0 ENSG00000179082 ENSG00000220992 - - 9 9 131127005 131032817 upstream upstream C9orf106 AL158151.16-2 131123116 131032672 + - 0 131080558 131074258 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 32 0.621332089913584 0.971277749749971 0.971277749749971 0.621332089913584 1 - - 33146 N Y 3.00087680095385 3.13855936026645 3.00087680095385 321 0.00999033193683518 0.412658670746989 Y 0.00999033193683518 0.779997851541519 N N 247001 275222 ENSG00000198786 ENSG00000198763 - + MT MT 14149 5512 coding coding MT-ND5 MT-ND2 12338 4471 + + 0.058115801912128 12418 5263 - + N 0.964548639392225 0.94718181329015 N HCC1954 2 1.66666666666667 1 4 5 N - - N - - 0 0 0 6 0.692749571512847 0.949852505270192 0.949852505270192 0.692749571512847 2 0 0 14031 Y Y 3.21960794753587 2.93292729402847 2.93292729402847 245 0 0.123103750464333 Y 0.982215743440233 0.964431486880467 N N 8168 388 ENSG00000100099 ENSG00000128203 + + 22 22 25209820 25169557 coding utr3p HPS4 ASPHD2 25177446 25155239 - + 0 25183829 25169522 - + N - 1.08091173046171 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.771308801272036 0.778450549431962 0.778450549431962 0.771308801272036 1 - 0 40952 Y Y 3.55128313764676 3.48230056095149 3.48230056095149 257 0 0.0425534269382551 Y 0 0 N N 661 0 ENSG00000124143 ENSG00000213959 - - 20 20 36712517 36677533 upstream upstream C20orf95 AL035419.12 36696740 36676970 + - 0 36688347 36685614 - + N - - N HCC1954 1 1 1 0 1 N - - Y DNA - 1 0 1 8 0.771308801272036 0.707033067832699 0.771308801272036 0.707033067832699 1 - - 46803 Y Y 3.40744620240479 3.51679652308403 3.40744620240479 317 0 0.898353009685928 Y 0 0 N N 584 560 ENSG00000197813 ENSG00000063127 + - 19 19 54535371 54520286 utr3p utr5p AC011450.4 SLC6A16 54523236 54484709 - - 0 54526686 54506480 - + N 0.53266534214399 15.300221629362 N HCC1954 1 1 1 0 4 N - - Y LTR,LTR - 0.739393939393939 0 0.739393939393939 21 1.17838844638783 1.20695543902754 1.20695543902754 1.17838844638783 4 0 0 42359 Y Y 3.55657227767558 3.33676820853032 3.33676820853032 233 0 0.674170430350576 Y 0.9741374505323 0.98706872526615 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 upstream downstream AFF1 AC093827.3 88147177 88089842 + - 0 88128615 88088748 - + N - - N HCC1954 13 10 2 5 5 N - - Y LINE - 1 0 1 5 0.557056356474248 0.421363141435649 0.557056356474248 0.421363141435649 1 - - 48929 Y Y 3.55504469436574 2.95121046126429 2.95121046126429 362 0 0.0286988870329439 Y 0.993919283115483 0.993919283115483 N N 2506 38037 ENSG00000214302 ENSG00000131446 + - 5 5 180210585 180175147 downstream upstream AC022413.4-2 MGAT1 180208398 180150147 - - 0 180193916 180190833 - + N - - N HCC1954 3 1.13333333333333 1 1 3 N - - Y SINE,SINE,LTR,LTR LTR 0.442105263157895 0.686046511627907 0.686046511627907 15 1.22123893534739 0.985561246069823 1.22123893534739 0.985561246069823 1 - - 40378 N N 3.45976132345673 3.46295381872224 3.45976132345673 5 0 0.084462683481724 N 0 0.617250515160436 N N 7644 3587 ENSG00000028528 ENSG00000198538 - + 15 19 62223486 58016697 utr3p utr5p SNX1 ZNF28 62175230 57992474 + - 0.00833088018840156 62219777 58003116 - - Y - - N HCC1954 294 119.888888888889 20 9 1 N - - N SINE - 1 0 1 9 0.321378667196682 0.692749571512847 0.692749571512847 0.321378667196682 2 - - 17912 Y Y 3.39653189510671 3.45248059180163 3.39653189510671 10 0.0396865203761757 0.105989595109613 Y 0.882225705329154 0.990940438871473 N N 82 279 ENSG00000215831 ENSG00000120341 + - 1 1 176273708 176258345 coding upstream AL359075.15 SEC16B 176267305 176164546 - - 0 176268253 176262012 - + N - - N HCC1954 2 1.33333333333333 1 2 1 N - - Y - - 0 0 0 6 0.771308801272036 0.842726282871298 0.842726282871298 0.771308801272036 2 - - 9521 Y N 3.75016368088976 2.94185468789063 2.94185468789063 0 0 0.539933918662093 Y 0 0.0494117647058822 N N 13858 5085 ENSG00000108439 ENSG00000167182 - + 17 17 43381673 43361320 upstream upstream PNPO SP2 43373916 43328515 + + 0.0494117647058822 43373704 43326267 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.492780623034912 0.28566992639705 0.492780623034912 0.28566992639705 1 - - 9476 Y Y 3.50165665075055 3.32423818963975 3.32423818963975 286 0 0.0315474747698112 Y 0 0.992618492618493 N N 1649619 109916 ENSG00000141736 ENSG00000161395 - - 17 17 35138441 35097836 upstream upstream ERBB2 PERLD1 35104766 35080902 + - 0 35104460 35098622 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 0.666666666666667 0.666666666666667 120 1.03555348318931 0.835584534711372 1.03555348318931 0.835584534711372 2 - - 7688 N N 3.62873800206655 3.11807691474166 3.11807691474166 0 0 0.0692450779702898 N 0 0 N N 0 1 ENSG00000183846 ENSG00000147655 + - 2 8 110575338 109165052 upstream intron AC112229.4-1 RSPO2 110574935 108980721 - - 0 110576484 109009228 - + Y - 0.92526158445441 N HCC1954 60 39.8666666666667 2 15 1 N - - N - LINE 0 1 1 15 0.978419497909897 0.521347615674617 0.978419497909897 0.521347615674617 2 - 0 45425 N Y 3.64759957832565 3.61567361684267 3.61567361684267 0 0 0.457026550935152 N 0.642893567421869 0.81204924601151 N N 0 38037 ENSG00000099256 ENSG00000131446 - - 10 5 25281539 180175147 intron upstream PRTFDC1 MGAT1 25177560 180150147 - - 0 25226120 180191409 + + Y 1 - N HCC1954 25 21 20 16 1 N - - N SINE,SINE - 1 0 1 16 0.371370904316165 0.871293275511003 0.871293275511003 0.371370904316165 1 0 - 26755 Y Y 3.53824925764641 3.34103362635907 3.34103362635907 327 0 0.008422501756708 Y 0 0.988540897746845 N N 18458 39 ENSG00000166530 ENSG00000140945 - + 16 16 82400529 82387705 upstream intron HSBP1 CDH13 82399094 81439761 + + 0 82394544 82381424 - + N - 0.342299349240781 N HCC1954 12 3.625 1 2 2 N - - Y SINE SINE 1 0.202127659574468 1 8 0.628473838073511 1.33550690590621 1.33550690590621 0.628473838073511 1 - 0 47045 N Y 3.37080016234644 3.54872248456702 3.37080016234644 313 0 0.0213297779064476 Y 0.366992374245004 0.992724050278678 N N 41 1744 ENSG00000130201 ENSG00000007255 + - 19 19 50429309 50373325 downstream upstream EXOC3L2 TRAPPC6A 50407719 50358027 - - 0 50397502 50382836 - + N - - N HCC1954 4 1.3 1 1 1 N - - N LINE DNA,DNA 1 0.401360544217687 1 10 0.978419497909897 1.04983697950916 1.04983697950916 0.978419497909897 3 - - 41557 N N 3.58320909912975 3.36976709257655 3.36976709257655 0 0 0.0838618012157731 Y 0.0753060615108988 0 N N 0 0 ENSG00000208525 ENSG00000207110 - + 8 8 130372654 129080722 downstream upstream AC103833.2-1 U1 130372411 129080559 + + 0 130412741 129070720 - + N - - N HCC1954 1 1 1 0 1 N 575 2.9574 N LTR - 1 0 1 5 0.757025304952183 0.814159290231593 0.814159290231593 0.757025304952183 1 - - 36966 N N 3.78105657260285 3.37655331069169 3.37655331069169 0 0 0.999935766762576 N 0 0 N N 12084 3 ENSG00000177119 ENSG00000179242 + + 12 20 44112391 59945671 coding intron ANO6 CDH4 43896170 59260965 + + 0 44047841 59589772 + + Y - 0.929733246584255 N HCC1954 1 1 1 0 8 N 451 26.2081 N - LTR 0 0.429347826086957 0.429347826086957 61 1.34264865406614 1.31408166142643 1.34264865406614 1.31408166142643 1 - 0 34290 Y Y 3.59784511035345 3.60103760561896 3.59784511035345 312 0 0.00456875174509874 Y 0.98534125188537 0.992670625942685 N N 0 147 ENSG00000223137 ENSG00000179082 + + 9 9 131172561 131127005 downstream downstream SRP_euk_arch C9orf106 131172274 131123116 - + 0 131157560 131144145 - + N - - N HCC1954 5 1.33333333333333 1 1 1 N - - Y SINE - 0.868055555555556 0 0.868055555555556 12 1.02841173502938 1.25694767614702 1.25694767614702 1.02841173502938 1 - - 46783 Y Y 3.30016202126533 2.91245419607349 2.91245419607349 292 0 0.0502792800823336 Y 0.19824389741477 0.992506952312288 N N 3446 6115 ENSG00000130158 ENSG00000197256 + - 19 19 11234157 11167496 downstream utr5p DOCK6 KANK2 11170973 11135947 - - 0.992506952312288 11169380 11167493 - + N - 23.4619093539055 N HCC1954 1 1 1 0 1 N - - Y Simple_repeat Simple_repeat 0.184931506849315 0.901515151515151 0.901515151515151 9 1.04269523134923 0.942710757110266 1.04269523134923 0.942710757110266 1 - 0 38451 Y Y 3.44871903508266 3.15057193767811 3.15057193767811 0 0 0.566400693800218 Y 0.99409965034965 0.99409965034965 N N 4025 8350 ENSG00000185024 ENSG00000179364 - - 14 14 104838374 104935529 coding intron BRF1 PACS2 104746670 104852126 - + 0 104823755 104852701 + - N - 0.328314398751677 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 1.21409718718746 1.15696320190805 1.21409718718746 1.15696320190805 1 - 0 13105 N Y 3.48553290901035 3.64656650855576 3.48553290901035 267 0 0.0156415373959569 N 0.950187265917603 0.941885143570537 N N 20793 3766 ENSG00000141027 ENSG00000132357 - + 17 5 16059570 40895948 utr5p utr3p NCOR1 CARD6 15875443 40877043 - + 0 16038677 40890593 + + Y - - N HCC1954 108 63.6 27 20 1 N - - N - SINE 0 1 1 20 0.978419497909897 0.735600060472404 0.978419497909897 0.735600060472404 1 - - 45507 N Y 3.25679254382414 3.57952209032428 3.25679254382414 0 0 0.0607080671713236 N 0 0.801307189542484 N N 4159 128 ENSG00000012061 ENSG00000204385 - - 19 6 50619017 31954802 utr5p utr3p ERCC1 SLC44A4 50604712 31938948 - - 0 50618890 31939071 + + Y - - N HCC1954 35 28 25 18 1 N - - N - SINE 0 1 1 18 0.628473838073511 0.385654400636018 0.628473838073511 0.385654400636018 1 - - 42228 Y Y 3.28296535696188 3.16679831294397 3.16679831294397 312 0 0.0381837837715847 Y 0 0 N N 340 16036 ENSG00000188981 ENSG00000197386 - + 4 4 3243263 3215485 intron intron C4orf44 HTT 3220565 3046206 + + 0 3240884 3199335 - + N 0.0742790072006345 3.92289041941679 N HCC1954 8 7.40740740740741 6 27 2 N - - Y - - 0 0 0 27 1.20695543902754 1.20695543902754 1.20695543902754 1.20695543902754 4 0 0 10232 Y Y 3.2802368700128 3.41166241987037 3.2802368700128 73 0 0.9698062150297 Y 0.466594946485711 0 N N 830 7432 ENSG00000185158 ENSG00000178691 - + 17 17 27404630 27352162 coding downstream LRRC37B SUZ12 27372156 27288185 + + 0 27375843 27359264 - + N - - N HCC1954 6 2 1 2 4 N - - Y - Low_complexity 0 0.494791666666667 0.494791666666667 6 0.792734045751814 0.892718519990782 0.892718519990782 0.792734045751814 4 - - 42255 Y Y 3.23420410596622 3.17511211436895 3.17511211436895 205 0 0.29893149607396 Y 0 0.986552406064601 N N 3206 0 ENSG00000109756 ENSG00000206978 - - 4 4 160500747 160205000 upstream upstream RAPGEF2 Y_RNA 160408448 160204899 + - 0 160333804 160244835 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 0.464213630395207 0.928427260790413 0.928427260790413 0.464213630395207 2 - - 29249 Y Y 3.27408249408343 3.23636353146184 3.23636353146184 235 0 0.0564492181440194 Y 0 0 N N 0 4260 ENSG00000218893 ENSG00000078401 - + 6 6 12427810 12404286 upstream downstream RP3-451B15.3 EDN1 12427671 12398599 + + 0 12420905 12404744 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE - 0.0135135135135135 0 0.0135135135135135 4 0.528489363834543 0.728458312312478 0.728458312312478 0.528489363834543 2 - - 28295 N N 3.21800065863931 3.51633251476761 3.21800065863931 8 0 0.237554673694511 N 0 0 N N 6328 1111 ENSG00000167508 ENSG00000182372 + + 16 8 87257019 1722134 intron utr3p MVD CLN8 87245849 1699277 - + 0 87256816 1719829 - + Y 1.07307248473141 - N HCC1954 35 33.75 32 4 1 N 296 13.7619 N - SINE 0 1 1 4 0.428504889595575 0.292811674556976 0.428504889595575 0.292811674556976 2 0 - 709 Y Y 3.31336373513502 3.64334350806672 3.31336373513502 0 0 0.162719098019383 Y 0.0282887402452618 0.98295243403939 N N 129 0 ENSG00000110375 ENSG00000223272 - + 11 11 118334478 118307394 coding upstream UPK2 SRP_euk_arch 118332236 118307130 + + 0 118333549 118301320 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.87843502367093 0.849868031031224 0.87843502367093 0.849868031031224 2 - - 23980 N N 3.50678730447985 2.86126543074728 2.86126543074728 0 0.279356829624817 0.565834804078244 N 0.406529153808673 0 N N 551733 362 ENSG00000204628 ENSG00000162913 + - 5 1 180603512 226467988 utr3p downstream GNB2L1 C1orf145 180596536 226457831 - - 0 180596557 226450217 - + Y - - N HCC1954 17 9.2 1 9 1 N - - N - - 0 0 0 10 0.707033067832699 0.264244681917271 0.707033067832699 0.264244681917271 2 - - 35949 N Y 3.34785034969775 3.34831435801417 3.34785034969775 149 0.814810601751792 0.00175419152706002 N 0.848481401433284 0.882152201114776 N N 10552 0 ENSG00000069431 ENSG00000217019 + - 12 6 21985603 116207531 utr3p downstream ABCC9 RP11-721G11.1 21841590 116205090 - - 0.848481401433284 21842498 115997933 - + Y - - N HCC1954 46 22.6363636363636 21 22 1 N - - N LINE LINE 1 1 1 22 0.499922371194838 0.314236919036755 0.499922371194838 0.314236919036755 1 - - 192 Y Y 3.35616415112274 3.41472693405989 3.35616415112274 312 0 0.0230956435311060 Y 0.00320512820512797 0.992980317804261 N N 107 0 ENSG00000196763 ENSG00000177848 + + 11 11 71317136 71282913 downstream upstream AP002490.4-1 AP002495.3-1 71306229 71282263 - + 0 71304767 71270326 - + N - - N HCC1954 3 1.8 1 3 2 N - - Y - LTR 0 1 1 5 0.5713398527941 0.949852505270192 0.949852505270192 0.5713398527941 1 - - 44277 N N 2.14172634875641 2.6718368118362 2.14172634875641 20 0 0.310717501249965 N 0.547196098920237 0.148728665970046 N N 20790 11502 ENSG00000099204 ENSG00000159921 - - 10 9 116434404 36248450 utr3p utr3p ABLIM1 GNE 116180862 36204430 - - 0.148728665970046 116184060 36206342 + + Y - - N HCC1954 38 35.8571428571429 34 7 1 N - - N Simple_repeat LINE 1 0.672897196261682 1 7 0.328520415356608 0.685607823352921 0.685607823352921 0.328520415356608 1 - - 10209 N Y 3.24831090852981 3.34884356667429 3.24831090852981 66 0.142059264622227 0.704513747842713 N 0.150230128768682 0.975487407560635 Y N 1053 0 ENSG00000176809 ENSG00000213330 - - 17 17 60360856 41020078 coding upstream LRRC37A3 AC126544.5-1 60280944 41019020 - + 0 60319180 41017721 + - N - - N HCC1954 8 4.82352941176471 2 17 1 N - - N - Low_complexity 0 0.031496062992126 0.031496062992126 17 1.22838068350732 0.907002016310634 1.22838068350732 0.907002016310634 4 - - 47655 N N 2.83908756804329 3.72721386824106 2.83908756804329 0 0 0.905650460282041 N 0 0.0789361702127659 N N 29248 1021 ENSG00000105738 ENSG00000028277 + - 19 19 43390849 47328470 utr5p upstream SIPA1L3 POU2F2 43089708 47284515 + - 0.0789361702127659 43089834 47356388 + + N 0.368125301781335 - Y HCC1954 1 1 1 0 3 N 330 6.24336 N - - 0 0 0 6 0.735600060472404 0.492780623034912 0.735600060472404 0.492780623034912 1 0 - 21686 N N 3.11704384497176 3.59169073442408 3.11704384497176 1 0 0.410376231914922 N 0 0 N N 23977 16186 ENSG00000160691 ENSG00000106723 - + 1 9 153213476 90283443 coding utr5p SHC1 SPIN1 153201398 90193117 - + 0 153209400 90221500 + + Y - - N HCC1954 22 21.5 21 4 2 N 477 22.2351 N - SINE 0 1 1 4 0.392796148795944 0.371370904316165 0.392796148795944 0.371370904316165 2 - - 17649 Y Y 3.28296535696188 3.63552422018169 3.28296535696188 0 0 0.659731694291234 Y 0 0 N N 11493 0 ENSG00000143774 ENSG00000217983 - - 1 1 226403308 226389316 coding downstream GUK1 RP11-520H14.1 226394286 226389118 + - 0 226394687 226385557 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 6 0.828442786551446 0.985561246069823 0.985561246069823 0.828442786551446 2 - - 4421 Y Y 3.92592657761471 2.41764212942916 2.41764212942916 217 0 0.951022579206488 Y 0.645708037178786 0.983128954151371 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding downstream CRCP ASL 65216341 65178207 + + 0 65230127 65202508 - + N 0.390248157880058 - N HCC1954 1 1 1 0 6 N - - Y - Simple_repeat,Simple_repeat 0 0.19375 0.19375 4 0.378512652476092 0.692749571512847 0.692749571512847 0.378512652476092 1 0 - 22935 N N 3.64809409186561 3.55334927718654 3.55334927718654 0 0 0.0282752753094628 N 0.00662251655629131 0 N N 49089 1215 ENSG00000117450 ENSG00000138660 - - 1 4 45760196 113410652 coding upstream PRDX1 C4orf16 45749295 113372430 - + 0 45757241 113361883 + - Y - - N HCC1954 11 5 2 8 1 N - - N - SINE 0 1 1 8 0.614190341753658 0.371370904316165 0.614190341753658 0.371370904316165 0 - - 38556 Y Y 3.2948728812365 3.70463477795295 3.2948728812365 181 0.0250430848772081 0.0324148414621953 Y 0.971658229211547 0.994331645842309 N N 2078 2999 ENSG00000080823 ENSG00000140153 + + 14 14 101841284 101759760 coding downstream RAGE WDR20 101762375 101675965 - + 0 101768627 101760886 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 22 1.73544480286208 1.28551466878673 1.73544480286208 1.28551466878673 1 - - 20829 N N 3.25256697878875 3.50206722590449 3.25256697878875 0 0 0.0745739497790673 N 0 0 N N 49089 2648 ENSG00000117450 ENSG00000093183 - - 1 3 45760196 42598432 coding intron PRDX1 SEC22C 45749295 42564479 - - 0 45757275 42575238 + + Y - 0.669842711446254 N HCC1954 10 6 2 6 1 N - - N - SINE 0 1 1 6 0.51420586751469 0.271386430077198 0.51420586751469 0.271386430077198 2 - 0 14972 N N 3.57592836747465 3.11116690544714 3.11116690544714 5 0.00418410041840989 0.810284138282628 N 0.105453513935182 0.476774696830012 N N 3 0 ENSG00000185177 ENSG00000218362 - + 7 1 57211513 245439418 coding intron ZNF733 RP11-488L18.4 57191270 245419776 - - 0.0716970427629247 57203935 245431942 + - Y - 1 N HCC1954 9 5.125 3 8 2 N 199 24.7532 N - - 0 0 0 8 0.39993789695587 0.735600060472404 0.735600060472404 0.39993789695587 3 - 0 267 Y Y 2.27429484578767 3.24678332521996 2.27429484578767 320 0 0.830933782404015 Y 0 0.988272058823529 N N 1289 3448 ENSG00000177595 ENSG00000177542 + - 11 11 795245 786221 downstream upstream LRDD SLC25A22 789180 780478 - - 0.988272058823529 788218 786368 - + N - - N HCC1954 1 1 1 0 4 N - - Y Low_complexity - 0.461538461538462 0 0.461538461538462 6 0.557056356474248 1.39978263934555 1.39978263934555 0.557056356474248 2 - - 543 Y Y 3.63296356710195 2.27429484578767 2.27429484578767 186 0 0.348747778339441 Y 0.977854142802597 0.988927071401298 N N 3448 1289 ENSG00000177542 ENSG00000177595 - + 11 11 786221 795245 utr5p downstream SLC25A22 LRDD 780478 789180 - - 0 786043 788218 + - N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity 0 0.28125 0.28125 91 1.06412047582901 0.914143764470561 1.06412047582901 0.914143764470561 1 - - 34755 Y Y 3.25781626602422 2.87635610271759 2.87635610271759 0 0 0.765965368280765 Y 0 0.99282911333271 N N 3463 188 ENSG00000160408 ENSG00000136840 - + 9 9 129701753 129719126 coding downstream ST6GALNAC6 ST6GALNAC4 129687421 129709987 - - 0 129698404 129707270 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 49 1.26408942430695 0.971277749749971 1.26408942430695 0.971277749749971 2 - - 46436 N N 3.57912086274016 3.34888341946764 3.34888341946764 0 0 0.0472649133860942 N 0.00316455696202522 0 N N 9325 20067 ENSG00000179115 ENSG00000101361 + - 19 20 12905558 2586976 intron upstream FARSA NOP56 12894284 2581178 - + 0 12897605 2580859 - - Y 0.555379991727937 - N HCC1954 3 2.83333333333333 2 6 1 N - - N SINE - 1 0 1 6 0.314236919036755 0.607048593593732 0.607048593593732 0.314236919036755 1 0 - 39155 N N 2.81559919916467 1.88428302257626 1.88428302257626 0 0.0526930375127717 0.121778627587070 N 0.132973288571011 0 N N 12465 5227 ENSG00000135956 ENSG00000137812 + + 2 15 96295459 38742173 utr3p intron TMEM127 CASC5 96280041 38673510 - + 0.0526930375127717 96280983 38739427 - + Y - 2.89054010058381 N HCC1954 40 18 3 4 1 N - - N SINE Simple_repeat,SINE 0.324607329842932 0.547169811320755 0.547169811320755 4 0.971277749749971 0.378512652476092 0.971277749749971 0.378512652476092 3 - 0 9513 N Y 2.75694313027168 3.52569296633162 2.75694313027168 0 0 0.570163441056411 Y 0.35657261592301 0.984306649168854 N N 0 1834 ENSG00000221462 ENSG00000178607 - - 17 17 59577563 59529654 upstream upstream SNORA76 ERN1 59577431 59474122 + - 0 59561066 59533894 - + N - - N HCC1954 1 1 1 0 2 N - - N Simple_repeat - 0.180555555555556 0 0.180555555555556 5 0.871293275511003 0.871293275511003 0.871293275511003 0.871293275511003 1 - - 14151 N Y 1.58496250072116 3.42936294528359 1.58496250072116 0 0 0.0299596243902792 N 0 0 N N 1612 3693 ENSG00000214367 ENSG00000198125 - + 4 22 2213658 34349347 utr3p utr5p C4orf15 MB 2199894 34332757 - - 0 2202989 34349263 + - Y - - N HCC1954 34 32.4 32 5 1 N - - N SINE SINE 1 0.395061728395062 1 5 0.492780623034912 0.578481600954027 0.578481600954027 0.492780623034912 1 - - 26878 Y Y 3.36613351693357 3.54400240599166 3.36613351693357 236 0 0.158301290318437 Y 0 0.983646541383447 N N 8642 3792 ENSG00000099381 ENSG00000175938 - + 16 16 30903482 30873757 upstream coding SETD1A ORAI3 30876116 30867916 + + 0 30875020 30872241 - + N - - N HCC1954 2 1.14285714285714 1 1 3 N - - Y SINE - 0.666666666666667 0 0.666666666666667 7 0.792734045751814 1.08554572030879 1.08554572030879 0.792734045751814 3 - - 757 N Y 3.24520654154694 3.56439156556061 3.24520654154694 436 0 0.00541973663967255 Y 0 0.993348623853211 N N 1654 1882 ENSG00000168569 ENSG00000162227 + + 11 11 62316056 62311390 coding intron TMEM223 TAF6L 62314503 62295451 - + 0 62314963 62296285 - + N - 0.639026362387382 N HCC1954 1 1 1 0 2 N - - N - SINE 0 0.708108108108108 0.708108108108108 5 0.914143764470561 0.692749571512847 0.914143764470561 0.692749571512847 3 - 0 33653 N N 3.2948728812365 3.36976709257655 3.2948728812365 0 0 0.0856657239217183 N 0 0 Y N 171855 0 ENSG00000198886 ENSG00000210195 - + MT MT 12138 15954 coding intron MT-ND4 AF347015.1-23 10761 15889 + + 0 11112 15925 - + N - 1 N HCC1954 2 1.33333333333333 1 2 1 N - - N - - 0 0 0 6 0.649899082553289 1.05697872766909 1.05697872766909 0.649899082553289 1 - 0 16435 N N 2.80881717094615 3.68783934123363 2.80881717094615 4 0 0.110015047145407 N 0 0 N N 122511 34471 ENSG00000187514 ENSG00000116251 - + 2 1 232286495 6182266 coding coding PTMA RPL22 232280638 6167668 + - 0 232284307 6169385 - - Y - - N HCC1954 14 7 2 5 1 Y - - N Low_complexity - 0.23696682464455 0 0.23696682464455 5 0.835584534711372 0.828442786551446 0.835584534711372 0.828442786551446 2 - - 12948 N N 3.47336426491055 3.72402137297555 3.47336426491055 7 0 0.33953531334246 N 0 0 N N 27 261771 ENSG00000184188 ENSG00000184009 + + 5 17 79631912 77094422 coding coding AC026410.5-4 ACTG1 79631253 77091594 - - 0 79631269 77092354 - - Y 1.25437572928821 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.299953422716903 0.442788385915428 0.442788385915428 0.299953422716903 1 0 - 45911 N N 3.45504124488137 3.30950889246021 3.30950889246021 2 0 0.086781081408302 N 0 0.00502512562814073 N N 9933 25286 ENSG00000085872 ENSG00000130429 - + 19 7 16514263 98830338 intron utr5p CHERP ARPC1B 16489700 98810265 - + 0.00502512562814073 16508782 98810330 + + Y 0.913143460851213 1.00285247934271 N HCC1954 20 10.4 7 5 1 N - - N SINE - 1 0 1 5 0.34280391167646 0.449930134075354 0.449930134075354 0.34280391167646 2 0 0 44873 Y Y 3.20804843356093 3.47834596772504 3.20804843356093 0 0 0.12411193881403 Y 0.461458333333333 0.804166666666667 N N 0 0 ENSG00000215129 ENSG00000221359 - + 10 10 112200988 112184133 upstream downstream RP11-525A16.3 AL355512.22 112200377 112183989 + + 0 112196957 112192044 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.705882352941177 0.705882352941177 4 0.628473838073511 0.714174815992626 0.714174815992626 0.628473838073511 2 - - 47303 Y Y 3.38396202342278 3.52357339362936 3.38396202342278 1 0 0.663238938284907 Y 0.382914610719801 0.985649176993484 N N 24791 11666 ENSG00000104881 ENSG00000117877 - - 19 19 50600136 50605864 utr5p utr5p PPP1R13L CD3EAP 50574741 50601307 - + 0 50593437 50601390 + - N - 0.0144891114964003 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 137 1.76401179550179 1.04983697950916 1.76401179550179 1.04983697950916 4 - 0 6417 N Y 3.44871903508266 3.55854103193824 3.44871903508266 326 0 0.00336425913023763 N 0 0.527768808524378 N N 71 250 ENSG00000163060 ENSG00000188681 - + 2 Y 94906295 11830682 upstream utr5p TEKT4 AC134878.3-1 94900959 11769481 + - 0 94896808 11830624 - - Y - - N HCC1954 5 2.33333333333333 1 10 1 N 384 15.2077 N - - 0 0 0 12 0.292811674556976 0.621332089913584 0.621332089913584 0.292811674556976 3 - - 30286 N Y 3.68850168864294 3.12023634023727 3.12023634023727 0 0 0.679002331247837 Y 0 0.98854079058032 N N 0 650 ENSG00000199920 ENSG00000170965 + - X X 133722044 133620179 upstream intron U4 PLAC1 133721904 133527539 - - 0 133725937 133528518 - + N - 2.68018880917824 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 35 0.707033067832699 1.17838844638783 1.17838844638783 0.707033067832699 2 - 0 19589 N Y 3.73808832274579 3.24893340314576 3.24893340314576 17 0 0.791795483718685 N 0.936981667394151 0.936981667394151 N N 0 0 ENSG00000219828 ENSG00000206696 - + 1 18 87023738 45272097 upstream upstream RP4-612B15.2 SNORD58 87023184 45272032 + - 0.936981667394151 87023175 45272639 - - Y - - N HCC1954 9 5.30666666666667 1 74 1 N - - N - - 0 0 0 75 0.857009779191151 0.678466075192994 0.857009779191151 0.678466075192994 3 - - 90 Y Y 3.56807857436608 3.5031842340604 3.5031842340604 266 0 0.415123557743996 Y 0.774185463659148 0.98671679197995 N N 0 138744 ENSG00000210948 ENSG00000152558 - - 11 11 101844353 101828985 downstream intron AP001830.5 TMEM123 101844288 101772268 + - 0 101846118 101824812 - + N - 1.45476260670474 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 18 1.02841173502938 0.449930134075354 1.02841173502938 0.449930134075354 1 - 0 565 Y Y 3.66273010308932 3.37655331069169 3.37655331069169 0 0 0.764618756264165 Y 0.0037878787878789 0 N Y 4289 193 ENSG00000110497 ENSG00000180423 - + 11 11 46572145 46595353 coding utr5p AMBRA1 HARBI1 46374540 46581124 - - 0 46472330 46595250 + - N - 1.78010321100917 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 0.928427260790413 0.857009779191151 0.928427260790413 0.857009779191151 4 - 0 32987 N N 3.1416492220063 3.50422665140011 3.1416492220063 0 0 0.99998135225929 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8648 14496 - + N 0.587987018616228 1.40918744733293 N HCC1954 3 2 1 6 10 N 189 4.09957 N - - 0 0 0 9 1.17838844638783 1.1141127129485 1.17838844638783 1.1141127129485 3 0 0 16385 N Y 3.41679307359967 3.6052936758779 3.41679307359967 1 0 0.170245357387118 N 0.903181189488243 0.903181189488243 N N 49089 7 ENSG00000117450 ENSG00000157884 - - 1 2 45760196 26717715 utr5p upstream PRDX1 CIB4 45749295 26657577 - - 0 45759868 26735021 + + Y - - N HCC1954 6 3.8 2 5 1 N - - N - SINE 0 1 1 5 0.757025304952183 0.421363141435649 0.757025304952183 0.421363141435649 2 - - 13264 N N 3.40591861909494 2.85079882778696 2.85079882778696 0 0.125066454013823 0.342801364802052 N 0.487107921318448 0.125066454013823 N N 78560 2205 ENSG00000112493 ENSG00000184979 - - 6 22 33390114 17040164 utr3p intron TAPBP USP18 33375449 17012758 - + 0.125066454013823 33376421 17026435 + - Y - 1.09112016915679 N HCC1954 147 48.6 2 25 1 N - - N SINE SINE 1 1 1 25 0.842726282871298 0.28566992639705 0.842726282871298 0.28566992639705 2 - 0 34987 Y Y 3.7297745213208 3.34256120966892 3.34256120966892 218 0 0.0767914843228893 Y 0.00458715596330272 0 N N 2515 0 ENSG00000137074 ENSG00000218769 + + 9 9 32991626 32937220 coding downstream APTX RP11-562M8.2 32962609 32935994 - + 0 32974629 32937616 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 4 0.621332089913584 0.292811674556976 0.621332089913584 0.292811674556976 4 - - 47496 N Y 3.25613019641484 3.11232376639641 3.11232376639641 0 0 0.224543187091263 Y 0 0.989497716894977 N Y 1118 1118 ENSG00000167744 ENSG00000167744 - + 19 19 54258936 54258936 utr5p upstream NTF4 NTF4 54256216 54256216 - - 0 54258808 54257078 + - N - - N HCC1954 1 1 1 0 1 Y - - N Low_complexity Low_complexity 0.291428571428571 0.0757575757575758 0.291428571428571 44 1.24980592798709 0.942710757110266 1.24980592798709 0.942710757110266 0 - - 4057 Y Y 3.42100929106525 3.73233517440054 3.42100929106525 387 0 0.487697847470701 Y 0.158025437095205 0.98056981777912 N N 32979 386 ENSG00000106105 ENSG00000196295 - - 7 7 30640168 30570758 upstream upstream GARS AC005154.1 30600706 30566129 + - 0 30591471 30585455 - + N - - N HCC1954 6 2 1 9 4 N - - Y SINE LTR,LTR 1 0.703703703703704 1 19 1.09268746846872 1.06412047582901 1.09268746846872 1.06412047582901 4 - - 8414 N N 3.67849247003875 3.42208221362849 3.42208221362849 1 0 0.601675561017117 N 0 0 N N 850768 0 ENSG00000075624 ENSG00000204458 + + 7 17 5536758 17086925 coding intron ACTB AC055811.5 5533313 17086049 - + 0 5534452 17086606 - + Y 1.19960355278068 1 N HCC1954 2 1.14285714285714 1 1 1 N - - N - - 0 0 0 7 0.464213630395207 0.264244681917271 0.464213630395207 0.264244681917271 1 0 0 26990 Y Y 3.46865776670432 3.48337348351473 3.46865776670432 100 0.00288184438040362 0.440869848620533 Y 0.00288184438040362 0 N N 2202 1174 ENSG00000182108 ENSG00000179583 + + 16 16 10943817 10926341 intron utr3p DEXI CIITA 10930278 10867648 - + 0 10936474 10924683 - + N 1.17074745692725 - N HCC1954 1 1 1 0 1 N - - Y SINE,DNA - 0.582278481012658 0 0.582278481012658 7 1.02841173502938 1.23552243166724 1.23552243166724 1.02841173502938 4 0 - 16338 N N 3.70512929149291 3.41315949795669 3.41315949795669 0 0 0.66248425526957 N 0 0 N N 8684 61 ENSG00000055044 ENSG00000132122 - - 2 1 202876627 48710432 coding intron NOP58 SPATA6 202838760 48536096 + - 0 202868804 48674538 - + Y - 1.02868661527242 N HCC1954 2 1.85380116959064 1 146 1 N - - N - - 0 0 0 171 1.32122340958636 1.24266417982717 1.32122340958636 1.24266417982717 2 - 0 48122 N N 3.51104337473878 3.43142908482337 3.43142908482337 0 0 0.999998850501805 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0.00340136054421769 117944558 2616724 - + Y - - N HCC1954 2 1.25 1 1 12 N 282 1.61558 N - - 0 0 0 4 0.742741808632331 0.749883556792257 0.749883556792257 0.742741808632331 1 - - 45292 N N 3.39657174790006 3.09087103183403 3.09087103183403 13 0 0.0720370163184638 N 0 0 N N 4 3891 ENSG00000160505 ENSG00000166295 + + 19 10 61085030 73665622 downstream intron NLRP4 C10orf104 61055199 73645812 + + 0 61085464 73645953 + + Y - 0.744979490524871 N HCC1954 28 21.7142857142857 20 7 1 N - - N SINE - 1 0 1 7 0.45707188223528 0.499922371194838 0.499922371194838 0.45707188223528 1 - 0 10342 Y Y 3.61616813038263 3.53039946453785 3.53039946453785 1 0 0.9999997905698 Y 0.233607720692591 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 coding utr5p ORMDL3 GSDMB 35330822 35314374 - - 0 35332385 35328377 - + N - 13.9337021458332 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 5 1.04983697950916 0.542772860154395 1.04983697950916 0.542772860154395 1 - 0 47336 Y Y 3.62464976567696 3.3414348539432 3.3414348539432 0 0 0.892299419551285 Y 0.990772128060264 0.990772128060264 N N 16146 7111 ENSG00000167491 ENSG00000129933 - + 19 19 19480736 19339989 utr5p downstream GATAD2A KIAA0892 19399336 19292614 + + 0 19407942 19357949 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity,Simple_repeat 0 0.270440251572327 0.270440251572327 32 0.799875793911741 1.13553795742827 1.13553795742827 0.799875793911741 2 - - 11 Y Y 3.50678730447985 3.51001030496889 3.50678730447985 0 0 0.848060324213582 Y 0.977590166987398 0.988795083493699 N N 1856 8597 ENSG00000149231 ENSG00000184384 + - 11 11 95757574 95466334 downstream coding CCDC82 MAML2 95725589 95351088 - - 0 95714195 95466329 - + N - 48.9145075524861 N HCC1954 1 1 1 0 1 N - - Y Simple_repeat - 0.420765027322404 0 0.420765027322404 197 1.3069399132665 1.35693215038599 1.35693215038599 1.3069399132665 4 - 0 39875 N Y 3.5010341561346 3.43361901554253 3.43361901554253 304 0 0.0272617544712505 Y 0 0.984547123623011 N N 273 0 ENSG00000140297 ENSG00000201704 - - 15 15 57700315 57653713 upstream downstream GCNT3 5S_rRNA 57691275 57653594 + - 0 57689226 57635664 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR,LINE SINE,LINE 0.583941605839416 0.947368421052632 0.947368421052632 4 0.871293275511003 0.792734045751814 0.871293275511003 0.792734045751814 4 - - 43466 N Y 3.40744620240479 3.44975210485255 3.40744620240479 8 0 0.0200538670774170 N 0 0.95743842364532 N N 0 4691 ENSG00000216994 ENSG00000152253 + + 10 2 93516933 169455190 downstream utr3p RP11-251A15.1 SPC25 93515636 169435648 - - 0.943251231527093 93484235 169435705 - - Y - - N HCC1954 620 590 500 4 1 N - - N LINE LINE 1 1 1 4 0.349945659836387 0.528489363834543 0.528489363834543 0.349945659836387 1 - - 33230 N N 3.08152416063915 3.62361669590707 3.08152416063915 14 0 0.152599972944134 N 0 0.0339667977282656 Y N 539404 336285 ENSG00000198712 ENSG00000198868 - + MT MT 8270 12138 coding coding MT-CO2 MT-ND4 7587 10471 + + 0.0339667977282656 8255 11476 - + N 3.13065601446849 - N HCC1954 2 1.5 1 2 1 N 189 4.09957 N - - 0 0 0 4 0.707033067832699 0.964136001590045 0.964136001590045 0.707033067832699 2 0 - 37894 N N 3.40591861909494 3.30591516961058 3.30591516961058 0 0 0.189381334763747 N 0 0 N N 5424 2601 ENSG00000033170 ENSG00000172197 + + 14 6 65279714 20320649 utr5p utr3p FUT8 MBOAT1 64947063 20208914 + - 0 65097939 20210097 + - Y - - N HCC1954 39 29.8333333333333 23 6 1 N - - N - SINE 0 1 1 6 0.742741808632331 0.907002016310634 0.907002016310634 0.742741808632331 2 - - 13728 Y Y 3.41269548964026 2.91341271792987 2.91341271792987 354 0 0.102636173859298 Y 0 0 N N 19152 9629 ENSG00000182457 ENSG00000133422 - - 22 22 29702049 29694187 intron upstream TUG1 MORC2 29696663 29652600 + - 0 29698840 29695371 - + N 0.63802764549611 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 30 1.18553019454776 1.26408942430695 1.26408942430695 1.18553019454776 1 0 - 18245 N Y 3.44143830342756 3.59594680468302 3.44143830342756 0 0 0.852489363455163 N 0.170986872792697 0.971013527020724 Y N 0 0 ENSG00000208696 ENSG00000213223 + + 1 1 147554054 147820286 upstream downstream AL356957.27-7 AL451058.16-1 147553983 147819627 - + 0 147557827 147843323 - + N - - N HCC1954 36 15.5714285714286 5 42 2 N 486 21.4198 N LTR - 1 0 1 42 1.24980592798709 1.20695543902754 1.24980592798709 1.20695543902754 1 - - 9307 Y Y 3.46807512488172 3.19024263913262 3.19024263913262 264 0 0.959956162067758 Y 0.0960297418630752 0.981551627384961 N N 1312 5490 ENSG00000120093 ENSG00000173917 + - 17 17 44006809 43977392 downstream upstream HOXB3 HOXB2 43981232 43975020 - - 0 43980736 43977925 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 20 0.814159290231593 1.12839620926835 1.12839620926835 0.814159290231593 4 - - 18484 Y Y 3.24053989613407 3.44682072941222 3.24053989613407 256 0.00390625 0.0090721208813751 Y 0.988680752840909 0.988680752840909 N N 673 22940 ENSG00000162616 ENSG00000162613 - - 1 1 78255581 78217365 coding upstream DNAJB4 FUBP1 78243224 78173191 + - 0 78251324 78217566 - + N 1.70823955263707 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 21 1.15696320190805 0.607048593593732 1.15696320190805 0.607048593593732 1 0 - 2531 N Y 3.5010341561346 3.27039548527796 3.27039548527796 1 0 0.410463534574173 N 0.88380187416332 0 N N 559 3567 ENSG00000178401 ENSG00000177951 - - 12 11 48031950 197428 utr3p coding DNAJC22 BET1L 48026967 157784 + - 0 48031823 170402 - + Y - 2.88658222152281 N HCC1954 190 142.470588235294 69 17 1 N - - N SINE - 1 0 1 17 0.349945659836387 0.864151527351077 0.864151527351077 0.349945659836387 2 - 0 12689 N N 3.353603498043 3.49528100778935 3.353603498043 0 0 0.027021661040307 N 0.493616814717732 0 N N 174 7525 ENSG00000105464 ENSG00000173894 - - 19 17 53639999 75375973 intron upstream GRIN2D CBX2 53589944 75366588 + + 0.477792340177662 53632438 75358159 - - Y 1.00851881072834 - N HCC1954 21 20.2 20 5 1 N - - N SINE LTR 1 1 1 5 0.307095170876829 0.45707188223528 0.45707188223528 0.307095170876829 1 0 - 24637 Y Y 3.49272035470961 3.11650947863845 3.11650947863845 185 0.0491859243697477 0.827547384096463 Y 0.994130777310924 0.988261554621849 N N 10593 4475 ENSG00000134779 ENSG00000134775 + + 18 18 32663156 32614016 coding downstream C18orf10 FHOD3 32630033 32131700 - + 0 32632411 32621041 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 88 1.63546032862311 1.27123117246687 1.63546032862311 1.27123117246687 1 - - 9317 N Y 2.51851081481407 3.1117894000631 2.51851081481407 347 0 0.00336047659461070 Y 0 0.988269198169181 N N 64784 4310 ENSG00000170004 ENSG00000183011 - - 17 17 7756803 7701897 coding coding CHD3 LSMD1 7728849 7700730 + - 0 7729062 7701240 - + N 0.13923419625232 11.6085948714976 N HCC1954 3 2.03508771929825 1 53 2 N - - N - - 0 0 0 57 0.842726282871298 0.635615586233437 0.842726282871298 0.635615586233437 1 0 0 6747 Y Y 2.84174150707887 3.48593413659447 2.84174150707887 293 0 0.0537899687697636 Y 0.965634929975285 0.993126985995057 N N 7139 2859 ENSG00000085449 ENSG00000152056 + - 2 2 224518296 224410563 utr3p upstream WDFY1 AP1S3 224448309 224325785 - - 0 224451490 224428877 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.763157894736842 0.763157894736842 7 1.04983697950916 0.792734045751814 1.04983697950916 0.792734045751814 4 - - 14553 N Y 3.04941093835673 3.38127338926705 3.04941093835673 217 0 0.0053514138367925 N 0.135580887703129 0 N N 0 24421 ENSG00000217043 ENSG00000177156 - + 1 11 54763192 755023 downstream utr3p RP5-866L20.2 TALDO1 54763085 737432 + + 0.659471258792142 54763361 755012 - + Y - 53.1139883942025 N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.176470588235294 0 0.176470588235294 5 0.242819437437493 0.478497126715059 0.478497126715059 0.242819437437493 1 - 0 7764 N Y 3.61038447681384 3.4439989565073 3.4439989565073 26 0 0.415549864123784 N 0 0 N N 3 0 ENSG00000222017 ENSG00000222231 + - 2 8 198347792 77340522 coding upstream AC011997.1 U2 198266075 77340333 + - 0.963458249105893 198266183 77381259 + + Y - - N HCC1954 25 22.6 21 10 1 N - - N LINE LTR,LTR 1 1 1 10 0.51420586751469 0.771308801272036 0.771308801272036 0.51420586751469 2 - - 7934 N Y 3.32523140661629 3.82402482245992 3.32523140661629 0 0 0.0224888867264597 N 0.865641503572538 0.932820751786269 N N 73 13154 ENSG00000109743 ENSG00000074054 - - 4 2 15343508 122123509 upstream intron BST1 CLASP1 15313739 121811825 + - 0 15292111 122106912 - + Y - 1.40456202047353 N HCC1954 28 20.9166666666667 20 12 1 N - - N - SINE 0 1 1 12 0.914143764470561 0.314236919036755 0.914143764470561 0.314236919036755 1 - 0 4606 Y Y 3.74337746277462 3.53312795148693 3.53312795148693 254 0 0.157320708518652 Y 0.610236220472441 0.978346456692913 N N 2192 2920 ENSG00000157764 ENSG00000090266 + + 7 7 140271033 140052911 downstream coding BRAF NDUFB2 140080751 140042950 - + 0 140067821 140043111 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.585623349113953 0.335662163516534 0.585623349113953 0.335662163516534 4 - - 34860 Y Y 3.42208221362849 3.7061623612628 3.42208221362849 90 0.119186046511628 0.0680239251024315 Y 0.953641370869033 0.953641370869033 N N 1173 9311 ENSG00000147912 ENSG00000175768 - + 9 9 37566250 37582594 utr5p utr3p FBXO10 TOMM5 37500899 37578410 - - 0 37531769 37578806 + - N - - N HCC1954 3 1.22222222222222 1 1 1 N - - Y - - 0 0 0 9 1.03555348318931 1.09982921662864 1.09982921662864 1.03555348318931 1 - - 44960 Y Y 3.3755202409218 3.43408302385895 3.3755202409218 262 0 0.0134266749267662 Y 0 0.957907751854639 N N 19160 21237 ENSG00000107959 ENSG00000067057 + + 10 10 3205003 3169762 coding coding PITRM1 PFKP 3169922 3099740 - + 0 3175954 3167961 - + N 0.769332107404885 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.564198104634174 0.607048593593732 0.607048593593732 0.564198104634174 1 0 - 4814 N N 3.45293525254824 3.36716658670346 3.36716658670346 10 0 0.0312969368396259 Y 0 0 N N 2424 6576 ENSG00000135272 ENSG00000106635 - - 7 7 114446501 72609960 utr3p coding MDFIC BCL7B 114349445 72588622 + - 0 114443830 72595851 - + N - 1.40522255187045 N HCC1954 37 35 31 4 1 N - - N SINE - 1 0 1 4 0.34280391167646 0.471355378555133 0.471355378555133 0.34280391167646 0 - 0 44463 N N 3.54040868314203 3.09087103183403 3.09087103183403 7 0 0.129256468701803 N 0 0 N N 383 3891 ENSG00000089091 ENSG00000166295 - + 20 10 18395829 73665622 utr3p intron C20orf12 C10orf104 18312011 73645812 - + 0 18312923 73645953 + + Y - 0.744979490524871 N HCC1954 35 30.9375 27 16 1 N - - N SINE - 1 0 1 16 0.335662163516534 0.692749571512847 0.692749571512847 0.335662163516534 1 - 0 26057 N Y 3.09400074636723 3.54400240599166 3.09400074636723 0 0 0.168514574512347 N 0.887553872273736 0.90361760480606 N N 9663 0 ENSG00000172775 ENSG00000213355 - + 16 2 55777477 94767690 utr5p upstream AC009090.12 AC073464.5-1 55743888 94766809 - + 0.90361760480606 55777235 94765856 + + Y - - N HCC1954 32 12 4 5 1 N - - N - SINE 0 1 1 5 0.542772860154395 0.299953422716903 0.542772860154395 0.299953422716903 1 - - 19190 N N 3.44296588673741 3.60781447616429 3.44296588673741 6 0.00338983050847474 0.99059396803787 N 0.0180458624127615 0 Y N 10857 14045 ENSG00000085832 ENSG00000117859 + + 1 1 51757583 52026729 intron coding EPS15 OSBPL9 51592523 51815439 - + 0 51684734 51890301 - + N 1.60195515387961 - N HCC1954 21 6.94444444444444 1 16 4 Y - - N SINE - 1 0 1 18 0.621332089913584 1.32122340958636 1.32122340958636 0.621332089913584 4 0 - 40976 Y Y 3.57489529770476 2.91550936269319 2.91550936269319 290 0 0.00223408955753834 Y 0.0555069480185281 0 N N 0 13533 ENSG00000201770 ENSG00000101294 - + 20 20 29632656 29621031 upstream downstream U6 HM13 29632553 29565892 + + 0 29629067 29624844 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR Low_complexity,SINE 1 0.338461538461538 1 12 1.09982921662864 1.19981369086761 1.19981369086761 1.09982921662864 1 - - 9493 Y N 3.49744043328497 3.38337003403037 3.38337003403037 0 0 0.108276688349351 Y 0 0 N N 0 0 ENSG00000221496 ENSG00000223094 - - 17 17 39737096 39724045 upstream downstream U3 SRP_euk_arch 39736890 39723752 + - 0.179292929292929 39732345 39717875 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR SINE 1 1 1 4 0.557056356474248 0.542772860154395 0.557056356474248 0.542772860154395 2 - - 33696 N Y 3.01191908932792 3.41103992525442 3.01191908932792 339 0 0.00202796056741616 Y 0 0.983382497541789 N N 171855 151141 ENSG00000198886 ENSG00000198888 - + MT MT 12138 4264 coding coding MT-ND4 MT-ND1 10761 3308 + + 0 10857 4130 - + N - - N HCC1954 4 2.33333333333333 1 4 1 Y - - N - - 0 0 0 6 1.17124669822791 0.842726282871298 1.17124669822791 0.842726282871298 1 - - 30549 N Y 3.40744620240479 3.44975210485255 3.40744620240479 4 0 0.0199385169172339 N 0 0.938815207780725 N N 140 6060 ENSG00000198934 ENSG00000079482 - + X X 75568148 67570372 downstream utr3p MAGEE1 OPHN1 75564521 67179440 + - 0.938815207780725 75661352 67179530 - - N - - Y HCC1954 620 610 600 4 1 N 83 28.0918 N LINE LINE 1 1 1 4 0.39993789695587 0.292811674556976 0.39993789695587 0.292811674556976 1 - - 43605 N N 3.50848272165904 3.09087103183403 3.09087103183403 0 0 0.165402323245386 N 0 0 N N 989 3891 ENSG00000181031 ENSG00000166295 + + 17 10 202576 73665622 downstream intron RPH3AL C10orf104 62297 73645812 - + 0 61194 73645953 - + Y - 0.744979490524871 N HCC1954 20 17.4444444444444 6 9 1 N - - N SINE - 1 0 1 9 0.328520415356608 0.757025304952183 0.757025304952183 0.328520415356608 1 - 0 29367 N N 3.01080631397133 3.53615261288309 3.01080631397133 0 0 0.839340984848833 Y 0 0 N N 343 52571 ENSG00000178729 ENSG00000096433 + + 6 6 48144384 33772324 intron coding C6orf138 ITPR3 47953998 33697139 - + 0 48102634 33716240 - + N 5.08738813241339 - N HCC1954 1 1 1 0 4 N 104 11.3593 N LTR - 1 0 1 26 0.528489363834543 0.578481600954027 0.578481600954027 0.528489363834543 2 0 - 22465 N N 3.47552369040616 3.51729103662399 3.47552369040616 14 0 0.553004862507712 N 0.618003913894325 0 N N 0 2833 ENSG00000206719 ENSG00000133019 - + 8 1 115032403 238139338 downstream utr5p Y_RNA CHRM3 115032291 237858996 + + 0 115729781 237859191 - + Y - - N HCC1954 25 24 23 5 1 N - - N LINE LINE 0.25 1 1 5 0.45707188223528 0.499922371194838 0.499922371194838 0.45707188223528 4 - - 31460 Y Y 3.54872248456702 3.31489131844487 3.31489131844487 314 0 0.208162310276834 Y 0 0.990770228827554 N N 168 73312 ENSG00000113946 ENSG00000163347 - - 3 3 191611027 191522909 upstream upstream CLDN16 CLDN1 191588535 191506197 + - 0 191571381 191523217 - + N - - N HCC1954 6 2.11111111111111 1 2 4 N - - Y LTR - 1 0 1 9 0.642757334393363 0.821301038391519 0.821301038391519 0.642757334393363 2 - - 2122 N N 3.28296535696188 3.50744965188915 3.28296535696188 22 0 0.338037774705268 N 0.0220625224577794 0.402371541501976 N N 0 19727 ENSG00000217068 ENSG00000110700 + + X 11 53383904 17055796 downstream utr3p RP6-29D12.3 RPS13P2 53383714 17052515 - - 0.402371541501976 53383672 17052541 - - Y - - N HCC1954 2 1.22222222222222 1 2 1 N - - N - - 0 0 0 9 0.271386430077198 0.678466075192994 0.678466075192994 0.271386430077198 1 - - 21840 N N 3.61360747730288 3.55401162459584 3.55401162459584 1 0 0.451446751296796 N 0 0 N N 4896 9856 ENSG00000175137 ENSG00000135677 + + 1 12 247086777 63439479 downstream utr3p SH3BP5L GNS 247071274 63393491 - - 0 247057528 63395447 - - Y - - N HCC1954 1 1 1 0 1 N - - N SINE SINE 1 0.456521739130435 1 6 0.28566992639705 0.328520415356608 0.328520415356608 0.28566992639705 2 - - 44798 N Y 3.71976530271662 3.24165267149067 3.24165267149067 0 0 0.282928084813597 N 0.408625 0.8755 Y N 6043 15659 ENSG00000099246 ENSG00000197321 - - 10 10 27869103 30064736 intron downstream RAB18 SVIL 27833255 29786283 + - 0 27838808 29738627 - + N 0.73030237699913 - N HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.271386430077198 0.614190341753658 0.614190341753658 0.271386430077198 1 0 - 24892 N N 3.21848159181014 3.55504469436573 3.21848159181014 0 0 0.0376341729011227 N 0 0 N N 0 9430 ENSG00000209951 ENSG00000139842 + + 7 13 86960 112967400 upstream intron AC097646.2-1 CUL4A 86858 112911151 - + 0 126185 112944557 - + Y - 1.75510366058849 N HCC1954 92 85 80 4 1 N - - N - SINE 0 1 1 4 0.435646637755502 0.385654400636018 0.435646637755502 0.385654400636018 1 - 0 48944 Y Y 3.48912663185998 3.56232542602083 3.48912663185998 281 0 0.0819127414848262 Y 0 0.98220640569395 N N 0 0 ENSG00000184550 ENSG00000221204 - + 5 5 177331888 177268164 upstream downstream AC136940.2 AC106795.3-2 177331334 177268072 + + 0 177311324 177299373 - + N - - N HCC1954 2 2 2 5 1 N - - Y - - 0 0 0 5 0.607048593593732 0.642757334393363 0.642757334393363 0.607048593593732 4 - - 43146 N Y 3.26824964015148 3.50000108636471 3.26824964015148 24 0 0.347112398269366 N 0.991340731307986 0.948044387847917 N N 8014 0 ENSG00000149084 ENSG00000178429 - - 11 10 43834736 86310999 utr3p downstream HSD17B12 AL356115.9 43658719 86310179 + + 0.212006549026742 43834016 86638343 - - Y 1.56799368003871 - N HCC1954 74 53 23 4 1 N - - N - SINE,SINE 0 1 1 4 0.635615586233437 0.585623349113953 0.635615586233437 0.585623349113953 1 0 - 43386 N N 3.34000055658918 3.11920327046738 3.11920327046738 0 0.00571428571428567 0.420732886988337 N 0.00571428571428567 0.00571428571428567 N N 53981 0 ENSG00000138326 ENSG00000220644 + + 10 Y 79470477 12876163 coding intron RPS24 AC004772.1 79463580 12875458 + + 0.00571428571428567 79467053 12876025 + + Y - 1 N HCC1954 6 3.28571428571429 1 6 1 N - - N - - 0 0 0 7 0.849868031031224 0.292811674556976 0.849868031031224 0.292811674556976 2 - 0 42319 Y Y 2.94268474037728 3.44975210485255 2.94268474037728 0 0 0.986764681667786 Y 0.607547169811321 0.969811320754717 N N 1 5644 ENSG00000189099 ENSG00000109686 - - 4 4 152432055 152367022 downstream utr5p AC104819.4 SH3D19 152417775 152260886 + - 0 152465843 152366688 - + N - 56.989680037046 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.464213630395207 0.364229156156239 0.464213630395207 0.364229156156239 4 - 0 18053 Y Y 3.34040178417331 3.16935896602371 3.16935896602371 222 0 0.00508578843561902 Y 0.913969525080636 0.987709932154377 N N 0 0 ENSG00000218510 ENSG00000142789 - + 1 1 22230209 22224238 upstream downstream AL031281.6 ELA3A 22229736 22200736 + + 0 22229383 22224661 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 129 1.20695543902754 0.949852505270192 1.20695543902754 0.949852505270192 3 - - 29128 N Y 3.52720696927234 3.44512531223303 3.44512531223303 221 0.0910879401927995 0.0231108294645558 Y 0.426519771788314 0.978359236671257 N N 4547 7887 ENSG00000044090 ENSG00000124541 + + 6 6 43129632 43105312 coding coding CUL7 C6orf153 43113336 43097351 - + 0 43113986 43103193 - + N 0.726237900353995 1.09475046534422 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.99270299422975 0.657040830713216 0.99270299422975 0.657040830713216 4 0 0 28989 N Y 3.65488030998075 3.50744965188915 3.50744965188915 0 0 0.0623069151978662 N 0 0 N N 4386 45068 ENSG00000062194 ENSG00000205336 + + 5 16 56594666 56256445 intron upstream GPBP1 GPR56 56505701 56220023 + + 0 56520240 56211648 + + Y 0.739651567889132 - N HCC1954 24 24 24 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.264244681917271 0.278528178237124 0.264244681917271 1 0 - 10426 Y Y 3.66016945000958 3.35719722089263 3.35719722089263 0 0 0.822009183245997 Y 0.993845262662467 0.993845262662467 N N 18893 6556 ENSG00000141551 ENSG00000141526 + + 17 17 77824862 77790658 coding downstream CSNK1D SLC16A3 77795535 77779582 - + 0 77795996 77791226 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 15 1.17124669822791 1.3069399132665 1.3069399132665 1.17124669822791 1 - - 5631 N Y 3.44785379918211 3.50425715662364 3.44785379918211 0 0 0.900909844526234 N 0 0.99012439705509 N N 120 0 ENSG00000163009 ENSG00000214018 - + 2 X 10269307 44054568 utr5p intron C2orf48 AL133344.28-2 10198960 44053504 + - 0 10199219 44053653 - - Y - 1 N HCC1954 2 1.95652173913043 1 22 1 N - - N LINE,LINE - 0.435251798561151 0 0.435251798561151 23 1.42120788382533 0.799875793911741 1.42120788382533 0.799875793911741 3 - 0 7089 Y Y 3.66848325143457 3.48333363072138 3.48333363072138 251 0 0.385520286905393 Y 0 0 N N 3237 633 ENSG00000003137 ENSG00000135636 + + 2 2 72228471 71767398 downstream downstream CYP26B1 DYSF 72209875 71534268 - + 0 72010427 71960514 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 19 0.757025304952183 0.956994253430118 0.956994253430118 0.757025304952183 2 - - 25571 N N 3.25252712599539 3.51423587000429 3.25252712599539 0 0 0.0431003059196525 N 0 0 N N 75177 6322 ENSG00000125107 ENSG00000196715 + + 16 7 57221251 65060252 intron utr3p CNOT1 VKORC1L1 57111359 64975759 - + 0 57220980 65059816 - + Y 2.02597604330693 - N HCC1954 21 20.9230769230769 20 13 1 N - - N - SINE 0 1 1 13 0.671324327033068 0.292811674556976 0.671324327033068 0.292811674556976 1 0 - 9512 Y Y 3.353603498043 3.42936294528359 3.353603498043 289 0 0.0159759572549388 Y 0 0.987385572248259 N N 265 752 ENSG00000161929 ENSG00000180626 + - 17 17 5078861 5035902 utr3p upstream C17orf87 ZNF594 5052980 5023554 - - 0 5053837 5036273 - + N 1.59528167142055 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 17 0.799875793911741 0.492780623034912 0.799875793911741 0.492780623034912 1 0 - 47023 Y Y 3.23842967100162 3.49015970162987 3.23842967100162 136 0 0.0183548192638353 Y 0 0.980910633484163 N N 13 7 ENSG00000188293 ENSG00000204866 - + 19 19 51425793 51356385 upstream downstream IGFL1 IGFL2 51424849 51274062 + + 0 51397992 51384290 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR 1 1 1 6 0.521347615674617 0.464213630395207 0.521347615674617 0.464213630395207 1 - - 28037 N Y 3.44296588673741 3.33424740824393 3.33424740824393 101 0.104196133899104 0.0104711761421139 N 0.0806223479490805 0.929278642149929 N N 13096 0 ENSG00000166164 ENSG00000214930 + - 16 X 48960346 137398714 utr3p downstream BRD7 Z81311.1 48910442 137397493 - - 0.0806223479490805 48940463 137018539 - + Y - - N HCC1954 620 610 600 4 1 N 531 26.2584 N LINE LINE 1 1 1 4 0.292811674556976 0.299953422716903 0.299953422716903 0.292811674556976 3 - - 8037 N N 3.47552369040616 3.37188666527882 3.37188666527882 2 0 0.114364551137237 N 0.818883818883819 0 N N 1992 11 ENSG00000003436 ENSG00000145451 - + 2 4 188127464 175987040 utr5p intron TFPI GLRA3 188037202 175799773 - - 0 188127364 175849148 + - Y - 0.949189630564094 N HCC1954 21 16 2 4 1 N - - N - Other 0 1 1 4 0.449930134075354 0.378512652476092 0.449930134075354 0.378512652476092 2 - 0 12440 N Y 3.71720464963688 3.07101108092519 3.07101108092519 1 0 0.70380884197256 N 0.624427901847257 0 N N 13563 1649619 ENSG00000163110 ENSG00000141736 - - 4 17 95808400 35138441 utr3p coding PDLIM5 ERBB2 95592061 35104766 + + 0 95804918 35125066 - - Y - - N HCC1954 22 21.7818181818182 20 55 2 N 453 21.9768 N SINE - 1 0 1 55 0.314236919036755 1.0069864905496 1.0069864905496 0.314236919036755 1 - - 43814 N Y 3.24893340314576 3.73808832274579 3.24893340314576 0 0 0.87310239199446 N 0.0861801242236022 0.944616977225673 N N 0 0 ENSG00000206696 ENSG00000217638 + - 18 10 45272097 120622104 upstream upstream SNORD58 RP11-215A21.2 45272032 120621556 - - 0.944616977225673 45272639 120622113 - + Y - - N HCC1954 4 3.75862068965517 2 29 1 N - - N - - 0 0 0 29 1.1426797055882 0.592765097273879 1.1426797055882 0.592765097273879 3 - - 38407 Y Y 3.52208566311286 3.53296011761759 3.52208566311286 0 0 0.470592329974311 Y 0.940639269406393 0.988127853881279 N Y 259 1147 ENSG00000100739 ENSG00000168398 - + 14 14 95800851 95780536 utr5p coding BDKRB1 BDKRB2 95792300 95740950 + + 0 95798742 95773271 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.706586826347305 0 0.706586826347305 17 1.19267194270768 1.4426331283051 1.4426331283051 1.19267194270768 4 - - 4075 N Y 3.5774559507845 3.20443756997885 3.20443756997885 284 0 0.0944288157119186 Y 0.992882293762575 0.978646881287726 N Y 12405 124 ENSG00000160862 ENSG00000176402 + - 7 7 99411623 99365260 coding coding AZGP1 GJC3 99402290 99358828 - - 0 99407305 99359162 - + N 0.739016906416787 4.5407124302546 N HCC1954 3 1.19047619047619 1 2 2 Y - - N - LTR 0 1 1 21 1.01412823870953 1.02126998686945 1.02126998686945 1.01412823870953 4 0 0 20354 N Y 3.41679307359967 3.50529022639353 3.41679307359967 1 0 0.579380014829102 N 0.833994708994709 0.81739417989418 N N 49089 4090 ENSG00000117450 ENSG00000112578 - - 1 6 45760196 42008762 utr5p intron PRDX1 BYSL 45749295 41996943 - + 0 45760088 41999047 + - Y - 0.834173037592588 N HCC1954 6 2 1 5 2 N - - N - SINE 0 1 1 17 0.842726282871298 0.335662163516534 0.842726282871298 0.335662163516534 2 - 0 37748 N N 2.62666928369017 3.03904526664885 2.62666928369017 0 0 0.0864984362473478 N 0.536382828993667 0 N N 0 4006 ENSG00000201027 ENSG00000090565 - - 14 16 89158304 512479 upstream utr3p 7SK RAB11FIP3 89158015 415669 + + 0 89140339 512029 - - Y - 1.81220154043646 N HCC1954 2 1.375 1 3 1 N - - N Simple_repeat - 1 0 1 8 0.321378667196682 0.464213630395207 0.464213630395207 0.321378667196682 1 - 0 23236 N N 3.3446273492087 3.41679307359967 3.3446273492087 0 0 0.0726804571449942 N 0.759652225169467 0.751068376068376 N N 0 49089 ENSG00000219955 ENSG00000117450 - - 10 1 22493241 45760196 upstream intron RP11-108B14.1 PRDX1 22492027 45749295 + - 0 22467047 45757314 - + Y - 3.42551017167268 N HCC1954 7 4.18181818181818 1 10 1 N - - N SINE - 1 0 1 11 0.278528178237124 0.599906845433805 0.599906845433805 0.278528178237124 0 - 0 13427 N Y 3.34458749641535 3.65913638023969 3.34458749641535 0 0.248813216026331 0.0972293897707274 N 0.608076460535477 0.608076460535477 N N 8393 0 ENSG00000164896 ENSG00000219956 - - 7 22 150408884 25613511 coding upstream FASTK RP1-40G4P.1 150404641 25612872 - - 0.608076460535477 150407940 25666035 + + Y - - N HCC1954 1 1 1 0 1 N - - N - SINE 0 0.974358974358974 0.974358974358974 4 0.357087407996313 0.278528178237124 0.357087407996313 0.278528178237124 1 - - 19353 N N 3.03806172861187 3.21696758886942 3.03806172861187 0 0.00431034482758585 0.251476712103813 N 0.159886853448276 0.128771551724138 N N 0 179175 ENSG00000212678 ENSG00000163191 - + 1 1 560165 150276135 intron utr3p RP5-857K21.11 S100A11 559619 150271606 + - 0.00431034482758585 559660 150271650 - - N 1 0.202855448381152 Y HCC1954 4 3.4 2 5 1 N - - N - - 0 0 0 5 0.264244681917271 0.521347615674617 0.521347615674617 0.264244681917271 2 0 0 36376 Y Y 3.5010341561346 3.60256518892881 3.5010341561346 222 0 0.10147792352544 Y 0.525954525954526 0.976297726297726 N N 19299 99057 ENSG00000089159 ENSG00000089157 + - 12 12 119187904 119123397 downstream upstream PXN RPLP0P2 119132637 119118893 - - 0 119128731 119123612 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.607048593593732 0.835584534711372 0.835584534711372 0.607048593593732 4 - - 41914 N N 2.96319769112561 3.38656252929588 2.96319769112561 2 0 0.967532435916895 N 0.0977757182576461 0 N N 29840 0 ENSG00000164830 ENSG00000212451 + + 8 8 107834093 127753081 utr5p downstream OXR1 U11 107739270 127752949 + + 0 107739589 128092359 + + N - - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - LINE 0 0.319148936170213 0.319148936170213 4 0.707033067832699 0.335662163516534 0.707033067832699 0.335662163516534 4 - - 4270 N Y 2.87846209505072 3.51377186168787 2.87846209505072 122 0 0.561979578479427 Y 0.77959927140255 0.981633272616879 N N 524 0 ENSG00000218609 ENSG00000201515 - - 7 7 65743252 65653116 upstream upstream KCTD7 5S_rRNA 65731380 65652992 + - 0.0265634486945961 65694761 65686853 - + N - - N HCC1954 20 3.625 1 7 5 N - - N - SINE 0 1 1 16 0.649899082553289 0.657040830713216 0.657040830713216 0.649899082553289 1 - - 3875 N N 2.54627399199396 3.47961192679575 2.54627399199396 0 0.0856605800214826 0.301146716862489 N 0.0856605800214826 0.0856605800214826 N N 850768 312 ENSG00000075624 ENSG00000046653 + - 7 X 5536758 13866758 utr3p intron ACTB GPM6B 5533313 13698983 - - 0.0856605800214826 5533797 13738789 - + Y 0.964319627074489 2.75769049304081 N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.558139534883721 0.558139534883721 7 0.51420586751469 0.307095170876829 0.51420586751469 0.307095170876829 2 0 0 20861 N N 1.29131830139072 3.32593360681895 1.29131830139072 4 0 0.0570575596398626 N 0.012909298729241 0 N N 767 50640 ENSG00000161267 ENSG00000175793 - + 3 1 198784591 27063534 utr3p intron BDH1 SFN 198721051 27062240 - + 0.012909298729241 198721941 27063483 + + Y - 1.81352195883919 N HCC1954 34 33.25 33 4 1 N - - N Simple_repeat - 0.972222222222222 0 0.972222222222222 4 0.257102933757345 0.364229156156239 0.364229156156239 0.257102933757345 2 - 0 26133 N N 3.44665289554288 3.5319270478477 3.44665289554288 0 0 0.0952656281592082 N 0 0 N N 15930 20747 ENSG00000102893 ENSG00000073605 - + 16 17 46291657 35328429 downstream intron PHKB GSDMB 46052739 35314374 + - 0 46430369 35327425 - - Y - 9.44764878355004 N HCC1954 36 13 3 5 1 N 277 24.701 N LTR LTR 1 0.950226244343891 1 5 0.271386430077198 0.749883556792257 0.749883556792257 0.271386430077198 1 - 0 3659 Y Y 3.29599923696223 3.41103992525442 3.29599923696223 281 0 0.0135547980098909 Y 0.00355871886121006 0 N N 21319 22838 ENSG00000184787 ENSG00000184900 - + 21 21 45046166 45062472 coding utr3p UBE2G2 SUMO3 45013384 45049960 - - 0 45032264 45051133 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.849868031031224 0.778450549431962 0.849868031031224 0.778450549431962 2 - - 45379 N Y 3.53143253430774 3.38333018123702 3.38333018123702 5 0.018096867596736 0.0794153835868553 N 0.018096867596736 0.786873738703167 N N 0 5961 ENSG00000220740 ENSG00000113456 + + 10 5 103835477 34954139 upstream utr3p RP11-302K17.3 RAD1 103835223 34938268 - - 0 103845619 34944620 - - Y - - N HCC1954 10 5.5 1 3 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.599906845433805 0.599906845433805 0.271386430077198 1 - - 36198 N N 3.35562978478943 3.31332388234167 3.31332388234167 0 0 0.979466303143301 N 0 0 Y N 11392 2251 ENSG00000175203 ENSG00000123297 + + 12 12 56227245 56476784 intron intron DCTN2 TSFM 56210361 56462826 - + 0 56215033 56465960 - + N 0.593459266099854 0.881451311801125 N HCC1954 3 1.02105263157895 1 1 3 N 463 0.0544881 N - DNA,DNA 0 1 1 95 1.26408942430695 1.54261760254407 1.54261760254407 1.26408942430695 2 0 0 30960 N N 3.45868840089349 3.59681204058356 3.45868840089349 0 0 0.413280652250757 N 0 0 N N 6539 9927 ENSG00000009413 ENSG00000114650 + - 6 3 111911125 47492449 coding intron REV3L SCAP 111726927 47430188 - - 0 111735942 47459725 - + Y - 2.86851798693008 N HCC1954 31 27.6 21 5 2 N - - N LINE - 1 0 1 5 0.714174815992626 0.535631111994469 0.714174815992626 0.535631111994469 3 - 0 36156 N Y 3.70040921291755 3.54975555433691 3.54975555433691 280 0.511185983827493 0.00799758821298324 N 0 0.924797843665768 N N 8806 9 ENSG00000137040 ENSG00000214776 + + 9 12 6005618 9598618 coding upstream RANBP6 AC006432.15-1 6001043 9563025 - + 0.924797843665768 6005415 9552302 - + Y 1.15409398735196 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.421363141435649 0.321378667196682 0.421363141435649 0.321378667196682 2 0 - 1147 N N 3.54872248456702 3.78105657260285 3.54872248456702 7 0 0.124615970073421 N 0 0 N N 0 153380 ENSG00000209665 ENSG00000185275 + + 11 Y 39745075 19614093 downstream utr3p AC021749.6-1 CD24L4 39745004 19611898 - - 0.0408836023789296 39561295 19612920 - - Y - - N HCC1954 5 3.5 2 10 1 N - - N SINE - 1 0 1 10 0.264244681917271 0.635615586233437 0.635615586233437 0.264244681917271 2 - - 13870 Y Y 3.38908332958227 3.56016600052522 3.38908332958227 0 0 0.336744889605378 Y 0 0.967211375212224 N N 956 0 ENSG00000128262 ENSG00000219862 - - 22 22 22991492 22975434 utr3p intron POM121L9P AP000354.4 22977589 22974042 + - 0 22984026 22975315 - + N - 1 N HCC1954 56 34 1 6 1 N - - Y - - 0 0 0 8 0.985561246069823 1.05697872766909 1.05697872766909 0.985561246069823 2 - 0 18250 Y Y 3.65488030998075 2.6748919784559 2.6748919784559 373 0 0.00206907886953656 Y 0 0.99307417336908 N N 500 528 ENSG00000164002 ENSG00000187815 - + 1 1 40754799 40734602 upstream intron DEM1 ZNF642 40747000 40715474 + + 0 40746763 40731930 - + N - 1.13200372611246 N HCC1954 1 1 1 0 2 N - - Y - LTR 0 0.852760736196319 0.852760736196319 9 0.928427260790413 0.928427260790413 0.928427260790413 0.928427260790413 1 - 0 43120 N N 3.12747721909902 2.79790802132126 2.79790802132126 0 0.252808988764045 0.062169176712256 N 0.377340823970038 0 N N 551733 0 ENSG00000204628 ENSG00000209247 + + 5 4 180603512 117438418 utr3p downstream GNB2L1 AC024248.7-1 180596536 117438348 - + 0 180596544 117519916 - + Y - - N HCC1954 21 10.5 2 10 1 N - - N - - 0 0 0 10 0.642757334393363 0.264244681917271 0.642757334393363 0.264244681917271 2 - - 18233 Y Y 2.67267154251321 3.37192651807217 2.67267154251321 0 0 0.9746430422066 Y 0 0.991835172545768 N N 0 2873 ENSG00000216933 ENSG00000127124 - - 1 1 42279987 42156965 upstream utr5p RP1-21K4.1 HIVEP3 42278855 41744623 + - 0 42274068 42156785 - + N - 6.15207717923113 N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.131782945736434 0 0.131782945736434 22 0.921285512630487 0.842726282871298 0.921285512630487 0.842726282871298 2 - 0 2783 N N 3.61360747730288 3.40169305405954 3.40169305405954 23 0 0.0567126256201834 N 0.0653068862275447 0 N N 3301 46806 ENSG00000070081 ENSG00000164733 - + 11 8 17309646 11763055 utr5p utr3p NUCB2 CTSB 17254860 11737442 + - 0 17260959 11737776 - - Y - - N HCC1954 37 29.7777777777778 24 9 1 N 567 23.8004 N - SINE 0 1 1 9 0.949852505270192 0.392796148795944 0.949852505270192 0.392796148795944 2 - - 39459 N Y 3.56807857436608 3.51782959285392 3.51782959285392 0 0 0.107487675284748 N 0 0.768654884634266 N N 11 75177 ENSG00000213471 ENSG00000125107 - + 15 16 88603303 57221251 intron utr5p TTLL13 CNOT1 88593766 57111359 + - 0 88594301 57190783 - - Y 0.639455782312925 - N HCC1954 20 20 20 20 1 N - - N SINE - 1 0 1 20 0.349945659836387 0.657040830713216 0.657040830713216 0.349945659836387 2 0 - 41717 Y Y 3.35719722089263 3.03379597941337 3.03379597941337 0 0 0.409000282888075 Y 0.980580933262321 0.987053955508214 N N 3661 30666 ENSG00000170873 ENSG00000147684 + + 8 8 125809911 125631407 intron coding MTSS1 NDUFB9 125632212 125620524 - + 0 125649069 125628535 - + N 0.815948353903233 - N HCC1954 2 1.36363636363636 1 4 1 N - - Y - - 0 0 0 11 1.18553019454776 1.33550690590621 1.33550690590621 1.18553019454776 4 0 - 24661 Y Y 3.48167806633553 3.67952553980864 3.48167806633553 382 0 0.00255418214713232 Y 0 0 N N 2054 314 ENSG00000154889 ENSG00000141404 + + 18 18 11898641 11872683 utr3p utr3p MPPE1 GNAL 11873470 11679563 - + 0.993481162098347 11873953 11872503 - + N - 0.35863546863291 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.0227272727272727 0.0227272727272727 5 0.799875793911741 0.842726282871298 0.842726282871298 0.799875793911741 2 - 0 21161 N N 3.4503745994685 3.34512186274866 3.34512186274866 2 0 0.0727834271620698 N 0.21329254727475 0.264599555061179 N N 6663 5782 ENSG00000163848 ENSG00000123836 + + 3 1 126576888 205320991 upstream utr3p ZNF148 PFKFB2 126427205 205293243 - + 0.264599555061179 126598916 205315546 - + Y - 4.08097043908831 N HCC1954 3 2.25 2 4 1 N - - N SINE - 1 0 1 4 0.264244681917271 0.307095170876829 0.307095170876829 0.264244681917271 2 - 0 31187 N Y 3.66336194527509 3.53768019619294 3.53768019619294 325 0 0.00494339997493132 Y 0 0.979230769230769 N N 397 7313 ENSG00000180432 ENSG00000181061 + - 3 3 42892661 42820986 upstream upstream CYP8B1 HIGD1D 42888688 42800797 - - 0 42903926 42825981 - + N - - N HCC1954 1 1 1 0 1 N - - N LINE LTR 0.839779005524862 1 1 40 1.25694767614702 0.742741808632331 1.25694767614702 0.742741808632331 3 - - 38277 N Y 3.69209541149257 3.39281019118108 3.39281019118108 246 0 0.134572057880175 Y 0 0.991769132567359 N N 3 0 ENSG00000211816 ENSG00000211812 - + 14 14 21810286 21741102 upstream upstream AE000661.1-1 AE000660.1-16 21809694 21740317 + + 0 21806502 21739118 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR - 1 0 1 5 0.557056356474248 0.857009779191151 0.857009779191151 0.557056356474248 2 - - 7425 Y Y 3.44785379918211 3.50425715662364 3.44785379918211 0 0 0.988859594586798 Y 0 0.993840847499384 N Y 120 38670 ENSG00000163009 ENSG00000171848 - + 2 2 10269307 10188996 utr5p coding C2orf48 RRM2 10198960 10179906 + + 0 10199432 10186732 - + N - - N HCC1954 2 1.55 1 22 2 N - - Y LINE,LINE - 0.410169491525424 0 0.410169491525424 40 1.49262536542459 1.19267194270768 1.49262536542459 1.19267194270768 4 - - 35941 N Y 3.43718223316862 3.39271690522525 3.39271690522525 0 0 0.367457818805265 N 0 0.860947935945924 N N 82 12 ENSG00000153303 ENSG00000205592 - + 6 12 168222706 39250827 utr5p downstream FRMD1 MUC19 168199333 39222629 - + 0 168209866 39372658 + + Y - - N HCC1954 31 28 25 4 1 N - - N SINE - 1 0 1 4 0.299953422716903 0.685607823352921 0.685607823352921 0.299953422716903 1 - - 16832 N Y 3.41679307359967 3.42953077915294 3.41679307359967 123 0 0.0410446634239314 N 0.849890201819513 0.849890201819513 N N 49089 47 ENSG00000117450 ENSG00000121101 - - 1 17 45760196 54124415 utr5p intron PRDX1 TEX14 45749295 53989041 - - 0 45759868 54058913 + + Y - 1.77656318320944 N HCC1954 10 2.04761904761905 1 54 1 N - - N - SINE 0 1 1 63 0.99270299422975 0.507064119354764 0.99270299422975 0.507064119354764 2 - 0 44622 N Y 3.58593758607883 3.40740634961144 3.40740634961144 0 0 0.766744732817532 N 0.955511083743842 0.982204433497537 N N 3849 104 ENSG00000138297 ENSG00000178440 + - 10 10 51293344 51403098 coding intron TIMM23 AL442003.8-2 51262096 51401190 - + 0 51276994 51402778 - - N 1.09466276080488 0.211032739669664 Y HCC1954 18 2.87272727272727 2 55 1 N - - N - - 0 0 0 55 0.849868031031224 1.31408166142643 1.31408166142643 0.849868031031224 4 0 0 6888 Y Y 3.45868840089349 3.353603498043 3.353603498043 309 0 0.0135127639639369 Y 0.766276085258342 0.993125767213481 N N 24774 2480 ENSG00000197756 ENSG00000138375 - + 2 2 217074428 217056021 upstream downstream RPL37A SMARCAL1 217071765 216985441 + + 0 217071577 217061213 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.155688622754491 0.155688622754491 10 0.907002016310634 1.12125446110842 1.12125446110842 0.907002016310634 3 - - 38528 Y Y 3.43465208531242 3.62192127872787 3.43465208531242 233 0 0.774946267800387 Y 0 0.990141503420728 N N 2447 4331 ENSG00000157379 ENSG00000100949 + - 14 14 23838770 23810643 coding utr5p DHRS1 RABGGTA 23829646 23804661 - - 0 23831242 23810354 - + N - 3.80639939049814 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 41 1.1141127129485 0.621332089913584 1.1141127129485 0.621332089913584 3 - 0 7383 Y Y 3.30484224704734 3.15571617177654 3.15571617177654 103 0.0226720647773279 0.0425542974805725 Y 0.0514170040485831 0.990418353576248 N N 184 1959 ENSG00000171174 ENSG00000163797 + + 2 2 27966727 27856112 intron coding RBKS MRPL33 27857770 27848088 - + 0 27858968 27855893 - + N 0.504608216974027 - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 9 0.93556900895034 0.664182578873142 0.93556900895034 0.664182578873142 2 0 - 16028 N Y 3.67952553980864 3.65488030998075 3.65488030998075 0 0.476850832783036 0.107502948238983 N 0.864993763298848 0.864993763298848 N N 25286 17 ENSG00000130429 ENSG00000172018 - + 7 1 98830338 155336224 utr5p downstream ARPC1B ETV3L 98810265 155328460 + - 0 98810339 155322786 - - Y - - N HCC1954 8 2.4 1 1 1 N - - N - SINE 0 1 1 5 0.607048593593732 0.299953422716903 0.607048593593732 0.299953422716903 1 - - 1319 N Y 3.47233119514066 3.4555052531978 3.4555052531978 3 0 0.110635944660510 N 0 0.914349276974416 N N 20739 9385 ENSG00000143951 ENSG00000129084 - + 2 11 63669355 14589108 utr3p intron C2orf86 PSMA1 63202041 14482999 - - 0.880088987764182 63309485 14575589 + - Y - 438.315757575758 N HCC1954 620 540 420 5 1 N - - N LINE LINE 1 1 1 5 0.357087407996313 0.299953422716903 0.357087407996313 0.299953422716903 4 - 0 44159 N Y 3.75488375946511 3.42680229220385 3.42680229220385 244 0.739168618266979 0.0106038136888600 N 0.739168618266979 0.739168618266979 N N 0 0 ENSG00000216946 ENSG00000201398 + + 10 3 29228419 155207981 intron upstream RP11-492M23.2 U8 29227931 155207846 - - 0.834016393442623 29228309 155224425 - - Y 1 - N HCC1954 42 41.1515151515151 36 33 1 N - - N - - 0 0 0 33 0.442788385915428 0.271386430077198 0.442788385915428 0.271386430077198 1 0 - 39845 Y Y 3.37655331069169 3.53039946453785 3.37655331069169 293 0 0.0394066436380842 Y 0.728869704878538 0.992672154185906 N N 0 4659 ENSG00000186690 ENSG00000173517 - - 15 15 75358134 75331928 downstream utr5p AC060773.10 AC107883.6 75357862 75187526 + - 0 75364358 75331926 - + N - 18.402118235134 N HCC1954 20 5.75 1 2 2 N - - Y SINE - 0.870748299319728 0 0.870748299319728 8 0.87843502367093 0.821301038391519 0.87843502367093 0.821301038391519 1 - 0 38416 Y Y 3.65657572715995 2.86700923152271 2.86700923152271 0 0 0.200685342370004 Y 0 0.994489950083688 N N 12363 5217 ENSG00000129559 ENSG00000100938 - - 14 14 23771412 23778285 utr5p intron NEDD8 GMPR2 23755897 23771488 - + 0 23771370 23772042 + - N - 0.349195705112127 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.592765097273879 0.678466075192994 0.678466075192994 0.592765097273879 1 - 0 10266 Y Y 3.55128313764676 3.6508225788147 3.55128313764676 0 0.0117368810051738 0.788213318055135 Y 0.0198373983739838 0.99189948263119 N N 31173 5003 ENSG00000132475 ENSG00000132478 - - 17 17 71287455 71333474 utr5p intron H3F3B UNK 71284112 71292532 - + 0 71287333 71293053 + - N - 1.2255062381494 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.814159290231593 0.642757334393363 0.814159290231593 0.642757334393363 2 - 0 42156 Y N 3.65488030998075 3.65254730560554 3.65254730560554 0 0 0.512256870518601 Y 0 0.382440476190476 N N 0 6139 ENSG00000213466 ENSG00000164056 - + 4 4 125203592 124544357 upstream downstream AC108075.3 SPRY1 125203103 124537406 + + 0.382440476190476 124969745 124849196 - + N - - N HCC1954 2 1.11111111111111 1 1 2 N - - Y - LINE 0 1 1 9 0.557056356474248 0.757025304952183 0.757025304952183 0.557056356474248 2 - - 27298 N N 3.66488952858494 3.22543357218168 3.22543357218168 0 0 0.957830293659344 Y 0 0 N N 69736 15881 ENSG00000181019 ENSG00000102908 + + 16 16 68318034 68296054 coding coding NQO1 NFAT5 68300808 68156498 - + 0 68306371 68284178 - + N - 1.35728074890337 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 8 0.778450549431962 0.578481600954027 0.778450549431962 0.578481600954027 1 - 0 14939 N N 3.61360747730288 3.41848849077886 3.41848849077886 0 0 0.047605263376661 N 0 0.0809209412561368 N N 49089 101048 ENSG00000117450 ENSG00000127954 - - 1 7 45760196 87774145 coding downstream PRDX1 STEAP4 45749295 87743687 - - 0.0809209412561368 45757256 87731881 + + Y - - N HCC1954 40 19.6521739130435 3 23 1 N - - N - SINE 0 1 1 23 0.792734045751814 0.335662163516534 0.792734045751814 0.335662163516534 1 - - 17714 N N 3.6272104187567 3.63552422018169 3.6272104187567 0 0 0.0336624583364665 N 0.730597680642284 0 N N 14411 3863 ENSG00000162521 ENSG00000219481 + + 1 1 32918845 146862781 intron upstream RBBP4 NBPF15 32889411 146827614 + + 0 32892527 146823370 + + N 1.22075032309497 - Y HCC1954 12 6.23809523809524 3 21 1 N - - N SINE - 1 0 1 21 0.392796148795944 0.864151527351077 0.864151527351077 0.392796148795944 2 0 - 40725 N Y 3.57332786160156 3.73080759109069 3.57332786160156 13 0.0717133536995807 0.0619353012228121 N 0.720395588463729 0.843421529539688 N N 4601 0 ENSG00000078699 ENSG00000182707 - + 20 X 31701503 73013524 utr3p downstream CBFA2T2 FXYD8 31541584 73011598 + + 0.0717133536995807 31697518 73081224 - + Y - - N HCC1954 29 29 29 4 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.499922371194838 0.499922371194838 0.271386430077198 2 - - 38378 Y Y 3.4033579660152 3.52105259334297 3.4033579660152 144 0 0.965244755294423 Y 0.11936378228513 0.987049467386546 N Y 333 438 ENSG00000181619 ENSG00000126790 - + 14 14 59001813 59020826 utr3p coding GPR135 C14orf149 58965493 59009159 - - 0 58997644 59012340 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 21 1.39978263934555 1.13553795742827 1.39978263934555 1.13553795742827 4 - - 38063 Y N 3.25103939547889 3.37916739693392 3.25103939547889 0 0 0.928743190237754 Y 0.75517890772128 0 N N 0 10336 ENSG00000221236 ENSG00000133961 - - 14 14 72985644 72892230 downstream upstream AC005280.3 NUMB 72985548 72811671 + - 0 72994926 72892231 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 35 0.721316564152552 1.03555348318931 1.03555348318931 0.721316564152552 2 - - 20334 N Y 3.66488952858494 3.31422897103557 3.31422897103557 0 0 0.0757051829604798 N 0 0 N N 10369 45068 ENSG00000117525 ENSG00000205336 - + 1 16 94779903 56256445 utr3p upstream F3 GPR56 94767461 56220023 - + 0 94768125 56211711 + + Y - - N HCC1954 7 5 3 6 1 N - - N SINE - 1 0 1 6 0.28566992639705 0.564198104634174 0.564198104634174 0.28566992639705 2 - - 41969 N N 3.34615493251855 3.39483647792751 3.34615493251855 0 0 0.0603541392859713 N 0 0.00338983050847474 N N 0 8783 ENSG00000209276 ENSG00000147697 + + X 8 95552437 130868316 downstream intron AL391865.9-2 GSDMC 95552205 130829625 - - 0.00338983050847474 95547863 130844053 - - Y - 0.654695145605657 N HCC1954 2 1.66666666666667 1 4 1 N - - N LTR - 1 0 1 6 0.371370904316165 0.5713398527941 0.5713398527941 0.371370904316165 1 - 0 39968 Y Y 3.34615493251855 3.23168330567983 3.23168330567983 354 0 0.634970454924186 Y 0 0.978322279538197 N N 1136 38799 ENSG00000104147 ENSG00000187446 + + 15 15 39412111 39361377 downstream downstream OIP5 AC012652.1 39388762 39310729 - + 0 39388057 39365590 - + N - - N HCC1954 40 11.5 2 4 4 N - - Y SINE - 1 0 1 4 0.499922371194838 0.528489363834543 0.528489363834543 0.499922371194838 4 - - 31225 Y Y 3.42783536197374 3.33267997214073 3.33267997214073 229 0 0.413271147544289 Y 0.315502183406114 0.987554585152838 N N 3882 5040 ENSG00000120756 ENSG00000175054 - - 3 3 143915191 143780358 intron upstream PLS1 ATR 143825034 143650770 + - 0 143846826 143797982 - + N 0.0233330598934899 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 1.05697872766909 0.757025304952183 1.05697872766909 0.757025304952183 2 0 - 19580 N Y 3.13180783727146 3.59887818012334 3.13180783727146 6 0 0.0693385978475463 N 0 0.859381595609962 N N 0 323 ENSG00000141650 ENSG00000183347 - + 18 1 53657194 89626307 upstream utr3p AC022724.8-1 GBP6 53656706 89602024 + + 0 53621260 89626050 - + Y - - N HCC1954 27 22.7142857142857 20 7 1 N - - N Low_complexity SINE 0.30327868852459 1 1 7 0.871293275511003 0.392796148795944 0.871293275511003 0.392796148795944 1 - - 34067 N Y 3.50997045217554 2.81507241011594 2.81507241011594 0 0 0.0707838085469836 N 0 0 N N 45208 0 ENSG00000119335 ENSG00000213526 + + 9 X 130498488 115981675 coding intron SET AL732604.5 130485996 115980035 + + 0 130495852 115981452 + + Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.478497126715059 0.242819437437493 0.478497126715059 0.242819437437493 1 - 0 48060 N N 3.43640385738336 3.28189243439864 3.28189243439864 0 0 0.119268811748349 N 0 0 N N 19339 0 ENSG00000177570 ENSG00000215233 - - 8 5 119703365 2841646 upstream upstream SAMD12 AC116359.2 119270880 2840558 - - 0.404511278195489 119845724 3244883 + + Y - - N HCC1954 1 1 1 0 1 N 287 4.21238 N LTR - 1 0 1 4 0.664182578873142 0.657040830713216 0.664182578873142 0.657040830713216 2 - - 22013 N N 3.31961139702023 3.55128313764676 3.31961139702023 11 0 0.329302830304479 N 0 0 N N 0 0 ENSG00000213224 ENSG00000213379 + + 1 14 147691578 76422846 intron intron AL109948.9-1 AF111169.2-1 147691189 76422500 - - 0.0885122410546141 147691303 76422599 - - Y 1 1 N HCC1954 27 15.4285714285714 9 7 1 N - - N - - 0 0 0 7 0.271386430077198 0.414221393275723 0.414221393275723 0.271386430077198 2 0 0 9612 Y Y 3.16567195721824 3.16038281718941 3.16038281718941 288 0 0.0254515484078039 Y 0 0.991258528265107 N N 520 14964 ENSG00000108352 ENSG00000108349 - + 17 17 35605426 35581957 upstream coding RAPGEFL1 CASC3 35588133 35550033 + + 0 35586704 35579223 - + N - 2.14053916935311 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 1.04983697950916 0.885576771830856 1.04983697950916 0.885576771830856 2 - 0 36194 Y Y 3.12907935032238 3.49953707804829 3.12907935032238 144 0 0.0114630217511108 Y 0.851041666666667 0.983449074074074 N N 1303 1864 ENSG00000185480 ENSG00000075188 - - 12 12 101119401 101036491 upstream coding C12orf48 NUP37 101038086 100992105 + - 0.983449074074074 101037988 101036401 - + N - 3.6028172904295 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 79 0.707033067832699 1.24266417982717 1.24266417982717 0.707033067832699 2 - 0 32428 N Y 3.62295434849776 3.4439989565073 3.4439989565073 0 0 0.375567278253116 N 0 0 N N 0 0 ENSG00000174944 ENSG00000222231 + - 3 8 152478920 77340522 intron upstream P2RY14 U2 152412595 77340333 - - 0.941411764705882 152442586 77381259 - + Y 1 - N HCC1954 21 20.5 20 6 1 N - - N LINE LTR,LTR 1 1 1 6 0.599906845433805 0.835584534711372 0.835584534711372 0.599906845433805 2 0 - 43278 N N 3.27870928670295 3.40169305405954 3.27870928670295 0 0 0.0591730388024518 N 0.300382102797978 0.251571551830396 N N 19481 6450 ENSG00000198074 ENSG00000185009 - + 7 10 133876693 75580832 downstream utr3p AKR1B10 AP3M1 133862884 75550022 + - 0.251571551830396 133900932 75550361 - - Y - - N HCC1954 36 33.75 31 4 1 N - - N - SINE 0 1 1 4 0.657040830713216 0.357087407996313 0.657040830713216 0.357087407996313 2 - - 9366 N N 3.14949901511487 3.4106386976703 3.14949901511487 2 0 0.933754904531274 Y 0 0 N N 3927 0 ENSG00000176155 ENSG00000211264 + + 17 17 77763978 67836854 coding downstream CCDC57 AC005243.1 77652635 67836654 - + 0 77752773 67912542 - + N 0.734829239828462 - N HCC1954 1 1 1 0 4 N 449 0.607786 N - - 0 0 0 6 0.621332089913584 0.45707188223528 0.621332089913584 0.45707188223528 1 0 - 46691 N Y 3.57800808738356 3.39227582484777 3.39227582484777 0 0 0.471380591974051 N 0 0 N N 17943 2197 ENSG00000105141 ENSG00000184178 + - 19 4 15027900 53926865 downstream intron CASP14 SCFD2 15024015 53433910 + - 0.710273466371027 15029502 53848992 + + Y - 0.58425930674745 N HCC1954 20 7.28947368421053 2 38 1 N - - N - SINE,LINE 0 0.86046511627907 0.86046511627907 38 0.807017542071667 0.307095170876829 0.807017542071667 0.307095170876829 3 - 0 45619 N N 3.63296356710195 1.90451039276595 1.90451039276595 23 0.347490888701991 0.161206764244455 N 0.450518643117465 0.416176058312307 N N 12272 0 ENSG00000105355 ENSG00000220898 + + 19 X 4818676 43023851 utr3p downstream M6PRBP1 RP11-315O19.1 4789346 43022318 - - 0.416176058312307 4789611 42919439 - - Y 0.708285818929947 - N HCC1954 18 15.25 13 4 1 N - - N SINE SINE,LTR 1 0.894736842105263 1 4 0.385654400636018 0.271386430077198 0.385654400636018 0.271386430077198 2 0 - 29233 Y Y 3.38809011260573 3.79143651356762 3.38809011260573 0 0 0.107177171431431 Y 0 0 N N 0 0 ENSG00000201523 ENSG00000218643 - + 6 6 19546601 19457273 downstream downstream 5S_rRNA RP11-686D16.2 19546493 19456391 + + 0 19571390 19471034 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 5 0.828442786551446 0.664182578873142 0.828442786551446 0.664182578873142 2 - - 31157 Y Y 3.47076375903745 3.59272380419397 3.47076375903745 164 0 0.355035033684057 Y 0 0.986195799457995 N N 46 46598 ENSG00000214217 ENSG00000118849 - - 3 3 159943998 159932969 upstream upstream AC080013.17 RARRES1 159940900 159897597 + - 0 159940874 159933437 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE - 0.82089552238806 0 0.82089552238806 5 0.478497126715059 0.749883556792257 0.749883556792257 0.478497126715059 2 - - 35058 N N 3.47336426491055 3.5727053669856 3.47336426491055 25 0.175672006516427 0.29370618975424 N 0.261539505837632 0.00393700787401563 N N 43374 0 ENSG00000130707 ENSG00000213738 + + 9 9 132366482 79984248 coding upstream ASS1 AL353705.23-2 132309915 79983952 + + 0.0554575074667393 132342092 79983636 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.364229156156239 0.235677689277566 0.364229156156239 0.235677689277566 2 - - 4734 Y Y 3.93849644929864 3.39909254818645 3.39909254818645 0 0 0.998486903746426 Y 0.981069506556507 0.987379671037671 N Y 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding coding CRCP ASL 65216341 65178207 + + 0 65230126 65195085 - + N - - N HCC1954 2 1.77777777777778 1 7 6 N - - Y - - 0 0 0 9 0.892718519990782 1.02126998686945 1.02126998686945 0.892718519990782 4 - - 46951 Y Y 3.15741158895574 3.43681151080804 3.15741158895574 288 0 0.0108058369486050 N 0 0.930474806201551 Y N 4590 1053 ENSG00000213015 ENSG00000171425 - + 19 19 60846647 60848800 intron upstream ZNF580 ZNF581 60844204 60846798 + + 0 60845551 60838221 - + N 0.420513125597042 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.471355378555133 0.535631111994469 0.535631111994469 0.471355378555133 1 0 - 42376 N Y 3.65913638023969 3.44296588673741 3.44296588673741 94 0 0.032644818085557 Y 0.0331237911025144 0.977514506769826 N N 7107 2425 ENSG00000109320 ENSG00000138821 - - 4 4 103757506 103485654 upstream upstream NFKB1 SLC39A8 103641518 103401844 + - 0 103570634 103559071 - + N - - N HCC1954 1 1 1 0 1 N - - N - LTR 0 1 1 5 0.771308801272036 0.649899082553289 0.771308801272036 0.649899082553289 1 - - 34351 Y Y 3.30128837699106 3.52361324642271 3.30128837699106 295 0 0.0499379517200926 Y 0.992981618524708 0.985963237049415 N N 18207 213 ENSG00000183354 ENSG00000120215 + + 9 9 5998003 5899822 coding downstream KIAA2026 MLANA 5909008 5880908 - + 0 5910544 5904062 - + N 0.725151987430437 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.914143764470561 0.99270299422975 0.99270299422975 0.914143764470561 4 0 - 8461 N Y 3.5482584762506 3.39653189510671 3.39653189510671 0 0 0.146101444254167 N 0 0.911388023537556 N N 2789 0 ENSG00000176208 ENSG00000209951 - + 17 7 26246421 86960 intron upstream ATAD5 AC097646.2-1 26183146 86858 + - 0 26242870 126062 - - Y 1.35584077394254 - N HCC1954 144 110 80 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.328520415356608 0.328520415356608 0.321378667196682 3 0 - 31823 Y Y 3.23999710710482 3.41782614336956 3.23999710710482 0 0 0.460008690574381 Y 0.992451891174519 0.992451891174519 N N 892 8 ENSG00000160145 ENSG00000065371 - - 3 3 125922726 125193674 coding upstream KALRN ROPN1 125296275 125170571 + - 0 125296440 125235348 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.907002016310634 0.742741808632331 0.907002016310634 0.742741808632331 1 - - 6075 N Y 3.64656650855576 3.35041100277749 3.35041100277749 1 0 0.597086859012374 N 0 0.907779265208984 N N 0 9904 ENSG00000183846 ENSG00000065883 + + 2 7 110575338 40101668 upstream intron AC112229.4-1 CDC2L5 110574935 39956484 - + 0 110576432 39970197 - + Y - 0.439996293843508 N HCC1954 40 40 40 5 1 N - - N - LINE 0 1 1 5 0.757025304952183 0.407079645115797 0.757025304952183 0.407079645115797 1 - 0 21452 N N 2.81029132109351 3.61633596425197 2.81029132109351 18 0 0.429949591871343 N 0 0 N N 29655 34471 ENSG00000136938 ENSG00000116251 - + 9 1 99818046 6182266 coding coding ANP32B RPL22 99785310 6167668 + - 0 99813381 6169341 - - Y - - N HCC1954 2 2 2 5 1 N - - N Low_complexity,Low_complexity,Low_complexity - 0.548223350253807 0 0.548223350253807 5 0.928427260790413 0.821301038391519 0.928427260790413 0.821301038391519 1 - - 48076 N N 3.62824348852659 3.77104735399867 3.62824348852659 0 0 0.999455958521174 N 0.00398406374502003 0 N N 12549 0 ENSG00000087206 ENSG00000212451 + + 5 8 176366358 127753081 coding downstream UIMC1 U11 176264612 127752949 - + 0 176302942 128114777 - + Y - - N HCC1954 1 1 1 0 5 N 573 7.11156 N - LINE 0 1 1 7 0.942710757110266 0.607048593593732 0.942710757110266 0.607048593593732 4 - - 42475 Y Y 3.66385645881505 3.55657227767559 3.55657227767559 0 0.00256410256410278 0.471211747614579 Y 0.0392795343715588 0.993880761365424 N N 735 2970 ENSG00000198515 ENSG00000163293 - - 4 4 47678276 47736947 utr5p upstream CNGA1 NPAL1 47632753 47713548 - + 0 47678273 47713256 + - N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.00436681222707424 0 0.00436681222707424 22 1.60689333598341 1.12839620926835 1.60689333598341 1.12839620926835 1 - - 26019 N Y 3.68680627146374 3.48809356209009 3.48809356209009 0 0 0.079442482460131 N 0 0 N N 1814 45068 ENSG00000163235 ENSG00000205336 + + 2 16 70634613 56256445 intron upstream TGFA GPR56 70527924 56220023 - + 0 70583081 56211646 - + Y 1.95448657810807 - N HCC1954 24 20.1111111111111 4 9 1 N - - N SINE - 1 0 1 9 0.385654400636018 0.599906845433805 0.599906845433805 0.385654400636018 1 0 - 42703 N N 3.12755176701253 3.42633828388743 3.12755176701253 2 0 0.0269345046963703 N 0.530330062444246 0.530330062444246 N N 9 470 ENSG00000132437 ENSG00000186212 + - 7 4 50596262 78038026 intron upstream DDC ANKRD56 50493630 78035645 - - 0 50494242 78038515 - + Y 0.922054173745649 - N HCC1954 20 20 20 6 1 N - - N Other - 1 0 1 6 0.34280391167646 0.635615586233437 0.635615586233437 0.34280391167646 1 0 - 31593 Y N 3.36145329115156 3.51104337473878 3.36145329115156 18 0 0.188421666386378 Y 0 0 N N 2911 701 ENSG00000163608 ENSG00000163607 + + 3 3 114221245 114202910 intron coding C3orf17 GTPBP8 114203981 114192490 - + 0 114215983 114202413 - + N 0.650936113741235 - N HCC1954 20 9.4 2 5 1 N - - Y SINE - 1 0 1 5 0.614190341753658 0.735600060472404 0.735600060472404 0.614190341753658 3 0 - 34371 Y Y 3.48077297764164 3.47332441211719 3.47332441211719 262 0 0.0139754302309869 Y 0.988806930268462 0.988806930268462 N N 2696 0 ENSG00000198642 ENSG00000220319 + + 9 9 21325379 21311826 utr3p downstream KLHL9 RP11-380P16.7 21319670 21311299 - + 0 21322907 21314322 - + N 0.359178718043935 - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 5 0.642757334393363 0.564198104634174 0.642757334393363 0.564198104634174 1 0 - 21927 N N 3.61360747730288 3.5816815158199 3.5816815158199 2 0 0.0634830530992245 N 0 0.740216830149716 N N 49089 15151 ENSG00000117450 ENSG00000082805 - - 1 12 45760196 1475360 coding intron PRDX1 ERC1 45749295 970665 - + 0 45757256 1176482 + - Y - 1.37696852269984 N HCC1954 21 16 7 4 1 N - - N - SINE 0 1 1 4 0.371370904316165 0.299953422716903 0.371370904316165 0.299953422716903 1 - 0 36389 Y Y 3.51633251476761 3.32163768376666 3.32163768376666 250 0 0.0144786924933775 Y 0 0.99183606557377 N N 8690 361 ENSG00000075856 ENSG00000198855 + + 12 12 107479295 107437510 coding coding SART3 FICD 107440122 107433181 - + 0 107443498 107435141 - + N 0.314192092056146 0.644383466050845 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.0538461538461538 0 0.0538461538461538 6 0.928427260790413 0.928427260790413 0.928427260790413 0.928427260790413 2 0 0 42440 Y Y 3.17142510556349 3.4446613039166 3.17142510556349 107 0 0.381997750395099 Y 0.991338854382333 0.991338854382333 N N 7896 12251 ENSG00000134852 ENSG00000134851 + + 4 4 56107754 55987095 intron coding CLOCK TMEM165 55993417 55956877 - + 0 56013162 55985566 - + N 1.38384862198753 - N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 8 0.657040830713216 0.542772860154395 0.657040830713216 0.542772860154395 1 0 - 21934 N Y 3.61360747730288 3.18615440274303 3.18615440274303 5 0 0.0613787392024172 N 0 0.788418445571412 N N 49089 3360 ENSG00000117450 ENSG00000090975 - - 1 12 45760196 122160928 coding intron PRDX1 PITPNM2 45749295 122033980 - - 0.218775799032905 45757256 122090573 + + Y - 3.19278199559692 N HCC1954 5 4.33333333333333 3 6 1 N - - N - SINE 0 1 1 6 0.392796148795944 0.257102933757345 0.392796148795944 0.257102933757345 1 - 0 24433 N N 3.63465898428114 3.68979027085925 3.63465898428114 0 0.43936170212766 0.100907985147593 N 0.406382978723404 0.43936170212766 N N 7 0 ENSG00000144847 ENSG00000215401 + - 3 18 120347588 1353874 utr5p upstream IGSF11 AP005119.2 120102173 1352441 - - 0.406382978723404 120314244 1503948 - + Y - - N HCC1954 23 21.6666666666667 21 6 2 N - - N LINE LTR 1 1 1 6 0.357087407996313 0.5713398527941 0.5713398527941 0.357087407996313 1 - - 39712 N Y 3.55390190756407 3.66592259835483 3.55390190756407 0 0 0.353449430217993 N 0.106197446278418 0.744627841793833 N N 0 269689 ENSG00000217558 ENSG00000067225 - + X 15 65635991 70310738 intron coding RP11-133K18.1 PKM2 65634315 70278424 + - 0.284957957022735 65635713 70281861 - - Y 1 - N HCC1954 1 1 1 0 1 N 596 26.6786 N - - 0 0 0 4 0.271386430077198 0.34280391167646 0.34280391167646 0.271386430077198 1 0 - 8641 N Y 3.60103760561896 3.82911562339586 3.60103760561896 1 0 0.679605166739815 N 0.857712009106432 0.766241157817709 N N 7731 0 ENSG00000167741 ENSG00000177418 - - 17 7 4410625 65659784 utr3p downstream GGT6 AC006001.2-1 4406978 65659267 - - 0 4407500 65657259 + + Y - - N HCC1954 22 21 20 4 1 N - - N SINE - 1 0 1 4 0.307095170876829 0.585623349113953 0.585623349113953 0.307095170876829 4 - - 31722 Y Y 3.70210463009675 3.70360170818306 3.70210463009675 0 0 0.457418070422766 Y 0.99155918698089 0.99155918698089 N N 18920 4 ENSG00000082781 ENSG00000173702 - + 3 3 126088834 126136270 coding downstream ITGB5 MUC13 125964488 126106979 - - 0 126075066 126102801 + - N - - N HCC1954 21 11.0769230769231 1 20 1 N - - Y - SINE 0 1 1 26 0.921285512630487 0.649899082553289 0.921285512630487 0.649899082553289 2 - - 13855 Y Y 3.65591337975064 3.48593413659447 3.48593413659447 0 0 0.812902348643143 Y 0 0 N N 0 94 ENSG00000198986 ENSG00000197182 - + 22 22 44887366 44884554 upstream coding hsa-let-7a-3 RP4-695O20__B.10 44887293 44828413 + + 0 44887238 44884452 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.09268746846872 1.02841173502938 1.09268746846872 1.02841173502938 4 - - 562 N Y 3.70210463009675 3.24103017687471 3.24103017687471 0 0.00910130718954238 0.999811612360475 Y 0.00910130718954238 0.986699346405229 N N 9074 0 ENSG00000166444 ENSG00000202276 - + 11 11 8817478 8855641 utr5p downstream ST5 Y_RNA 8671478 8855540 - - 0 8789458 8848958 + - N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 18 1.46405837278488 1.04269523134923 1.46405837278488 1.04269523134923 4 - - 35657 N N 3.41175185377493 3.60103760561896 3.41175185377493 2 0 0.236652387005796 N 0.181994047619048 0 N N 2726 23800 ENSG00000177663 ENSG00000067182 + + 22 12 15971387 6321522 utr3p coding IL17RA TNFRSF1A 15945849 6308185 + - 0 15971294 6310286 + - Y - - N HCC1954 21 21 21 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.521347615674617 0.521347615674617 0.328520415356608 2 - - 34436 Y Y 3.35823029066252 3.55976477294109 3.35823029066252 418 0 0.00447519435427712 Y 0 0 N N 0 29655 ENSG00000212521 ENSG00000136938 - + 9 9 99834438 99818046 upstream downstream U6 ANP32B 99834333 99785310 + + 0 99828481 99820590 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,SINE - 1 0 1 5 1.06412047582901 1.04269523134923 1.06412047582901 1.04269523134923 3 - - 26941 N Y 3.55550870268216 3.53465553479678 3.53465553479678 212 0.0302370585389452 0.803294526029117 Y 0.0302370585389452 0.987239961296565 N N 69736 15881 ENSG00000181019 ENSG00000102908 + + 16 16 68318034 68296054 coding coding NQO1 NFAT5 68300808 68156498 - + 0 68302537 68284256 - + N 0.280010811649238 - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 6 0.93556900895034 0.778450549431962 0.93556900895034 0.778450549431962 1 0 - 41492 Y Y 3.49744043328497 3.46973068926756 3.46973068926756 274 0 0.279531549264504 Y 0.990419708029197 0.980839416058394 N N 3478 5969 ENSG00000205268 ENSG00000066855 + + 8 8 66916853 66785339 coding coding PDE7A MTFR1 66793537 66719528 - + 0 66794169 66782800 - + N 2.27135902182758 3.03539807888833 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 22 0.764167053112109 1.05697872766909 1.05697872766909 0.764167053112109 4 0 0 18228 Y Y 3.6035982586987 3.47336426491055 3.47336426491055 326 0 0.00305953737256326 Y 0 0.993218146154167 N N 19965 7703 ENSG00000143398 ENSG00000163159 - - 1 1 149488629 149429290 upstream coding PIP5K1A VPS72 149437652 149415562 + - 0 149434022 149425049 - + N - 0.8026570312325 N HCC1954 20 6.61538461538461 1 7 1 N - - Y SINE - 1 0 1 13 0.921285512630487 0.971277749749971 0.971277749749971 0.921285512630487 1 - 0 30676 N N 3.11232376639641 3.73403059157974 3.11232376639641 0 0 0.489895479375462 N 0.741694177814247 0 N Y 8617 190 ENSG00000221867 ENSG00000184750 - + X X 151621480 151673020 utr5p utr5p MAGEA6 MAGEA2 151617901 151669043 + - 0 151619902 151670689 - - N - - Y HCC1954 6 4.66666666666667 4 12 1 Y - - N - - 0 0 0 12 0.528489363834543 0.364229156156239 0.528489363834543 0.364229156156239 4 - - 48058 N N 3.50421730383029 3.36447795254773 3.36447795254773 0 0.00338983050847452 0.244902880698656 N 0.364797913950456 0.00338983050847452 N N 21549 29840 ENSG00000063438 ENSG00000164830 - - 5 8 491392 107834093 coding upstream PDCD6 OXR1 324736 107739270 + + 0 325827 107604124 - - Y - - N HCC1954 1 1 1 0 1 N 263 18.0934 N - SINE 0 0.857142857142857 0.857142857142857 5 1.06412047582901 0.649899082553289 1.06412047582901 0.649899082553289 1 - - 38390 Y Y 3.62192127872787 3.22948402739086 3.22948402739086 268 0 0.0784545936450887 Y 0.947564807541241 0.989512961508248 N N 4331 2447 ENSG00000100949 ENSG00000157379 - + 14 14 23810643 23838770 utr5p intron RABGGTA DHRS1 23804661 23829646 - - 0 23810354 23837658 + - N - 1.7936746240795 N HCC1954 6 1.07692307692308 1 2 3 N - - Y - SINE,DNA 0 0.685483870967742 0.685483870967742 104 0.757025304952183 0.885576771830856 0.885576771830856 0.757025304952183 3 - 0 23469 N Y 3.45976132345673 3.27192306858781 3.27192306858781 2 0 0.444019534769029 N 0.674444802059865 0.904248471194078 N N 2 32027 ENSG00000219073 ENSG00000064666 - - 1 19 22188432 990060 intron coding ELA3B CNN2 22175999 977298 + + 0 22186581 988625 - - Y 1.17012858555885 1.1204043270164 N HCC1954 5 3 2 4 1 N 193 18.2211 N srpRNA - 0.978260869565217 0 0.978260869565217 4 0.328520415356608 0.628473838073511 0.628473838073511 0.328520415356608 1 0 0 4598 Y Y 3.61207989399303 3.52105259334297 3.52105259334297 99 0 0.82050464460503 Y 0 0.877196420406297 N N 8965 4751 ENSG00000127359 ENSG00000006530 + + 7 7 141048422 141000678 coding coding KIAA1147 AGK 141002997 140901712 - + 0 141010441 140999152 - + N 0.684330387626116 - N HCC1954 2 1.25 1 1 2 N - - Y - - 0 0 0 4 0.507064119354764 0.45707188223528 0.507064119354764 0.45707188223528 4 0 - 28166 N Y 3.64809409186561 3.50744965188915 3.50744965188915 0 0 0.101725047210952 N 0 0 N N 12076 45068 ENSG00000148219 ENSG00000205336 - + 9 16 119217138 56256445 intron upstream ASTN2 GPR56 118227328 56220023 - + 0 118540516 56211648 + + Y 177.982040362896 - N HCC1954 21 21 21 11 1 N - - N SINE - 1 0 1 11 0.321378667196682 0.442788385915428 0.442788385915428 0.321378667196682 2 0 - 41803 N Y 3.69937614314766 3.52208566311286 3.52208566311286 158 0.0420931380615435 0.0322106104281736 Y 0.0420931380615435 0 N N 38251 2253 ENSG00000156802 ENSG00000156795 - - 8 8 124477868 124523441 coding upstream ATAD2 WDYHV1 124401922 124498146 - + 0 124462097 124497668 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 11 1.07840397214886 0.721316564152552 1.07840397214886 0.721316564152552 1 - - 37130 N N 3.57014471390586 3.4561676006071 3.4561676006071 8 0 0.840643084942062 N 0.0742857142857144 0 N N 6175 234233 ENSG00000221983 ENSG00000150991 + + 19 12 18546960 123965530 coding coding UBA52 UBC 18545111 123962147 + - 0 18546680 123962283 + - Y - - N HCC1954 5 4.35714285714286 2 14 2 N - - N - - 0 0 0 14 0.271386430077198 0.821301038391519 0.821301038391519 0.271386430077198 3 - - 38029 N Y 3.85425536676371 3.74015446228557 3.74015446228557 2 0 0.555207923140565 N 0.853536556322934 0.809597523219814 N N 2963 12 ENSG00000133983 ENSG00000120156 + + 14 9 69896147 27220171 coding intron COX16 TEK 69680762 27099286 - + 0 69895989 27103577 - + Y 0.803532643437988 0.827031219701377 N HCC1954 10 2.81818181818182 1 6 1 N - - N - SINE 0 1 1 11 0.5713398527941 0.292811674556976 0.5713398527941 0.292811674556976 3 0 0 37803 N N 3.51104337473878 3.40740634961144 3.40740634961144 11 0 0.571799361329841 N 0.628935239434419 0.609405515194126 N N 64575 0 ENSG00000092199 ENSG00000215054 - + 14 16 20807478 11244910 intron upstream HNRNPC AC009121.8-1 20747135 11244008 - + 0.00398406374501992 20801828 11243947 + + Y 0.38955189038318 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.364229156156239 0.257102933757345 0.364229156156239 0.257102933757345 2 0 - 4374 Y Y 3.39590940049075 3.31741211873126 3.31741211873126 124 0 0.0419165294577784 Y 0.680563149261892 0.949562602515036 N N 11 0 ENSG00000164707 ENSG00000212303 + - 7 7 135063474 135000990 intron downstream SLC13A4 U6 135016579 135000887 - - 0 135024249 134997826 - + N 1.9434874105094 - N HCC1954 2 1.2 1 1 2 N - - Y SINE - 1 0 1 5 0.664182578873142 0.335662163516534 0.664182578873142 0.335662163516534 2 0 - 48793 N N 3.53937561337214 3.30119509103522 3.30119509103522 0 0 0.181213198420196 N 0.192116477272727 0 N N 1458 6627 ENSG00000188818 ENSG00000113269 + + 5 5 904101 179431719 intron intron ZDHHC11 RNF130 848722 179315111 - - 0 896714 179367738 - - N 1.24266249109517 1.40481845160553 Y HCC1954 2 1.62962962962963 1 17 2 N 48 1.73211 N - LINE 0 1 1 27 0.914143764470561 0.921285512630487 0.921285512630487 0.914143764470561 1 0 0 1167 N N 3.49640736351508 3.60785432895764 3.49640736351508 1 0 0.141750516659867 N 0 0 N N 2004 3301 ENSG00000115525 ENSG00000070081 - + 2 11 85969668 17309646 utr5p utr5p ST3GAL5 NUCB2 85919778 17254860 - + 0 85923671 17261019 + + Y - - N HCC1954 27 26.1666666666667 25 6 1 N - - N SINE SINE 1 0.376106194690265 1 6 0.357087407996313 0.899860268150708 0.899860268150708 0.357087407996313 3 - - 1393 N Y 3.6272104187567 3.50744965188915 3.50744965188915 1 0 0.238818332995576 N 0.875475285171103 0.903147444021969 N N 3346 20793 ENSG00000149311 ENSG00000141027 - - 11 17 107745036 16059570 utr3p utr5p ATM NCOR1 107598769 15875443 + - 0 107741838 16038675 - + Y - - N HCC1954 30 27 21 5 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.564198104634174 0.564198104634174 0.299953422716903 1 - - 19626 N N 3.41600968859956 3.69681549006792 3.41600968859956 0 0 0.0649444644978209 N 0.39777836551177 0 N N 35256 0 ENSG00000212664 ENSG00000206696 + - 1 18 109337022 45272097 utr5p downstream RPL17 SNORD58 109336399 45272032 + - 0 109336415 45271950 + + Y 0.786577312137681 - N HCC1954 6 4.8 3 5 1 N - - N - - 0 0 0 5 0.371370904316165 0.87843502367093 0.87843502367093 0.371370904316165 1 0 - 24342 N N 3.64553343878587 3.58217602935986 3.58217602935986 0 0 0.52188662264019 N 0 0.0024330900243309 N N 0 5754 ENSG00000218426 ENSG00000168461 + - 6 18 153645587 9852547 downstream upstream RP11-475C16.1 RAB31 153645112 9764874 - + 0.0024330900243309 153645091 9724787 - - Y - - N HCC1954 2 1.75 1 3 1 N - - N Simple_repeat - 0.0283400809716599 0 0.0283400809716599 4 0.849868031031224 0.307095170876829 0.849868031031224 0.307095170876829 2 - - 47724 Y Y 3.39384326095097 2.99615672237849 2.99615672237849 93 0.00409836065573776 0.995446533173196 Y 0.00409836065573776 0 N Y 3492 6250 ENSG00000123815 ENSG00000105245 + - 19 19 45914440 45888396 coding intron ADCK4 NUMBL 45889274 45863650 - - 0 45890696 45884740 - + N - 5.77660762383018 N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 9 0.692749571512847 0.628473838073511 0.692749571512847 0.628473838073511 4 - 0 46033 N N 3.6272104187567 3.30521516096314 3.30521516096314 4 0 0.0447969952644738 N 0 0.0102040816326531 N N 9933 25286 ENSG00000085872 ENSG00000130429 + - 19 7 16514263 98830338 intron coding CHERP ARPC1B 16489700 98810265 - + 0.0102040816326531 16508700 98822325 - - Y 0.913143460851213 0.90615093929141 N HCC1954 20 10.5 7 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.378512652476092 0.378512652476092 0.328520415356608 1 0 0 34921 N Y 3.44871903508266 3.13011242009227 3.13011242009227 0 0 0.734322471876789 Y 0.993310523314471 0.986621046628942 N Y 2993 4646 ENSG00000107201 ENSG00000197579 - + 9 9 32516322 32542601 coding coding DDX58 TOPORS 32445300 32530545 - - 0 32490937 32540772 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.892718519990782 0.685607823352921 0.892718519990782 0.685607823352921 4 - - 42906 N N 3.17932833183454 3.38912318237562 3.17932833183454 1 0 0.804797066300401 N 0.154852619764901 0 N N 11640 21519 ENSG00000137038 ENSG00000164111 + + 9 4 7789799 122837585 upstream coding C9orf123 ANXA5 7786490 122808598 - - 0 7790339 122825348 - - Y - - N HCC1954 20 8 1 3 4 N - - N SINE - 1 0 1 5 0.428504889595575 0.449930134075354 0.449930134075354 0.428504889595575 2 - - 7105 Y Y 3.55401162459584 3.42680229220385 3.42680229220385 186 0 0.0395990748624125 Y 0 0 N N 19744 7234 ENSG00000068878 ENSG00000115239 + - 2 2 54051481 53940801 coding intron PSME4 ASB3 53944708 53613314 - - 0 53946766 53935471 - + N 0.394869022351296 55.1412090843106 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.778450549431962 0.814159290231593 0.814159290231593 0.778450549431962 1 0 0 36564 Y Y 3.49640736351508 3.33424740824393 3.33424740824393 5 0 0.896021101172796 Y 0.980846462774174 0.980846462774174 N N 1240 0 ENSG00000139354 ENSG00000012504 - + 12 12 99542812 99481775 utr5p downstream GAS2L3 NR1H4 99512769 99391810 + + 0 99512784 99491694 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat 0 0.227722772277228 0.227722772277228 18 0.99270299422975 0.721316564152552 0.99270299422975 0.721316564152552 4 - - 9409 Y Y 3.47233119514066 3.52720696927234 3.47233119514066 283 0 0.300137637269034 Y 0.990687229615931 0.990687229615931 N N 0 12836 ENSG00000222777 ENSG00000167258 + + 17 17 34955984 34941095 downstream intron U6 CRKRS 34955883 34871265 - + 0 34954031 34936098 - + N - 2.62354953389778 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 24 0.842726282871298 1.19981369086761 1.19981369086761 0.842726282871298 1 - 0 37052 N N 3.41167176744019 3.18400855761655 3.18400855761655 0 0 0.294453539797825 N 0.454018109790606 0.389784946236559 N N 106 71224 ENSG00000163633 ENSG00000089009 - - 4 12 88032599 111331793 downstream coding C4orf36 RPL6P27 88016383 111327378 - - 0.389784946236559 88010371 111330839 + + Y - 1.65031016012083 N HCC1954 4 2.75 2 12 1 N - - N - - 0 0 0 12 0.264244681917271 0.728458312312478 0.728458312312478 0.264244681917271 1 - 0 36538 N Y 3.38383404234679 3.18143432416767 3.18143432416767 43 0 0.0917182541425037 Y 0 0.904640813731723 N N 1823 0 ENSG00000126749 ENSG00000207713 - + 12 12 6955232 6943190 coding upstream EMG1 hsa-mir-200c 6950348 6943123 + + 0 6953825 6942703 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 16 0.557056356474248 0.714174815992626 0.714174815992626 0.557056356474248 2 - - 36298 Y Y 3.75847748231474 3.3012485241977 3.3012485241977 370 0 0.00125638823546237 Y 0 0.987837837837838 N N 0 0 ENSG00000221617 ENSG00000207365 - + 12 12 92015251 91939619 upstream upstream AC138123.2 Y_RNA 92015158 91939513 + + 0 91998942 91922494 - + N - - N HCC1954 3 1.28571428571429 1 1 1 N - - Y LTR SINE 0.265060240963855 0.277777777777778 0.277777777777778 7 0.592765097273879 0.51420586751469 0.592765097273879 0.51420586751469 2 - - 29097 N Y 3.40016547074969 3.46720988898117 3.40016547074969 272 0.699223085460599 0.00609719210247783 N 0.868410099889012 0.887208657047725 N N 99 95833 ENSG00000204623 ENSG00000204525 + + 6 6 30136900 31432935 intron coding C6orf12 HLA-C 30076768 31344505 - - 0.887208657047725 30082769 31347412 - - N 0.455072933993676 0.99720082069125 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.264244681917271 0.314236919036755 0.314236919036755 0.264244681917271 3 0 0 22618 N Y 3.33680806132368 3.23065023590994 3.23065023590994 366 0 0.00232253824681161 N 0 0.948858063612162 N N 0 0 ENSG00000223225 ENSG00000220261 + - 4 1 119747156 222242479 upstream upstream U6 RP11-504P24.2 119747053 222237079 + - 0 119732391 222242676 + + Y - - N HCC1954 26 13.8888888888889 10 9 1 N 387 25.288 N - - 0 0 0 9 0.471355378555133 0.642757334393363 0.642757334393363 0.471355378555133 3 - - 43096 N N 3.45872825368684 3.448886868952 3.448886868952 0 0 0.979602655747297 N 0.143299798792757 0.206498993963783 N N 9848 13 ENSG00000164134 ENSG00000152495 + + 4 5 140531972 110848645 intron intron NARG1 CAMK4 140442126 110587981 + + 0.206498993963783 140442476 110646627 + + Y 1.36681297140778 1.03487135990953 N HCC1954 1 1 1 0 5 N 370 4.32528 N - DNA 0 1 1 11 1.13553795742827 1.12125446110842 1.13553795742827 1.12125446110842 2 0 0 9353 Y Y 3.02111537489174 3.39401109482032 3.02111537489174 0 0 0.125806334502998 Y 0.0114942528735632 0 N N 69569 12647 ENSG00000108424 ENSG00000141279 - + 17 17 43116003 43055640 upstream downstream KPNB1 NPEPPS 43082274 42963443 + + 0 43081895 43068928 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE,LINE 0 1 1 6 0.478497126715059 0.507064119354764 0.507064119354764 0.478497126715059 3 - - 38397 N Y 3.09446475468366 3.60256518892881 3.09446475468366 0 0 0.374072657490884 Y 0 0.939743923893921 N N 2963 2822 ENSG00000133983 ENSG00000213463 - + 14 14 69896147 69953497 coding utr3p COX16 SYNJ2BP 69680762 69907901 - - 0 69879137 69909461 + - N - - N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 6 0.985561246069823 0.742741808632331 0.985561246069823 0.742741808632331 1 - - 32975 N N 2.99376390316809 3.29652844562235 2.99376390316809 1 0 0.999966658419563 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8399 14200 - + N 0.806109216236245 0.632974497059645 N HCC1954 4 1.81818181818182 1 5 10 N 189 4.09957 N - - 0 0 0 11 0.93556900895034 0.971277749749971 0.971277749749971 0.93556900895034 2 0 0 19777 N N 3.48809356209009 3.75065819442972 3.48809356209009 0 0 0.095761791626382 N 0 0 N N 45068 1 ENSG00000205336 ENSG00000122223 + - 16 1 56256445 159099316 upstream intron GPR56 CD244 56220023 159066623 + - 0 56211646 159098167 + + Y - 1.03241782980639 N HCC1954 21 20.2142857142857 20 14 1 N - - N - SINE 0 1 1 14 0.599906845433805 0.307095170876829 0.599906845433805 0.307095170876829 1 - 0 9830 N Y 3.13073491470822 3.11080976345569 3.11080976345569 191 0.00338983050847463 0.104578602513859 Y 0.990033898305085 0.990033898305085 N N 4310 64784 ENSG00000183011 ENSG00000170004 - - 17 17 7701897 7756803 coding upstream LSMD1 CHD3 7700730 7728849 - + 0 7701243 7727280 + - N - - N HCC1954 4 2.95752895752896 1 254 2 N - - N - - 0 0 0 259 1.45691662462496 0.771308801272036 1.45691662462496 0.771308801272036 2 - - 33019 N N 3.16423765986423 2.90613198627477 2.90613198627477 0 0 0.307133008803863 N 0 0.275531340057637 Y N 0 171855 ENSG00000210156 ENSG00000198886 - + MT MT 8365 12138 intron coding AF347015.1-16 MT-ND4 8296 10761 + + 0.275531340057637 8365 10965 - + N 1 0.531460044217095 N HCC1954 2 1.5 1 3 1 N 189 4.09957 N - - 0 0 0 6 1.27123117246687 0.899860268150708 1.27123117246687 0.899860268150708 2 0 0 18289 Y Y 3.65554265739006 2.83908756804329 2.83908756804329 289 0 0.167234468034804 Y 0 0 N N 24548 0 ENSG00000134369 ENSG00000218820 - + 1 1 200062720 199756301 upstream downstream NAV1 RP11-134G8.6 199859224 199755807 + + 0 199824290 199775093 - + N - - N HCC1954 14 3.8 1 2 2 N - - Y SINE,LINE - 0.922413793103448 0 0.922413793103448 5 0.828442786551446 0.857009779191151 0.857009779191151 0.828442786551446 4 - - 47166 Y Y 3.3755202409218 3.47911741325579 3.3755202409218 371 0 0.369462691478242 Y 0 0.987131553777932 N N 6 14186 ENSG00000213052 ENSG00000171570 + + 19 19 46048180 46006176 downstream utr3p CYP2A6 EGLN2 46041284 45996959 - + 0 46024309 46005958 - + N - - N HCC1954 2 1.75 1 6 3 N - - Y - - 0 0 0 8 1.12839620926835 1.24266417982717 1.24266417982717 1.12839620926835 4 - - 41540 N N 3.38912318237562 3.58320909912975 3.38912318237562 0 0 0.970702023212013 Y 0.0136671504596033 0 N N 0 0 ENSG00000208525 ENSG00000222501 - - 8 8 130372654 129092039 downstream downstream AC103833.2-1 U4 130372411 129091912 + - 0 130395857 129091871 - + N - - N HCC1954 1 1 1 0 4 N 575 2.9574 N SINE,LINE - 0.130841121495327 0 0.130841121495327 9 0.764167053112109 0.714174815992626 0.764167053112109 0.714174815992626 1 - - 48036 N N 3.40319013214585 3.41679307359967 3.40319013214585 0 0 0.997888615326164 N 0.400029266865031 0 N N 10798 0 ENSG00000113761 ENSG00000212451 - - 5 8 176426349 127753081 coding downstream ZNF346 U11 176382303 127752949 + + 0 176421665 128092284 - - Y - - N HCC1954 1 1 1 0 5 N 185 21.3767 N - - 0 0 0 5 0.407079645115797 0.478497126715059 0.478497126715059 0.407079645115797 4 - - 726 Y Y 3.44508545943967 3.43408302385895 3.43408302385895 0 0.160711692084241 0.692584221271288 Y 0.990777051561365 0.990777051561365 N Y 17 7254 ENSG00000186652 ENSG00000134802 - + 11 11 56914688 56951629 utr5p coding PRG2 SLC43A3 56910843 56931005 - - 0 56914005 56933224 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.778450549431962 0.728458312312478 0.778450549431962 0.728458312312478 4 - - 42653 N N 3.54296933622177 3.38552945952599 3.38552945952599 0 0 0.488960036499147 N 0 0.637433155080214 N N 4574 42670 ENSG00000188917 ENSG00000128050 - - X 4 100193758 57022291 utr3p utr3p TRMT2B PAICS 100150992 56996672 - + 0 100151997 57020869 + - Y - - N HCC1954 35 33.25 30 4 1 N - - N SINE SINE 1 1 1 4 0.392796148795944 0.478497126715059 0.478497126715059 0.392796148795944 2 - - 38461 Y Y 3.59847695253922 3.45400817511148 3.45400817511148 243 0 0.0486785474008598 Y 0.0250812215724495 0.9895170023825 N N 3195 681 ENSG00000126804 ENSG00000089775 - - 14 14 64070161 64041055 utr5p intron ZBTB1 ZBTB25 64040456 64023310 + - 0 64047855 64038700 - + N - 4.49586174847168 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.47887323943662 0.47887323943662 4 0.45707188223528 0.507064119354764 0.507064119354764 0.45707188223528 2 - 0 31792 Y Y 3.37767966641742 3.66745018166468 3.37767966641742 2 0 0.308683765058929 Y 0.96308519740863 0.992617039481726 N N 1241 480 ENSG00000073803 ENSG00000113790 - - 3 3 186683293 186454531 utr5p upstream MAP3K13 EHHADH 186529396 186391108 + - 0 186628981 186486127 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.971277749749971 0.821301038391519 0.971277749749971 0.821301038391519 1 - - 16862 N Y 3.48167806633553 3.52936639476796 3.48167806633553 33 0 0.192561413929517 N 0 0.816476826394344 N N 46217 2162 ENSG00000131746 ENSG00000162458 - + 17 1 35911380 15985676 utr3p utr3p TNS4 FBLIM1 35885606 15955741 - + 0.0386881382560881 35886742 15984331 + + Y - - N HCC1954 37 36.25 36 4 1 N 616 29.8497 N SINE SINE 0.256410256410256 1 1 4 0.557056356474248 0.385654400636018 0.557056356474248 0.385654400636018 1 - - 34016 N N 3.44359772892318 3.6344911504118 3.44359772892318 10 0 0.792526883307255 N 0.0476977307777041 0 N N 0 115137 ENSG00000216739 ENSG00000147403 + + 9 X 118983195 153283874 intron coding RPL10P3 RPL10 118982728 153278689 - + 0 118982800 153282376 - + Y 1 - N HCC1954 14 8.14285714285714 3 7 1 N - - N - - 0 0 0 7 0.664182578873142 1.07126222398894 1.07126222398894 0.664182578873142 2 0 - 29421 Y Y 3.45872825368684 3.40272612382943 3.40272612382943 0 0 0.443512121197689 Y 0.401993355481728 0.992617201919527 N N 10024 850 ENSG00000137266 ENSG00000180822 + + 6 6 3401734 3213013 intron coding SLC22A23 AL445309.13-1 3214694 3200327 - + 0 3248089 3208990 - + N 2.3483022031484 - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 4 0.585623349113953 0.807017542071667 0.807017542071667 0.585623349113953 3 0 - 33975 N Y 3.37232774565629 3.13855936026645 3.13855936026645 455 0.00219780219780219 0.0063856624166505 Y 0.00219780219780219 0.994265504610332 N N 59837 275222 ENSG00000198695 ENSG00000198763 + + MT MT 14674 5512 coding coding MT-ND6 MT-ND2 14150 4471 - + 0 14191 5263 - + N - 0.94718181329015 N HCC1954 2 1.75 1 3 3 N - - N - - 0 0 0 4 0.978419497909897 0.885576771830856 0.978419497909897 0.885576771830856 2 - 0 33537 N Y 3.08507803069543 3.63399663687184 3.08507803069543 333 0.00300300300300294 0.909267086089374 Y 0.00300300300300294 0.96189820393642 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0 12381 9077 - + N - 0.586743334843155 N HCC1954 2 1.66666666666667 1 4 7 Y - - N - - 0 0 0 6 0.871293275511003 1.04983697950916 1.04983697950916 0.871293275511003 2 - 0 20618 N N 3.49487978020523 3.54400240599166 3.49487978020523 0 0 0.0821497809462945 N 0 0 N N 3 975 ENSG00000198821 ENSG00000198487 + + 1 6 165754456 42218335 intron coding CD247 AL512274.9 165666509 42183124 - - 0 165710730 42183238 - - Y 1.1237322515213 - N HCC1954 5 2.6 2 5 1 N - - N SINE - 1 0 1 5 0.271386430077198 0.421363141435649 0.421363141435649 0.271386430077198 2 0 - 3576 N N 3.51832410639388 3.5074097990958 3.5074097990958 0 0 0.37740620809832 N 0 0.00374531835206005 N N 4 21326 ENSG00000166265 ENSG00000182240 + - 21 21 26867452 41570378 upstream upstream CYYR1 BACE2 26760402 41461598 - + 0.00374531835206005 26906322 41450465 - - N - - Y HCC1954 1 1 1 0 1 N 355 7.16371 N - SINE 0 0.736842105263158 0.736842105263158 4 0.671324327033068 0.628473838073511 0.671324327033068 0.628473838073511 1 - - 1213 N N 3.50016892023405 3.45612774781375 3.45612774781375 1 0 0.044328157796272 N 0 0 N N 3748 8014 ENSG00000168887 ENSG00000149084 + + 2 11 85692666 43834736 utr3p utr3p C2orf68 HSD17B12 85687290 43658719 - + 0 85691261 43833980 - + Y - 1.60098572907956 N HCC1954 36 34.9285714285714 33 14 1 N 72 23.8484 N SINE - 1 0 1 14 0.428504889595575 0.835584534711372 0.835584534711372 0.428504889595575 1 - 0 13917 Y Y 3.53461568200343 3.4283298755137 3.4283298755137 0 0 0.878763080515233 Y 0.465284515122116 0.986797148521534 N N 12589 9158 ENSG00000100348 ENSG00000100350 - + 22 22 35207633 35233033 coding coding TXN2 FOXRED2 35193039 35214235 - - 0 35206830 35216181 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 18 0.949852505270192 1.1426797055882 1.1426797055882 0.949852505270192 4 - - 624 Y Y 3.77104735399867 3.69784855983781 3.69784855983781 420 0 0.000630907657476532 Y 0.932134758665371 0.993213475866537 N N 3781 308 ENSG00000110218 ENSG00000181333 - + 11 11 93554781 93487022 coding coding PANX1 HEPHL1 93501742 93394026 + + 0 93502143 93440558 - + N - 1.28296975539514 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.742741808632331 0.642757334393363 0.742741808632331 0.642757334393363 2 - 0 22529 N N 3.25256697878875 3.61720120015252 3.25256697878875 0 0 0.0446664539366163 N 0 0 N N 49089 1244 ENSG00000117450 ENSG00000156735 - - 1 8 45760196 38189966 coding intron PRDX1 BAG4 45749295 38153469 - + 0 45757275 38179008 + - Y - 1.30298810136759 N HCC1954 10 5.66666666666667 3 6 1 N - - N - SINE 0 1 1 6 0.585623349113953 0.264244681917271 0.585623349113953 0.264244681917271 1 - 0 9871 Y N 3.39024953810134 3.41952156054875 3.39024953810134 13 0.107486797141969 0.480605741887377 N 0 0 N N 1649619 109916 ENSG00000141736 ENSG00000161395 - + 17 17 35138441 35097836 utr5p upstream ERBB2 PERLD1 35104766 35080902 + - 0 35104810 35098525 - - N - - Y HCC1954 1 1 1 0 2 N 298 9.39526 N - LINE 0 0.628318584070796 0.628318584070796 5 0.842726282871298 0.771308801272036 0.842726282871298 0.771308801272036 1 - - 33114 N N 3.66951632120446 3.50848272165904 3.50848272165904 5 0 0.069590700610027 N 0 0 Y N 1291380 171855 ENSG00000198804 ENSG00000198886 - + MT MT 7446 12138 coding coding MT-CO1 MT-ND4 5905 10761 + + 0 6321 11569 - + N 1.05941304751534 1.0617458527768 N HCC1954 2 1.5 1 2 1 Y 106 8.09281 N - - 0 0 0 4 0.821301038391519 0.914143764470561 0.914143764470561 0.821301038391519 1 0 0 42635 N N 3.61207989399303 3.56591914887046 3.56591914887046 0 0 0.66272208160763 N 0 0 N N 0 0 ENSG00000202536 ENSG00000217588 + + 4 X 113896522 54267220 upstream intron Y_RNA RP3-390O13.1 113896421 54266482 - + 0 113929057 54266923 - + Y - 1 N HCC1954 26 13.2 8 5 1 N - - N - - 0 0 0 5 0.521347615674617 0.257102933757345 0.521347615674617 0.257102933757345 2 - 0 10319 Y Y 3.25832012713399 3.20803129282848 3.20803129282848 0 0 0.999801774303019 Y 0 0.98652520715558 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 coding coding C17orf37 ERBB2 35138937 35104766 - + 0 35139464 35133703 - + N - 1.16900995319948 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 10 1.03555348318931 1.02841173502938 1.03555348318931 1.02841173502938 4 - 0 814 N N 3.47592491799029 3.41423242051993 3.41423242051993 0 0 0.47738570145508 N 0 0 N N 698 23248 ENSG00000183570 ENSG00000172927 + + 21 11 46186796 68821329 intron downstream PCBP3 MYEOV 45888036 68818198 + + 0 45913292 68911608 + + Y 0.151052771284475 - N HCC1954 1 1 1 0 2 N - - N LINE SINE 1 1 1 9 0.721316564152552 0.978419497909897 0.978419497909897 0.721316564152552 1 0 - 47090 Y Y 3.22266730405219 3.42254622194492 3.22266730405219 137 0 0.0662119838832463 Y 0.0253483742534839 0.981950895819509 N N 8067 3492 ENSG00000086544 ENSG00000123815 - - 19 19 45938603 45914440 coding intron ITPKC ADCK4 45914848 45889274 + - 0 45915941 45912383 - + N 0.967964592257441 9.7997253419117 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.392796148795944 0.435646637755502 0.435646637755502 0.392796148795944 1 0 0 31165 Y Y 3.48908677906663 2.88274380859372 2.88274380859372 313 0 0.51526722567287 Y 0.983658932593097 0.983658932593097 N N 2216 1131 ENSG00000185485 ENSG00000214116 + - 3 3 197201530 197173943 downstream coding AC024937.21-3 AC024937.21-2 197174603 197171055 - - 0 197174568 197171354 - + N - 1.93046968027974 N HCC1954 8 4.34782608695652 2 23 3 N - - Y - LINE 0 0.673575129533679 0.673575129533679 23 0.985561246069823 1.37835739486577 1.37835739486577 0.985561246069823 4 - 0 21701 N N 3.78208964237274 2.23906232173876 2.23906232173876 0 0 0.0198291231313515 N 0 0 N N 2833 0 ENSG00000133019 ENSG00000222581 - + 1 9 238139338 12290451 utr5p upstream CHRM3 U2 237858996 12290266 + - 0 237859411 12330581 - - Y - - N HCC1954 23 22.25 22 4 1 N - - N LINE - 1 0 1 4 0.314236919036755 0.628473838073511 0.628473838073511 0.314236919036755 0 - - 40630 N N 3.32895826821511 3.37655331069169 3.32895826821511 0 0 0.115310844344229 N 0 0 N N 14089 975 ENSG00000124201 ENSG00000198487 + + 20 6 47328163 42218335 intron intron ZNFX1 AL512274.9 47288858 42183124 - - 0 47300628 42204322 - - Y 0.848719715489186 0.755947860259476 N HCC1954 23 21.2 20 5 1 N 201 21.7755 N SINE - 1 0 1 5 0.321378667196682 0.549914608314322 0.549914608314322 0.321378667196682 2 0 0 7699 N Y 3.7297745213208 3.35616415112274 3.35616415112274 2 0 0.0196695617262120 N 0 0.806124106562703 N N 20739 0 ENSG00000143951 ENSG00000201763 - - 2 8 63669355 60531123 utr3p downstream C2orf86 5S_rRNA 63202041 60530998 - + 0.750730994152047 63309655 60566958 + - Y - - N HCC1954 660 575 400 4 1 N - - N LINE LINE 1 1 1 4 0.414221393275723 0.307095170876829 0.414221393275723 0.307095170876829 1 - - 34623 Y Y 3.7061623612628 3.36191729946799 3.36191729946799 222 0 0.124050636213797 Y 0 0.984684684684685 N N 394 3243 ENSG00000183784 ENSG00000107099 - - 9 9 205741 455255 intron intron C9orf66 DOCK8 202824 263048 - + 0 205408 276399 + - N - 0.0469142419002762 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.421363141435649 0.599906845433805 0.599906845433805 0.421363141435649 1 - 0 33276 N Y 2.94806716636195 1.79459101063324 1.79459101063324 418 0.0345732366105881 0.458671279174289 Y 0.00239234449760761 0.922765858928847 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding downstream MT-CO3 MT-ND1 8367 3308 + + 0 8497 4287 - + N 0.603627792848188 - N HCC1954 6 3.27586206896552 1 25 6 N - - N - - 0 0 0 29 1.1426797055882 1.45691662462496 1.45691662462496 1.1426797055882 2 0 - 13707 Y Y 3.57167229721571 3.27394935533424 3.27394935533424 233 0.0304946916647842 0.0277895265787453 Y 0.0304946916647842 0 N N 140 1817 ENSG00000100156 ENSG00000100151 + + 22 22 36809116 36801653 downstream coding SLC16A8 PICK1 36804093 36783208 - + 0 36803608 36800990 - + N - 1.90974643360554 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.542772860154395 0.585623349113953 0.585623349113953 0.542772860154395 1 - 0 3323 N N 3.14640915337501 3.45553575842133 3.14640915337501 20 0 0.617245877331674 N 0 0 N N 2273 0 ENSG00000177556 ENSG00000210558 + + 5 11 151118405 80942666 utr3p upstream ATOX1 AP002783.3-3 151102577 80942598 - + 0.0934741488020174 151106034 80576517 - + Y - - N HCC1954 20 20 20 4 1 N - - N - LTR 0 1 1 4 0.371370904316165 0.521347615674617 0.521347615674617 0.371370904316165 3 - - 45327 N N 3.30587531681723 3.42424163912411 3.30587531681723 0 0 0.0520317589011271 N 0 0.00355871886121006 N N 551733 1490 ENSG00000204628 ENSG00000138190 + + 5 10 180603512 94809241 coding upstream GNB2L1 EXOC6 180596536 94584450 - + 0.00355871886121006 180597248 94578543 - + Y 0.533804592371237 - N HCC1954 8 4.42857142857143 1 6 1 N - - N - SINE,LINE 0 0.891891891891892 0.891891891891892 7 0.642757334393363 0.264244681917271 0.642757334393363 0.264244681917271 1 0 - 40982 Y Y 3.32952732966858 3.50000108636471 3.32952732966858 254 0 0.534889516245926 Y 0.750984251968504 0.983398950131234 N N 52353 525 ENSG00000088832 ENSG00000125775 + - 20 20 1321753 1257838 downstream intron FKBP1A SDCBP2 1297623 1238619 - - 0 1288343 1254173 - + N - 1.57072633895818 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.428504889595575 0.528489363834543 0.528489363834543 0.428504889595575 4 - 0 35225 N Y 3.36976709257655 3.61104682422314 3.36976709257655 0 0 0.439908922302458 N 0.961688117330141 0.961688117330141 N N 267 4382 ENSG00000166153 ENSG00000115993 - - 12 2 99184988 202024499 upstream intron DEPDC4 TRAK2 99121578 201950176 - - 0 99185309 201986300 + + Y - 1.0229220538285 N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.402597402597403 0 0.402597402597403 11 0.549914608314322 0.28566992639705 0.549914608314322 0.28566992639705 3 - 0 33130 N Y 3.52567938596249 3.6035982586987 3.52567938596249 354 0 0.0266184884839880 Y 0 0.993992920835886 N N 171855 539404 ENSG00000198886 ENSG00000198712 - + MT MT 12138 8270 coding coding MT-ND4 MT-CO2 10761 7587 + + 0 11164 7781 - + N 0.782121531774436 1.0258786505853 N HCC1954 2 1.75 1 3 3 Y - - N - - 0 0 0 4 0.671324327033068 0.728458312312478 0.728458312312478 0.671324327033068 2 0 0 12116 N Y 2.93909101752765 3.60463132846859 2.93909101752765 103 0 0.344795803527608 N 0 0.956070087609512 N N 1021 4310 ENSG00000104714 ENSG00000183011 + - 8 17 671226 7701897 upstream coding ERICH1 LSMD1 604201 7700730 - - 0 913662 7700801 - + Y - 3.7328361102682 N HCC1954 3 2.6 2 5 3 N - - N Other - 0.0120481927710843 0 0.0120481927710843 5 0.799875793911741 0.549914608314322 0.799875793911741 0.549914608314322 1 - 0 46279 N Y 3.77104735399867 3.37655331069169 3.37655331069169 0 0 0.531362479237784 N 0.919018013709549 0.910919815080504 N N 2827 52 ENSG00000119574 ENSG00000214164 - - 19 2 63722733 110569923 coding intron ZBTB45 AC112229.4-2 63716711 110569013 - - 0 63719646 110569183 + + Y - 1.39776386634722 N HCC1954 21 7.30434782608696 6 23 2 N - - N - - 0 0 0 23 0.392796148795944 0.821301038391519 0.821301038391519 0.392796148795944 1 - 0 46280 N Y 3.47076375903745 3.53146303953127 3.47076375903745 261 0 0.063816371682581 N 0.852419469277707 0.852419469277707 N N 3966 2827 ENSG00000175772 ENSG00000119574 - - 2 19 110111006 63722733 coding intron AC013268.5-1 ZBTB45 110103138 63716711 + - 0.594153540513694 110103264 63720853 - + Y - 8.55053704756341 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.278528178237124 0.385654400636018 0.385654400636018 0.278528178237124 2 - 0 35195 N Y 3.40488554932505 2.93335144955154 2.93335144955154 1 0 0.0652427461939296 N 0 0 N N 1194 4442 ENSG00000212691 ENSG00000139116 - + 2 12 201257138 38123190 coding downstream AC007163.3-1 KIF21A 201255742 37973298 + - 0 201255861 37891111 - - Y - - N HCC1954 400 100.857142857143 22 7 1 N - - N Other LINE 1 1 1 7 0.685607823352921 0.578481600954027 0.685607823352921 0.578481600954027 2 - - 29245 Y Y 3.58271458558979 3.63399663687184 3.58271458558979 287 0 0.0510931006793592 Y 0 0.992830822450054 N N 0 41 ENSG00000216906 ENSG00000164520 - - 6 6 150269246 150253863 upstream upstream RP11-350J20.9 RAET1E 150267069 150251014 + - 0.992830822450054 150260852 150258863 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 8 0.635615586233437 0.849868031031224 0.849868031031224 0.635615586233437 1 - - 4331 Y Y 3.47592491799029 3.29652844562235 3.29652844562235 436 0 0.00683086611890948 N 0 0.993725116842652 Y N 0 0 ENSG00000223189 ENSG00000208561 - + 7 7 128054565 128054565 downstream downstream U6 AC018638.5-1 128054462 128054463 + + 0 128068338 128059159 - + N - - N HCC1954 196 55.1666666666667 14 6 3 N - - N - SINE,LTR 0 0.50609756097561 0.50609756097561 6 0.885576771830856 0.999844742389676 0.999844742389676 0.885576771830856 2 - - 26244 N Y 3.12804628055249 3.59421153471047 3.12804628055249 0 0 0.234729686598868 N 0.900389105058366 0.900389105058366 N N 1649619 4690 ENSG00000141736 ENSG00000034713 - - 17 16 35138441 74169279 coding upstream ERBB2 GABARAPL2 35104766 74157750 + + 0 35122227 74156138 - - Y - - N HCC1954 20 5.8 1 4 1 N - - N - SINE 0 1 1 5 0.478497126715059 0.314236919036755 0.478497126715059 0.314236919036755 2 - - 7252 Y Y 3.37704782423165 3.81657625693547 3.37704782423165 0 0 0.252279793367204 Y 0.978577336641853 0.989288668320926 N N 6 0 ENSG00000177519 ENSG00000200377 + - 2 2 154043568 154011643 upstream downstream RPRM SNORD56 154042098 154011573 - - 0 154157621 153986725 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 7 0.678466075192994 0.621332089913584 0.678466075192994 0.621332089913584 1 - - 36061 N N 3.52101274054962 3.66016945000958 3.52101274054962 2 0 0.631928208025403 N 0 0 N N 0 0 ENSG00000221617 ENSG00000181260 - + 12 3 92015251 180665801 upstream downstream AC138123.2 AC007620.30 92015158 180664828 + + 0 92001402 180694541 - + Y - - N HCC1954 16 15 14 6 1 N 447 23.1319 N - - 0 0 0 6 0.407079645115797 0.264244681917271 0.407079645115797 0.264244681917271 1 - - 20224 N Y 3.59425138750382 3.74234439300473 3.59425138750382 248 0.729907053034445 0.00987559319671605 N 0.729907053034445 0.729907053034445 N N 0 8013 ENSG00000214873 ENSG00000143367 + + 16 1 21469333 149822683 intron intron AC005632.2-2 TUFT1 21451791 149779405 - + 0.69614543466375 21457310 149796726 - + Y 1 1.06832450817703 N HCC1954 12 9.55555555555556 8 9 1 N - - N - - 0 0 0 9 0.257102933757345 0.34280391167646 0.34280391167646 0.257102933757345 2 0 0 5817 N N 3.38230645903694 3.66592259835483 3.38230645903694 12 0 0.457394604779156 N 0.456856702619415 0.0559652212194586 N N 250 4355 ENSG00000125618 ENSG00000073711 + - 2 3 113752958 137349423 intron intron PAX8 PPP2R3A 113690045 137167257 - + 0.0559652212194586 113729437 137308331 - - Y 4.6738572162301 1.80975333760807 N HCC1954 20 13.8 2 5 1 N - - N - SINE 0 1 1 5 0.357087407996313 0.299953422716903 0.357087407996313 0.299953422716903 3 0 0 36551 Y Y 3.40062947906611 3.26460248413936 3.26460248413936 1 0.00230414746543761 0.799400133512776 Y 0.91636082673363 0.994025773338116 N N 16017 12 ENSG00000018236 ENSG00000205592 - + 12 12 39750361 39250827 utr5p downstream CNTN1 MUC19 39588423 39222629 + + 0 39588427 39372662 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 358 1.60689333598341 1.1426797055882 1.60689333598341 1.1426797055882 1 - - 32968 N Y 3.19446820416802 3.17407904459906 3.17407904459906 295 0 0.166851003201606 Y 0 0.991180440977951 N N 171855 539404 ENSG00000198886 ENSG00000198712 - + MT MT 12138 8270 coding coding MT-ND4 MT-CO2 10761 7587 + + 0 10904 8253 - + N 0.411787399530623 - N HCC1954 2 1.25 1 1 3 N - - N - - 0 0 0 4 0.842726282871298 0.649899082553289 0.842726282871298 0.649899082553289 2 0 - 23761 N Y 3.68953475841283 3.41103992525442 3.41103992525442 315 0.800634920634921 0.00146274035509986 N 0 0.861978021978022 N N 50714 10721 ENSG00000154380 ENSG00000007047 + + 1 19 223907468 50500381 coding intron ENAH MARK4 223741157 50446390 - + 0 223821628 50457366 - + Y - 0.532219683716373 N HCC1954 20 20 20 4 1 N 173 26.9615 N - SINE 0 1 1 4 0.728458312312478 0.278528178237124 0.728458312312478 0.278528178237124 3 - 0 39859 Y Y 3.49015970162987 3.17720875913227 3.17720875913227 239 0 0.446354669641211 Y 0.683149486496767 0.96982376061874 N N 1304 0 ENSG00000186073 ENSG00000210354 - - 15 15 34889724 34649513 upstream upstream C15orf41 AC103988.7 34770651 34649295 + - 0 34723771 34659454 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 23 0.478497126715059 1.22123893534739 1.22123893534739 0.478497126715059 4 - - 45460 N N 3.05683907801791 3.50678730447985 3.05683907801791 0 0.279325572059414 0.567682292014439 N 0.385307105580088 0.279325572059414 N N 24895 551733 ENSG00000099250 ENSG00000204628 + + 10 5 33665196 180603512 utr5p utr3p NRP1 GNB2L1 33506426 180596536 - - 0.279325572059414 33663611 180596557 - - Y - - N HCC1954 22 18.2173913043478 1 21 1 N - - N Simple_repeat - 0.486486486486487 0 0.486486486486487 23 0.264244681917271 0.671324327033068 0.671324327033068 0.264244681917271 2 - - 6760 Y Y 3.28143777365203 3.48064499656564 3.28143777365203 0 0 0.446467644196872 Y 0 0.991556580259222 N N 606 11936 ENSG00000186132 ENSG00000115107 + + 2 2 119840876 119739698 coding downstream C2orf76 STEAP3 119776271 119697854 - + 0 119785669 119756574 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.799875793911741 0.864151527351077 0.864151527351077 0.799875793911741 1 - - 16512 N Y 3.64656650855576 3.48553290901035 3.48553290901035 1 0 0.368268608760935 N 0.91703869047619 0.958519345238095 N N 6903 20793 ENSG00000077254 ENSG00000141027 + - 1 17 77998125 16059570 utr3p utr5p USP33 NCOR1 77934264 15875443 - - 0 77935229 16038677 - + Y - 4.2421966926149 N HCC1954 44 26.3636363636364 10 11 1 N - - N SINE - 1 0 1 11 0.428504889595575 0.685607823352921 0.685607823352921 0.428504889595575 1 - 0 2499 N Y 3.61360747730288 3.52361324642271 3.52361324642271 0 0 0.890198536658439 N 0 0.00423728813559332 N N 18434 9042 ENSG00000136868 ENSG00000137692 + + 9 11 115068495 102468079 utr3p coding SLC31A1 DCUN1D5 115023638 102438032 + - 0.00423728813559332 115066412 102458687 + - Y - - N HCC1954 39 34.3636363636364 23 11 1 N - - N SINE - 1 0 1 11 0.449930134075354 0.678466075192994 0.678466075192994 0.449930134075354 4 - - 20415 N N 3.59930878696866 3.44040523365767 3.44040523365767 6 0 0.0411784473362683 N 0 0 N N 260 975 ENSG00000143515 ENSG00000198487 - + 1 6 152590403 42218335 utr3p coding ATP8B2 AL512274.9 152564654 42183124 + - 0 152589288 42204405 - - Y - 0.811586469073095 N HCC1954 33 31.2 29 5 1 N 109 25.7277 N SINE - 1 0 1 5 0.328520415356608 0.449930134075354 0.449930134075354 0.328520415356608 1 - 0 7701 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.0813314143128978 N 0 0.93483606557377 N N 20739 0 ENSG00000143951 ENSG00000210349 - + 2 8 63669355 21500598 utr3p upstream C2orf86 AC022716.13 63202041 21500252 - + 0 63309485 21336575 + + Y - - N HCC1954 620 572 420 5 1 N - - N LINE LINE 1 1 1 5 0.39993789695587 0.292811674556976 0.39993789695587 0.292811674556976 4 - - 33938 N N 3.77208042376856 3.13863390817995 3.13863390817995 0 0 0.0664396989715448 N 0 0 N N 240508 275222 ENSG00000198899 ENSG00000198763 + + MT MT 9208 5512 coding coding MT-ATP6 MT-ND2 8528 4471 + + 0 9056 5361 + + N - 1.32301945939418 Y HCC1954 4 4 4 4 1 N 301 4.17858 N - - 0 0 0 4 0.885576771830856 0.5713398527941 0.885576771830856 0.5713398527941 1 - 0 29718 N Y 3.66169703331943 2.76484635654273 2.76484635654273 0 0 0.436518613240663 Y 0 0 N N 3755 48732 ENSG00000204387 ENSG00000204389 - + 6 6 31915520 31893702 coding downstream C6orf48 HSPA1A 31910383 31891299 + + 0 31911167 31898221 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.692749571512847 0.599906845433805 0.692749571512847 0.599906845433805 2 - - 1784 N N 3.19645056666323 3.60103760561896 3.19645056666323 1 0 0.0240140771906465 N 0 0 N N 218 14402 ENSG00000088386 ENSG00000156689 - + 13 11 98202909 58368833 utr3p utr5p SLC15A1 GLYATL2 98134057 58358118 - - 0 98171182 58363695 + - Y - - N HCC1954 39 34 30 4 1 N 210 20.5309 N SINE - 1 0 1 4 0.307095170876829 0.478497126715059 0.478497126715059 0.307095170876829 0 - - 3882 N N 3.32060461399677 3.43358851031899 3.32060461399677 12 0.055031924597142 0.807795860411511 N 0.157190635451505 0.157190635451505 N N 0 850768 ENSG00000217920 ENSG00000075624 + + X 7 46033507 5536758 downstream utr3p RP1-30G7.1 ACTB 46032395 5533313 - - 0.157190635451505 46031990 5533541 - - Y - 0.816165638786703 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 11 0.292811674556976 0.678466075192994 0.678466075192994 0.292811674556976 2 - 0 35670 N N 3.79040344379773 3.80144573217181 3.79040344379773 5 0 0.659933851400876 N 0 0.0262459990855055 N N 94 164905 ENSG00000183785 ENSG00000123416 + + 22 12 16994498 47811571 coding coding TUBA8 TUBA1B 16973453 47807836 + - 0.0262459990855055 16989386 47808735 + - Y - - N HCC1954 6 3.09090909090909 2 11 1 N 127 15.3989 N - - 0 0 0 11 0.371370904316165 0.771308801272036 0.771308801272036 0.371370904316165 1 - - 36926 N Y 3.03589262417669 3.49744043328497 3.03589262417669 0 0 0.778514042158433 N 0.0647745358090186 0.969336870026525 N N 0 542 ENSG00000219787 ENSG00000135482 - + 20 12 21683988 54802545 intron upstream RPL41P1 ZC3H10 21683908 54798297 + + 0.969336870026525 21683920 54796850 - + Y 1 - N HCC1954 9 7.17721518987342 2 237 1 N - - N - - 0 0 0 237 0.642757334393363 1.37835739486577 1.37835739486577 0.642757334393363 4 0 - 29269 Y Y 3.53824925764641 3.57639237579107 3.53824925764641 273 0 0.0247845617765312 Y 0 0.990859293611587 N N 0 0 ENSG00000223286 ENSG00000218757 - - 6 6 155244196 155208446 downstream upstream AL121952.18-2 RP3-472M2.2 155244108 155207900 + - 0 155270553 155223821 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 1 1 4 0.864151527351077 0.592765097273879 0.864151527351077 0.592765097273879 2 - - 46217 N N 3.53871326596283 3.43784458057793 3.43784458057793 4 0 0.236199580306685 N 0 0.486514522821577 N N 0 20398 ENSG00000220830 ENSG00000105216 - + 9 19 11003096 39412048 downstream intron RP11-109M17.1 LSM14A 11001748 39355283 + + 0.346473029045643 11054933 39388192 - + Y - 2.02371728678309 N HCC1954 23 7.5 3 6 1 N - - N LTR SINE 1 1 1 6 0.599906845433805 0.349945659836387 0.599906845433805 0.349945659836387 1 - 0 42465 N N 3.48280442206126 3.44615838200292 3.44615838200292 0 0 0.938885345963311 N 0 0 N N 2269 0 ENSG00000056050 ENSG00000174473 + - 4 4 170915637 174199266 coding upstream C4orf27 GALNTL6 170887205 172971229 - + 0 170895387 172839868 - - N 0.715326055392117 - Y HCC1954 1 1 1 0 3 N - - N - - 0 0 0 5 0.621332089913584 0.599906845433805 0.621332089913584 0.599906845433805 1 0 - 16824 N N 3.34831435801417 2.98272161479402 2.98272161479402 9 0 0.245241775959099 N 0.330524553571429 0.096986607142857 N N 443941 0 ENSG00000172057 ENSG00000220375 - - 17 1 35337380 558984 utr3p intron ORMDL3 RP5-857K21.14 35330822 558778 - + 0.096986607142857 35331837 558819 + - Y - 1 N HCC1954 2 2 2 4 1 N 506 15.0412 N - - 0 0 0 4 0.628473838073511 0.407079645115797 0.628473838073511 0.407079645115797 2 - 0 40634 N Y 3.57336771439491 3.54872248456702 3.54872248456702 17 0 0.280344087055853 N 0 0 N N 6782 5881 ENSG00000101079 ENSG00000112664 - + 20 6 34807895 34468419 utr3p downstream NDRG3 NUDT3 34713583 34363982 - - 0 34714047 34362769 + - Y - - N HCC1954 34 28.8 24 5 1 N - - N SINE - 1 0 1 5 0.471355378555133 0.792734045751814 0.792734045751814 0.471355378555133 1 - - 10890 N N 3.54616183148728 3.39483647792751 3.39483647792751 6 0 0.0857823950707958 N 0 0.315047021943574 N N 11507 252027 ENSG00000065833 ENSG00000141738 + - 6 17 84197498 35157070 intron utr5p ME1 GRB7 83976827 35147713 - + 0.315047021943574 84115224 35147875 - - Y 0.886738494281714 0.410465831783318 N HCC1954 22 20.2857142857143 20 7 1 N - - N SINE - 1 0 1 7 0.328520415356608 0.664182578873142 0.664182578873142 0.328520415356608 2 0 0 31395 Y Y 3.23632367866849 3.70256863841317 3.23632367866849 0 0 0.998272184372378 Y 0 0.986351364863513 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 intron upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42854176 42826141 - + N 0.0692123342775211 - N HCC1954 1 1 1 0 6 N - - Y DNA,LTR LTR 0.680851063829787 1 1 7 0.964136001590045 0.5713398527941 0.964136001590045 0.5713398527941 2 0 - 16263 N N 3.64553343878587 3.35992570784171 3.35992570784171 0 0 0.119162718059298 N 0 0 N N 1992 26061 ENSG00000003436 ENSG00000143324 - - 2 1 188127464 179122106 utr5p intron TFPI XPR1 188037202 178867763 - + 0 188127391 178947239 + - Y - 0.7407822719534 N HCC1954 21 20.25 19 4 1 N - - N - Other 0 1 1 4 0.557056356474248 0.39993789695587 0.557056356474248 0.39993789695587 2 - 0 45642 N N 3.15592385843924 3.25364368345618 3.15592385843924 0 0.341772151898734 0.0180295454434680 N 0 0 N N 5018 7339 ENSG00000000003 ENSG00000141905 - + X 19 99778450 3414603 utr3p upstream TSPAN6 NFIC 99770451 3310616 - + 0 99770484 3290666 + + Y - - N HCC1954 483 466.142857142857 440 7 1 N - - N LINE SINE 1 1 1 7 0.299953422716903 0.307095170876829 0.307095170876829 0.299953422716903 2 - - 17488 N Y 3.64553343878587 3.22998788850064 3.22998788850064 304 0 0.0187709177330651 Y 0 0 N N 17324 17324 ENSG00000185499 ENSG00000185499 - + 1 1 153429330 153429330 coding upstream MUC1 MUC1 153424924 153424924 - - 0.99302999631947 153429201 153429921 + - N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 10 0.707033067832699 0.435646637755502 0.707033067832699 0.435646637755502 1 - - 33086 N N 3.31592438821476 2.95382031470719 2.95382031470719 5 0 0.625907337957642 N 0 0 Y N 171855 247001 ENSG00000198886 ENSG00000198786 - + MT MT 12138 14149 coding coding MT-ND4 MT-ND5 10761 12338 + + 0 10825 13902 - + N 0.28629595620082 1.1071556937776 N HCC1954 2 1.33333333333333 1 2 3 N 189 4.09957 N - - 0 0 0 6 1.0069864905496 0.785592297591888 1.0069864905496 0.785592297591888 2 0 0 26726 N Y 3.74656995804013 3.66951632120446 3.66951632120446 0 0 0.827670900837679 Y 0.00340136054421769 0.993030778745064 N N 7487 568 ENSG00000188603 ENSG00000196877 + - 16 16 28411124 28275423 intron intron CLN3 NPIPL1 28396101 28262355 - - 0 28396558 28271882 - + N 1.13856838932361 22.22221131631 N HCC1954 20 8.4 4 5 2 N - - N - SINE 0 0.549618320610687 0.549618320610687 5 0.792734045751814 0.807017542071667 0.807017542071667 0.792734045751814 1 0 0 11893 N N 2.6718368118362 1.39998898407635 1.39998898407635 0 0.208645336963921 0.0896603669596874 N 0.89788972089857 0.208645336963921 N N 11502 14964 ENSG00000159921 ENSG00000108349 - + 9 17 36248450 35581957 utr3p utr5p GNE CASC3 36204430 35550033 - + 0.208645336963921 36206342 35550171 + + Y - - N HCC1954 38 35.4 30 5 1 N - - N LINE Simple_repeat 0.404580152671756 0.96551724137931 0.96551724137931 5 0.93556900895034 0.414221393275723 0.93556900895034 0.414221393275723 1 - - 2620 N N 3.36042022138167 3.56232542602083 3.36042022138167 1 0 0.136223542082512 N 0.1072 0.718933333333333 N N 193 4 ENSG00000180423 ENSG00000103569 + + 11 15 46595353 56265402 intron downstream HARBI1 AQP9 46581124 56217700 - + 0.173333333333333 46583842 56339667 - + Y 0.851931146110886 - N HCC1954 360 58.4444444444444 20 9 1 N 47 23.7983 N SINE LTR 1 1 1 9 0.314236919036755 0.39993789695587 0.39993789695587 0.314236919036755 3 0 - 14445 N Y 3.22846030519079 3.31588453542141 3.22846030519079 0 0.926255144032922 0.299074268005022 N 0.926255144032922 0.889382716049383 N N 15935 0 ENSG00000205531 ENSG00000177173 + - 11 1 2970183 116878237 coding intron NAP1L4 AL390066.5-1 2922237 116877117 - - 0.557530864197531 2929065 116877119 - + Y - 1 N HCC1954 1 1 1 0 1 N - - N - Low_complexity 0 0.18 0.18 7 0.792734045751814 0.357087407996313 0.792734045751814 0.357087407996313 3 - 0 33106 N N 3.40744620240479 3.5246463161926 3.40744620240479 0 0.0115714285714283 0.999933091410466 N 0.0204761904761905 0.0115714285714283 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0.0115714285714283 8548 15513 - + N 0.655744413572778 1.16857738568299 N HCC1954 2 1.375 1 3 8 Y 189 4.09957 N - - 0 0 0 8 0.835584534711372 1.20695543902754 1.20695543902754 0.835584534711372 3 0 0 31325 Y Y 3.54296933622177 3.58999531724489 3.54296933622177 300 0 0.0124413407666688 Y 0.0392492492492491 0.991021021021021 N N 0 5523 ENSG00000203643 ENSG00000051382 - - 3 3 139961738 139960875 downstream upstream AC117389.5 PIK3CB 139961461 139856921 + - 0.991021021021021 139962304 139960897 - + N - - N HCC1954 2 1.28571428571429 1 2 1 N - - Y SINE - 1 0 1 7 0.671324327033068 1.25694767614702 1.25694767614702 0.671324327033068 3 - - 3610 N N 3.58064844605001 3.5246463161926 3.5246463161926 0 0 0.984994419711306 Y 0 0 N Y 5796 16900 ENSG00000159267 ENSG00000185658 - + 21 21 37284373 39607426 coding coding HLCS BRWD1 37045066 39479274 - - 0 37191301 39506462 + - N - - N HCC1954 1 1 1 0 2 Y 508 8.9854 N - - 0 0 0 40 1.40692438750547 1.3069399132665 1.40692438750547 1.3069399132665 4 - - 47127 N Y 3.33743990350944 3.18292205468417 3.18292205468417 277 0 0.069738143484681 Y 0 0.99261933413558 N N 0 0 ENSG00000203305 ENSG00000203305 - + 19 19 60900406 60900406 downstream upstream AC010525.6-1 AC010525.6-1 60899900 60899900 + + 0.99261933413558 60900521 60899475 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.814159290231593 0.749883556792257 0.814159290231593 0.749883556792257 1 - - 25875 N Y 3.17511211436896 3.53824925764641 3.17511211436896 235 0 0.0096455473735122 N 0.800851063829787 0.900425531914894 N N 0 0 ENSG00000200434 ENSG00000222088 - + 16 Y 33873078 10647930 intron intron 5_8S_rRNA AC010970.3-1 33872927 10647846 + + 0.900425531914894 33873041 10647878 - + Y 1 1 N HCC1954 1 1 1 0 1 N 4 12.1279 N - - 0 0 0 50 0.821301038391519 1.04983697950916 1.04983697950916 0.821301038391519 2 0 0 34871 Y Y 3.15099609320118 2.69164756238188 2.69164756238188 104 0 0.459145203562602 Y 0.531309297912714 0.988282732447818 N N 364 1351 ENSG00000137070 ENSG00000213930 - + 9 9 34651883 34640571 utr5p downstream IL11RA GALT 34643932 34636635 + + 0 34643995 34642228 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.870967741935484 0.870967741935484 9 0.835584534711372 0.664182578873142 0.835584534711372 0.664182578873142 1 - - 44784 Y Y 3.04430905912733 3.45144752203174 3.04430905912733 320 0 0.00531987693091762 Y 0 0.9800625 N N 40 36 ENSG00000165429 ENSG00000204043 - + 10 10 81600608 81462701 upstream downstream AL135925.10 FAM22C 81591094 81453188 + + 0 81555595 81516176 - + N - - N HCC1954 16 9.29032258064516 3 31 2 N - - Y - SINE 0 0.149122807017544 0.149122807017544 31 0.685607823352921 0.814159290231593 0.814159290231593 0.685607823352921 1 - - 17877 N Y 3.42204236083514 3.03226839610352 3.03226839610352 0 0 0.492869527307216 N 0.845595766473199 0.794127688630932 N N 2252 3863 ENSG00000181873 ENSG00000219481 + + 1 1 226436581 146862781 utr3p upstream C1orf69 NBPF15 226420139 146827614 + + 0.794127688630932 226432877 146822896 + + N - - Y HCC1954 44 36.2857142857143 21 7 1 N - - N SINE - 1 0 1 7 0.28566992639705 0.914143764470561 0.914143764470561 0.28566992639705 4 - - 141 Y Y 3.42783536197374 3.42360979693834 3.42360979693834 226 0 0.894594779736313 Y 0 0.989841069171031 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 upstream utr3p C11orf66 C11orf79 61005168 60954173 + + 0 60996795 60970163 - + N - 1.98651781809781 N HCC1954 1 1 1 0 6 N - - Y LTR - 1 0 1 4 0.707033067832699 0.849868031031224 0.849868031031224 0.707033067832699 1 - 0 47142 N N 3.44193281696752 3.52105259334297 3.44193281696752 0 0 0.912030367913398 N 0 0 Y N 302 7 ENSG00000167637 ENSG00000204866 - + 19 19 42062306 51356385 intron upstream ZNF345 IGFL2 42033103 51274062 + + 0 42033444 51261297 - + N 0.191267882868105 - N HCC1954 1 1 1 0 2 N 138 5.8892 N - DNA 0 0.0722222222222222 0.0722222222222222 9 0.492780623034912 1.13553795742827 1.13553795742827 0.492780623034912 2 0 - 36661 Y Y 3.40528677690917 3.48743121468078 3.40528677690917 0 0 0.627815046754172 Y 0 0.937781531531532 N N 32 3670 ENSG00000123096 ENSG00000123095 - - 12 12 26277134 26169113 coding coding SSPN BHLHE41 26239789 26164228 + - 0 26240140 26166290 - + N - 0.825111180165878 N HCC1954 2 1.16666666666667 1 1 2 N - - Y - - 0 0 0 6 0.685607823352921 0.685607823352921 0.685607823352921 0.685607823352921 2 - 0 44106 N Y 3.43933231109443 3.32316526707651 3.32316526707651 0 0 0.48263383132989 N 0.944217898832685 0.936249027237354 N N 18316 217 ENSG00000215136 ENSG00000156500 - + 10 X 45259678 133816282 intron coding AL731567.6 FAM122C 45189635 133768890 + + 0 45206580 133790978 - + Y - - N HCC1954 24 22.75 21 4 1 N - - N Other - 1 0 1 4 0.478497126715059 0.535631111994469 0.535631111994469 0.478497126715059 3 - - 36668 N Y 3.47911741325579 3.25360004855864 3.25360004855864 0 0 0.461215261938416 Y 0.952215146378339 0.986347184679525 N Y 52 68 ENSG00000111215 ENSG00000212127 - + 12 12 10893344 11215465 coding coding PRR4 TAS2R14 10889717 10982120 - - 0 10892273 11078648 + - N - - N HCC1954 2 1.2 1 1 1 Y - - N - LINE,SINE,LTR 0 0.469194312796209 0.469194312796209 5 0.628473838073511 1.06412047582901 1.06412047582901 0.628473838073511 4 - - 2793 N Y 3.66745018166468 3.26824964015148 3.26824964015148 1 0 0.106409771718061 N 0.962250933997509 0.924501867995019 N N 2216 8014 ENSG00000197217 ENSG00000149084 - - 8 11 23371081 43834736 utr3p utr3p ENTPD4 HSD17B12 23299386 43658719 - + 0 23346255 43834016 + - Y - - N HCC1954 74 58.5714285714286 38 7 1 N - - N SINE - 1 0 1 7 0.657040830713216 0.999844742389676 0.999844742389676 0.657040830713216 1 - - 48480 N N 3.55401162459584 3.29280674169672 3.29280674169672 24 0 0.065574823133102 N 0.611239914680516 0.149587313363628 N N 0 0 ENSG00000113263 ENSG00000209951 - + 5 7 156614687 86960 intron upstream ITK AC097646.2-1 156540432 86858 + - 0.149587313363628 156578758 126097 - - Y 1 - N HCC1954 160 117 80 4 1 N - - N SINE - 1 0 1 4 0.449930134075354 0.528489363834543 0.528489363834543 0.449930134075354 2 0 - 33424 N Y 3.42680229220385 3.40740634961144 3.40740634961144 426 0 0.38649427434849 Y 0 0.994830815636479 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding coding MT-CO3 MT-ND1 8367 3308 + + 0 8549 3865 - + N - - N HCC1954 4 2.5 1 3 6 N - - N - - 0 0 0 4 0.807017542071667 0.942710757110266 0.942710757110266 0.807017542071667 2 - - 43760 N N 3.52783881145811 3.21279122419719 3.21279122419719 9 0 0.0717008729207397 N 0 0 N N 0 3891 ENSG00000219717 ENSG00000166295 + + 22 10 35147635 73665622 upstream intron WI2-80423F1.1 C10orf104 35147264 73645812 - + 0 35154975 73645955 - + Y - 0.744979490524871 N HCC1954 20 19.6 18 5 1 N - - N SINE - 1 0 1 5 0.535631111994469 0.407079645115797 0.535631111994469 0.407079645115797 1 - 0 30781 Y Y 3.4869807867335 3.48743121468078 3.4869807867335 0 0 0.130839523237372 Y 0 0 N N 79891 9069 ENSG00000160211 ENSG00000071889 + - X X 153428981 153397757 coding upstream G6PD FAM3A 153412800 153387696 - - 0 153413448 153399818 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.671324327033068 0.907002016310634 0.907002016310634 0.671324327033068 2 - - 19120 N Y 3.57848902055439 3.61616813038263 3.57848902055439 0 0 0.84050213034461 N 0.550215489094946 0.892908449784511 Y N 1843 3863 ENSG00000142794 ENSG00000219481 - + 1 1 21684085 146862781 intron upstream NBPF3 NBPF15 21639217 146827614 + + 0.892908449784511 21641321 146823434 - + N 0.707256802427417 - N HCC1954 6 4.33333333333333 3 6 1 N 264 24.5347 N SINE - 1 0 1 6 0.271386430077198 0.464213630395207 0.464213630395207 0.271386430077198 3 0 - 17892 N N 3.71191550960805 3.31961139702023 3.31961139702023 11 0 0.325332682137 N 0 0 Y N 34471 0 ENSG00000116251 ENSG00000219978 + + 1 1 6182266 204347066 coding intron RPL22 RP11-38J22.2 6167668 204346677 - + 0.00411522633744854 6169458 204346952 - + N - 1 N HCC1954 27 15.4285714285714 9 7 1 N - - N - - 0 0 0 7 0.414221393275723 0.271386430077198 0.414221393275723 0.271386430077198 2 - 0 33009 N N 2.7459636226299 3.67320333000993 2.7459636226299 6 0.013404297260004 0.999996127242658 N 0 0.327321111768184 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8474 11426 - + N 0.683366249773457 0.980330327290683 N HCC1954 3 1.53846153846154 1 6 12 N 189 4.09957 N - - 0 0 0 13 1.29979816510658 1.34979040222606 1.34979040222606 1.29979816510658 1 0 0 26744 Y Y 3.82658547553966 3.37232774565629 3.37232774565629 256 0 0.276058652963334 Y 0 0.977101293103448 N N 0 0 ENSG00000221286 ENSG00000207514 + + 16 16 71171037 70968219 downstream downstream AC092289.3 U6 71170942 70968104 - + 0 71113953 71018857 - + N - - N HCC1954 1 1 1 0 2 N - - Y DNA,LINE - 0.909090909090909 0 0.909090909090909 4 0.549914608314322 0.871293275511003 0.871293275511003 0.549914608314322 4 - - 12362 N N 3.17101453040955 3.47825217735525 3.17101453040955 0 0 0.661225881614675 N 0.613075789608559 0.66247036965853 N N 1649619 13563 ENSG00000141736 ENSG00000163110 - - 17 4 35138441 95808400 coding upstream ERBB2 PDLIM5 35104766 95592061 + + 0 35125065 95570967 - - Y - - N HCC1954 20 17.2857142857143 1 6 2 N - - N - SINE 0 1 1 7 0.407079645115797 0.292811674556976 0.407079645115797 0.292811674556976 2 - - 39072 N N 3.47552369040616 3.35715736809928 3.35715736809928 2 0 0.0651677961685972 N 0.887310890009541 0 N N 1992 4017 ENSG00000003436 ENSG00000214482 - + 2 15 188127464 83018061 utr5p utr3p TFPI AC115102.7 188037202 83013781 - - 0 188127364 83016534 + - Y - - N HCC1954 24 20.4857142857143 8 35 1 N - - N - Other 0 1 1 35 0.849868031031224 0.999844742389676 0.999844742389676 0.849868031031224 2 - - 29262 Y Y 3.33833564463353 3.5351195431132 3.33833564463353 366 0 0.051454120606695 Y 0 0.986149058894961 N N 176 0 ENSG00000124635 ENSG00000222800 + - 6 6 27208520 27185738 utr3p downstream HIST1H2BJ U2 27202037 27185548 - - 0 27202073 27173411 - + N 0.278090249371269 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.949852505270192 0.814159290231593 0.949852505270192 0.814159290231593 4 0 - 17301 Y Y 3.33168675516419 3.33590297262978 3.33168675516419 0 0 0.875499756388565 Y 0 0 N N 2003 24302 ENSG00000160781 ENSG00000198952 - + 1 1 154484471 154519240 coding utr3p PAQR6 SMG5 154479831 154485641 - - 0 154484444 154486872 + - N - 0.561336638118265 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.749883556792257 0.93556900895034 0.93556900895034 0.749883556792257 1 - 0 44245 N N 3.53039946453785 3.09087103183403 3.09087103183403 6 0 0.0753273443300757 N 0 0 N N 4429 3891 ENSG00000137075 ENSG00000166295 + + 9 10 36391195 73665622 upstream intron RNF38 C10orf104 36326401 73645812 - + 0 36402867 73645953 - + Y - 0.744979490524871 N HCC1954 28 25 23 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.321378667196682 0.321378667196682 0.28566992639705 1 - 0 46745 Y Y 3.38552945952599 3.44615838200292 3.38552945952599 245 0 0.113666046220720 Y 0.00408163265306116 0.989291200351108 N Y 7761 1457 ENSG00000129455 ENSG00000169035 + - 19 19 56196770 56179106 coding intron KLK8 KLK7 56191076 56171541 - - 0 56196166 56176982 - + N 0.875293755289509 37.0552029096617 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 93 0.728458312312478 0.828442786551446 0.828442786551446 0.728458312312478 4 0 0 16016 N Y 3.09872082494259 3.59421153471047 3.09872082494259 0 0 0.479362148029894 N 0.960647400710365 0.960647400710365 N N 6576 30525 ENSG00000106635 ENSG00000134202 - - 7 1 72609960 110085183 coding utr3p BCL7B GSTM3 72588622 110078077 - - 0 72609753 110079929 + + Y - - N HCC1954 37 33.625 29 8 1 N - - N - SINE 0 1 1 8 1.09268746846872 0.335662163516534 1.09268746846872 0.335662163516534 3 - - 46830 Y Y 3.24740581983591 3.51525959220437 3.24740581983591 203 0 0.249566917754871 Y 0 0.987076962446421 N N 106 280 ENSG00000213793 ENSG00000183022 - + 19 19 58645397 58637941 upstream intron AC022137.6-2 AC022137.6-1 58644449 58627067 + + 0 58642272 58627148 - + N - 0.269063083904262 N HCC1954 3 1.82142857142857 1 22 3 N - - Y - - 0 0 0 28 0.621332089913584 0.421363141435649 0.621332089913584 0.421363141435649 3 - 0 46348 N Y 3.49760826715431 3.46448140203209 3.46448140203209 238 0.561848739495798 0.0216975606822984 N 0.561848739495798 0.322857142857143 N N 7771 0 ENSG00000172081 ENSG00000219751 + + 19 2 2047304 22266690 utr3p downstream MOBKL2A AC068044.1 2022037 22264713 - + 0 2023087 22305027 - + Y - - N HCC1954 23 17.75 5 4 1 N - - N SINE srpRNA,SINE 1 0.675675675675676 1 4 0.628473838073511 0.264244681917271 0.628473838073511 0.264244681917271 1 - - 318 Y Y 3.55401162459584 3.37717580530765 3.37717580530765 393 0 0.0816623730285757 Y 0.0560991854090885 0.986611335963249 N N 0 1020 ENSG00000200983 ENSG00000166436 - - 11 11 8662479 8649989 upstream upstream SNORA3 TRIM66 8662350 8590160 + - 0 8657743 8653006 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE,DNA 0 0.819277108433735 0.819277108433735 5 0.942710757110266 0.814159290231593 0.942710757110266 0.814159290231593 4 - - 46826 Y Y 3.62464976567696 3.3414348539432 3.3414348539432 279 0 0.158245637870491 Y 0.935016362786349 0.989169393797725 N N 16146 7111 ENSG00000167491 ENSG00000129933 - + 19 19 19480736 19339989 utr5p downstream GATAD2A KIAA0892 19399336 19292614 + + 0 19407942 19357949 - + N 0.114681546538879 - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity,Simple_repeat 0 0.26875 0.26875 31 0.692749571512847 1.02841173502938 1.02841173502938 0.692749571512847 2 0 - 47285 N N 3.06782793322949 2.59156017451149 2.59156017451149 0 0.0392840062854412 0.297665313262067 N 0.00280112044817915 0 N N 16224 4351 ENSG00000141867 ENSG00000105127 - - 19 19 15252262 15351603 coding downstream BRD4 AKAP8 15209301 15325341 - - 0 15244770 15304267 + + N - - Y HCC1954 1 1 1 0 1 N 524 25.9511 N - Simple_repeat,Simple_repeat 0 0.946107784431138 0.946107784431138 5 0.771308801272036 1.02841173502938 1.02841173502938 0.771308801272036 2 - - 31629 N N 2.55520575950186 2.98721107876773 2.55520575950186 0 0 0.381114957770099 N 0.0643598615916955 0 Y N 614 7845 ENSG00000185614 ENSG00000004534 - + 3 3 49817465 50089685 coding utr5p C3orf54 RBM6 49815691 49952481 + + 0 49816750 49952642 - + N - 0.345358292041282 N HCC1954 1 1 1 0 2 N 568 9.12122 N Simple_repeat - 0.170886075949367 0 0.170886075949367 45 1.12839620926835 0.899860268150708 1.12839620926835 0.899860268150708 3 - 0 48723 N Y 3.15525216346012 2.9920684859889 2.9920684859889 1 0.157033248081841 0.0436212254231193 N 0.157033248081841 0.882921284455811 N N 12188 0 ENSG00000168724 ENSG00000218534 - + 5 9 34994825 45306461 utr3p downstream DNAJA5 RP11-187C18.1 34965455 45304083 + - 0.00483091787439605 34991677 45290591 - - Y - - N HCC1954 116 97.6 92 5 1 N - - N SINE - 1 0 1 5 0.45707188223528 0.521347615674617 0.521347615674617 0.45707188223528 1 - - 45529 N Y 3.12449241049621 2.39788152983156 2.39788152983156 0 0 0.0432712786796732 N 0 0 N N 297 0 ENSG00000204655 ENSG00000182225 - + 6 19 29748128 5527949 utr3p downstream MOG AC011533.6 29732788 5527671 + - 0 29747854 5518621 - - Y - - N HCC1954 38 34.3333333333333 32 6 1 N - - N SINE - 1 0 1 6 0.349945659836387 0.599906845433805 0.599906845433805 0.349945659836387 1 - - 44867 N N 3.49168728493972 3.09087103183403 3.09087103183403 13 0 0.0476151704930237 Y 0.336336336336336 0.312634062634063 N N 3907 3891 ENSG00000156650 ENSG00000166295 - + 10 10 76462645 73665622 upstream intron MYST4 C10orf104 76255346 73645812 + + 0.312634062634063 76237779 73645953 - + N - 0.744979490524871 N HCC1954 26 21.2 20 5 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.34280391167646 0.34280391167646 0.314236919036755 1 - 0 5608 N N 3.5774559507845 3.38912318237562 3.38912318237562 1 0 0.789983988553197 N 0 0 N N 0 0 ENSG00000214199 ENSG00000217946 + + 2 X 106681564 97532574 intron intron AC096663.1-1 RP11-390F10.1 106680219 97531164 - + 0 106680716 97532107 - + Y 1 1 N HCC1954 12 9.27272727272727 8 11 1 N - - N - - 0 0 0 11 0.328520415356608 0.278528178237124 0.328520415356608 0.278528178237124 3 0 0 33000 N Y 2.57495130970384 3.3697272397832 2.57495130970384 306 0 0.0430325613811725 Y 0.0634732640259683 0.926415756459183 N N 59837 151141 ENSG00000198695 ENSG00000198888 + + MT MT 14674 4264 coding coding MT-ND6 MT-ND1 14150 3308 - + 0 14486 4245 - + N 1.38453395394424 5.27407832110376 N HCC1954 8 4 2 4 2 N - - N - - 0 0 0 4 0.828442786551446 0.842726282871298 0.842726282871298 0.828442786551446 2 0 0 15243 N N 3.75744441254485 3.38593068711011 3.38593068711011 12 0.00862068965517238 0.0672350801452634 N 0.0260133091349063 0.130369026013309 N N 3863 0 ENSG00000219481 ENSG00000211244 + - 1 7 146862781 66502053 utr5p upstream NBPF15 AC099758.4 146827614 66501982 + - 0.130369026013309 146827699 66613609 + + Y - - N HCC1954 40 35 20 4 1 N 247 22.5611 N - SINE 0 1 1 4 0.614190341753658 0.292811674556976 0.614190341753658 0.292811674556976 2 - - 6428 N N 3.61104682422314 3.52208566311286 3.52208566311286 10 0 0.145616130075206 N 0.505681675655337 0.10352439483256 N N 9911 153380 ENSG00000071073 ENSG00000185275 - + 2 Y 98714021 19614093 utr3p utr3p MGAT4A CD24L4 98602001 19611898 - - 0.0448764580459051 98607067 19612776 + - Y - - N HCC1954 39 33.2 12 5 1 N - - N SINE SINE 1 0.372093023255814 1 5 0.535631111994469 0.921285512630487 0.921285512630487 0.535631111994469 1 - - 18130 Y Y 3.51423587000429 3.74656995804013 3.51423587000429 0 0 0.98155103390265 Y 0 0 N N 17101 0 ENSG00000162407 ENSG00000219539 + - 1 1 56817845 56446716 downstream upstream PPAP2B RP4-710M16.1 56733023 56445827 - - 0 56613662 56487460 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LINE 0 0.470588235294118 0.470588235294118 25 1.07126222398894 0.849868031031224 1.07126222398894 0.849868031031224 2 - - 37463 N N 2.91774333610232 3.16567195721824 2.91774333610232 0 0.0551646495918942 0.463576158843564 N 0 0.0926581158779303 N N 131026 169845 ENSG00000115053 ENSG00000080824 - + 2 14 232037449 101675494 coding coding NCL HSP90AA2 232027706 101617139 - - 0.0926581158779303 232034687 101621049 + - Y - - N HCC1954 1 1 1 0 1 Y - - N Simple_repeat,Simple_repeat,Simple_repeat Low_complexity 0.296296296296296 0.225961538461538 0.296296296296296 4 0.928427260790413 0.956994253430118 0.956994253430118 0.928427260790413 3 - - 47983 N N 3.26616992024256 3.73080759109069 3.26616992024256 0 0.0709677419354839 0.734095910850064 N 0.137327188940092 0.0709677419354839 N N 0 6627 ENSG00000223281 ENSG00000113269 + + 8 5 100002954 179431719 downstream coding 7SK RNF130 100002637 179315111 - - 0.0709677419354839 99997280 179372763 - - Y - - N HCC1954 1 1 1 0 2 N 272 23.0717 N - - 0 0 0 4 0.385654400636018 0.5713398527941 0.5713398527941 0.385654400636018 3 - - 25508 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.0833183828336453 N 0 0 N N 7284 45068 ENSG00000156299 ENSG00000205336 + + 21 16 31853161 56256445 intron upstream TIAM1 GPR56 31412607 56220023 - + 0 31586657 56211646 - + Y 1.63905605053672 - N HCC1954 24 20.7083333333333 20 24 1 N - - N SINE - 1 0 1 24 0.378512652476092 0.599906845433805 0.599906845433805 0.378512652476092 1 0 - 34787 Y Y 3.36291051644453 3.43101850966944 3.36291051644453 0 0 0.786426670818953 Y 0 0 N N 71 0 ENSG00000160339 ENSG00000219785 - + 9 9 136919745 136900142 coding upstream FCN2 RP11-263F14.3 136912475 136899686 + + 0 136912576 136896318 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 0.892718519990782 0.864151527351077 0.892718519990782 0.864151527351077 1 - - 26771 Y Y 3.41423242051993 3.71720464963688 3.41423242051993 278 0 0.805829318098176 Y 0.250705035971223 0.992028776978417 N N 1747 10006 ENSG00000157312 ENSG00000132612 + + 16 16 67921999 67916446 downstream downstream COG8 VPS4A 67920025 67895081 - + 0.992028776978417 67918880 67916888 - + N - - N HCC1954 2 1.42857142857143 1 3 4 N - - Y SINE SINE,DNA,SINE 0.0419161676646707 0.533333333333333 0.533333333333333 7 1.19267194270768 0.821301038391519 1.19267194270768 0.821301038391519 2 - - 22380 N Y 3.62192127872787 3.2216204045696 3.2216204045696 204 0 0.0304569337489986 N 0 0 N N 0 3567 ENSG00000217333 ENSG00000156011 - - 1 8 169680726 18915476 upstream intron RP1-81F6.1 PSD3 169680447 18429093 - - 0.838530838530838 169691448 18850872 + + Y - 1.78065816235911 N HCC1954 140 56.8 20 5 1 N - - N SINE SINE 0.925 1 1 5 0.28566992639705 0.278528178237124 0.28566992639705 0.278528178237124 3 - 0 41743 Y Y 3.2216342342823 3.28503149650166 3.2216342342823 1 0 0.996556072509958 Y 0.0517091035926056 0.983650156958493 N N 9799 0 ENSG00000076554 ENSG00000222697 - - 8 8 81155565 81279688 coding upstream TPD52 SRP_euk_arch 81109662 81279396 - + 0 81139383 81246082 + - N - - N HCC1954 1 1 1 0 6 N - - Y - Simple_repeat 0 0.296650717703349 0.296650717703349 8 0.949852505270192 1.19981369086761 1.19981369086761 0.949852505270192 3 - - 1488 N N 1.55910242553179 2.04239882705049 1.55910242553179 2 0 0.351059380440535 N 0.015433673469388 0 N N 14964 153581 ENSG00000108349 ENSG00000110092 - + 17 11 35581957 69178422 utr5p utr3p CASC3 CCND1 35550033 69165054 + + 0 35550129 69176752 - + Y 0.138909074928949 1.71816677396659 N HCC1954 20 4.8 1 1 1 N - - N Simple_repeat - 0.96969696969697 0 0.96969696969697 5 0.564198104634174 0.928427260790413 0.928427260790413 0.564198104634174 3 0 0 45863 N Y 3.60256518892881 3.63655728995158 3.60256518892881 0 0.737838915470495 0.757669813202701 N 0 0.895135566188198 N N 355 0 ENSG00000106066 ENSG00000207553 - + 7 19 29201417 58903901 coding upstream CPVL hsa-mir-518c 29001772 58903801 - + 0 29098843 58903432 + + Y - - N HCC1954 20 17.2 6 5 1 N - - N - SINE 0 1 1 5 0.949852505270192 0.357087407996313 0.949852505270192 0.357087407996313 4 - - 27426 Y Y 3.47449062063627 3.56761456604966 3.47449062063627 119 0 0.100858030102533 Y 0.981370509516565 0.990685254758282 N N 300 1618 ENSG00000157429 ENSG00000167377 + - 16 16 70080755 70053651 coding upstream ZNF19 ZNF23 70065477 70039001 - - 0 70069634 70055054 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 4 0.907002016310634 0.5713398527941 0.907002016310634 0.5713398527941 2 - - 33215 N Y 3.22639416565101 3.49744043328497 3.22639416565101 457 0 0.00357371953310703 Y 0 0.994934965400038 N N 339915 247001 ENSG00000198727 ENSG00000198786 - + MT MT 15882 14149 coding coding MT-CYB MT-ND5 14748 12338 + + 0.994934965400038 15356 13725 - + N 0.959800492111642 - N HCC1954 2 1.25 1 1 2 N - - N - - 0 0 0 4 0.614190341753658 0.764167053112109 0.764167053112109 0.614190341753658 3 0 - 14637 N N 3.09868097214924 2.93400021659171 2.93400021659171 0 0 0.0830766261303846 N 0 0.0187181663837011 N N 24457 0 ENSG00000142186 ENSG00000220375 - - 11 1 65062758 558984 upstream intron SCYL1 RP5-857K21.14 65049124 558778 + + 0.0187181663837011 65023661 558815 - - Y - 1 N HCC1954 2 2 2 4 1 N - - N LINE - 1 0 1 4 0.792734045751814 0.585623349113953 0.792734045751814 0.585623349113953 2 - 0 3670 N N 3.54503547576155 3.01706258767976 3.01706258767976 0 0.297638842700366 0.0255168712444607 N 0.457266378450283 0.584968407050216 N N 581 49 ENSG00000173198 ENSG00000186842 + - X 21 77469743 32870062 downstream intron CYSLTR1 C21orf77 77414787 32866420 - - 0.457266378450283 77364715 32868363 - + Y - 3.7798074459128 N HCC1954 23 20.6 20 5 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.349945659836387 0.349945659836387 0.299953422716903 1 - 0 39396 N Y 3.53039946453785 2.81248125181267 2.81248125181267 81 0.117952600256556 0.126999032293870 N 0.604315185161819 0.942295964502765 N N 1278 110 ENSG00000214611 ENSG00000198312 - + 15 22 19634453 20993088 utr5p upstream AC126335.16-4 D87018.1-3 19624910 20991471 + + 0 19624929 20982553 - + Y - - N HCC1954 8 3.2 1 33 2 N 364 23.3546 N Satellite Satellite 0.00716845878136201 0.903703703703704 0.903703703703704 55 1.64974382494297 0.964136001590045 1.64974382494297 0.964136001590045 2 - - 29701 Y Y 3.75694989900489 3.30488209984069 3.30488209984069 6 0 0.100823144328735 Y 0 0.975470254158779 N N 291864 19742 ENSG00000196230 ENSG00000137337 - - 6 6 30801182 30793437 coding upstream TUBB MDC1 30796136 30775564 + - 0 30798352 30793491 - + N - - N HCC1954 2 1.25 1 1 1 N - - Y - - 0 0 0 4 0.814159290231593 0.657040830713216 0.814159290231593 0.657040830713216 1 - - 25195 Y Y 3.3446273492087 3.77104735399867 3.3446273492087 266 0 0.00821703948888775 Y 0.992155585814931 0.992155585814931 N N 2546 3633 ENSG00000136159 ENSG00000136143 - - 13 13 47519283 47473463 utr5p upstream NUDT15 SUCLA2 47509704 47414792 + - 0 47509744 47477139 - + N - - N HCC1954 22 4.75 1 4 2 N - - Y - LTR 0 1 1 12 0.849868031031224 0.87843502367093 0.87843502367093 0.849868031031224 1 - - 40820 N N 3.26616992024256 3.51001030496889 3.26616992024256 0 0.347355397463656 0.0628831814027743 N 0.363671512527065 0.347355397463656 N N 0 28646 ENSG00000209130 ENSG00000125835 - + 7 20 79785748 2399499 downstream utr3p AC004862.1 SNRPB 79785505 2390281 + - 0.347355397463656 79844664 2390313 - - Y - - N HCC1954 1 1 1 0 1 N - - N LINE - 0.552631578947368 0 0.552631578947368 5 0.271386430077198 0.828442786551446 0.828442786551446 0.271386430077198 2 - - 28880 N N 3.02963319511028 3.10812112929996 3.02963319511028 0 0.222846715328467 0.0654348828972522 N 0.282627737226278 0 N N 0 551733 ENSG00000140873 ENSG00000204628 + + 16 5 76026512 180603512 downstream utr3p ADAMTS18 GNB2L1 75873527 180596536 - - 0 75858083 180596543 - - Y - - N HCC1954 19 11.84375 1 31 1 N - - N LINE - 1 0 1 32 0.28566992639705 1.02126998686945 1.02126998686945 0.28566992639705 2 - - 3362 Y Y 3.34934742778406 3.20124507471334 3.20124507471334 6 0 0.194838571939232 Y 0 0.989937691087116 N N 18589 0 ENSG00000180530 ENSG00000217388 + - 21 21 15359192 15124181 utr5p upstream NRIP1 AF127936.8 15255427 15123346 - - 0 15337689 15151845 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 6 0.821301038391519 0.921285512630487 0.921285512630487 0.821301038391519 2 - - 35676 N Y 3.53039946453785 3.75913982972405 3.53039946453785 119 0 0.0250796347919396 N 0.0656108597285068 0.885585003232062 N N 10403 13271 ENSG00000066084 ENSG00000081923 - - 12 18 49428717 53550037 intron coding DIP2B ATP8B1 49185035 53464656 + - 0.294440853264383 49259566 53549994 - + Y 0.481257329725143 1.91652705132396 N HCC1954 21 20.5 20 4 1 N - - N SINE - 1 0 1 4 0.357087407996313 0.585623349113953 0.585623349113953 0.357087407996313 2 0 0 47994 N N 3.61464054707278 3.54193626645188 3.54193626645188 0 0 0.982022402634643 N 0.328804265041889 0.00307692307692298 N N 0 10798 ENSG00000212451 ENSG00000113761 - - 8 5 127753081 176426349 downstream intron U11 ZNF346 127752949 176382303 + + 0.00307692307692298 128113175 176410307 - - Y - 1.34575632127257 N HCC1954 1 1 1 0 5 N - - N SINE,SINE - 1 0 1 90 0.807017542071667 1.6854525657426 1.6854525657426 0.807017542071667 1 - 0 34242 N Y 3.37808089400154 3.51104337473878 3.37808089400154 290 0 0.0214295087832513 Y 0.992830563135698 0.992830563135698 N N 3688 3 ENSG00000125485 ENSG00000188523 + + 9 9 134535609 134438527 coding coding DDX31 C9orf171 134458205 134275251 - + 0 134477297 134402856 - + N 0.354217655377354 0.835114503816794 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 11 0.899860268150708 0.93556900895034 0.93556900895034 0.899860268150708 3 0 0 4249 Y Y 3.58271458558979 3.33680806132368 3.33680806132368 0 0 0.653625451328262 Y 0.963543455857094 0.975695637238063 N N 16361 188 ENSG00000198420 ENSG00000159860 + + 7 7 143230181 143146099 downstream intron FAM115B AC099548.6 143180984 143138257 - + 0 143164667 143141806 - + N - 1.14656037452309 N HCC1954 4 3.45454545454545 2 11 2 N - - Y Simple_repeat - 0.2125 0 0.2125 11 0.5713398527941 1.3069399132665 1.3069399132665 0.5713398527941 1 - 0 17977 Y Y 3.3414348539432 2.90397256077916 2.90397256077916 0 0 0.234094689865654 Y 0 0.985334629719657 N N 4645 576 ENSG00000196517 ENSG00000159214 + + 1 1 44269721 44234783 coding intron SLC6A9 CCDC24 44234742 44229867 - + 0 44239027 44230281 - + N - 0.252570214091706 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.814159290231593 0.821301038391519 0.821301038391519 0.814159290231593 2 - 0 21985 N N 3.42424163912411 3.61360747730289 3.42424163912411 2 0 0.0449466959021095 N 0 0 N N 15994 49089 ENSG00000119707 ENSG00000117450 - - 14 1 72657740 45760196 intron coding RBM25 PRDX1 72595021 45749295 + - 0 72599356 45757256 - + Y 0.463880906532033 3.16366837851847 N HCC1954 42 9.88888888888889 5 18 1 N - - N SINE - 1 0 1 18 0.335662163516534 0.449930134075354 0.449930134075354 0.335662163516534 1 0 0 27413 Y Y 3.48081283043499 3.20976656280103 3.20976656280103 134 0.0612648221343876 0.764372643555391 Y 0.934123847167325 0.991765480895916 N N 4968 172 ENSG00000104731 ENSG00000205047 + - 16 16 86357056 86292831 coding upstream KLHDC4 AC010536.8 86298920 86291389 - - 0 86299067 86294541 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 1.04269523134923 0.692749571512847 1.04269523134923 0.692749571512847 3 - - 9248 N Y 3.35087501109391 3.3991324009798 3.35087501109391 0 0 0.66932772606452 N 0.66812865497076 0.935766836445954 N N 7721 473 ENSG00000108854 ENSG00000154251 + + 17 17 60088854 63635979 intron downstream SMURF2 AC005332.1-1 59971197 63633345 - - 0 60087326 63622158 - - N 5.32601130531616 - Y HCC1954 4 2.44444444444444 2 18 2 N - - N - - 0 0 0 18 0.428504889595575 0.542772860154395 0.542772860154395 0.428504889595575 1 0 - 39920 Y Y 3.81554318716558 3.5816815158199 3.5816815158199 256 0 0.0181283899370576 Y 0.979248046875 0.9688720703125 N N 374 236 ENSG00000189227 ENSG00000103599 - + 15 15 65605946 65581193 upstream intron C15orf61 IQCH 65600632 65334221 + + 0 65598392 65539367 - + N - 2.03737738653902 N HCC1954 1 1 1 0 1 N - - Y SINE SINE 0.95 0.685534591194969 0.95 6 0.714174815992626 1.13553795742827 1.13553795742827 0.714174815992626 4 - 0 45593 N N 3.30012216847198 3.45972147066338 3.30012216847198 2 0 0.0685644384044113 N 0.793512195121951 0 N N 561 975 ENSG00000183401 ENSG00000198487 - + 19 6 11326619 42218335 coding coding AC024575.6-1 AL512274.9 11316357 42183124 + - 0 11319985 42204389 - - Y - - N HCC1954 34 23.5 6 4 1 N - - N SINE - 1 0 1 4 0.428504889595575 0.585623349113953 0.585623349113953 0.428504889595575 1 - - 23628 N Y 3.57489529770476 3.34785034969775 3.34785034969775 0 0 0.474315103498204 N 0.912627418348242 0.912627418348242 N N 4806 342 ENSG00000196352 ENSG00000219665 - + 1 19 205600934 11999553 intron utr5p CD55 AC008770.7-4 205561488 11959471 + + 0 205565022 11998009 - + Y 2.38556922946302 - N HCC1954 3 1.18181818181818 1 1 1 N - - N SINE - 0.648148148148148 0 0.648148148148148 11 0.385654400636018 1.08554572030879 1.08554572030879 0.385654400636018 2 0 - 38030 N N 3.48912663185998 3.3038490300708 3.3038490300708 4 0 0.0729397190039489 N 0 0 N N 20795 0 ENSG00000198805 ENSG00000220830 - + 14 9 20015086 11003096 downstream upstream NP RP11-109M17.1 19992539 11001748 + + 0.0585641449634835 20024001 10938426 - + Y - - N HCC1954 11 10 9 4 1 N 255 20.6965 N LTR - 1 0 1 4 0.307095170876829 0.735600060472404 0.735600060472404 0.307095170876829 2 - - 26756 Y Y 3.35785956830193 3.60682125918775 3.35785956830193 241 0 0.0500518999592207 Y 0 0.986358210651964 N N 18458 39 ENSG00000166530 ENSG00000140945 - + 16 16 82400529 82387705 upstream intron HSBP1 CDH13 82399094 81439761 + + 0 82394681 82381326 - + N - 0.342299349240781 N HCC1954 1 1 1 0 2 N - - Y DNA SINE 1 0.0608108108108108 1 4 0.349945659836387 0.564198104634174 0.564198104634174 0.349945659836387 2 - 0 26300 N N 3.48809356209009 3.66745018166468 3.48809356209009 8 0 0.0711997689408661 N 0 0.00381679389312994 N N 45068 16 ENSG00000205336 ENSG00000108370 + + 16 17 56256445 60654281 upstream intron GPR56 RGS9 56220023 60564011 + + 0.00381679389312994 56211646 60580803 + + Y - 0.799107275025336 N HCC1954 24 20.5416666666667 18 24 1 N - - N - SINE 0 1 1 24 0.742741808632331 0.428504889595575 0.742741808632331 0.428504889595575 1 - 0 30174 N Y 3.45889608755619 3.24272559405391 3.24272559405391 25 0.101007189365166 0.159326170960142 N 0.107569180683668 0.67846242539338 N N 0 78560 ENSG00000222476 ENSG00000112493 - + 9 6 9432367 33390114 intron utr3p SRP_euk_arch TAPBP 9432060 33375449 + - 0.101007189365166 9432090 33376318 - - Y 1 - N HCC1954 266 92.8461538461538 5 13 1 N - - N srpRNA SINE,SINE 1 0.491666666666667 1 13 0.735600060472404 0.821301038391519 0.821301038391519 0.735600060472404 2 0 - 40161 Y Y 3.53358261223354 3.22167408707565 3.22167408707565 353 0 0.00162442260184781 Y 0 0.985116908375967 N N 2246 90 ENSG00000140395 ENSG00000140403 + + 15 15 76378995 76361591 coding intron WDR61 DNAJA4 76362635 76343551 - + 0 76365450 76357676 - + N - 0.852540429171202 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity,DNA 0 0.288888888888889 0.288888888888889 9 1.13553795742827 1.2783729206268 1.2783729206268 1.13553795742827 2 - 0 39942 Y Y 3.38912318237562 3.22167408707565 3.22167408707565 291 0 0.08807692269556 Y 0 0 N N 172 110 ENSG00000166819 ENSG00000166813 + - 15 15 88023595 87992583 downstream upstream PLIN KIF7 88008607 87972211 - - 0 88007159 87997189 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.871293275511003 0.849868031031224 0.871293275511003 0.849868031031224 4 - - 6673 N Y 3.64400585547602 3.20803129282848 3.20803129282848 182 0.00348432055749126 0.033385595840816 N 0.923344947735192 0.961672473867596 N N 2713 2755 ENSG00000222041 ENSG00000153094 + + 2 2 87687439 111642493 utr3p downstream AC133644.1 BCL2L11 87536002 111594962 + + 0 87687402 111722290 + + N - - Y HCC1954 2 1.98076923076923 1 51 1 N 398 27.3048 N SINE,LINE - 0.926315789473684 0 0.926315789473684 52 1.35693215038599 0.785592297591888 1.35693215038599 0.785592297591888 1 - - 20352 N N 3.61360747730288 3.42424163912411 3.42424163912411 0 0 0.0478607324979291 N 0 0.0500181554103122 N N 49089 677 ENSG00000117450 ENSG00000164663 - + 1 6 45760196 41971077 coding intron PRDX1 USP49 45749295 41870085 - - 0.0500181554103122 45757256 41883231 + - Y - 3.43360179808953 N HCC1954 14 7.70588235294118 7 17 1 N - - N - SINE 0 1 1 17 0.664182578873142 0.299953422716903 0.664182578873142 0.299953422716903 1 - 0 42820 N N 3.44512531223303 3.71720464963688 3.44512531223303 1 0 0.101630661622407 N 0.775767918088737 0.634584755403868 N N 14738 73 ENSG00000172115 ENSG00000109743 - - 7 4 25131480 15343508 utr3p upstream CYCS BST1 25124802 15313739 - + 0.634584755403868 25127681 15292002 + - Y - - N HCC1954 27 23.875 21 8 1 N - - N SINE - 1 0 1 8 0.34280391167646 0.735600060472404 0.735600060472404 0.34280391167646 2 - - 1732 N Y 3.58999531724489 3.47548383761281 3.47548383761281 0 0 0.651261106290538 N 0.00416666666666654 0.862278368794326 N N 9180 13271 ENSG00000014138 ENSG00000081923 - - 11 18 64821663 53550037 upstream upstream POLA2 ATP8B1 64786006 53464656 + - 0 64774178 53550058 - + Y - - N HCC1954 22 21 20 5 1 N - - N SINE - 1 0 1 5 0.357087407996313 0.549914608314322 0.549914608314322 0.357087407996313 1 - - 41138 N Y 3.38383404234679 3.39909254818645 3.38383404234679 147 0 0.351459771986648 Y 0.84398531626506 0.975997740963855 N Y 289 2529 ENSG00000204070 ENSG00000198641 - + 20 20 43472664 43431263 coding coding DBNDD2 SYS1 43468085 43423991 + + 0 43470514 43427740 - + N - 0.866908304998631 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.657040830713216 0.499922371194838 0.657040830713216 0.499922371194838 4 - 0 3706 N N 3.35832357661836 3.76848670091893 3.35832357661836 10 0 0.761596826267319 N 0.309126247901758 0.0449686368053716 N Y 14800 18486 ENSG00000142207 ENSG00000055609 + - 21 7 32687206 151764023 coding intron URB1 MLL3 32605200 151462947 - - 0.0449686368053716 32666687 151601885 - + Y 0.850966307309652 1.54185517748269 N HCC1954 2 1.75 1 3 1 N 407 26.1595 N - - 0 0 0 4 0.449930134075354 0.699891319672773 0.699891319672773 0.449930134075354 4 0 0 10285 N Y 3.62617734898681 3.5587317031712 3.5587317031712 0 0 0.308576896937468 N 0.864718812969408 0.97101117420773 N N 1572 473 ENSG00000136447 ENSG00000154251 - - 17 17 42012364 63635979 intron downstream ARL17P1 AC005332.1-1 41949797 63633345 - - 0 41983594 63622256 + + N 0.108713167154875 - Y HCC1954 12 5.23529411764706 2 34 1 N - - N - - 0 0 0 34 0.849868031031224 0.785592297591888 0.849868031031224 0.785592297591888 1 0 - 9852 Y Y 3.43887765034782 3.40744620240479 3.40744620240479 99 0 0.997774411628245 Y 0 0 N N 170868 252027 ENSG00000141741 ENSG00000141738 - - 17 17 35140314 35157070 coding utr5p C17orf37 GRB7 35138937 35147713 - + 0 35140070 35147803 + - N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 14 0.93556900895034 0.892718519990782 0.93556900895034 0.892718519990782 4 - - 38374 Y Y 3.08677344787462 3.48912663185998 3.08677344787462 0 0 0.176490694169472 Y 0 0 N N 2224 4712 ENSG00000020426 ENSG00000100625 - - 14 14 60505149 60260545 coding coding MNAT1 SIX4 60271223 60246009 + - 0 60332688 60259762 - + N - 1.19682972359529 N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.157446808510638 0.157446808510638 24 0.757025304952183 1.14982145374813 1.14982145374813 0.757025304952183 3 - 0 38805 N N 3.38912318237562 3.425274708894 3.38912318237562 0 0 0.0437046382284141 N 0 0 N N 206 3163 ENSG00000095752 ENSG00000151327 - + 19 14 60573626 34622340 utr3p intron IL11 C14orf24 60567569 34583864 - + 0 60568467 34585717 + + Y - 0.578766413872441 N HCC1954 30 29.8888888888889 29 9 1 N 497 25.1807 N SINE,SINE - 1 0 1 9 0.307095170876829 0.821301038391519 0.821301038391519 0.307095170876829 1 - 0 32102 N Y 3.234707967076 3.57336771439491 3.234707967076 7 0 0.262463942356263 N 0 0.849425391367297 N N 0 2723 ENSG00000209951 ENSG00000114744 + + 7 3 86960 150952968 upstream utr3p AC097646.2-1 COMMD2 86858 150941222 - - 0 126103 150941616 - - Y - - N HCC1954 156 138.578947368421 105 19 1 N - - N - SINE 0 1 1 19 0.871293275511003 0.34280391167646 0.871293275511003 0.34280391167646 2 - - 9131 N N 3.07101108092519 3.61360747730288 3.07101108092519 0 0 0.0745949078523367 N 0 0 N N 1649619 13069 ENSG00000141736 ENSG00000055332 - - 17 2 35138441 37405184 coding intron ERBB2 EIF2AK2 35104766 37179857 + - 0 35125066 37320044 - + Y - 102.423188968732 N HCC1954 22 18.4615384615385 6 13 1 N - - N - SINE 0 1 1 13 0.649899082553289 0.364229156156239 0.649899082553289 0.364229156156239 1 - 0 44683 Y Y 3.44143830342756 3.49168728493972 3.44143830342756 301 0 0.256481217997947 Y 0 0 N N 11 573 ENSG00000178363 ENSG00000205488 - - 10 10 5558225 5555140 downstream utr5p CALML3 AL732437.12 5556924 5546207 + - 0 5582964 5554092 - + N - 13.6695482668023 N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 34 1.06412047582901 1.02126998686945 1.06412047582901 1.02126998686945 4 - 0 32995 N N 3.46115868944844 3.19616362134721 3.19616362134721 0 0 0.999991404901815 N 0.0893280632411064 0.0608695652173911 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0.0608695652173911 8756 14303 - + N 0.560423695130388 0.838285990444985 N HCC1954 3 2 1 3 10 N 189 4.09957 N - - 0 0 0 4 0.657040830713216 0.621332089913584 0.657040830713216 0.621332089913584 2 0 0 27222 N Y 3.30910766487608 3.71976530271662 3.30910766487608 0 0.561249163965633 0.135151988617328 Y 0.967896280290168 0.957195040386891 N Y 173 2248 ENSG00000185710 ENSG00000183604 - + 16 16 21837978 30254196 utr5p coding AC092375.4-5 AC106782.5-2 21822947 30186415 - - 0 21837887 30224775 + - N - - N HCC1954 10 7.66666666666667 6 6 1 N - - N - - 0 0 0 6 0.314236919036755 0.728458312312478 0.728458312312478 0.314236919036755 1 - - 26880 Y Y 3.60000453584907 3.44193281696752 3.44193281696752 170 0.157529794149512 0.0977923125590244 Y 0.164550379198267 0 N N 6267 6875 ENSG00000040199 ENSG00000140832 + + 16 16 70306205 70233367 coding coding PHLPPL MARVELD3 70232304 70217571 - + 0 70236222 70220897 - + N 0.0602222399912835 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 1.04269523134923 1.1141127129485 1.1141127129485 1.04269523134923 1 0 - 36996 N N 3.41745542100897 3.00935843624818 3.00935843624818 0 0 0.157677819443136 N 0 0 N N 13 0 ENSG00000139220 ENSG00000217620 + - 12 8 80672131 103888783 intron upstream PPFIA2 AP003356.2 80177487 103888246 - + 0 80246971 103838036 - - Y 0.92068159931115 - N HCC1954 20 18.1818181818182 7 33 1 N 421 28.2287 N SINE - 1 0 1 33 0.28566992639705 0.714174815992626 0.714174815992626 0.28566992639705 2 0 - 24880 N Y 3.54552998930151 3.26936241550807 3.26936241550807 249 0 0.0173755869707413 N 0.189933065595716 0.867202141900937 N N 167 5397 ENSG00000197462 ENSG00000091164 - - 5 18 121842681 52456874 intron downstream AC022101.4 TXNL1 121800093 52421053 - - 0 121838154 52236462 + + Y 0.0455877289833909 - N HCC1954 80 56.75 36 4 1 N - - N LTR LTR 1 1 1 4 0.435646637755502 0.34280391167646 0.435646637755502 0.34280391167646 2 0 - 39645 N Y 3.46145674063593 3.69784855983781 3.46145674063593 0 0 0.0497945569428833 N 0.697712973134925 0.864935583741137 N N 1346 12271 ENSG00000103707 ENSG00000177479 - + 15 3 63109018 48997971 utr3p utr5p MTFMT ARIH2 63081904 48931285 - + 0 63082352 48935246 + + Y - - N HCC1954 40 38.8 37 5 1 N - - N SINE - 1 0 1 5 0.271386430077198 0.721316564152552 0.721316564152552 0.271386430077198 1 - - 4761 N Y 3.14488157006516 3.51675667029068 3.14488157006516 1 0.0110762253619396 0.768425052377958 N 0.0196014303157159 0.991474795046224 N Y 497 222 ENSG00000135205 ENSG00000174384 - + 7 7 76762457 74352585 utr5p coding CCDC146 AC138783.10-2 76589870 74340864 + - 0 76634911 74348689 - - N - - Y HCC1954 28 18.6 6 10 1 N - - N - LTR 0 0.233333333333333 0.233333333333333 10 0.949852505270192 1.07126222398894 1.07126222398894 0.949852505270192 4 - - 49057 Y Y 3.3241983368464 3.67423639977982 3.3241983368464 269 0 0.396204852339963 Y 0 0 N N 46607 3556 ENSG00000146063 ENSG00000146054 - - 5 5 180595414 180564783 upstream upstream TRIM41 TRIM7 180582912 180553531 + - 0 180577127 180567325 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.592765097273879 0.728458312312478 0.728458312312478 0.592765097273879 1 - - 2587 N N 3.33560915840422 3.34728128824428 3.33560915840422 0 0 0.0141072242081454 N 0.226708074534161 0.226708074534161 N N 8304 5574 ENSG00000087299 ENSG00000135365 - + 14 11 49848697 46099561 utr3p intron L2HGDH PHF21A 49774064 45907447 - - 0.269668737060042 49780395 46091774 + - Y - 1.6212105228056 N HCC1954 483 456.6 420 5 1 N - - N LINE SINE 1 1 1 5 0.39993789695587 0.314236919036755 0.39993789695587 0.314236919036755 1 - 0 29800 Y Y 3.47233119514066 3.76273355257368 3.47233119514066 245 0 0.159711810133810 Y 0 0.974463631606489 N N 140 37845 ENSG00000204444 ENSG00000204463 - - 6 6 31733965 31728461 coding utr5p APOM BAT3 31728172 31714784 + - 0 31733520 31727532 - + N - 3.24573274929389 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.857009779191151 0.5713398527941 0.857009779191151 0.5713398527941 4 - 0 43824 N Y 3.81657625693547 3.07311707325832 3.07311707325832 0 0 0.0998658645339406 N 0 0.868023061497326 N N 0 0 ENSG00000156395 ENSG00000215401 - - 10 18 107014983 1353874 downstream upstream SORCS3 AP005119.2 106391076 1352441 + - 0 107133077 1504575 - + Y - - N HCC1954 23 22.25 22 4 1 N 134 28.0078 N LINE - 1 0 1 4 0.321378667196682 0.428504889595575 0.428504889595575 0.321378667196682 2 - - 30637 Y N 3.47911741325579 3.40125197368207 3.40125197368207 18 0 0.122608083748859 Y 0.992088449635619 0 N N 153 0 ENSG00000129682 ENSG00000173954 - - X X 137894912 138272206 coding upstream FGF13 CXorf19 137541401 138271925 - + 0 137767391 138113887 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 1.48548361726466 0.749883556792257 1.48548361726466 0.749883556792257 2 - - 30513 Y Y 3.53465553479678 3.70360170818306 3.53465553479678 322 0 0.248256626010657 Y 0 0.986528453919758 N N 1011 1542 ENSG00000205663 ENSG00000205664 + - X X 3810322 3771898 upstream coding BX890604.9-1 RP11-706O15.1 3792439 3745569 - - 0 3821156 3757432 - + N - 2.74806728039013 N HCC1954 9 7.09090909090909 3 11 2 Y - - Y - - 0 0 0 11 0.764167053112109 0.964136001590045 0.964136001590045 0.764167053112109 2 - 0 42477 Y Y 3.68321254861411 3.48271113610543 3.48271113610543 0 0 0.169261011881449 Y 0.977589321250345 0.988794660625172 N N 735 2970 ENSG00000198515 ENSG00000163293 - - 4 4 47678276 47736947 utr5p upstream CNGA1 NPAL1 47632753 47713548 - + 0 47678276 47707570 + - N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 9 0.599906845433805 0.664182578873142 0.664182578873142 0.599906845433805 1 - - 47827 N N 3.66488952858494 3.63399663687184 3.63399663687184 2 0 0.137064986841104 N 0 0.39440846627705 N N 551733 0 ENSG00000204628 ENSG00000207507 - + 5 19 180603512 844590 coding downstream GNB2L1 U6 180596536 844484 - + 0.00205338809034905 180597807 844732 + + Y - - N HCC1954 20 20 20 5 1 N - - N - snRNA 0 1 1 5 0.885576771830856 0.464213630395207 0.885576771830856 0.464213630395207 2 - - 29929 N N 3.26191384998362 3.3038490300708 3.26191384998362 35 0.0416795545932572 0.29715531210614 N 0.680559851531086 0.0792607485307766 N N 78560 0 ENSG00000112493 ENSG00000217035 - - 6 X 33390114 44379422 utr3p downstream TAPBP CHTF8P 33375449 44377882 - + 0.0416795545932572 33376425 44385726 + - Y - - N HCC1954 21 10.9375 1 15 1 N - - N SINE SINE 1 0.710526315789474 1 16 0.542772860154395 0.271386430077198 0.542772860154395 0.271386430077198 2 - - 17666 N N 3.63296356710195 3.44768596531277 3.44768596531277 0 0 0.287685376587017 N 0 0 Y N 4543 12071 ENSG00000132680 ENSG00000116580 - + 1 1 154170814 154093710 coding coding KIAA0907 GON4L 154149460 153986132 - - 0 154163236 154089712 + - N - 1.10997514430511 N HCC1954 1 1 1 0 2 Y 495 6.71914 N - - 0 0 0 13 1.02126998686945 1.02126998686945 1.02126998686945 1.02126998686945 1 - 0 18846 Y Y 3.28503149650166 3.52105259334297 3.28503149650166 246 0 0.116037568068675 Y 0.556432329029173 0.991630798660928 N N 12653 12308 ENSG00000160818 ENSG00000163382 + + 1 1 154837894 154830715 intron utr3p GPATCH4 APOA1BP 154830908 154828178 - + 0 154833121 154830504 - + N 1.33495603817759 1.75875697080145 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.592765097273879 0.592765097273879 0.592765097273879 0.592765097273879 3 0 0 26073 N N 3.54144175291192 3.35823029066252 3.35823029066252 2 0 0.633005467008935 N 0.300615026595745 0 N N 16390 8194 ENSG00000140950 ENSG00000144036 - - 16 2 83095794 72906685 utr5p intron KIAA1609 EXOC6B 83068608 72256621 - - 0 83095714 72698306 + + Y - 0.464323603265729 N HCC1954 13 2.88 1 11 2 N - - N - SINE 0 1 1 25 0.678466075192994 0.299953422716903 0.678466075192994 0.299953422716903 3 - 0 9585 Y Y 3.09355966598976 3.12911920311573 3.09355966598976 334 0 0.132662582074992 Y 0 0.993957539466522 N N 5477 1954 ENSG00000169992 ENSG00000205544 - - 17 17 7263903 7248142 upstream upstream NLGN2 C17orf61 7252226 7247038 + - 0 7251659 7249654 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.453488372093023 0.453488372093023 11 1.21409718718746 1.14982145374813 1.21409718718746 1.14982145374813 1 - - 7045 Y Y 3.07168277590431 3.39487633072086 3.07168277590431 219 0 0.0209811561004373 Y 0 0.984446347031963 N N 0 0 ENSG00000216921 ENSG00000188011 + + 2 2 242493375 242464155 downstream downstream AC131097.4 C2orf85 242484809 242460559 - + 0 242478487 242472239 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 8 0.435646637755502 0.264244681917271 0.435646637755502 0.264244681917271 1 - - 31524 N N 3.64656650855576 3.27973300890302 3.27973300890302 0 0 0.0250833618906366 N 0 0 N N 1974 837 ENSG00000172113 ENSG00000188315 + + 3 3 48317852 49289456 upstream utr3p NME6 C3orf62 48310595 49281223 - - 0 48344790 49281291 - - N - - Y HCC1954 33 30.5 28 10 1 N 456 26.7939 N - SINE 0 1 1 10 0.635615586233437 0.314236919036755 0.635615586233437 0.314236919036755 0 - - 42329 Y Y 3.05103249651017 2.7614461108465 2.7614461108465 252 0 0.569870368616569 Y 0 0.980079365079365 N N 3011 0 ENSG00000018189 ENSG00000207058 - - 4 4 71891789 71787704 upstream upstream RIPX U6 71806560 71787599 + - 0 71802139 71789875 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE Simple_repeat 0.0487804878048781 0.329545454545455 0.329545454545455 5 0.585623349113953 0.628473838073511 0.628473838073511 0.585623349113953 4 - - 7504 Y Y 3.34528969661801 2.94029086755001 2.94029086755001 0 0 0.146583538019316 Y 0 0.886466165413534 N N 1163 20 ENSG00000042493 ENSG00000152292 - - 2 2 85499066 85517661 coding intron CAPG SH2D6 85475382 85499565 - + 0 85482763 85500132 + - N - 0.575229357798165 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 0.99270299422975 0.671324327033068 0.99270299422975 0.671324327033068 2 - 0 41465 N N 3.74081680969488 3.35463656781289 3.35463656781289 0 0 0.76761289071142 Y 0 0 N N 38251 0 ENSG00000156802 ENSG00000206719 + + 8 8 124477868 115032403 coding upstream ATAD2 Y_RNA 124401922 115032291 - + 0 124437812 114899716 - + N 0.718166915015522 - N HCC1954 1 1 1 0 2 N 405 1.47521 N - LINE,LINE 0 1 1 22 0.692749571512847 1.1141127129485 1.1141127129485 0.692749571512847 1 0 - 41558 Y Y 3.53089397807781 3.4503745994685 3.4503745994685 354 0 0.0858318405094481 Y 0 0.993170033279158 N N 293 3661 ENSG00000180938 ENSG00000170873 - - 8 8 126060809 125809911 upstream upstream ZNF572 MTSS1 126054733 125632212 + - 0 125949376 125931377 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.413793103448276 0.413793103448276 7 0.835584534711372 0.999844742389676 0.999844742389676 0.835584534711372 1 - - 12331 N Y 3.07101108092519 3.6052936758779 3.07101108092519 0 0 0.3159790342795 N 0 0.759621305418719 N N 1649619 1203 ENSG00000141736 ENSG00000085871 - + 17 4 35138441 140844857 coding upstream ERBB2 MGST2 35104766 140806372 + + 0 35125066 140764608 - + Y 0.990793461175642 - N HCC1954 21 20.2 20 5 1 N - - N - SINE 0 1 1 5 0.349945659836387 0.278528178237124 0.349945659836387 0.278528178237124 1 0 - 11473 N N 3.40169305405954 3.38912318237562 3.38912318237562 26 0.148696066539595 0.175442871326178 N 0 0 N N 261771 0 ENSG00000184009 ENSG00000178631 + + 17 3 77094422 140695911 coding downstream ACTG1 AC097103.8 77091594 140695599 - + 0 77092446 140696365 - + Y - - N HCC1954 5 1.75 1 4 1 N - - N - - 0 0 0 12 0.87843502367093 0.278528178237124 0.87843502367093 0.278528178237124 1 - - 46708 N Y 3.57800808738356 3.30847582269032 3.30847582269032 0 0 0.425126883599407 N 0.00427350427350448 0 N N 17943 135 ENSG00000105141 ENSG00000174137 + - 19 4 15027900 1655516 downstream intron CASP14 FAM53A 15024015 1611607 + - 0 15029502 1632106 + + Y - 0.880364398319055 N HCC1954 4 3.5 3 4 1 N - - N - SINE 0 0.868421052631579 0.868421052631579 4 0.671324327033068 0.271386430077198 0.671324327033068 0.271386430077198 3 - 0 40650 N Y 3.63874722067073 3.45972147066338 3.45972147066338 8 0 0.248562297016128 N 0.816251747195044 0.032903932605493 N N 6721 975 ENSG00000130703 ENSG00000198487 - + 20 6 60304664 42218335 utr3p coding OSBPL2 AL512274.9 60246975 42183124 + - 0 60303423 42204389 - - Y - - N HCC1954 39 37 35 5 1 N - - N SINE - 1 0 1 5 0.349945659836387 0.478497126715059 0.478497126715059 0.349945659836387 1 - - 38089 Y Y 3.58593758607883 3.4439989565073 3.4439989565073 177 0 0.140116647581698 Y 0 0.937853107344633 N N 2447 4331 ENSG00000157379 ENSG00000100949 + - 14 14 23838770 23810643 intron utr5p DHRS1 RABGGTA 23829646 23804661 - - 0 23831511 23810306 - + N 1.01059105817224 4.14155161589639 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 15 0.956994253430118 0.521347615674617 0.956994253430118 0.521347615674617 1 0 0 6551 Y Y 3.11704384497176 3.69784855983781 3.11704384497176 200 0 0.0601733777769717 Y 0.005 0.954076923076923 N N 13398 0 ENSG00000196950 ENSG00000213107 - - 2 2 196310671 196156625 utr5p upstream SLC39A10 AC064834.5-1 196229716 196155759 + - 0 196253001 196186059 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.735600060472404 0.407079645115797 0.735600060472404 0.407079645115797 4 - - 11007 N Y 3.12804628055249 3.47233119514066 3.12804628055249 0 0 0.241061472149253 N 0.797062099693679 0.852408799777221 N N 1649619 11178 ENSG00000141736 ENSG00000096070 - - 17 6 35138441 36308544 coding upstream ERBB2 BRPF3 35104766 36272528 + + 0 35122227 36265458 - - Y - - N HCC1954 4 1.8 1 2 1 N - - N - SINE 0 1 1 5 0.39993789695587 0.299953422716903 0.39993789695587 0.299953422716903 2 - - 45634 N Y 3.24057974892742 3.30272267434507 3.24057974892742 0 0 0.118990793904689 N 0 0 N N 0 3007 ENSG00000177051 ENSG00000182378 + + 19 X 50906933 160023 upstream utr3p FBXO46 PLCXD1 50906323 132989 - + 0 50925782 158396 - + Y - - N HCC1954 36 30.8571428571429 21 7 1 N - - N - SINE 0 1 1 7 0.378512652476092 0.307095170876829 0.378512652476092 0.307095170876829 3 - - 22709 N Y 3.61360747730289 3.58424216889964 3.58424216889964 113 0 0.00569576738500632 N 0.858407079646018 0.919089759797724 N N 0 3240 ENSG00000187980 ENSG00000087008 + - 1 4 20374274 8493352 downstream intron PLA2G2C ACOX3 20363071 8418911 - - 0.0897597977243996 20358811 8487235 - + Y - 5.31652105834416 N HCC1954 8 5.23529411764706 3 17 1 N - - N LTR LTR 1 1 1 17 0.685607823352921 0.307095170876829 0.685607823352921 0.307095170876829 1 - 0 7747 N Y 3.45976132345673 3.51001030496889 3.45976132345673 6 0 0.103641930612287 N 0 0.820988392963982 N N 1 1 ENSG00000219041 ENSG00000147655 + - 2 8 91318999 109165052 intron intron AC027612.6-2 RSPO2 91042814 108980721 + - 0 91089634 109009187 + + Y 1.23920265780731 0.92526158445441 N HCC1954 240 226.666666666667 200 9 1 N 394 26.9477 N - LINE 0 1 1 9 0.51420586751469 0.34280391167646 0.51420586751469 0.34280391167646 3 0 0 29111 Y Y 3.49744043328497 3.24255776018456 3.24255776018456 285 0 0.83130032343473 Y 0.963763955342903 0.972822966507177 N N 1789 0 ENSG00000204599 ENSG00000203481 - - 6 6 30419485 30360468 upstream upstream TRIM39 AL662795.5 30402600 30360104 + - 0 30402110 30371993 - + N - - N HCC1954 1 1 1 0 5 N - - Y - LTR 0 1 1 13 0.964136001590045 0.757025304952183 0.964136001590045 0.757025304952183 4 - - 47056 Y Y 3.30761058678977 3.29553522864581 3.29553522864581 287 0 0.0201976268524880 Y 0 0.9778552071235 N N 22 0 ENSG00000185792 ENSG00000203305 + + 19 19 60941580 60900406 downstream upstream NLRP9 AC010525.6-1 60911610 60899900 - + 0 60907653 60899605 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 1 0 1 4 0.51420586751469 0.499922371194838 0.51420586751469 0.499922371194838 2 - - 6669 N Y 3.44975210485255 3.44615838200292 3.44615838200292 2 0 0.0202983095465632 Y 0.00581395348837199 0.898896334253055 N N 4691 0 ENSG00000152253 ENSG00000212025 + + 2 2 169455190 34482328 utr3p downstream SPC25 AC011748.7 169435648 34482235 - + 0.865195112337406 169435705 34548520 - + N - - N HCC1954 640 600 500 4 1 N - - N LINE LINE 1 1 1 4 0.371370904316165 0.321378667196682 0.371370904316165 0.321378667196682 1 - - 288 Y Y 3.45872825368684 3.06320114060997 3.06320114060997 334 0 0.00252603355644809 Y 0 0.985119313611583 N N 0 103869 ENSG00000216482 ENSG00000117984 - - 11 11 1770676 1741798 upstream upstream AC139143.1 CTSD 1770359 1730561 + - 0.985119313611583 1756353 1755053 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.0515463917525773 0.0515463917525773 5 0.307095170876829 0.642757334393363 0.642757334393363 0.307095170876829 2 - - 44661 Y Y 3.61144805180727 3.40744620240479 3.40744620240479 413 0 0.0854804943634936 Y 0.994831198484487 0.989662396968975 N N 0 282831 ENSG00000212325 ENSG00000099194 + + 10 10 102148193 102114577 downstream downstream Y_RNA SCD 102148099 102096762 - + 0.674365504522701 102137784 102131195 - + N - - N HCC1954 44 2.05833333333333 1 39 2 N - - Y LTR,LTR LTR,LTR 0.909871244635193 0.751243781094527 0.909871244635193 120 1.66402732126282 1.43549138014518 1.66402732126282 1.43549138014518 4 - - 10764 N Y 3.11080976345569 3.13073491470822 3.11080976345569 103 0 0.483403269529701 N 0.953063407181054 0.958930481283422 N N 2906 4310 ENSG00000079819 ENSG00000183011 - - 6 17 131426017 7701897 downstream coding EPB41L2 LSMD1 131202180 7700730 - - 0 131164594 7701243 + + Y - 11.8312907194667 N HCC1954 4 2.97887323943662 1 281 2 N - - N - - 0 0 0 284 1.29265641694665 1.2783729206268 1.29265641694665 1.2783729206268 2 - 0 21849 N N 3.31270138772572 3.19612376855386 3.19612376855386 0 0 0.0709323488307603 N 0 0 N N 6477 3863 ENSG00000151176 ENSG00000219481 - - 12 1 112311584 146862781 intron upstream PLBD2 NBPF15 112280761 146827614 + + 0 112284472 146827333 - - Y 0.347283054506111 - N HCC1954 44 25.5 8 4 1 N - - N SINE - 1 0 1 4 0.307095170876829 0.542772860154395 0.542772860154395 0.307095170876829 2 0 - 34289 Y Y 3.33358506083463 3.21232721588077 3.21232721588077 220 0 0.0209887356391418 Y 0.152020202020202 0.987710437710438 N N 901 0 ENSG00000137033 ENSG00000218509 - + 9 9 6247982 6187470 utr5p downstream IL33 RP11-575C20.1 6231678 6185934 + + 0 6231682 6205850 - + N 0.0636932480903646 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.728458312312478 0.578481600954027 0.728458312312478 0.578481600954027 3 0 - 32869 N N 2.42680847320244 2.11422534208663 2.11422534208663 0 0.191350710900474 0.0976502665716246 N 0.751184834123223 0 N N 5996 767 ENSG00000187678 ENSG00000161267 - + 5 3 141684750 198784591 utr3p utr3p SPRY4 BDH1 141670189 198721051 - - 0.191350710900474 141671703 198721921 + - Y - - N HCC1954 38 35.2222222222222 33 9 1 N - - N - Simple_repeat 0 0.986111111111111 0.986111111111111 9 0.364229156156239 0.51420586751469 0.51420586751469 0.364229156156239 1 - - 44804 N Y 3.09719324163274 3.59169073442408 3.09719324163274 170 0 0.0116511329443395 Y 0 0 N N 0 0 ENSG00000217359 ENSG00000217137 + - 10 10 76812608 76699309 downstream downstream SPA17P1 RP11-399K21.2 76812157 76699156 - - 0 76788340 76692530 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 14 0.99270299422975 0.564198104634174 0.99270299422975 0.564198104634174 2 - - 45024 Y Y 3.33524062522047 3.41472693405989 3.33524062522047 0 0 0.620260425981896 Y 0 0.993079419625811 N N 4494 136 ENSG00000122861 ENSG00000222047 - - 10 10 75347260 75352541 utr5p downstream PLAU C10orf55 75340896 75339733 + - 0 75340982 75339057 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 1.09268746846872 0.885576771830856 1.09268746846872 0.885576771830856 1 - - 30456 Y Y 3.32267075353655 3.37295958784206 3.32267075353655 261 0 0.192515814420032 Y 0.454022988505747 0.980842911877395 N N 0 0 ENSG00000219493 ENSG00000216396 - - X X 117957125 117897176 upstream upstream RP13-347D8.1 RP4-562J12.1 117956144 117895877 + - 0 117933348 117910193 - + N - - N HCC1954 20 9.125 1 5 2 N - - Y SINE,SINE LINE 1 0.476744186046512 1 8 1.03555348318931 0.614190341753658 1.03555348318931 0.614190341753658 4 - - 4730 Y Y 3.93849644929864 2.41764212942916 2.41764212942916 8 0.0094503710575139 0.99851659108182 Y 0.993525819418677 0.993525819418677 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding downstream CRCP ASL 65216341 65178207 + + 0 65230127 65202508 - + N - - N HCC1954 3 1.51219512195122 1 20 6 N - - Y - Simple_repeat,Simple_repeat 0 0.197452229299363 0.197452229299363 41 1.29265641694665 1.12125446110842 1.29265641694665 1.12125446110842 1 - - 19540 N Y 3.45653832296769 3.44057306752701 3.44057306752701 0 0.0708333333333333 0.738343433424308 N 0.911507936507936 0.911507936507936 N Y 1843 3299 ENSG00000142794 ENSG00000179571 - + 1 1 21684085 16812569 utr5p utr5p NBPF3 NBPF1 21639217 16762999 + - 0.115079365079365 21666076 16793674 - - N - - Y HCC1954 1 1 1 0 1 N - - N SINE - 0.104166666666667 0 0.104166666666667 4 0.34280391167646 0.599906845433805 0.599906845433805 0.34280391167646 4 - - 48560 N N 1.46400562653446 2.45725668237607 1.46400562653446 0 0 0.184138716386542 N 0.004 0 N N 850768 8953 ENSG00000075624 ENSG00000154122 - + 7 5 5536758 14924876 utr3p intron ACTB ANKH 5533313 14762019 - - 0 5533818 14825005 + - Y - 2.56672255467393 N HCC1954 34 15.5 5 4 1 N 0 20.7652 N - SINE 0 0.711864406779661 0.711864406779661 4 0.585623349113953 0.421363141435649 0.585623349113953 0.421363141435649 3 - 0 33008 N N 3.40744620240479 3.52720696927234 3.40744620240479 0 0 0.999998816682554 N 0.00243902439024402 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8548 11663 - + N 0.655744413572778 1.1601984934822 N HCC1954 4 1.71428571428571 1 3 12 Y 189 4.09957 N - - 0 0 0 7 0.956994253430118 1.15696320190805 1.15696320190805 0.956994253430118 3 0 0 14296 N N 3.30232144676095 3.56488607910057 3.30232144676095 0 0 0.0448714096123612 N 0 0 N N 3693 0 ENSG00000198125 ENSG00000213864 + - 22 5 34349347 67491477 coding downstream MB AC104120.2 34332757 67490802 - - 0 34343239 67478557 - + Y - - N HCC1954 16 6.5 1 2 1 N - - N - SINE 0 1 1 4 0.357087407996313 0.257102933757345 0.357087407996313 0.257102933757345 1 - - 8308 N N 3.55397177180249 3.46551447180198 3.46551447180198 0 0 0.0878849776229753 N 0 0.00324675324675305 N N 551733 42 ENSG00000204628 ENSG00000144057 + - 5 2 180603512 106869996 coding intron GNB2L1 ST6GAL2 180596536 106784492 - - 0.00324675324675305 180597265 106796214 - + Y 0.562989757040652 1.5591227513985 N HCC1954 15 9.625 7 8 1 Y - - N - SINE 0 0.864864864864865 0.864864864864865 8 0.51420586751469 0.264244681917271 0.51420586751469 0.264244681917271 2 0 0 44001 N Y 3.6344911504118 3.00762316627563 3.00762316627563 5 0 0.0603299539984187 N 0.728529534981148 0.922437009994614 N N 3209 3891 ENSG00000011638 ENSG00000166295 + + 16 10 21099438 73665622 utr3p intron TMEM159 C10orf104 21077199 73645812 + + 0 21099353 73645904 + + Y - 0.744979490524871 N HCC1954 37 33 22 5 1 N - - N SINE - 1 0 1 5 0.357087407996313 0.821301038391519 0.821301038391519 0.357087407996313 2 - 0 4196 N Y 3.83489927696465 3.20959872893168 3.20959872893168 262 0 0.108926430503669 Y 0.900381679389313 0.991698473282443 N N 0 0 ENSG00000201959 ENSG00000186704 - + 7 7 76509001 76483049 upstream intron Y_RNA PMS2L11 76508900 76469431 + + 0 76507208 76473027 - + N - 1 N HCC1954 2 1.84615384615385 1 11 2 N - - N - - 0 0 0 13 0.45707188223528 0.785592297591888 0.785592297591888 0.45707188223528 1 - 0 7180 Y Y 3.44256465915329 3.2038150753629 3.2038150753629 286 0 0.0374835723471558 Y 0 0.981198047235783 N N 0 347 ENSG00000202479 ENSG00000115137 + - 2 2 25045850 25048435 upstream upstream SNORD14 DNAJC27 25045761 25020009 - - 0 25055433 25048605 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,LINE - 0.572727272727273 0 0.572727272727273 7 0.771308801272036 0.578481600954027 0.771308801272036 0.578481600954027 4 - - 19481 N N 3.25256697878875 3.48912663185998 3.25256697878875 0 0 0.244021220943313 N 0 0 N N 49089 2080 ENSG00000117450 ENSG00000067208 - - 1 1 45760196 93030549 coding intron PRDX1 EVI5 45749295 92746841 - - 0 45757275 92875473 + + N - 0.589774829039507 Y HCC1954 22 3.10810810810811 1 109 2 N - - N - SINE 0 1 1 111 1.14982145374813 0.328520415356608 1.14982145374813 0.328520415356608 2 - 0 31650 Y Y 2.88274380859372 3.63552422018169 2.88274380859372 115 0 0.60463602618118 Y 0.96932783305023 0.992331958262558 N N 1131 2216 ENSG00000214116 ENSG00000185485 - + 3 3 197173943 197201530 coding coding AC024937.21-2 AC024937.21-3 197171055 197174603 - - 0 197171356 197176699 + - N - - N HCC1954 12 5.26086956521739 2 23 3 N - - Y LINE - 0.492753623188406 0 0.492753623188406 23 0.985561246069823 1.12839620926835 1.12839620926835 0.985561246069823 2 - - 1153 N N 3.54296933622177 1.14851232086445 1.14851232086445 0 0 0.139788949956029 N 0 0 N N 74637 0 ENSG00000089597 ENSG00000206951 - - 11 2 62170680 33024022 coding downstream GANAB Y_RNA 62148876 33023910 - - 0 62163732 32995158 + + Y - - N HCC1954 4 2 1 2 2 N 604 19.3493 N - Simple_repeat 0 0.978723404255319 0.978723404255319 4 0.549914608314322 1.0069864905496 1.0069864905496 0.549914608314322 1 - - 27433 Y Y 3.37023110089298 3.5010341561346 3.37023110089298 157 0.00636942675159236 0.0071569136672297 Y 0.983158803843247 0.966317607686495 N N 13096 2486 ENSG00000166164 ENSG00000121281 + + 16 16 48960346 48909547 coding utr3p BRD7 ADCY7 48910442 48857979 - + 0 48911300 48907400 - + N - 1.44233191202134 N HCC1954 2 1.88888888888889 1 8 1 N - - Y - - 0 0 0 9 0.892718519990782 0.835584534711372 0.892718519990782 0.835584534711372 2 - 0 4569 Y Y 3.62295434849776 3.33631354778371 3.33631354778371 136 0 0.0581454250352068 Y 0 0.991260438920179 N N 0 1798 ENSG00000201138 ENSG00000174353 - + 7 7 74848952 74834926 downstream coding Y_RNA STAG3L2 74848851 74826391 + + 0 74849942 74833954 - + N - - N HCC1954 9 6.2 4 10 1 N - - Y LTR - 0.541666666666667 0 0.541666666666667 10 0.857009779191151 0.914143764470561 0.914143764470561 0.857009779191151 1 - - 36446 Y Y 3.33577499155379 3.08824759802198 3.08824759802198 0 0 0.10329650220563 Y 0 0.976936382856045 N N 18261 44572 ENSG00000139613 ENSG00000092841 + + 12 12 54869618 54841633 downstream coding SMARCC2 MYL6 54843034 54838367 - + 0 54842945 54840330 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.535631111994469 0.721316564152552 0.721316564152552 0.535631111994469 1 - - 42450 N N 3.39487633072086 3.48280442206126 3.39487633072086 6 0.0149450549450549 0.870828014032196 N 0.0368351648351649 0 N N 0 2269 ENSG00000174473 ENSG00000056050 - + 4 4 174199266 170915637 upstream coding GALNTL6 C4orf27 172971229 170887205 + - 0 172843109 170895387 - - N - - Y HCC1954 1 1 1 0 3 N - - N - - 0 0 0 4 0.614190341753658 0.685607823352921 0.685607823352921 0.614190341753658 1 - - 39747 N N 2.94537337453302 2.56547129975977 2.56547129975977 0 0.304771557773273 0.241820863704998 N 0.304771557773273 0.304771557773273 N N 10338 18564 ENSG00000107164 ENSG00000140319 - + 9 15 132503560 38118657 upstream coding FUBP3 SRP14P1 132444781 38115535 + - 0.304771557773273 132408853 38115914 - - Y - - N HCC1954 2 1.15384615384615 1 2 1 N - - N Simple_repeat - 0.604651162790698 0 0.604651162790698 13 0.307095170876829 0.778450549431962 0.778450549431962 0.307095170876829 2 - - 40913 Y Y 3.70889084821189 3.49847350305486 3.49847350305486 332 0 0.0604667832539716 Y 0 0 N N 1 1149 ENSG00000124092 ENSG00000124097 + - 20 20 55534041 55497489 downstream upstream CTCFL HMGB1L1 55505630 55496854 - - 0 55503666 55497676 - + N - - N HCC1954 6 1.15068493150685 1 7 2 N - - Y - LINE 0 0.326315789473684 0.326315789473684 73 0.928427260790413 1.35693215038599 1.35693215038599 0.928427260790413 1 - - 42117 N N 3.26191384998362 3.07151494203496 3.07151494203496 0 0.0514133940428763 0.191111745359706 N 0.50199203187251 0.0751280591918043 N N 78560 0 ENSG00000112493 ENSG00000216027 - - 6 4 33390114 61212351 utr3p downstream TAPBP AC095061.3 33375449 61212262 - - 0.0751280591918043 33376425 60902136 + + Y - - N HCC1954 168 21.7887323943662 1 68 1 N 95 22.1645 N SINE SINE,SINE 1 0.884615384615385 1 71 1.12125446110842 0.371370904316165 1.12125446110842 0.371370904316165 1 - - 784 Y Y 3.51360402781852 3.40422320191574 3.40422320191574 0 0.209087445227662 0.529292432963234 Y 0.982806248809297 0.982806248809297 N N 3045 5429 ENSG00000172922 ENSG00000172977 + + 11 11 65244985 65243650 utr3p intron RNASEH2C KAT5 65241720 65236065 - + 0 65243728 65239364 - + N - 1.09412777614618 N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.236842105263158 0.236842105263158 5 1.07840397214886 0.814159290231593 1.07840397214886 0.814159290231593 4 - 0 44475 N N 3.44719145177281 3.09087103183403 3.09087103183403 7 0 0.0800770786542764 N 0 0 N N 0 3891 ENSG00000213881 ENSG00000166295 - + 8 10 62278340 73665622 upstream intron AC105015.3 C10orf104 62277464 73645812 + + 0 62198180 73645953 - + Y - 0.744979490524871 N HCC1954 20 18.8 14 5 1 N 361 22.7069 N SINE - 1 0 1 5 0.385654400636018 0.371370904316165 0.385654400636018 0.371370904316165 1 - 0 24453 N N 3.33420755545058 3.3755202409218 3.33420755545058 1 0 0.106676745608187 N 0 0.00245700245700231 N N 37 850768 ENSG00000183287 ENSG00000075624 + + 18 7 55515554 5536758 intron utr3p CCBE1 ACTB 55252129 5533313 - - 0.00245700245700231 55511348 5533538 - - Y 2.00832500832501 0.817582063631692 N HCC1954 5 1.83333333333333 1 5 1 N - - N - - 0 0 0 12 0.28566992639705 1.07840397214886 1.07840397214886 0.28566992639705 2 0 0 260 N Y 3.67849247003875 3.1971966911171 3.1971966911171 299 0 0.0043210234992318 Y 0 0.98688611160007 N N 0 0 ENSG00000206653 ENSG00000207487 + - 11 11 62378016 62377083 upstream downstream SNORD29 SNORD22 62377952 62376958 - - 0.98688611160007 62378062 62376890 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 23 0.421363141435649 0.757025304952183 0.757025304952183 0.421363141435649 2 - - 17900 Y Y 3.21063179870157 3.63296356710195 3.21063179870157 3 0 0.0760969443489544 Y 0 0 N N 81453 12034 ENSG00000143321 ENSG00000143314 + - 1 1 154988864 154977547 utr3p upstream HDGF MRPL24 154978526 154973718 - - 0.994578703204229 154979809 154978019 - + N - - N HCC1954 1 1 1 0 1 N - - Y Simple_repeat LINE 0.231292517006803 0.0266666666666667 0.231292517006803 4 0.585623349113953 0.785592297591888 0.785592297591888 0.585623349113953 1 - - 49462 Y Y 3.6491271616355 3.03486890197662 3.03486890197662 243 0 0.06097772372974 Y 0 0.991340132402934 N N 1658 551733 ENSG00000183718 ENSG00000204628 + - 5 5 180620725 180603512 utr3p upstream TRIM52 GNB2L1 180615994 180596536 - - 0 180616301 180606941 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 1.02841173502938 1.26408942430695 1.26408942430695 1.02841173502938 1 - - 47568 Y Y 3.37808089400154 3.63552422018169 3.37808089400154 248 0 0.529238813202793 Y 0 0 N N 49782 15 ENSG00000089327 ENSG00000221946 - + 19 19 40352625 40337045 utr5p intron FXYD5 FXYD7 40337467 40325994 + + 0 40337825 40331365 - + N - 0.350908025776216 N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 4 0.357087407996313 0.378512652476092 0.378512652476092 0.357087407996313 4 - 0 36441 Y Y 3.43784458057793 3.3012485241977 3.3012485241977 0 0 0.732166334629683 Y 0.480897009966778 0.993078626799557 N Y 2251 1532 ENSG00000123297 ENSG00000123427 - + 12 12 56476784 56462588 coding coding TSFM FAM119B 56462826 56452650 + + 0 56463160 56453178 - + N 0.888136429544554 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.857009779191151 1.05697872766909 1.05697872766909 0.857009779191151 4 0 - 5172 N N 3.2378376816092 3.64297278570613 3.2378376816092 3 0.00386100386100396 0.111363711536151 N 0.375302663438257 0.00386100386100396 N N 6759 850768 ENSG00000148218 ENSG00000075624 + + 9 7 115203434 5536758 downstream utr3p ALAD ACTB 115188416 5533313 - - 0.00386100386100396 115186868 5533865 - - Y - - N HCC1954 14 3.58333333333333 1 6 1 N - - N SINE - 1 0 1 12 0.235677689277566 0.707033067832699 0.707033067832699 0.235677689277566 1 - - 37874 N N 3.40591861909494 2.6221451245963 2.6221451245963 22 0.0914127423822716 0.376848911407847 N 0.510760707436608 0.353505220541232 N N 78560 32016 ENSG00000112493 ENSG00000092148 - - 6 14 33390114 30746440 utr3p intron TAPBP HECTD1 33375449 30639075 - - 0.353505220541232 33376420 30675791 + + Y 0.849760068573764 1.4639885942594 N HCC1954 20 10.3333333333333 1 18 1 N - - N SINE SINE 1 0.815789473684211 1 21 0.585623349113953 0.271386430077198 0.585623349113953 0.271386430077198 2 0 0 35126 N N 3.48333363072138 3.39380340815762 3.39380340815762 5 0.0174330174330175 0.0762006745274761 N 0.0562185562185563 0.0174330174330175 N N 2661 2636 ENSG00000139531 ENSG00000154642 - - 12 21 54685576 18113574 utr5p downstream SUOX C21orf91 54677310 18083156 + - 0 54679387 18039532 - + Y - - N HCC1954 28 25.1428571428571 24 7 1 N - - N LTR LTR 1 1 1 7 0.321378667196682 0.671324327033068 0.671324327033068 0.321378667196682 0 - - 33555 N Y 3.28126993978269 3.03652446636246 3.03652446636246 405 0 0.185367926336820 Y 0 0.991889992974004 N N 247001 275222 ENSG00000198786 ENSG00000198763 - + MT MT 14149 5512 coding coding MT-ND5 MT-ND2 12338 4471 + + 0 12424 5492 - + N - 163.649702896659 N HCC1954 2 1.33333333333333 1 3 5 Y - - N - - 0 0 0 9 0.978419497909897 1.56404284702385 1.56404284702385 0.978419497909897 2 - 0 9609 Y Y 3.2802368700128 3.41166241987037 3.2802368700128 283 0 0.644561927765455 Y 0 0 N N 830 7432 ENSG00000185158 ENSG00000178691 - + 17 17 27404630 27352162 coding downstream LRRC37B SUZ12 27372156 27288185 + + 0 27375843 27359264 - + N 0.852804786717399 - N HCC1954 6 2 1 1 4 N - - Y - Low_complexity 0 0.494791666666667 0.494791666666667 5 0.51420586751469 0.892718519990782 0.892718519990782 0.51420586751469 4 0 - 16150 N Y 3.19293127328835 3.48639814491089 3.19293127328835 266 0 0.00656461452835855 N 0.809230523116301 0.851623740201568 N N 10665 0 ENSG00000115233 ENSG00000220337 - - 2 1 161976474 142087113 upstream downstream PSMD14 BX571672.7 161872795 142086687 + + 0.798632218844985 161843310 142120036 - - Y - - N HCC1954 11 7.5 1 3 1 N 283 12.9779 N LINE LINE 0.888198757763975 0.645669291338583 0.888198757763975 4 0.642757334393363 0.721316564152552 0.721316564152552 0.642757334393363 3 - - 21145 N N 3.39165333023182 3.40591861909494 3.39165333023182 3 0 0.129454231477566 N 0.0846566410768748 0.367336207803134 N N 0 31120 ENSG00000222873 ENSG00000142910 - + 3 1 15755319 31825872 intron utr3p SRP_euk_arch TINAGL1 15755026 31814700 + + 0.286570617309917 15755041 31825568 - + Y 1 3.07419298161371 N HCC1954 12 6.6 3 5 1 N - - N LTR SINE 1 0.89344262295082 1 5 0.649899082553289 0.814159290231593 0.814159290231593 0.649899082553289 2 0 0 27401 Y Y 3.21484801616716 3.51832410639388 3.21484801616716 0 0 0.492920786806187 Y 0.963125406107862 0.963125406107862 N N 1864 6656 ENSG00000154102 ENSG00000131153 + - 16 16 84342190 84280089 coding upstream C16orf74 GINS2 84298624 84268782 - - 0 84301357 84281886 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 12 1.19267194270768 1.05697872766909 1.19267194270768 1.05697872766909 2 - - 18508 Y Y 3.29912895149544 3.53039946453785 3.29912895149544 118 0 0.0582458501559395 Y 0.239061884115096 0.838588884509263 N N 0 0 ENSG00000218833 ENSG00000220261 - - 1 1 222257979 222242479 upstream intron RP11-504P24.3 RP11-504P24.2 222250220 222237079 + - 0 222246866 222242397 - + N - 1 N HCC1954 14 11.6875 9 16 2 N - - Y - - 0 0 0 16 0.628473838073511 0.549914608314322 0.628473838073511 0.549914608314322 1 - 0 41043 N N 3.55657227767559 3.73552766966605 3.55657227767559 0 0 0.978046199241724 N 0 0 Y N 9407 7469 ENSG00000101346 ENSG00000126001 - + 20 20 30290125 33563218 downstream coding POFUT1 CEP250 30259357 33506564 + + 0 30306813 33527834 - + N - - N HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 6 0.942710757110266 0.928427260790413 0.942710757110266 0.928427260790413 4 - - 5281 N N 3.60785432895764 3.51782959285392 3.51782959285392 4 0 0.0602450203006787 N 0.0174631620868179 0 N N 165508 0 ENSG00000196262 ENSG00000219149 + - 7 9 44807754 78354504 utr3p intron PPIA AL161626.20-1 44802805 78354018 + - 0 44807594 78354116 + + Y - 1 N HCC1954 38 22.2142857142857 4 14 1 N - - N - - 0 0 0 14 0.857009779191151 0.278528178237124 0.857009779191151 0.278528178237124 1 - 0 14003 N N 3.53717633508317 2.84852772519401 2.84852772519401 44 0 0.0396505468941951 Y 0 0 N N 314 318 ENSG00000169662 ENSG00000133475 + - 22 22 19976715 19911926 coding intron AP000552.1-3 GGT2 19972519 19892261 - - 0 19973899 19893627 - + N - 0.591273113786721 N HCC1954 63 54.6 49 5 1 N - - N - - 0 0 0 5 0.699891319672773 0.721316564152552 0.721316564152552 0.699891319672773 1 - 0 43403 N Y 3.3184850412945 3.63296356710195 3.3184850412945 0 0.735193884130054 0.0784094951930553 N 0.766970618034448 0.809339596573639 N N 1637 249 ENSG00000180251 ENSG00000150076 - + 2 10 102516862 33211797 utr3p intron SLC9A4 C10orf68 102456194 32896657 + + 0.766970618034448 102516712 33113488 - + Y - 13.7178929359707 N HCC1954 30 26.2666666666667 22 15 1 N - - N LINE LINE 1 1 1 15 0.742741808632331 0.264244681917271 0.742741808632331 0.264244681917271 0 - 0 29286 N Y 3.47080361183081 3.31588453542141 3.31588453542141 274 0.167229545702146 0.00198415437833266 Y 0.524131168972655 0.985129099030395 N N 99 0 ENSG00000204623 ENSG00000219322 + + 6 6 30136900 30004988 intron intron C6orf12 HLA-K 30076768 30002215 - + 0 30082761 30002640 - + N 0.455072933993676 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.364229156156239 0.271386430077198 0.364229156156239 0.271386430077198 1 0 0 18351 Y Y 3.66336194527509 3.37126417066287 3.37126417066287 240 0 0.0195648342488389 Y 0.988420542635659 0.988420542635659 N N 2211 0 ENSG00000143036 ENSG00000217711 - - 1 1 95133389 94912305 upstream upstream SLC44A3 RP11-86H7.2 95058523 94911066 + - 0 95058104 94982141 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.621332089913584 1.0069864905496 1.0069864905496 0.621332089913584 1 - - 36302 Y Y 3.3755202409218 3.27820542559317 3.27820542559317 273 0 0.00506499124473159 Y 0 0.983394383394383 N N 14247 542 ENSG00000139641 ENSG00000135482 - + 12 12 54824719 54802545 coding utr5p FAM62A ZC3H10 54808318 54798297 + + 0 54808509 54798359 - + N 0.367239943837921 0.603118836291913 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.499922371194838 0.292811674556976 0.499922371194838 0.292811674556976 1 0 0 47584 Y Y 3.34040178417331 3.30803474231284 3.30803474231284 236 0 0.00654328889841427 Y 0.782176906779661 0.989627471751412 N N 18 2053 ENSG00000214212 ENSG00000099203 - - 19 19 10841043 10807983 coding upstream C19orf38 TMED1 10820160 10804115 + - 0 10820199 10808376 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.0731707317073171 0.0731707317073171 10 0.921285512630487 0.928427260790413 0.928427260790413 0.921285512630487 3 - - 44199 N N 3.50848272165904 3.21279122419719 3.21279122419719 1 0 0.0425108508618774 N 0 0 N N 1974 3891 ENSG00000172113 ENSG00000166295 - + 3 10 48317852 73665622 utr3p intron NME6 C10orf104 48310595 73645812 - + 0 48310786 73645955 + + Y - 0.744979490524871 N HCC1954 26 24 21 9 1 N - - N SINE - 1 0 1 9 0.314236919036755 0.564198104634174 0.564198104634174 0.314236919036755 1 - 0 8292 N N 3.79722016713641 3.7297745213208 3.7297745213208 0 0 0.930691819971607 N 0 0.0302850061957869 N N 0 51 ENSG00000182152 ENSG00000115290 + - 5 2 117142614 165186606 downstream intron AC114322.2 GRB14 117142420 165057579 - - 0.0302850061957869 116869229 165138554 - + Y - 1.67260042593817 N HCC1954 2 2 2 61 3 N - - N Unknown - 0.368159203980099 0 0.368159203980099 61 1.43549138014518 0.464213630395207 1.43549138014518 0.464213630395207 2 - 0 38119 Y Y 3.54975555433691 3.53296011761759 3.53296011761759 2 0.00436681222707413 0.951798311171112 Y 0.00436681222707413 0.966812227074236 N N 51898 4802 ENSG00000100644 ENSG00000027075 - + 14 14 61284729 61087443 upstream coding HIF1A PRKCH 61231992 60858186 + + 0 61194076 61067066 - + N - 1.4127374906466 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.549914608314322 0.764167053112109 0.764167053112109 0.549914608314322 4 - 0 3346 N N 3.28126993978269 3.58320909912975 3.28126993978269 15 0 0.447632405850624 Y 0 0 N N 16900 5796 ENSG00000185658 ENSG00000159267 + - 21 21 39607426 37284373 coding coding BRWD1 HLCS 39479274 37045066 - - 0 39503891 37191264 - + N - 1.08126826964697 N HCC1954 1 1 1 0 2 N 508 8.9854 N - - 0 0 0 23 1.07840397214886 1.15696320190805 1.15696320190805 1.07840397214886 2 - 0 29438 Y Y 3.4780843434859 3.43568515508231 3.43568515508231 0 0 0.844859202421153 Y 0 0.977689676616916 N N 0 1209 ENSG00000219891 ENSG00000197279 - + 6 6 28168598 28165320 upstream coding ZSCAN12L1 ZNF165 28168305 28154551 + + 0 28168097 28164431 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.892718519990782 0.928427260790413 0.928427260790413 0.892718519990782 1 - - 46357 N Y 3.28292550416853 3.8333716936548 3.28292550416853 0 0 0.752166598091772 N 0.269003266531297 0.968217533327448 N N 0 3966 ENSG00000205243 ENSG00000175772 + + 19 2 33907087 110111006 upstream upstream AC005524.1 AC013268.5-1 33886996 110103138 - + 0.279597422088814 33989089 110102056 - + Y - - N HCC1954 40 40 40 4 1 N 333 26.3085 N LINE - 1 0 1 4 0.328520415356608 0.39993789695587 0.39993789695587 0.328520415356608 3 - - 15232 N Y 3.55401162459584 3.52936639476796 3.52936639476796 3 0 0.0159918754116094 N 0 0.85598972665566 N N 1702 7816 ENSG00000170379 ENSG00000159023 + + 7 1 143058435 29319545 utr3p utr3p FAM115C EPB41 143028667 29086215 + + 0.0207301412584848 143057700 29317494 + + Y - - N HCC1954 672 604.75 546 4 1 N - - N LINE SINE 1 1 1 4 0.449930134075354 0.307095170876829 0.449930134075354 0.307095170876829 1 - - 40619 N Y 3.61464054707278 3.58064844605001 3.58064844605001 12 0 0.0649143340639523 N 0 0.964909894593675 N N 2078 556 ENSG00000182621 ENSG00000196284 - + 20 6 8813547 45453669 intron utr5p PLCB1 SUPT3H 8061296 44904447 + - 0.0525671540292416 8300025 45252126 - - Y 0.389104197622807 - N HCC1954 23 14.6 2 5 1 N - - N - LINE 0 1 1 5 0.507064119354764 0.607048593593732 0.607048593593732 0.507064119354764 1 0 - 23262 N Y 3.52936639476796 3.41679307359967 3.41679307359967 1 0 0.0807018369959065 N 0.794592491733126 0.763781365493095 N N 6191 5137 ENSG00000169905 ENSG00000148429 - - 1 10 178113557 11693759 utr5p intron TOR1AIP2 USP6NL 178080577 11542517 - - 0 178112998 11660105 + + Y - 1.65766832988279 N HCC1954 21 20.5714285714286 20 7 1 N - - N - SINE 0 1 1 7 0.528489363834543 0.328520415356608 0.528489363834543 0.328520415356608 1 - 0 4345 Y Y 3.22639416565101 3.31535532676129 3.22639416565101 257 0 0.103151664928141 Y 0 0.71655436398722 N N 0 3838 ENSG00000212568 ENSG00000154710 - + 7 7 65993713 65913881 upstream downstream U6 RABGEF1 65993610 65843078 + + 0 65958094 65951088 - + N - - N HCC1954 4 1.8 1 6 1 N - - Y SINE - 0.374045801526718 0 0.374045801526718 10 0.93556900895034 0.892718519990782 0.93556900895034 0.892718519990782 4 - - 33144 N N 3.53871326596283 3.57848902055439 3.53871326596283 0 0 0.0732058022933868 N 0 0 Y N 0 544065 ENSG00000211459 ENSG00000198744 - + MT MT 1603 9988 intron coding AF347015.1-2 MT-CO3 650 8367 + + 0 1452 9414 - + N 1 1.17756096167547 N HCC1954 4 3 2 6 1 N 368 9.72153 N - - 0 0 0 6 0.28566992639705 0.699891319672773 0.699891319672773 0.28566992639705 1 0 0 41667 N Y 3.54189641365853 3.57332786160156 3.54189641365853 337 0 0.00299426566257266 Y 0.456164014027515 0.990936066900459 N N 5793 13 ENSG00000185803 ENSG00000214597 - - 8 8 145555754 145549313 intron coding GPR172A AF205589.5 145553033 145547782 + - 0 145553651 145549194 - + N 0.127539640541859 1.78951857295806 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.785592297591888 0.478497126715059 0.785592297591888 0.478497126715059 3 0 0 44052 N N 3.09087103183403 3.57233464462502 3.09087103183403 7 0 0.0587082845648518 N 0 0 N N 3891 1098 ENSG00000166295 ENSG00000065615 + + 10 6 73665622 84726863 intron intron C10orf104 CYB5R4 73645812 84626089 + + 0 73645953 84705494 + + Y 0.744979490524871 2.31841970306234 N HCC1954 20 17.75 11 4 1 N - - N - SINE 0 1 1 4 0.299953422716903 0.328520415356608 0.328520415356608 0.299953422716903 1 0 0 36359 Y Y 3.46704205511183 3.59681204058356 3.46704205511183 165 0 0.0196148870608983 Y 0 0 N N 1188 2 ENSG00000177675 ENSG00000215009 + + 12 12 7488016 7372236 downstream intron CD163L1 ACSM4 7398826 7348209 - + 0 7390902 7370733 - + N - 1.11293499671701 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.907002016310634 0.707033067832699 0.907002016310634 0.707033067832699 2 - 0 5730 N N 3.36042022138167 3.81657625693547 3.36042022138167 0 0 0.0641834897293072 N 0 0.443850267379679 N N 411 7 ENSG00000183023 ENSG00000144847 - + 2 3 40691697 120347588 coding utr5p SLC8A1 IGSF11 40192790 120102173 - - 0 40509134 120314236 + - Y - - N HCC1954 23 22.6 22 5 1 N - - N - LINE 0 1 1 5 0.499922371194838 0.314236919036755 0.499922371194838 0.314236919036755 1 - - 30569 N Y 3.60256518892881 3.34252135687557 3.34252135687557 79 0.00363636363636366 0.596300592576497 Y 0.012080123266564 0.983112480739599 N N 0 3991 ENSG00000208602 ENSG00000165704 + + X X 133488116 133462354 downstream coding AC004383.1 HPRT1 133487977 133421923 - + 0 133475631 133460380 - + N - - N HCC1954 4 1.61111111111111 1 6 1 N - - N SINE - 0.950819672131147 0 0.950819672131147 18 0.871293275511003 1.05697872766909 1.05697872766909 0.871293275511003 4 - - 8013 N N 2.73208080244326 2.71123698212769 2.71123698212769 15 0.198395593869732 0.381137327024121 N 0.198395593869732 0.252873563218391 N N 122511 24465 ENSG00000187514 ENSG00000164104 - + 2 4 232286495 174492167 coding coding PTMA HMGB2 232280638 174489363 + - 0.276221264367816 232284932 174489844 - - Y - - N HCC1954 4 2.5 1 3 1 Y - - N Low_complexity Low_complexity 0.0921985815602837 0.0410958904109589 0.0921985815602837 4 0.842726282871298 0.521347615674617 0.842726282871298 0.521347615674617 3 - - 36009 N Y 2.12058993319223 3.31947825827104 2.12058993319223 0 0.135670731707317 0.0527403853050625 N 0.135670731707317 0.135670731707317 N N 20535 122756 ENSG00000101972 ENSG00000135480 - + X 12 123064187 50928976 utr5p coding STAG2 KRT7 122921743 50913221 + + 0.135670731707317 122922217 50915291 - + Y - 0.684652537509957 N HCC1954 6 3 1 2 1 N - - N Simple_repeat - 0.72972972972973 0 0.72972972972973 4 0.264244681917271 0.385654400636018 0.385654400636018 0.264244681917271 2 - 0 13964 N Y 3.58441000276898 3.54872248456702 3.54872248456702 0 0 0.216353030953477 Y 0 0 N N 6053 1267 ENSG00000100097 ENSG00000221912 - + 22 22 36405753 36392885 coding coding LGALS1 PDXP 36401559 36384683 + + 0 36402991 36391596 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.671324327033068 0.899860268150708 0.899860268150708 0.671324327033068 3 - - 29386 Y Y 3.45144752203174 3.39384326095097 3.39384326095097 95 0.0412785094763894 0.844396973213016 Y 0.977353035656923 0.962255059428204 N N 446 3909 ENSG00000111837 ENSG00000137210 + + 6 6 10946714 10865200 intron coding MAK TMEM14B 10870942 10856024 - + 0 10878296 10857917 - + N 0.775378924760826 - N HCC1954 2 1.66666666666667 1 4 3 N - - Y - - 0 0 0 6 0.857009779191151 1.3069399132665 1.3069399132665 0.857009779191151 4 0 - 41911 N N 3.74913061111987 3.61720120015252 3.61720120015252 0 0.122904842510538 0.790301003721394 N 0.122904842510538 0 N N 29840 0 ENSG00000164830 ENSG00000212451 + + 8 8 107834093 127753081 coding downstream OXR1 U11 107739270 127752949 + + 0 107765655 128072234 + + N - - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - - 0 0 0 6 0.5713398527941 0.535631111994469 0.5713398527941 0.535631111994469 1 - - 31732 Y Y 3.82402482245992 2.9976538004648 2.9976538004648 82 0 0.556020061009861 Y 0.00323624595469263 0.990131051940146 N N 46 46598 ENSG00000214217 ENSG00000118849 - - 3 3 159943998 159932969 utr5p upstream AC080013.17 RARRES1 159940900 159897597 + - 0 159942556 159933013 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE,SINE - 0.234042553191489 0 0.234042553191489 8 1.20695543902754 0.99270299422975 1.20695543902754 0.99270299422975 2 - - 31224 Y Y 3.33528047801382 3.45976132345673 3.33528047801382 285 0 0.0152372658771818 Y 0 0.976825785393717 N N 0 2527 ENSG00000199306 ENSG00000186001 - + 3 3 199105881 199082851 upstream coding U6 LRCH3 199105775 199002542 + + 0 199094697 199082728 - + N - 28.2065709392822 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 19 0.721316564152552 0.699891319672773 0.721316564152552 0.699891319672773 0 - 0 20789 N N 3.51935717616377 3.51729103662399 3.51729103662399 18 0 0.232152733740368 N 0.0943396226415093 0 N N 94 2833 ENSG00000147255 ENSG00000133019 - + X 1 130361358 238139338 utr5p utr5p IGSF1 CHRM3 130235161 237858996 - + 0.0218867924528301 130361358 237859192 + + Y - - N HCC1954 25 23 21 4 1 N - - N - LINE 0 1 1 4 0.557056356474248 0.421363141435649 0.557056356474248 0.421363141435649 1 - - 23789 N Y 3.57063922744582 3.61360747730288 3.57063922744582 0 0 0.330706568695927 N 0 0.973406593406594 N N 1186 2 ENSG00000137968 ENSG00000205462 - + 1 5 75849389 81718091 coding downstream SLC44A5 AC026698.6 75440404 81714520 - + 0 75577903 81766652 + + Y - - N HCC1954 24 18.875 1 7 1 N - - N - LINE 0 1 1 8 0.899860268150708 0.478497126715059 0.899860268150708 0.478497126715059 4 - - 49307 Y Y 3.43358851031899 3.73808832274579 3.43358851031899 0 0 0.877548136816 Y 0 0.98155961869042 N N 336 1955 ENSG00000179978 ENSG00000205570 - + 5 5 69460019 69590632 coding utr3p AC140134.2-1 AC140134.2-2 69424621 69470446 - - 0 69460017 69528838 + - N - 0.196429205275905 N HCC1954 40 33.75 15 4 1 N - - Y - - 0 0 0 4 0.742741808632331 0.557056356474248 0.742741808632331 0.557056356474248 4 - 0 26889 Y Y 3.58337693299909 3.34528969661801 3.34528969661801 336 0 0.0430552548292334 Y 0 0.993483504512916 N N 6938 516 ENSG00000198211 ENSG00000182289 - + 16 16 88530006 88510383 upstream coding TUBB3 AC092143.4-2 88513168 88508026 + + 0 88511784 88509048 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat 0 0.0930232558139535 0.0930232558139535 19 1.5783263433437 1.19981369086761 1.5783263433437 1.19981369086761 1 - - 49091 Y Y 3.59681204058356 3.2965682984157 3.2965682984157 3 0 0.866605788241082 Y 0.0146116380415278 0.00401606425702794 N N 5 2781 ENSG00000215159 ENSG00000082196 - - 5 5 34232139 34160396 intron intron AC138409.1-1 AMACR 34210910 34023069 + - 0 34211309 34100579 - + N 0.899963885879379 22.4681704598243 N HCC1954 2 1.2 1 1 3 N - - Y - LTR 0 1 1 5 0.542772860154395 0.87843502367093 0.87843502367093 0.542772860154395 3 0 0 31413 Y Y 3.48912663185998 3.01187923653457 3.01187923653457 263 0.00380228136882121 0.0147296944703437 Y 0.00380228136882121 0.990943657103353 N N 182 1404 ENSG00000131378 ENSG00000154814 + + 3 3 16530226 16322597 intron utr3p RFTN1 OXNAD1 16332357 16281718 - + 0 16353624 16320104 - + N 1.03907022942961 10.3524386737588 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 5 0.721316564152552 0.956994253430118 0.956994253430118 0.721316564152552 1 0 0 18440 Y Y 3.55128313764676 3.54040868314203 3.54040868314203 300 0 0.0411141200596066 Y 0.978489208633094 0.992829736211031 N N 0 56940 ENSG00000215899 ENSG00000168528 + + 1 1 31733954 31680111 downstream intron AC114494.2-1 SERINC2 31733019 31654999 - + 0 31716502 31673045 - + N - 0.695246759919559 N HCC1954 1 1 1 0 2 N - - Y LTR SINE,LINE 1 0.514084507042254 1 17 1.03555348318931 1.01412823870953 1.03555348318931 1.01412823870953 3 - 0 400 Y Y 3.61616813038263 3.17245817533338 3.17245817533338 70 0 0.96988773766832 Y 0.116373991457048 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.98984337921215 1816506 1814825 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 9 1.16410495006798 1.02126998686945 1.16410495006798 1.02126998686945 1 - - 43327 N Y 2.97933078043563 3.1165493314318 2.97933078043563 3 0 0.0911365255601726 N 0 0.668384879725086 N N 1673 2 ENSG00000212774 ENSG00000108242 - - 7 10 23644794 96485514 coding intron AC006026.2-1 CYP2C18 23643291 96433368 - + 0 23644435 96448462 + - Y - 1.12641126740339 N HCC1954 414 276.714285714286 126 7 1 N - - N Other LINE 1 1 1 7 0.45707188223528 0.371370904316165 0.45707188223528 0.371370904316165 3 - 0 46461 N Y 3.43677165801469 3.51935717616377 3.43677165801469 263 0 0.0339772246407842 N 0.755649616184805 0.699261066073607 N N 3 0 ENSG00000079102 ENSG00000187534 + - 8 19 93176619 45141507 downstream intron RUNX1T1 AC007842.1 93040328 45140401 - - 0.699261066073607 92991593 45141446 - + Y - 1 N HCC1954 3 2.17647058823529 2 34 1 N - - N - - 0 0 0 34 0.385654400636018 0.685607823352921 0.685607823352921 0.385654400636018 1 - 0 2023 N Y 3.26824964015148 3.66745018166468 3.26824964015148 21 0.00414937759336098 0.461695388793923 N 0.969200496214228 0.948667493690379 N N 8014 111 ENSG00000149084 ENSG00000112319 - - 11 6 43834736 133894358 utr3p upstream HSD17B12 EYA4 43658719 133604188 + + 0.117080891474526 43834016 133567317 - - Y 1.56799368003871 - N HCC1954 46 46 46 4 1 N - - N - SINE 0 1 1 4 0.578481600954027 0.39993789695587 0.578481600954027 0.39993789695587 2 0 - 27209 N Y 3.30910766487608 3.47907756046244 3.30910766487608 0 0 0.777653984350688 N 0.93502778685845 0.924199084668192 N N 211 0 ENSG00000157341 ENSG00000197017 - + 16 16 22385434 29532462 utr5p intron AC106788.3-1 AC009086.6-2 22370389 29531923 + - 0 22370442 29531925 - - N - 1 Y HCC1954 6 5.14285714285714 2 7 1 N - - N - - 0 0 0 7 0.314236919036755 0.692749571512847 0.692749571512847 0.314236919036755 4 - 0 9771 N Y 3.29127915838687 3.64127736852694 3.29127915838687 0 0 0.795991825425478 N 0 0.859520969986086 N N 9789 2668 ENSG00000159842 ENSG00000188522 + + 17 17 1029881 18848842 coding utr3p ABR FAM83G 853510 18812827 - - 0 958924 18819450 - - N 5.89626599502189 - Y HCC1954 39 37 35 4 1 N - - N - SINE 0 1 1 4 0.335662163516534 0.321378667196682 0.335662163516534 0.321378667196682 2 0 - 47729 Y Y 3.33528047801382 2.99615672237849 2.99615672237849 270 0.00370370370370365 0.711868238414049 Y 0.107967269595177 0 N N 3492 6250 ENSG00000123815 ENSG00000105245 + - 19 19 45914440 45888396 utr3p intron ADCK4 NUMBL 45889274 45863650 - - 0 45889339 45884742 - + N - 5.77660762383018 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 6 0.842726282871298 0.635615586233437 0.842726282871298 0.635615586233437 2 - 0 1669 N N 3.57912086274016 3.52105259334297 3.52105259334297 1 0 0.336995043709304 N 0 0 N N 2518 313916 ENSG00000135378 ENSG00000131748 - + 11 17 32832679 35073248 utr3p intron PRRG4 STARD3 32808065 35046938 + + 0 32832563 35065079 - + Y - 1.048146045815 N HCC1954 25 6.6 1 2 1 N - - N SINE DNA,SINE 1 0.768115942028985 1 5 0.28566992639705 0.492780623034912 0.492780623034912 0.28566992639705 1 - 0 45204 Y Y 3.45823374014688 3.12279699331701 3.12279699331701 7 0 0.282502226177175 Y 0.0357304387155133 0.985165083672546 N N 753 3745 ENSG00000203791 ENSG00000189319 + - 10 10 126470429 126422920 coding utr5p METTL10 FAM53B 126437396 126297853 - - 0 126441091 126385427 - + N - 3.90280830737247 N HCC1954 1 1 1 0 2 N - - Y SINE - 0.0652173913043478 0 0.0652173913043478 4 0.328520415356608 0.521347615674617 0.521347615674617 0.328520415356608 1 - 0 1285 N N 3.08462336994882 1.74518490395198 1.74518490395198 37 0 0.0611109217035453 N 0 0.493275792854276 N N 10635 0 ENSG00000048649 ENSG00000206951 + - 11 2 77209528 33024022 intron downstream RSF1 Y_RNA 77054923 33023910 - - 0.493275792854276 77123809 32994825 - + Y 1.29167088559693 - N HCC1954 14 7.75 1 3 1 N 400 11.0246 N - Simple_repeat 0 1 1 4 0.328520415356608 0.299953422716903 0.328520415356608 0.299953422716903 2 0 - 47370 Y Y 3.17151839151932 3.73808832274579 3.17151839151932 261 0 0.601863250874894 Y 0.493021346469622 0.991105637657362 N N 4159 60677 ENSG00000012061 ENSG00000125740 - - 19 19 50619017 50670254 utr5p downstream ERCC1 FOSB 50604712 50663093 - + 0 50618479 50673816 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.671324327033068 0.621332089913584 0.671324327033068 0.621332089913584 2 - - 5468 N N 3.59784511035345 3.42936294528359 3.42936294528359 0 0 0.0500076676052664 N 0 0 N N 13069 8332 ENSG00000055332 ENSG00000124788 - - 2 6 37405184 16869666 utr3p intron EIF2AK2 ATXN1 37179857 16407322 - - 0 37184742 16436787 + + Y - 0.560278166444937 N HCC1954 29 26 25 4 1 N - - N SINE,SINE - 1 0 1 4 0.264244681917271 0.307095170876829 0.307095170876829 0.264244681917271 1 - 0 16342 N Y 3.61360747730288 3.57233464462502 3.57233464462502 0 0 0.59067302613082 N 0.708870967741935 0.693548387096774 N N 33725 14131 ENSG00000143819 ENSG00000091436 - + 1 2 224099884 173840979 utr5p downstream EPHX1 ZAK 224064459 173648688 + + 0 224083049 173877201 - + Y - - N HCC1954 20 18.75 17 4 1 N - - N - LTR 0 1 1 4 0.549914608314322 0.292811674556976 0.549914608314322 0.292811674556976 4 - - 42397 Y Y 3.32423818963975 3.50472116494007 3.32423818963975 222 0 0.0377678556877836 Y 0 0.985141858276187 N N 4707 0 ENSG00000125386 ENSG00000206738 - - 4 4 2704097 2586749 intron downstream C4orf8 Y_RNA 2596957 2586649 + - 0 2597932 2567930 - + N 0.0145154996266201 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.328520415356608 0.435646637755502 0.435646637755502 0.328520415356608 1 0 - 13578 N N 3.68953475841283 3.42680229220385 3.42680229220385 0 0 0.0562544948314162 N 0.854492229540661 0 N N 265 147 ENSG00000100206 ENSG00000179082 + + 22 9 37296135 131127005 utr3p downstream DMC1 C9orf106 37244900 131123116 - + 0 37245211 131144161 - + Y - - N HCC1954 34 26.6666666666667 22 6 1 N - - N SINE - 1 0 1 6 0.428504889595575 0.578481600954027 0.578481600954027 0.428504889595575 1 - - 33055 N Y 3.00463835767282 2.89211846966702 2.89211846966702 305 0 0.9997973532737 Y 0.0196183821553346 0.983660306369256 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8414 5443 - + N 1.08080409485149 1.36651119851212 N HCC1954 3 1.6 1 12 9 Y - - N - - 0 0 0 25 1.14982145374813 0.93556900895034 1.14982145374813 0.93556900895034 2 0 0 9394 Y Y 3.48912663185998 3.25616070163838 3.25616070163838 296 0.0135479867622724 0.614808766717702 Y 0.0135479867622724 0.989830391616106 N N 0 12836 ENSG00000222777 ENSG00000167258 + + 17 17 34955984 34941095 downstream coding U6 CRKRS 34955883 34871265 - + 0 34954030 34940802 - + N - 3.14108936845148 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 18 0.749883556792257 1.0069864905496 1.0069864905496 0.749883556792257 1 - 0 33917 N N 3.14160936921295 3.779528989293 3.14160936921295 0 0 0.0675315166664529 N 0 0 N N 544065 339915 ENSG00000198744 ENSG00000198727 + + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8677 15834 + + N 0.567956504381133 2.74556537998934 Y HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.828442786551446 0.757025304952183 0.828442786551446 0.757025304952183 1 0 0 49061 N N 3.60682125918775 3.51935717616377 3.51935717616377 0 0 0.241991487779155 Y 0 0 N N 6627 51629 ENSG00000113269 ENSG00000165671 + + 5 5 179431719 176655369 intron coding RNF130 NSD1 179315111 176493532 - + 0 179387721 176571799 - + N 2.25757575493198 1.41971483172397 N HCC1954 1 1 1 0 1 N 286 5.49859 N - - 0 0 0 15 0.999844742389676 1.02126998686945 1.02126998686945 0.999844742389676 1 0 0 23443 N Y 3.41969076197147 2.97991342225823 2.97991342225823 0 0.374882260596546 0.264229896810027 N 0.374882260596546 0.744270015698587 N N 1303 9618 ENSG00000197573 ENSG00000122417 - + 19 1 46148403 86634591 downstream utr3p CYP2B7P1 ODF2L 46122010 86581341 + - 0.374882260596546 46162175 86588617 - - Y - - N HCC1954 50 31.5 25 4 1 N - - N LINE LINE 1 1 1 4 0.549914608314322 0.328520415356608 0.549914608314322 0.328520415356608 2 - - 25116 Y Y 3.39760481766995 3.62770493229666 3.39760481766995 282 0 0.0426196092041949 Y 0.992153906293628 0.992153906293628 N N 2333 987 ENSG00000005812 ENSG00000102805 + + 13 13 76499286 76474652 coding utr3p FBXL3 CLN5 76477391 76462796 - + 0 76487547 76474187 - + N - 1.66492866746751 N HCC1954 1 1 1 0 2 N - - Y - RNA 0 0.82 0.82 9 0.907002016310634 1.07126222398894 1.07126222398894 0.907002016310634 2 - 0 31330 Y Y 3.53209488171704 3.48015048302568 3.48015048302568 271 0 0.176797215366572 Y 0.146020031628888 0 N N 708 14912 ENSG00000012171 ENSG00000114353 - + 3 3 50289574 50271775 upstream downstream SEMA3B GNAI2 50280044 50248640 + + 0 50279107 50275502 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.93556900895034 0.735600060472404 0.93556900895034 0.735600060472404 1 - - 36189 N Y 3.46869761949767 3.56591914887046 3.46869761949767 0 0 0.194218681344577 N 0 0 N N 889 7684 ENSG00000002016 ENSG00000094916 + + 12 12 929124 52960153 intron downstream RAD52 CBX5 891516 52921003 - - 0 917971 52918123 - - N 1.52282387447273 - Y HCC1954 9 6 5 5 1 N - - N SINE SINE 1 0.507246376811594 1 5 0.264244681917271 0.492780623034912 0.492780623034912 0.264244681917271 1 0 - 44910 N N 3.39128260787123 3.8097595335968 3.39128260787123 0 0 0.103088267098468 Y 0 0 N N 0 269 ENSG00000220006 ENSG00000203772 + - 10 10 135239525 135088111 downstream upstream RP11-108K14.7 SPRN 135238616 135084161 - - 0 135237382 135088820 - + N - - N HCC1954 2 2 2 4 1 N - - N LINE - 1 0 1 4 0.335662163516534 0.364229156156239 0.364229156156239 0.335662163516534 2 - - 16132 N Y 3.13846607431061 3.01125674191862 3.01125674191862 319 0 0.00226101186386363 N 0 0.803250288731232 N N 71 0 ENSG00000163060 ENSG00000222289 - + 2 1 94906295 142279986 upstream upstream TEKT4 BX004987.9-1 94900959 142279905 + - 0 94897028 142308926 - - Y - - N HCC1954 2 1.58333333333333 1 7 1 N 310 21.3208 N - - 0 0 0 12 0.414221393275723 0.321378667196682 0.414221393275723 0.321378667196682 2 - - 36244 Y Y 3.49847350305486 3.20653421474217 3.20653421474217 172 0 0.092244427918127 Y 0.0510042283298098 0 N N 1803 27079 ENSG00000139055 ENSG00000111341 + - 12 12 14982750 14930025 downstream upstream ERP27 MGP 14958241 14925119 - - 0 14949371 14930040 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 16 0.821301038391519 0.93556900895034 0.93556900895034 0.821301038391519 1 - - 41383 Y Y 3.29396779254261 3.24099032408136 3.24099032408136 0 0 0.99888708069032 Y 0.991481866481866 0.991481866481866 N N 0 9799 ENSG00000222697 ENSG00000076554 - - 8 8 81279688 81155565 upstream coding SRP_euk_arch TPD52 81279396 81109662 + - 0 81246213 81139381 - + N - 31.6570974291493 N HCC1954 1 1 1 0 6 N - - Y Low_complexity - 0.121794871794872 0 0.121794871794872 755 1.1141127129485 0.885576771830856 1.1141127129485 0.885576771830856 2 - 0 43440 N Y 3.7061623612628 3.60785432895764 3.60785432895764 0 0 0.435260628025819 N 0 0.959071166054126 N N 401 24 ENSG00000172650 ENSG00000188452 + - 10 2 75127645 182230079 coding intron AGAP5 CERKL 75104049 182109644 - - 0 75105838 182134206 - + Y - 1.80098481739844 N HCC1954 38 27.1666666666667 8 6 1 N - - N - SINE,SINE 0 1 1 6 0.949852505270192 0.421363141435649 0.949852505270192 0.421363141435649 2 - 0 31776 N Y 3.52614339427891 3.1060761045112 3.1060761045112 164 0 0.125148899711009 N 0.787886698864378 0.985859113257625 N Y 2906 2216 ENSG00000214135 ENSG00000185485 - + 3 3 196895854 197201530 coding intron AC069513.28-1 AC024937.21-3 196874647 197174603 + - 0 196876138 197201458 - - N - 3.22140037873952 Y HCC1954 8 4.71428571428571 1 6 1 Y - - N - Simple_repeat 0 0.012987012987013 0.012987012987013 7 0.728458312312478 1.09982921662864 1.09982921662864 0.728458312312478 4 - 0 16936 N N 3.37911396377143 3.61360747730289 3.37911396377143 0 0 0.0447161032496208 N 0 0 N N 989 49089 ENSG00000181031 ENSG00000117450 - - 17 1 202576 45760196 utr3p coding RPH3AL PRDX1 62297 45749295 - - 0 62988 45757256 + + Y - - N HCC1954 42 17.5217391304348 1 22 1 N - - N SINE - 1 0 1 23 0.314236919036755 0.87843502367093 0.87843502367093 0.314236919036755 1 - - 5492 N N 3.38127338926705 3.45976132345673 3.38127338926705 6 0 0.074518177415883 N 0 0 N N 3780 7581 ENSG00000115020 ENSG00000142166 - + 2 21 208931720 33653993 utr3p coding PIP5K3 IFNAR1 208839236 33619084 + + 0 208929428 33639445 - + Y - - N HCC1954 36 23.5 20 6 1 N - - N SINE - 1 0 1 6 0.435646637755502 0.949852505270192 0.949852505270192 0.435646637755502 2 - - 38365 Y Y 3.71873223294673 3.79362644428678 3.71873223294673 2 0.0117761390270393 0.999229301225626 Y 0.815754873377923 0.983250443034357 N N 10336 0 ENSG00000133961 ENSG00000221236 - - 14 14 72892230 72985644 coding upstream NUMB AC005280.3 72811671 72985548 - + 0 72820835 72946398 + - N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 4 0.914143764470561 0.857009779191151 0.914143764470561 0.857009779191151 4 - - 4092 Y Y 3.78105657260285 3.35781971550858 3.35781971550858 334 0 0.214725396561662 N 0.139275406022488 0.992827295050188 Y N 0 0 ENSG00000223189 ENSG00000208561 - + 7 7 128054565 128054565 downstream downstream U6 AC018638.5-1 128054462 128054463 + + 0 128066232 128059157 - + N - - N HCC1954 221 123.272727272727 14 11 3 N - - N SINE,LTR,LTR SINE,LTR 0.559782608695652 0.548611111111111 0.559782608695652 11 1.24266417982717 0.899860268150708 1.24266417982717 0.899860268150708 1 - - 31879 Y Y 3.45513453083721 3.6052936758779 3.45513453083721 0 0 0.817225458519918 Y 0.992672768408062 0.992672768408062 N N 90 3914 ENSG00000206115 ENSG00000085276 + - 3 3 170582016 170347054 coding intron MDS1 EVI1 170581663 170283981 - - 0 170581670 170344315 - + N - 5.48779034056929 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 51 1.07126222398894 0.999844742389676 1.07126222398894 0.999844742389676 1 - 0 48283 N N 3.40232489624531 3.17720875913227 3.17720875913227 9 0 0.069690205584851 N 0 0 N N 2273 0 ENSG00000177556 ENSG00000146477 + + 5 6 151118405 160796004 utr3p intron ATOX1 SLC22A3 151102577 160689415 - + 0 151106049 160791821 - + Y - 1 N HCC1954 20 20 20 5 1 N - - N - LTR 0 1 1 5 0.39993789695587 0.307095170876829 0.39993789695587 0.307095170876829 2 - 0 3337 N N 2.98098634482147 3.63655728995158 2.98098634482147 0 0 0.393137601928853 N 0 0 N N 21326 17298 ENSG00000182240 ENSG00000182871 + + 21 21 41570378 45758062 upstream intron BACE2 COL18A1 41461598 45649480 + + 0 41450663 45683052 + + N - 0.138337720616552 Y HCC1954 1 1 1 0 1 N - - N SINE - 1 0 1 7 0.657040830713216 0.549914608314322 0.657040830713216 0.549914608314322 2 - 0 18280 N Y 3.22998788850064 3.64553343878587 3.22998788850064 304 0 0.0187709177330651 Y 0 0 N N 17324 17324 ENSG00000185499 ENSG00000185499 + - 1 1 153429330 153429330 upstream coding MUC1 MUC1 153424924 153424924 - - 0.99302999631947 153429921 153428699 - + N - 2.36997282556327 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 10 0.435646637755502 0.707033067832699 0.707033067832699 0.435646637755502 1 - 0 1274 N N 3.41369636351399 3.61936062564813 3.41369636351399 0 0 0.0264027467146084 N 0 0 N N 6632 3153 ENSG00000158636 ENSG00000204104 - + 11 2 75940234 238974202 upstream intron C11orf30 TRAF3IP1 75833717 238893821 + + 0 75833056 238921285 - + Y - 2.39984715716921 N HCC1954 21 20.1666666666667 20 6 1 N - - N - SINE 0 1 1 6 0.449930134075354 0.299953422716903 0.449930134075354 0.299953422716903 0 - 0 27320 N N 3.4780843434859 3.73552766966605 3.4780843434859 13 0.0526160503540517 0.794551666275421 N 0.174075531077892 0 N N 30870 21349 ENSG00000179889 ENSG00000103226 + + 16 16 15140696 16296168 coding downstream PDXDC1 NOMO3 14976487 16233890 + + 0 15031414 16304413 + + N - - Y HCC1954 6 3.75 3 4 2 N 266 11.9069 N - LINE 0 1 1 4 0.87843502367093 0.585623349113953 0.87843502367093 0.585623349113953 4 - - 47901 N N 3.38656252929588 3.51360402781852 3.38656252929588 0 0 0.0973586667057711 N 0 0.092852175822567 N N 117 551733 ENSG00000196223 ENSG00000204628 + + 19 5 53399021 180603512 utr3p coding AC011466.6 GNB2L1 53375839 180596536 - - 0.092852175822567 53375848 180599176 - - Y - - N HCC1954 21 21 21 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.799875793911741 0.799875793911741 0.28566992639705 1 - - 38109 Y Y 3.79362644428678 3.56554842650988 3.56554842650988 236 0 0.924325827263136 Y 0.842774308652988 0.979036574487065 N N 0 10336 ENSG00000221236 ENSG00000133961 - - 14 14 72985644 72892230 upstream upstream AC005280.3 NUMB 72985548 72811671 + - 0 72946398 72903442 - + N - - N HCC1954 1 1 1 0 5 N - - Y - SINE 0 1 1 77 1.02841173502938 0.771308801272036 1.02841173502938 0.771308801272036 4 - - 9253 Y N 2.65607444488677 3.67589196416566 2.65607444488677 0 0 0.364854024419369 N 0 0 N N 0 0 ENSG00000221462 ENSG00000199753 - - 17 17 59577563 59577244 upstream upstream SNORA76 SNORND104 59577431 59577175 + + 0 59561069 59576731 - - N - - Y HCC1954 1 1 1 0 1 N 499 23.7168 N Simple_repeat - 0.176829268292683 0 0.176829268292683 29 1.07840397214886 1.04269523134923 1.07840397214886 1.04269523134923 1 - - 36151 N N 2.12829848505008 3.16783138271386 2.12829848505008 0 0 0.0322998225316166 N 0 0 N N 1375 41507 ENSG00000219410 ENSG00000188846 + + 12 3 6647454 40478862 coding coding AC125494.2-2 RPL14 6646689 40473834 + + 0 6647361 40478645 + + Y - - N HCC1954 44 26.2 12 5 1 N - - N Simple_repeat - 1 0 1 5 0.271386430077198 0.378512652476092 0.378512652476092 0.271386430077198 1 - - 14079 Y Y 3.47336426491055 3.32163768376666 3.32163768376666 356 0 0.346716922192209 Y 0 0.981702917225028 N Y 4030 855 ENSG00000185214 ENSG00000099910 + - 22 22 19180122 19122146 coding coding KLHL22 SCARF2 19125806 19108874 - - 0 19130730 19116275 - + N - 17.213042250171 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 14 0.814159290231593 0.714174815992626 0.814159290231593 0.714174815992626 4 - 0 32982 N N 2.76022891149302 2.8061819699529 2.76022891149302 1 0 0.999979562905594 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8492 14511 - + N 0.619501286280727 1.51584380467864 N HCC1954 3 1.42857142857143 1 4 10 N 189 4.09957 N - - 0 0 0 14 1.45691662462496 1.29979816510658 1.45691662462496 1.29979816510658 3 0 0 6548 Y Y 3.64656650855576 3.28651922701816 3.28651922701816 1 0 0.686855398906941 Y 0.99032762445002 0.98065524890004 N N 514 0 ENSG00000176771 ENSG00000200708 - - 2 2 134042504 134070447 utr5p downstream AC010974.1 7SK 133145844 134070132 - + 0 134033158 134115398 + - N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.0309278350515464 0 0.0309278350515464 6 0.692749571512847 0.528489363834543 0.692749571512847 0.528489363834543 4 - - 9646 Y N 3.4561676006071 3.30856910864616 3.30856910864616 0 0 0.0279899866649044 Y 0.969444444444445 0 N N 1772 0 ENSG00000187451 ENSG00000210710 - + 17 17 42483361 42474469 downstream upstream AC068152.11-2 AC068152.11-1 42480430 42474194 + + 0 42486515 42465682 - + N - - N HCC1954 4 2 1 2 1 N - - Y - - 0 0 0 5 0.585623349113953 0.507064119354764 0.585623349113953 0.507064119354764 1 - - 45530 N N 3.79040344379773 3.3755202409218 3.3755202409218 0 0 0.128964186654838 N 0 0.073095995508982 N N 8826 23280 ENSG00000167747 ENSG00000124767 - - 19 6 55999786 38778930 utr5p downstream C19orf48 GLO1 55992774 38751682 - - 0 55997677 38741002 + + Y - - N HCC1954 21 16.5 12 4 1 N - - N - SINE 0 1 1 4 0.335662163516534 0.257102933757345 0.335662163516534 0.257102933757345 3 - - 41696 N N 3.72874145155091 3.66505736245428 3.66505736245428 0 0 0.757176410140872 N 0 0 N N 249 79632 ENSG00000155897 ENSG00000182197 + + 8 8 132123854 119193119 upstream coding ADCY8 EXT1 131861736 118875910 - - 0 132371321 119191512 - - N - - Y HCC1954 1 1 1 0 2 N - - N - - 0 0 0 8 1.15696320190805 0.564198104634174 1.15696320190805 0.564198104634174 3 - - 8778 N N 3.06425985366392 2.90903555097135 2.90903555097135 0 0 0.591666669641366 N 0 0 N N 0 43386 ENSG00000215597 ENSG00000196535 - - Y 17 24080904 24531533 upstream intron AC009947.2 MYO18A 24078856 24424654 + - 0 24056446 24467769 - + Y - 1.44809082788858 N HCC1954 20 12.2 3 5 1 N - - N Simple_repeat - 0.738095238095238 0 0.738095238095238 5 0.299953422716903 0.585623349113953 0.585623349113953 0.299953422716903 2 - 0 13768 Y Y 3.65591337975064 3.48593413659447 3.48593413659447 345 0 0.0475156555104614 Y 0 0 N N 0 94 ENSG00000198986 ENSG00000197182 - + 22 22 44887366 44884554 upstream coding hsa-let-7a-3 RP4-695O20__B.10 44887293 44828413 + + 0 44887238 44884452 - + N - 1.65648624610889 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.971277749749971 0.778450549431962 0.971277749749971 0.778450549431962 4 - 0 19009 Y Y 3.32320511986986 3.54144175291192 3.32320511986986 293 0 0.0162917160534877 Y 0.00341296928327639 0 N N 2470 69209 ENSG00000143303 ENSG00000143320 - - 1 1 154973365 154942232 intron downstream C1orf66 CRABP2 154964902 154936034 + - 0 154968405 154926238 - + N 1.38179432324497 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 1.06412047582901 0.735600060472404 1.06412047582901 0.735600060472404 1 0 - 10198 Y Y 3.56331864299737 3.63296356710195 3.56331864299737 278 0 0.032827698874464 Y 0.979023097311625 0.968534645967436 N N 45264 31 ENSG00000131473 ENSG00000204815 - - 17 17 37328798 37371174 utr5p upstream ACLY TTC25 37276696 37340424 - + 0 37328662 37340137 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.671324327033068 0.907002016310634 0.907002016310634 0.671324327033068 2 - - 26900 Y Y 3.55297855482595 3.33255199106474 3.33255199106474 279 0 0.0116878468209524 Y 0 0 N N 2826 385 ENSG00000103037 ENSG00000103034 - + 16 16 57111932 57105024 intron utr3p SETD6 NDRG4 57106887 57055118 + + 0 57107173 57103580 - + N 0.727897065851525 - N HCC1954 1 1 1 0 1 Y - - Y Low_complexity - 0.0571428571428571 0 0.0571428571428571 4 0.942710757110266 0.899860268150708 0.942710757110266 0.899860268150708 1 0 - 47931 N N 3.79722016713641 3.7297745213208 3.7297745213208 0 0 0.99997729001051 N 0 0.013041408852927 N N 0 86504 ENSG00000182152 ENSG00000104408 + + 5 8 117142614 109330135 downstream coding AC114322.2 EIF3E 117142420 109283149 - - 0.013041408852927 116869229 109296012 - - Y - - N HCC1954 2 1.14598540145985 1 60 7 N 241 0.00319582 N Unknown - 0.364532019704433 0 0.364532019704433 411 1.44977487646503 1.36407389854591 1.44977487646503 1.36407389854591 4 - - 39828 Y Y 2.87316360745208 3.19971749140349 2.87316360745208 420 0 0.000792447484718517 N 0.989973677913376 0.994986838956688 Y N 33005 0 ENSG00000166145 ENSG00000210485 - - 15 15 38937144 38925032 utr5p downstream SPINT1 AC012476.8 38923538 38924962 + - 0 38923671 38918178 - + N 0.263427080343323 - N HCC1954 1 1 1 0 1 N - - N - LTR,LTR 0 1 1 69 1.33550690590621 1.38549914302569 1.38549914302569 1.33550690590621 1 0 - 47937 N N 3.40744620240479 3.00869608883888 3.00869608883888 0 0 0.670023572688192 N 0 0.015839651677802 N N 10798 29840 ENSG00000113761 ENSG00000164830 - + 5 8 176426349 107834093 intron coding ZNF346 OXR1 176382303 107739270 + + 0.015839651677802 176410317 107760614 - + Y 1.34575632127257 - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 39 1.49976711358451 1.16410495006798 1.49976711358451 1.16410495006798 2 0 - 29616 Y Y 3.5010341561346 3.68105312311849 3.5010341561346 0 0 0.672887591339035 Y 0 0 N N 4424 8 ENSG00000204427 ENSG00000204428 + - 6 6 31779172 31759796 utr3p intron BAT5 LY6G5C 31762711 31752440 - - 0 31762937 31759098 - + N - 1.52887029288703 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.764167053112109 0.592765097273879 0.764167053112109 0.592765097273879 1 - 0 44303 N Y 3.45872825368684 3.70719543103269 3.45872825368684 246 0 0.0384277186437508 N 0 0.446702800361337 N N 41134 0 ENSG00000035403 ENSG00000220830 + + 10 9 75549916 11003096 intron downstream VCL RP11-109M17.1 75427878 11001748 + + 0 75455948 11036660 + + Y 0.725776949372927 - N HCC1954 180 21.75 9 32 2 N - - N LTR SINE 1 1 1 32 0.314236919036755 0.971277749749971 0.971277749749971 0.314236919036755 1 0 - 36248 Y Y 3.44359772892318 3.26460248413936 3.26460248413936 304 0 0.00544542463264175 Y 0.0428938654583478 0.993399268037644 N N 16017 12 ENSG00000018236 ENSG00000205592 - + 12 12 39750361 39250827 upstream downstream CNTN1 MUC19 39588423 39222629 + + 0 39443115 39372662 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 12 0.642757334393363 0.692749571512847 0.692749571512847 0.642757334393363 1 - - 33099 N N 3.24913645959595 2.9438017485332 2.9438017485332 0 0.00467289719626152 0.441327512581664 Y 0.336448598130841 0.00467289719626152 N N 339915 275222 ENSG00000198727 ENSG00000198763 - + MT MT 15882 5512 coding coding MT-CYB MT-ND2 14748 4471 + + 0.00467289719626152 15542 5461 - + N 1.27437966361768 2.11782405234804 N HCC1954 2 1.28571428571429 1 2 2 N - - N - - 0 0 0 7 0.621332089913584 1.10697096478857 1.10697096478857 0.621332089913584 2 0 0 31363 N N 3.25931334411053 3.71976530271662 3.25931334411053 0 0 0.0476837453622593 Y 0.686159844054581 0 N N 0 37 ENSG00000201991 ENSG00000189283 + - 3 3 61043677 60497735 downstream upstream 5S_rRNA FHIT 61043568 59712992 - - 0 61002761 60497754 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR - 0.933333333333333 0 0.933333333333333 4 0.428504889595575 0.357087407996313 0.428504889595575 0.357087407996313 1 - - 21130 N Y 3.47233119514066 3.16104516459872 3.16104516459872 8 0 0.0701829192454942 N 0 0.846859562455893 N N 266 18437 ENSG00000135835 ENSG00000163932 + + 1 3 179181862 53201771 utr3p utr5p KIAA1614 PRKCD 179148936 53170263 + + 0 179181799 53187469 + + Y - - N HCC1954 21 21 21 4 1 N - - N SINE Low_complexity 1 0.089171974522293 1 4 0.264244681917271 0.907002016310634 0.907002016310634 0.264244681917271 1 - - 10063 Y Y 3.70144228268745 3.13739315174737 3.13739315174737 0 0 0.999871150172958 N 0 0.994169046647627 Y N 1482 317991 ENSG00000171345 ENSG00000171346 - + 17 17 36938167 36932191 coding upstream KRT19 KRT15 36933396 36923523 - - 0 36937607 36946767 + - N - - N HCC1954 2 1.03333333333333 1 1 8 N - - N - - 0 0 0 30 1.08554572030879 0.99270299422975 1.08554572030879 0.99270299422975 1 - - 36662 Y Y 3.47911741325579 3.45447218342791 3.45447218342791 44 0 0.251091133713901 Y 0 0.981613756613757 N N 32 3670 ENSG00000123096 ENSG00000123095 - - 12 12 26277134 26169113 coding upstream SSPN BHLHE41 26239789 26164228 + - 0 26268549 26170629 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.449930134075354 0.499922371194838 0.499922371194838 0.449930134075354 1 - - 17934 Y Y 3.4722913423473 3.40591861909494 3.40591861909494 145 0 0.00726307642601187 Y 0.0259946949602121 0.0832891246684351 N N 413 0 ENSG00000179743 ENSG00000216318 + + 1 1 16047229 16027751 utr3p upstream AL450998.19 RP11-169K16.8 16033561 16027314 - + 0.102387267904509 16033887 16018872 - + N - - N HCC1954 20 8.5 1 3 1 N - - Y - SINE 0 1 1 6 0.585623349113953 0.628473838073511 0.628473838073511 0.585623349113953 1 - - 24769 Y Y 3.64400585547602 3.56807857436608 3.56807857436608 100 0 0.068092092316578 N 0 0 Y N 48 0 ENSG00000215474 ENSG00000201825 + - 18 18 43029552 43014917 downstream downstream AC051635.7-1 U6 43011492 43014811 - - 0 43010852 42992484 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.428504889595575 0.499922371194838 0.499922371194838 0.428504889595575 3 - - 30260 Y Y 3.40488554932505 3.24368411591029 3.24368411591029 293 0 0.0263991194679551 Y 0 0.991482162130626 N N 35 0 ENSG00000102349 ENSG00000196163 - + X X 56328252 56118739 upstream downstream KLF8 AL353698.17 56275632 56117482 + + 0 56248129 56150770 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 15 0.685607823352921 1.16410495006798 1.16410495006798 0.685607823352921 1 - - 47311 Y Y 3.60000453584907 3.15848451151898 3.15848451151898 13 0 0.999510886166734 Y 0.805260263929619 0.992210410557185 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 coding upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10597344 10574234 - + N - - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.142857142857143 0.142857142857143 454 1.40692438750547 0.999844742389676 1.40692438750547 0.999844742389676 3 - - 33924 N N 3.56335849579072 3.425274708894 3.425274708894 0 0 0.0743534630860792 N 0 0 N N 544065 171855 ENSG00000198744 ENSG00000198886 + + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8985 11159 + + N 0.575390189395912 0.775977923154699 Y HCC1954 4 2.6 2 5 1 N 301 4.17858 N - - 0 0 0 5 0.814159290231593 1.07126222398894 1.07126222398894 0.814159290231593 1 0 0 13610 Y Y 3.28296535696188 3.60785432895764 3.28296535696188 300 0 0.0330249180371746 Y 0.939798657718121 0.99331096196868 N N 480 0 ENSG00000159496 ENSG00000220101 - - 22 22 22371363 22325521 upstream upstream RGL4 AP000347.3 22360329 22321400 + - 0 22355915 22332190 - + N - - N HCC1954 9 3.55670103092783 1 39 1 N - - Y - - 0 0 0 97 1.12839620926835 1.09982921662864 1.12839620926835 1.09982921662864 2 - - 47462 Y Y 3.45553575842133 3.58424216889964 3.45553575842133 251 0 0.629790693898804 Y 0 0.986540325185744 N N 2309 8 ENSG00000131398 ENSG00000131401 - + 19 19 55524446 55539830 coding downstream KCNC3 NAPSB 55507006 55528871 - - 0 55518044 55528539 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 5 0.464213630395207 0.45707188223528 0.464213630395207 0.45707188223528 1 - - 4166 Y Y 3.45872825368684 3.51935717616377 3.45872825368684 0 0 0.971697964676097 Y 0.402643171806167 0.98468315825144 N N 0 0 ENSG00000219142 ENSG00000217741 + + 7 7 17039627 16944706 upstream upstream AC098592.8 AC098592.7 17039238 16944374 - + 0 17059026 16922534 - + N - - N HCC1954 20 5.75 1 1 4 N - - Y LINE,LINE LTR 0.80952380952381 1 1 4 0.749883556792257 0.307095170876829 0.749883556792257 0.307095170876829 3 - - 41961 N N 3.26191384998363 3.34512186274866 3.26191384998363 0 0.00409836065573754 0.322691825221608 N 0.399024872809497 0.141464104013567 N N 0 0 ENSG00000217035 ENSG00000147434 - - X 8 44379422 42742776 downstream intron CHTF8P CHRNA6 44377882 42726939 + - 0.467707744488412 44385724 42732342 - + Y - 1 N HCC1954 21 20.25 20 4 1 N - - N SINE SINE 0.65625 1 1 4 0.22853594111764 0.28566992639705 0.28566992639705 0.22853594111764 2 - 0 18769 N Y 3.43681151080804 3.64656650855576 3.43681151080804 0 0 0.805714715176411 Y 0.237581413434432 0.975405852046272 N N 1120 1120 ENSG00000078900 ENSG00000078900 - + 1 1 3639716 3639716 downstream downstream TP73 TP73 3558989 3558989 + + 0 3649228 3646811 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.557056356474248 0.635615586233437 0.635615586233437 0.557056356474248 4 - - 47475 Y Y 3.40740634961144 3.4210491438586 3.40740634961144 35 0.209097404143844 0.647795202269975 N 0.209097404143844 0.985353655632293 Y N 1219 232 ENSG00000173480 ENSG00000204514 - + 19 19 63119790 63092182 coding coding ZNF417 AC010326.7-2 63108954 63076002 - - 0 63119560 63078338 + - N - 1.35369476506576 N HCC1954 9 6.25 4 4 1 N - - N SINE - 0.454545454545455 0 0.454545454545455 4 0.549914608314322 0.642757334393363 0.642757334393363 0.549914608314322 2 - 0 48901 Y Y 3.58064844605001 2.96787791690762 2.96787791690762 247 0 0.00865301818624131 N 0 0.821620641730618 Y N 0 0 ENSG00000222533 ENSG00000208333 - + 5 5 180661677 180661677 downstream upstream U6 AC138036.2-1 180661574 180661575 + + 0.21215783431023 180666010 180655178 - + N - - N HCC1954 189 141.75 126 4 1 N - - N SINE - 1 0 1 4 0.307095170876829 0.349945659836387 0.349945659836387 0.307095170876829 1 - - 6235 N N 2.9420707098628 2.6718368118362 2.6718368118362 0 0.170305676855895 0.191448489665837 N 0.60589519650655 0.170305676855895 N N 3242 11502 ENSG00000163032 ENSG00000159921 + - 2 9 17701766 36248450 utr3p utr3p VSNL1 GNE 17583874 36204430 + - 0.170305676855895 17700223 36206342 + + Y - 0.659918255598569 N HCC1954 37 34.2 25 5 1 N - - N Simple_repeat LINE 0.938775510204082 0.45 0.938775510204082 5 0.349945659836387 0.428504889595575 0.428504889595575 0.349945659836387 1 - 0 10217 Y Y 3.47655676017605 3.47705127371601 3.47655676017605 0 0 0.859579290329259 Y 0 0.983792289535799 N N 45 922 ENSG00000171403 ENSG00000186847 - + 17 17 36981836 36996673 coding downstream KRT9 KRT14 36975622 36992059 - - 0 36979998 36990717 + - N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.539393939393939 0.539393939393939 7 0.964136001590045 1.16410495006798 1.16410495006798 0.964136001590045 4 - - 34229 Y Y 3.33424740824393 3.09343168491377 3.09343168491377 382 0 0.00427662458134725 Y 0 0 N N 526 3337 ENSG00000177943 ENSG00000054148 - + 9 9 138875070 138865308 upstream downstream MAMDC4 PHPT1 138866640 138862997 + + 0.982029149568417 138866462 138865379 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.564198104634174 0.792734045751814 0.792734045751814 0.564198104634174 1 - - 37851 N N 3.40591861909494 2.6221451245963 2.6221451245963 19 0.0915524104378593 0.373535443180563 N 0.510835913312693 0.283724015922158 N N 78560 32016 ENSG00000112493 ENSG00000092148 - - 6 14 33390114 30746440 utr3p intron TAPBP HECTD1 33375449 30639075 - - 0.353604599734631 33376420 30675791 + + Y - 1.4639885942594 N HCC1954 21 11.8333333333333 1 21 1 N - - N SINE SINE 1 0.815789473684211 1 24 0.735600060472404 0.271386430077198 0.735600060472404 0.271386430077198 2 - 0 37029 N Y 3.68527868815389 3.23739660123173 3.23739660123173 0 0 0.764217334808816 N 0.745166176601622 0.915055392200541 N N 871 27 ENSG00000084453 ENSG00000164749 + + 12 8 21439638 76641600 utr5p upstream SLCO1A2 HNF4G 21311651 76482732 - + 0 21439221 76299157 - + Y - - N HCC1954 23 21.7173913043478 4 46 2 N - - N LINE,LINE LINE 1 1 1 46 0.599906845433805 0.956994253430118 0.956994253430118 0.599906845433805 2 - - 30326 Y Y 3.5465630590714 3.41319935075004 3.41319935075004 230 0 0.0448368049055886 Y 0 0 N N 5963 137 ENSG00000123575 ENSG00000176274 - - X X 103322781 103288364 coding upstream CXorf39 MCART6 103297957 103230555 + - 0 103307038 103288550 - + N 1.0953871995529 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 0.978419497909897 0.685607823352921 0.978419497909897 0.685607823352921 2 0 - 4577 Y N 2.12808527889139 3.18664891628299 2.12808527889139 0 0.0161290322580645 0.35146809556529 Y 0.139112903225806 0.0161290322580645 N N 11641 25286 ENSG00000106244 ENSG00000130429 + + 7 7 98844228 98830338 coding utr3p PDAP1 ARPC1B 98830525 98810265 - + 0.0161290322580645 98833551 98830303 - + N 0.275906224505138 - N HCC1954 3 1.55555555555556 1 4 2 N - - Y - - 0 0 0 9 0.5713398527941 0.407079645115797 0.5713398527941 0.407079645115797 3 0 - 48113 N N 3.49847350305486 3.41952156054875 3.41952156054875 0 0 0.999999212109432 N 0.0356379044992106 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117944557 2598623 - + Y - - N HCC1954 1 1 1 0 12 N 282 1.61558 N - - 0 0 0 6 1.17838844638783 1.02126998686945 1.17838844638783 1.02126998686945 2 - - 31798 Y Y 3.47911741325579 3.43614916339873 3.43614916339873 0 0 0.939792372918923 Y 0.11570163834334 0.85529663172891 N N 1907 18718 ENSG00000160799 ENSG00000160796 - - 3 3 46993242 47026197 utr5p intron CCDC12 AC094020.2 46938225 46996177 - + 0 46993237 46998352 + - N - 0.283672096413374 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 10 0.764167053112109 0.649899082553289 0.764167053112109 0.649899082553289 1 - 0 35136 N Y 3.03589262417669 3.49744043328497 3.03589262417669 0 0 0.190904294196880 N 0.983427495291902 0.966854990583804 N N 0 542 ENSG00000157680 ENSG00000135482 + + 7 12 137182149 54802545 intron upstream DGKI ZC3H10 136724925 54798297 - + 0.966854990583804 136849157 54796850 - + Y 1 - N HCC1954 8 6.625 3 8 1 N - - N - - 0 0 0 8 0.635615586233437 1.02841173502938 1.02841173502938 0.635615586233437 4 0 - 9441 Y Y 3.73912139251568 3.51207644450867 3.51207644450867 124 0 0.292486789243068 Y 0.685887096774194 0.966935483870968 N N 13858 5085 ENSG00000108439 ENSG00000167182 - + 17 17 43381673 43361320 upstream intron PNPO SP2 43373916 43328515 + + 0 43373711 43331651 - + N - 0.47794028798386 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.378512652476092 0.449930134075354 0.449930134075354 0.378512652476092 2 - 0 39002 N N 3.4594316186373 3.53209488171704 3.4594316186373 0 0 0.130936486849829 N 0 0 N N 14038 2113 ENSG00000115183 ENSG00000074410 - - 2 15 159797412 61461128 intron upstream TANC1 CA12 159533392 61402784 + - 0 159661333 61469486 - + Y 0.766365622465559 - N HCC1954 5 3.46666666666667 2 15 1 N - - N LTR - 1 0 1 15 0.464213630395207 0.607048593593732 0.607048593593732 0.464213630395207 3 0 - 46765 N N 3.20384558058643 2.64508558967518 2.64508558967518 0 0 0.999030479068863 N 0 0 Y N 8665 5583 ENSG00000079313 ENSG00000104885 + + 19 19 1799452 2181007 downstream intron REXO1 DOT1L 1766245 2115148 - + 0 1765595 2160139 - + N - 1.64923594430015 N HCC1954 1 1 1 0 5 N 279 3.37031 N - Low_complexity 0 0.205882352941176 0.205882352941176 48 1.22123893534739 1.21409718718746 1.22123893534739 1.21409718718746 2 - 0 26015 N Y 3.58999531724489 3.58424216889964 3.58424216889964 0 0 0.223807417137384 N 0 0 N N 3042 45068 ENSG00000156973 ENSG00000205336 + + 2 16 232354245 56256445 intron upstream PDE6D GPR56 232305388 56220023 - + 0 232335414 56211650 - + Y 1.24315410678976 - N HCC1954 21 20.25 20 4 1 N - - N SINE - 1 0 1 4 0.257102933757345 0.435646637755502 0.435646637755502 0.257102933757345 3 0 - 2707 N Y 3.33573513876043 3.56331864299737 3.33573513876043 0 0 0.109579202110412 N 0 0.941344058991118 N N 22 19569 ENSG00000150672 ENSG00000088812 - + 11 20 85015962 3579760 intron intron DLG2 ATRN 82843701 3399676 - + 0 82901424 3533062 + + Y 0.734335448047145 2.06818515404193 N HCC1954 21 19.9 18 10 1 N - - N LINE - 1 0 1 10 0.314236919036755 0.492780623034912 0.492780623034912 0.314236919036755 2 0 0 36026 N Y 3.51001030496889 3.37920724972727 3.37920724972727 224 0.466677295918367 0.0209455004661508 N 0.697783801020408 0.697783801020408 N N 5950 0 ENSG00000028203 ENSG00000217548 + - 12 X 94219075 46201578 coding intron VEZT RP11-75A9.3 94135715 46198476 + - 0.697783801020408 94184538 46200802 + + Y - 1 N HCC1954 1 1 1 0 1 N 151 21.7783 N - Simple_repeat 0 0.0819672131147541 0.0819672131147541 5 0.535631111994469 0.435646637755502 0.535631111994469 0.435646637755502 2 - 0 31172 Y Y 3.49268050191626 3.46448140203209 3.46448140203209 285 0 0.309270518860128 Y 0.985237166991553 0.985237166991553 N N 397 6473 ENSG00000180432 ENSG00000144648 + + 3 3 42892661 42883778 upstream intron CYP8B1 CCBP2 42888688 42836115 - + 0 42904034 42855775 - + N - 0.0692123342775211 N HCC1954 1 1 1 0 3 N - - Y LINE LTR 0.970802919708029 1 1 11 0.857009779191151 0.978419497909897 0.978419497909897 0.857009779191151 4 - 0 43256 N Y 3.53718568265298 3.00762316627563 3.00762316627563 16 0 0.0194661702472548 N 0.741420765027323 0.900546448087432 N N 4259 3891 ENSG00000157741 ENSG00000166295 - + 7 10 138643522 73665622 intron intron UBN2 C10orf104 138566991 73645812 + + 0 138609838 73645904 - + Y 1.80756106321472 0.744979490524871 N HCC1954 28 22.1666666666667 20 6 1 N - - N SINE - 1 0 1 6 0.321378667196682 0.371370904316165 0.371370904316165 0.321378667196682 1 0 0 16377 N N 3.68105312311849 3.48912663185998 3.48912663185998 0 0 0.0793880400136998 N 0 0 N N 49089 8194 ENSG00000117450 ENSG00000144036 - - 1 2 45760196 72906685 coding intron PRDX1 EXOC6B 45749295 72256621 - - 0 45757265 72896742 + + Y - 1.00135810846817 N HCC1954 20 6.36363636363636 3 11 1 N - - N - SINE 0 1 1 11 0.857009779191151 0.407079645115797 0.857009779191151 0.407079645115797 2 - 0 33826 Y N 2.9114211263036 2.97933078043563 2.9114211263036 0 0 0.99881247222447 N 0 0 Y N 59837 247001 ENSG00000198695 ENSG00000198786 - - MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0 14426 12376 + - N - 1.05585117299816 N HCC1954 3 1.21 1 13 7 N 189 4.09957 N - - 0 0 0 100 1.6854525657426 1.39264089118562 1.6854525657426 1.39264089118562 3 - 0 22089 N N 3.43101850966944 3.71976530271662 3.43101850966944 0 0 0.0443595004548814 N 0 0 N N 30350 4 ENSG00000143420 ENSG00000103569 - + 1 15 148868722 56265402 coding downstream ENSA AQP9 148840214 56217700 - + 0 148840311 56339885 + + Y - - N HCC1954 34 31.2 25 5 1 N - - N SINE LTR 1 1 1 5 0.357087407996313 0.378512652476092 0.378512652476092 0.357087407996313 1 - - 49315 N Y 3.59272380419397 3.29652844562235 3.29652844562235 372 0.0329097425871619 0.00063113904761769 Y 0.915379602476377 0.99395568589117 N N 232 232 ENSG00000205464 ENSG00000205464 - + 5 5 81649981 81649981 utr5p upstream ATP6AP1L ATP6AP1L 81611037 81611037 + + 0 81636837 81610569 - + N - - N HCC1954 3 1.5 1 1 1 Y - - N SINE SINE,SINE 0.386046511627907 0.686567164179104 0.686567164179104 4 0.899860268150708 0.628473838073511 0.899860268150708 0.628473838073511 1 - - 41923 N N 3.74081680969488 3.35463656781289 3.35463656781289 0 0 0.8469239391581 Y 0 0 N N 38251 0 ENSG00000156802 ENSG00000206719 + + 8 8 124477868 115032403 coding upstream ATAD2 Y_RNA 124401922 115032291 - + 0 124437812 114899716 - + N - - N HCC1954 1 1 1 0 2 N 405 1.47521 N - LINE,LINE 0 1 1 44 1.12125446110842 1.22123893534739 1.22123893534739 1.12125446110842 1 - - 7250 Y Y 3.64400585547602 2.97896005807504 2.97896005807504 0 0 0.123713131961515 Y 0 0.374456165444901 N N 0 17723 ENSG00000208433 ENSG00000136720 + - 2 2 128824954 128792641 upstream intron AC013277.9 HS6ST1 128824876 128739525 - - 0.374456165444901 128825890 128791825 - + N - 1.46013599917433 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 4 0.749883556792257 0.842726282871298 0.842726282871298 0.749883556792257 2 - 0 19597 N N 2.95425204751485 3.40591861909494 2.95425204751485 0 0 0.0710508262324963 N 0 0.0128205128205127 N N 0 4519 ENSG00000217260 ENSG00000085415 + - 1 18 653390 12977533 upstream intron RP11-206L10.1 SEH1L 651474 12937983 - + 0.0128205128205127 664128 12944554 - - Y - 0.946649041420742 N HCC1954 40 10 2 5 1 N - - N DNA,SINE SINE 0.86046511627907 1 1 5 0.307095170876829 0.364229156156239 0.364229156156239 0.307095170876829 2 - 0 36527 Y Y 3.51310951427856 3.4561676006071 3.4561676006071 154 0 0.0689677977253185 Y 0.948835838491011 0.993604479811376 N N 2597 853 ENSG00000139651 ENSG00000139631 - - 12 12 51870921 51860959 coding upstream ZNF740 CSAD 51864534 51837714 + - 0 51864538 51862239 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.797385620915033 0.797385620915033 33 1.60689333598341 1.09268746846872 1.60689333598341 1.09268746846872 2 - - 18135 Y Y 3.84594156533872 3.05421564420587 3.05421564420587 225 0 0.147128988948505 Y 0 0.950222222222222 N N 0 33 ENSG00000209354 ENSG00000177757 + + 1 1 798820 745077 downstream downstream AL669831.13-2 FAM87B 798710 742614 - + 0.00444444444444414 772987 753094 - + N - - N HCC1954 3 2.125 1 6 3 N - - Y - - 0 0 0 8 0.849868031031224 0.835584534711372 0.849868031031224 0.835584534711372 2 - - 28712 N N 3.6581033104698 3.68527868815389 3.6581033104698 0 0 0.463187862099181 N 0.788503011824199 0.779690637316874 N N 6328 841 ENSG00000167508 ENSG00000181896 - - 16 19 87257019 19652412 coding utr3p MVD ZNF101 87245849 19640605 - + 0 87252628 19652302 + - Y - - N HCC1954 35 27.2 7 5 1 N 300 22.8496 N - SINE 0 1 1 5 0.635615586233437 0.421363141435649 0.635615586233437 0.421363141435649 1 - - 20686 N N 3.60103760561896 2.64318545646472 2.64318545646472 0 0 0.111405269983261 N 0.0887573964497042 0.0887573964497042 N N 0 4377 ENSG00000207623 ENSG00000169891 + + 1 X 207672210 17081324 upstream utr5p hsa-mir-205 REPS2 207672101 16874735 + + 0.0887573964497042 207670432 16874774 + + Y - 0.0227419656069074 N HCC1954 6 3.83333333333333 3 6 1 N - - N - Simple_repeat 0 1 1 6 0.478497126715059 0.299953422716903 0.478497126715059 0.299953422716903 3 - 0 19270 Y Y 3.71823771940677 1.9371763897703 1.9371763897703 81 0 0.0167847625015316 Y 0.901234567901234 0.901234567901234 N N 3130 2348 ENSG00000135766 ENSG00000010072 + + 1 1 229627413 229556611 intron coding EGLN1 C1orf124 229568054 229540305 - + 0.901234567901234 229572023 229553889 - + N 1.79847078704602 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.585623349113953 0.428504889595575 0.585623349113953 0.428504889595575 1 0 - 23280 N Y 3.33680806132368 3.50000108636471 3.33680806132368 34 0.004 0.427311556907169 N 0.970415841584158 0.250534653465346 N N 2806 1814 ENSG00000143674 ENSG00000178229 + + 1 19 231587517 62533956 utr3p utr3p MAP3K19 ZNF543 231530137 62523689 + + 0.457623762376238 231585767 62532991 + + Y - - N HCC1954 34 23.8333333333333 22 12 1 N - - N - SINE 0 1 1 12 0.692749571512847 0.499922371194838 0.692749571512847 0.499922371194838 3 - - 33605 N N 3.28292550416853 3.32064446679012 3.28292550416853 0 0 0.350642190319757 N 0 0.193045112781955 Y N 336285 59837 ENSG00000198868 ENSG00000198695 - - MT MT 12138 14674 coding coding MT-ND4 MT-ND6 10471 14150 + - 0 11237 14604 - + N - 1.68519414393926 N HCC1954 4 1.8 1 2 2 N 189 4.09957 N - - 0 0 0 5 0.87843502367093 0.87843502367093 0.87843502367093 0.87843502367093 2 - 0 39518 N Y 3.29912895149544 3.56232542602083 3.29912895149544 1 0 0.172635964730011 N 0 0.932754581783106 N N 4991 4 ENSG00000103042 ENSG00000103569 - + 16 15 57276175 56265402 downstream downstream SLC38A7 AQP9 57257799 56217700 - + 0.0921868540719306 57253459 56339667 + + Y - - N HCC1954 120 26.9411764705882 4 17 1 N 385 18.2542 N SINE LTR 1 1 1 17 0.328520415356608 0.45707188223528 0.45707188223528 0.328520415356608 3 - - 5050 N N 3.46232197653647 3.24359082995445 3.24359082995445 0 0 0.990289213638336 Y 0 0 N Y 28646 3396 ENSG00000164880 ENSG00000188191 + - 7 7 1510772 733813 coding utr5p INTS1 PRKAR1B 1476439 555361 - - 0 1500978 717690 - + N - 3.19613220326386 N HCC1954 1 1 1 0 3 Y 22 4.15045 N - - 0 0 0 57 1.37835739486577 1.4140661356654 1.4140661356654 1.37835739486577 4 - 0 32862 N N 2.7465279996206 2.72029709021333 2.72029709021333 0 0.283972537878788 0.205182257092379 N 0.75094696969697 0 N N 767 5996 ENSG00000161267 ENSG00000187678 - + 3 5 198784591 141684750 utr3p utr3p BDH1 SPRY4 198721051 141670189 - - 0 198721884 141671688 + - Y - 1.14614386371356 N HCC1954 36 32.4 30 15 1 N 161 25.0602 N Simple_repeat - 0.960526315789474 0 0.960526315789474 15 0.542772860154395 0.814159290231593 0.814159290231593 0.542772860154395 1 - 0 5184 N Y 3.1352735790451 3.59268395140062 3.1352735790451 160 0 0.006668191805832 N 0 0.921546052631579 N N 0 1675 ENSG00000209951 ENSG00000148120 + - 7 9 86960 96889261 upstream intron AC097646.2-1 C9orf3 86858 96528804 - + 0 126183 96691193 - - Y - 0.382548521147188 N HCC1954 88 82.4 80 5 1 N - - N - SINE 0 1 1 5 0.414221393275723 0.321378667196682 0.414221393275723 0.321378667196682 1 - 0 31321 Y Y 3.51679652308403 3.35104284496326 3.35104284496326 301 0 0.705968260253424 Y 0 0.99317344013107 N N 18718 1907 ENSG00000160796 ENSG00000160799 - - 3 3 47026197 46993242 upstream upstream AC094020.2 CCDC12 46996177 46938225 + - 0 46995969 46993275 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 15 0.978419497909897 1.08554572030879 1.08554572030879 0.978419497909897 1 - - 29193 Y Y 3.66016945000958 3.29231222815676 3.29231222815676 239 0 0.111685913285033 Y 0 0.991560882206936 N N 30978 0 ENSG00000112245 ENSG00000213312 - - 6 6 64351447 64317378 utr5p downstream PTP4A1 RPL7AP34 64339879 64316572 + - 0 64344361 64295904 - + N 0.58068000993836 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 59 1.33550690590621 1.08554572030879 1.33550690590621 1.08554572030879 2 0 - 4295 Y Y 3.71976530271662 3.33887420086346 3.33887420086346 216 0 0.194122322139397 Y 0.585262345679012 0.988150352733686 N N 0 524 ENSG00000203446 ENSG00000218609 + + 7 7 65814279 65743252 downstream downstream AC027644.9 KCTD7 65814003 65731380 - + 0 65787782 65757014 - + N - - N HCC1954 15 6.75 1 3 3 N - - Y SINE - 1 0 1 4 0.785592297591888 0.614190341753658 0.785592297591888 0.614190341753658 2 - - 41494 Y Y 3.32320511986986 3.33424740824393 3.32320511986986 297 0 0.269527188105911 Y 0.993126668988738 0.986253337977476 N N 4 45 ENSG00000184090 ENSG00000214789 + + 8 8 129029462 128893866 downstream downstream TMEM75 AC084123.9 129029046 128875961 - + 0 128972017 128936747 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 15 1.1426797055882 1.02126998686945 1.1426797055882 1.02126998686945 4 - - 4207 Y N 3.28230300955258 3.448886868952 3.28230300955258 0 0 0.908883246036142 Y 0 0.389050515736578 N N 0 0 ENSG00000219142 ENSG00000217741 + + 7 7 17039627 16944706 downstream downstream AC098592.8 AC098592.7 17039238 16944374 - + 0.389050515736578 17027550 16964211 - + N - - N HCC1954 14 5.25 1 3 4 N - - Y - SINE 0 1 1 4 0.335662163516534 0.364229156156239 0.364229156156239 0.335662163516534 2 - - 47920 N N 3.40744620240479 2.96319769112561 2.96319769112561 0 0 0.949690339930787 N 0 0 N N 10798 29840 ENSG00000113761 ENSG00000164830 - + 5 8 176426349 107834093 intron utr5p ZNF346 OXR1 176382303 107739270 + + 0 176410310 107739589 - + Y 1.34575632127257 1.03199430721578 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 34 1.49976711358451 1.16410495006798 1.49976711358451 1.16410495006798 4 0 0 13997 Y N 3.44975210485255 3.55401162459584 3.44975210485255 0 0 0.171718999036778 N 0 0 N N 110 238 ENSG00000198312 ENSG00000211643 + + 22 22 20993088 21003581 downstream coding D87018.1-3 IGLV5-52 20991471 21003021 + + 0 20994770 21003372 + + N - 0.500482431454531 Y HCC1954 11 8.5 3 4 1 N - - N - - 0 0 0 4 0.564198104634174 0.592765097273879 0.592765097273879 0.564198104634174 0 - 0 17923 N N 3.02606058701167 3.68168496530426 3.02606058701167 3 0 0.949259350033888 N 0.00404858299595134 0 Y Y 12071 4543 ENSG00000116580 ENSG00000132680 + - 1 1 154093710 154170814 coding coding GON4L KIAA0907 153986132 154149460 - - 0 154089691 154163571 - + N - 0.575440753711907 N HCC1954 1 1 1 0 2 N 495 6.71914 N - - 0 0 0 4 0.449930134075354 0.378512652476092 0.449930134075354 0.378512652476092 4 - 0 549 N Y 3.31216283149579 3.63552422018169 3.31216283149579 134 0 0.976666135028084 Y 0.235292843058655 0.992502871010379 N N 9074 0 ENSG00000166444 ENSG00000202276 - + 11 11 8817478 8855641 utr5p downstream ST5 Y_RNA 8671478 8855540 - - 0 8817475 8849459 + - N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 6 1.1141127129485 0.835584534711372 1.1141127129485 0.835584534711372 3 - - 36702 Y Y 3.53296011761759 3.01191908932792 3.01191908932792 324 0 0.0199993923054778 Y 0 0.986707818930041 N N 48182 10291 ENSG00000010292 ENSG00000111639 - - 12 12 6511381 6472718 coding upstream NCAPD2 MRPL51 6473529 6471579 + - 0.986707818930041 6474544 6473046 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.642757334393363 0.785592297591888 0.785592297591888 0.642757334393363 2 - - 41565 Y Y 3.20720590972129 3.76848670091893 3.20720590972129 224 0 0.0527187091841972 Y 0.0874255952380952 0.976296768707483 N N 0 0 ENSG00000221176 ENSG00000222501 - - 8 8 129130666 129092039 downstream upstream hsa-mir-1207 U4 129130580 129091912 + - 0 129151629 129102080 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE,LINE LTR 1 1 1 4 0.799875793911741 0.885576771830856 0.885576771830856 0.799875793911741 1 - - 19992 N N 3.66745018166468 3.48809356209009 3.48809356209009 11 0 0.0612571622780484 N 0 0 N N 8 45068 ENSG00000184144 ENSG00000205336 - + 1 16 203313759 56256445 intron upstream CNTN2 GPR56 203278963 56220023 + + 0 203286471 56211646 - + Y 0.921830550401979 - N HCC1954 24 21.5555555555556 20 9 1 N - - N SINE - 1 0 1 9 0.335662163516534 0.428504889595575 0.428504889595575 0.335662163516534 1 0 - 31898 Y Y 3.46977054206092 3.40757418348078 3.40757418348078 0 0 0.952990482061905 Y 0 0.984554190982202 N Y 3350 240 ENSG00000070950 ENSG00000180914 + - 3 3 8980146 8786300 coding coding RAD18 OXTR 8896561 8767114 - - 0 8907073 8769910 - + N - 1.61706460687128 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.792734045751814 0.764167053112109 0.792734045751814 0.764167053112109 4 - 0 27329 N Y 3.44768596531277 3.448886868952 3.44768596531277 0 0 0.802990187041507 N 0.993957166977695 0.981871500933085 N N 30870 21349 ENSG00000179889 ENSG00000103226 + + 16 16 15140696 16296168 coding downstream PDXDC1 NOMO3 14976487 16233890 + + 0 15031411 16305393 + + N - - Y HCC1954 8 4.41860465116279 3 43 2 N 266 11.9069 N - LINE,LINE 0 1 1 43 1.29265641694665 1.20695543902754 1.29265641694665 1.20695543902754 2 - - 24833 Y N 3.52567938596249 3.2965682984157 3.2965682984157 0 0 0.95601851663622 Y 0.146631408423861 0 N N 962 0 ENSG00000184828 ENSG00000206944 - + 18 18 43821492 43950259 utr5p upstream ZBTB7C U6 43807746 43950153 - - 0 43821492 43965693 + - N - - N HCC1954 1 1 1 0 3 N - - Y - LINE 0 1 1 4 0.757025304952183 0.849868031031224 0.849868031031224 0.757025304952183 4 - - 28707 N N 3.22423474015539 3.57800808738356 3.22423474015539 1 0 0.403629110656727 N 0 0 N N 560 17943 ENSG00000197471 ENSG00000105141 - + 16 19 29589312 15027900 intron downstream SPN CASP14 29581801 15024015 + + 0.0202659093842777 29587459 15029502 - + Y - - N HCC1954 25 9.8 1 3 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.507064119354764 0.507064119354764 0.299953422716903 3 - - 6127 N Y 3.47233119514066 3.37126417066287 3.37126417066287 1 0 0.124444835315669 N 0 0.845835199283475 N N 20739 0 ENSG00000143951 ENSG00000218140 - - 2 7 63669355 148662881 utr3p downstream C2orf86 AC004941.4 63202041 148662048 - + 0.811576354679803 63309485 148670145 + - Y - - N HCC1954 620 470 420 4 1 N - - N LINE LINE 1 1 1 4 0.34280391167646 0.364229156156239 0.364229156156239 0.34280391167646 4 - - 8002 N Y 3.47233119514066 3.37126417066287 3.37126417066287 3 0 0.0812812899773043 N 0 0.935877261998426 N N 20739 0 ENSG00000143951 ENSG00000200521 - + 2 4 63669355 158908715 utr3p upstream C2orf86 Y_RNA 63202041 158908615 - - 0 63309485 159064967 + - Y - - N HCC1954 620 580 420 6 1 N - - N LINE LINE 1 1 1 6 0.357087407996313 0.39993789695587 0.39993789695587 0.357087407996313 4 - - 3930 N N 3.34718800228844 3.6052936758779 3.34718800228844 283 0.441006636214772 0.000915316390834864 N 0.441006636214772 0.0278376281996036 N N 850768 0 ENSG00000075624 ENSG00000217920 + - 7 X 5536758 46033507 coding intron ACTB RP1-30G7.1 5533313 46032395 - - 0.0278376281996036 5534169 46032562 - + Y - 1 N HCC1954 8 1.65217391304348 1 9 1 N - - N - - 0 0 0 23 0.799875793911741 0.271386430077198 0.799875793911741 0.271386430077198 1 - 0 48851 Y Y 3.32679884271949 3.43681151080804 3.32679884271949 275 0 0.494035061856595 Y 0 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883894 140816150 - + N 0.484630852928673 0.194212665568841 N HCC1954 7 1.23809523809524 1 6 2 N - - Y - LTR 0 1 1 63 0.721316564152552 1.12839620926835 1.12839620926835 0.721316564152552 4 0 0 32886 N Y 3.31233066536513 3.54552998930151 3.31233066536513 20 0 0.0264777165724250 N 0.769105691056911 0 N N 193 1294 ENSG00000080709 ENSG00000144681 - + 5 3 113860096 36564500 utr5p coding KCNN2 STAC 113725565 36397101 + + 0 113797242 36460135 - + Y - 1.36990340242264 N HCC1954 22 21.4 21 5 1 N - - N LTR - 1 0 1 5 0.292811674556976 0.535631111994469 0.535631111994469 0.292811674556976 1 - 0 47654 N N 3.40847927217468 3.56807857436608 3.40847927217468 0 0 0.209953210119604 N 0 0 N N 2321 9271 ENSG00000127226 ENSG00000073050 + - 19 19 18168552 48771555 utr3p intron AC068499.1 XRCC1 18165040 48739304 + - 0 18168392 48770528 + + N 2.85797650802464 1.09010023396784 Y HCC1954 2 2 2 4 1 N - - N SINE Low_complexity,SINE 0.488888888888889 0.53125 0.53125 4 0.5713398527941 0.22853594111764 0.5713398527941 0.22853594111764 2 0 0 38213 N Y 3.61360747730289 3.28189243439864 3.28189243439864 193 0 0.987485549594094 Y 0.820213496472938 0.976028466196392 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 upstream downstream SIPA1L1 SNORD56 71065795 70934807 + + 0 71049213 70950484 - + N - - N HCC1954 1 1 1 0 6 N - - N LTR - 1 0 1 9 0.799875793911741 0.528489363834543 0.799875793911741 0.528489363834543 4 - - 30300 Y Y 3.47382827322697 3.38805025981237 3.38805025981237 326 0 0.589224426604092 Y 0.963076573506021 0.992615314701204 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 upstream intron STS HDHD1A 7147472 6976961 + - 0 7118922 7075644 - + N - 0.638327297478365 N HCC1954 2 1.04444444444444 1 4 5 N - - Y - DNA 0 0.733333333333333 0.733333333333333 90 1.01412823870953 1.28551466878673 1.28551466878673 1.01412823870953 1 - 0 19274 Y N 3.21808036422602 3.53039946453785 3.21808036422602 0 0 0.213767688821126 N 0 0 N N 568 13757 ENSG00000215828 ENSG00000135823 + + 1 1 179212241 179258669 intron coding AL162431.17-1 STX6 179179798 179208801 - - 0 179186573 179220436 - - N 0.0731551073274452 0.397982148574853 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.742741808632331 0.671324327033068 0.742741808632331 0.671324327033068 3 0 0 36423 Y Y 3.56232542602083 3.67952553980864 3.56232542602083 306 0 0.00535680425824825 Y 0 0 N N 727 34637 ENSG00000139625 ENSG00000197111 + + 12 12 52179538 52159872 intron coding MAP3K12 PCBP2 52160547 52132161 - + 0 52165021 52151831 - + N 2.51080407750642 2.06496059858819 N HCC1954 3 1.5 1 1 1 N - - Y - - 0 0 0 4 0.749883556792257 0.757025304952183 0.757025304952183 0.749883556792257 2 0 0 35844 N Y 3.63296356710195 3.45976132345673 3.45976132345673 0 0 0.0985031017059068 N 0 0.800716845878136 N N 332 75177 ENSG00000123094 ENSG00000125107 + + 12 16 26124091 57221251 utr3p utr5p RASSF8 CNOT1 26003229 57111359 + - 0 26123695 57190813 + - Y - - N HCC1954 23 22.0833333333333 22 12 1 N - - N SINE - 1 0 1 12 0.292811674556976 0.599906845433805 0.599906845433805 0.292811674556976 1 - - 22521 N Y 3.61616813038263 3.61360747730288 3.61360747730288 1 0 0.601806772590356 N 0.667892156862745 0.653452685421995 N N 79 33725 ENSG00000132297 ENSG00000143819 - - 8 1 133167084 224099884 utr5p utr5p OC90 EPHX1 133105667 224064459 - + 0 133167021 224083049 + - Y - - N HCC1954 21 20.741935483871 17 31 1 N - - N LTR - 0.958333333333333 0 0.958333333333333 31 0.34280391167646 0.857009779191151 0.857009779191151 0.34280391167646 4 - - 48894 Y Y 2.72142344593906 3.47961192679575 2.72142344593906 194 0 0.0230886312947011 Y 0.774501718213058 0.986735395189003 N N 746 682 ENSG00000049167 ENSG00000164181 + - 5 5 60276648 60119016 downstream utr5p ERCC8 ELOVL7 60205415 60083376 - - 0 60175745 60119016 - + N - 15.7819063004847 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.464213630395207 0.414221393275723 0.464213630395207 0.414221393275723 2 - 0 45569 N N 3.38656252929588 3.22904294701339 3.22904294701339 0 0 0.447077431583474 N 0.280725623582766 0.225396825396826 N N 2818 5345 ENSG00000105048 ENSG00000135341 + + 19 6 60352385 91353628 coding upstream TNNT1 MAP3K7 60336008 91282074 - - 0.225396825396826 60349870 91528318 - - Y 22.2898171792768 - N HCC1954 1 1 1 0 1 N - - N - DNA 0 1 1 5 0.607048593593732 0.271386430077198 0.607048593593732 0.271386430077198 1 0 - 33038 N Y 3.02448896101185 3.54040868314203 3.02448896101185 445 0 0.79944394741472 Y 0 0.994692804207507 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0.994692804207507 10854 8869 - + N 0.345779280503889 0.574912726696822 N HCC1954 2 1.75 1 3 7 N - - N - - 0 0 0 4 1.12839620926835 0.949852505270192 1.12839620926835 0.949852505270192 3 0 0 44935 N Y 3.37824872787089 3.33420755545058 3.33420755545058 0 0 0.415634219792098 Y 0.947577276524645 0.982525758841548 N N 590 104 ENSG00000204149 ENSG00000178440 - + 10 10 51440265 51403098 upstream intron AGAP6 AL442003.8-2 51418356 51401190 + + 0 51416931 51402908 - + N - - N HCC1954 20 12.75 4 4 1 N - - N LTR - 1 0 1 4 0.749883556792257 0.857009779191151 0.857009779191151 0.749883556792257 4 - - 41537 Y Y 3.34718800228844 3.03383583220673 3.03383583220673 305 0 0.347713781459698 Y 0 0 N Y 1097 1486 ENSG00000221850 ENSG00000181638 - + 8 8 144430474 144416250 intron intron GLI4 ZFP41 144420982 144400484 + + 0 144422905 144404885 - + N 0.605786828551664 1.80371748005096 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 14 1.05697872766909 1.03555348318931 1.05697872766909 1.03555348318931 4 0 0 41231 Y Y 3.42783536197374 2.79101916968047 2.79101916968047 0 0 0.230921077621857 Y 0.57466251298027 0.993354101765317 N N 3725 0 ENSG00000174306 ENSG00000218353 - - 20 20 39362153 39393714 utr5p upstream ZHX3 RP3-450M14.1 39240502 39393177 - + 0 39331136 39379562 + - N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.790419161676647 0.790419161676647 6 0.971277749749971 1.10697096478857 1.10697096478857 0.971277749749971 1 - - 34782 Y Y 3.62464976567696 2.77693106225651 2.77693106225651 0 0 0.990699406608215 Y 0 0.981011719329476 N N 4263 0 ENSG00000187764 ENSG00000218102 - - 9 9 91260688 91277427 utr5p downstream SEMA4D RP13-93L13.1 91181972 91276972 - + 0 91223172 91302654 + - N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity,Simple_repeat 0 0.433962264150943 0.433962264150943 31 1.52833410622422 0.757025304952183 1.52833410622422 0.757025304952183 4 - - 3678 N N 3.5514509715161 3.25153390901886 3.25153390901886 0 0 0.043953531584219 N 0.456493506493507 0.150771103896104 N N 1582 0 ENSG00000185917 ENSG00000213113 - + 21 3 36373557 199332046 utr5p downstream SETD4 AC073135.3-1 36328709 199330983 - + 0.150771103896104 36353502 199368970 + + Y - - N HCC1954 160 139.872340425532 84 47 1 N - - N SINE - 1 0 1 47 0.428504889595575 1.09982921662864 1.09982921662864 0.428504889595575 1 - - 19168 N Y 3.51001030496889 3.37232774565629 3.37232774565629 8 0 0.981566843795805 Y 0.0353057889822596 0.984185340802988 N N 0 7600 ENSG00000203341 ENSG00000157978 - + 1 1 25784586 25767964 downstream coding AL606491.19-2 LDLRAP1 25784093 25742663 + + 0 25789247 25764285 - + N - - N HCC1954 1 1 1 0 2 N - - N LTR - 0.126984126984127 0 0.126984126984127 12 0.899860268150708 0.814159290231593 0.899860268150708 0.814159290231593 4 - - 33830 N N 2.94703409659206 2.93975336493696 2.93975336493696 13 0 0.999992126676833 N 0.00865359730848869 0.00865359730848869 Y N 59837 544065 ENSG00000198695 ENSG00000198744 - - MT MT 14674 9988 coding coding MT-ND6 MT-CO3 14150 8367 - + 0.00865359730848869 14647 8409 + - N - 1.020127342997 N HCC1954 8 2.13333333333333 1 6 10 N 189 4.09957 N - - 0 0 0 15 1.37835739486577 1.37121564670584 1.37835739486577 1.37121564670584 2 - 0 9098 N Y 3.12804628055249 3.65913638023969 3.12804628055249 2 0 0.221050960258416 N 0.89234997709574 0.89234997709574 N N 1649619 0 ENSG00000141736 ENSG00000213319 - + 17 2 35138441 100574218 coding downstream ERBB2 AC068538.8 35104766 100573947 + - 0 35122227 100570370 - - Y - - N HCC1954 23 22 21 5 1 N 267 17.0042 N - SINE 0 1 1 5 0.599906845433805 0.278528178237124 0.599906845433805 0.278528178237124 2 - - 24713 N Y 3.32320511986986 3.4561676006071 3.32320511986986 329 0 0.00916777484608977 Y 0 0.984175230375838 N N 0 13271 ENSG00000141650 ENSG00000081923 - - 18 18 53657194 53550037 upstream upstream AC022724.8-1 ATP8B1 53656706 53464656 + - 0 53620212 53550195 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 10 0.678466075192994 0.664182578873142 0.678466075192994 0.664182578873142 2 - - 3436 Y Y 3.23164345288648 3.7061623612628 3.23164345288648 223 0 0.0499170398028213 Y 0 0 N N 0 0 ENSG00000217578 ENSG00000216501 + - 21 21 31096616 31057071 downstream upstream KRTAP8P1 AP000244.11 31096431 31056871 - - 0 31080655 31073400 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.792734045751814 0.478497126715059 0.792734045751814 0.478497126715059 4 - - 37286 N Y 3.41103992525442 3.61889661733171 3.41103992525442 80 0.364266666666667 0.0887071419161025 N 0.920533333333333 0.920533333333333 N N 34637 0 ENSG00000197111 ENSG00000213731 + + 12 5 52159872 90808593 coding downstream PCBP2 AC008923.9 52132161 90808096 + + 0.364266666666667 52142616 91175595 + + Y - - N HCC1954 2 1.8 1 4 1 N - - N - SINE 0 0.65 0.65 5 0.557056356474248 0.28566992639705 0.557056356474248 0.28566992639705 2 - - 10868 N N 3.16360581767846 3.55401162459584 3.16360581767846 0 0 0.073639598354766 N 0 0 N N 37605 21542 ENSG00000131771 ENSG00000152894 - - 17 6 35046404 128883453 downstream intron PPP1R1B PTPRK 35036705 128331627 + - 0 35046596 128812689 - + Y - 3.68186953807432 N HCC1954 20 18.8333333333333 13 6 1 N - - N - SINE 0 0.977272727272727 0.977272727272727 6 0.507064119354764 0.314236919036755 0.507064119354764 0.314236919036755 2 - 0 591 Y Y 3.51360402781852 3.56807857436608 3.51360402781852 0 0 0.938890313811718 Y 0.987137223177268 0.993568611588634 N N 138744 0 ENSG00000152558 ENSG00000210948 - - 11 11 101828985 101844353 coding downstream TMEM123 AP001830.5 101772268 101844288 - + 0 101828465 101846116 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 33 1.10697096478857 1.19981369086761 1.19981369086761 1.10697096478857 2 - - 36798 Y Y 3.67593181695901 3.43784458057793 3.43784458057793 12 0 0.754315755612491 Y 0 0.972587155963303 N N 1680 16 ENSG00000139190 ENSG00000139193 + + 12 12 6450326 6431145 coding intron VAMP1 CD27 6440603 6424312 - + 0 6444317 6428184 - + N - 0.591675675675676 N HCC1954 17 6.33333333333333 2 6 1 N - - Y - SINE 0 1 1 6 0.857009779191151 0.692749571512847 0.857009779191151 0.692749571512847 4 - 0 23284 N Y 3.5010341561346 3.68577320169385 3.5010341561346 0 0 0.393655819990494 N 0 0 N N 40617 168 ENSG00000130164 ENSG00000186543 + + 19 1 11105490 16843765 utr3p utr3p LDLR AL137798.8-2 11061132 16828752 + - 0 11104135 16828997 + - Y - - N HCC1954 21 20.6666666666667 20 6 1 N - - N - SINE 0 1 1 6 0.564198104634174 0.264244681917271 0.564198104634174 0.264244681917271 3 - - 4078 Y Y 3.46128890676658 3.82911562339586 3.46128890676658 329 0.916919959473151 0.0655005545944083 N 0.993609227651781 0.987218455303562 Y N 0 0 ENSG00000201515 ENSG00000177418 + - 7 7 65653116 65659784 upstream downstream 5S_rRNA AC006001.2-1 65652992 65659267 - - 0 65675807 65657259 - + N - - N HCC1954 6 1.95 1 26 2 N - - N - - 0 0 0 60 1.16410495006798 1.2783729206268 1.2783729206268 1.16410495006798 4 - - 7798 N Y 3.8333716936548 3.46551447180198 3.46551447180198 0 0.167187599668304 0.871643733418178 N 0.167187599668304 0.918351725457677 N N 0 0 ENSG00000183846 ENSG00000217928 + + 2 22 110575338 15435527 upstream upstream AC112229.4-1 KB-67B5.12 110574935 15432917 - + 0 110576428 15410147 - + Y - - N HCC1954 16 13.7142857142857 2 7 2 N 359 26.8809 N - - 0 0 0 7 1.1141127129485 0.314236919036755 1.1141127129485 0.314236919036755 1 - - 6467 N Y 3.2720510496638 3.0448781205808 3.0448781205808 160 0 0.0773036696470172 Y 0.988000193545265 0.904001548362123 N N 4881 4174 ENSG00000118640 ENSG00000115486 - - 2 2 85662665 85642090 coding upstream VAMP8 GGCX 85658227 85629718 + - 0 85659643 85642278 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 1.09982921662864 0.535631111994469 1.09982921662864 0.535631111994469 4 - - 43123 N N 3.09555125761603 2.81559919916467 2.81559919916467 0 0.355539806283959 0.0677483995581951 N 0.375068903063233 0 N N 551733 88 ENSG00000204628 ENSG00000184795 + + 5 4 180603512 9108757 utr3p downstream GNB2L1 UNC93B5 180596536 9104381 - + 0 180596545 9133381 - + Y - - N HCC1954 22 16 2 11 1 N - - N - LINE 0 1 1 11 0.785592297591888 0.357087407996313 0.785592297591888 0.357087407996313 2 - - 3827 N Y 3.56129235625094 3.54719490125717 3.54719490125717 1 0 0.0637724013992678 N 0 0.898513753327418 N N 0 2004 ENSG00000156687 ENSG00000105793 - + 8 7 35771722 89854586 intron utr3p UNC5D GTPBP10 35212845 89813926 + + 0 35502325 89854507 - + Y 1 - N HCC1954 68 63 60 4 1 N - - N - SINE 0 1 1 4 0.449930134075354 0.442788385915428 0.449930134075354 0.442788385915428 1 0 - 17323 Y Y 3.43681151080804 3.56914214935951 3.43681151080804 0 0 0.992847984756036 Y 0.168760469011725 0.813802345058627 N Y 10731 43044 ENSG00000160741 ENSG00000143570 - + 1 1 152197725 152206812 coding coding CRTC2 SLC39A1 152186775 152198210 - - 0 152194266 152201320 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 30 1.7140195583823 1.13553795742827 1.7140195583823 1.13553795742827 4 - - 33763 N N 2.85381686522283 3.05228683331189 2.85381686522283 0 0 0.999354585847117 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8462 10635 - + N - 0.92382906116619 N HCC1954 1 1 1 0 7 Y 189 4.09957 N - - 0 0 0 4 0.757025304952183 0.899860268150708 0.899860268150708 0.757025304952183 2 - 0 3483 N N 3.42254622194492 3.46448140203209 3.42254622194492 0 0 0.538209407684912 N 0 0 N N 83 166846 ENSG00000154645 ENSG00000142192 - + 21 21 18561561 26465003 intron coding CHODL APP 18195451 26174733 + - 0 18542227 26347535 - - N 0.599113918166545 - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.87843502367093 0.914143764470561 0.914143764470561 0.87843502367093 1 0 - 29109 Y Y 3.42936294528359 3.18871505582277 3.18871505582277 358 0 0.00206508123345828 Y 0.0349612542800506 0.991958010452334 N N 56438 5275 ENSG00000204256 ENSG00000204257 - - 6 6 33057260 33028863 upstream intron BRD2 HLA-DMA 33044415 33024368 + - 0 33043922 33025736 - + N - 1.06693090120767 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.607048593593732 0.592765097273879 0.607048593593732 0.592765097273879 2 - 0 4409 N Y 3.17251160849586 3.40488554932505 3.17251160849586 227 0 0.249423574084806 Y 0.990239267513173 0.990239267513173 N N 524 0 ENSG00000218609 ENSG00000201515 - - 7 7 65743252 65653116 upstream upstream KCTD7 5S_rRNA 65731380 65652992 + - 0 65694702 65681120 - + N - - N HCC1954 2 1.66666666666667 1 4 5 N - - N - LTR 0 1 1 6 0.599906845433805 1.07840397214886 1.07840397214886 0.599906845433805 1 - - 7877 N Y 3.58999531724489 3.5816815158199 3.5816815158199 1 0 0.165983790336932 N 0.960716093117409 0.960716093117409 N N 1738 148 ENSG00000144366 ENSG00000205682 - - 2 4 189168898 61976534 utr5p utr3p GULP1 AC020741.4 188864641 61968559 + - 0 188956859 61968993 - + Y - - N HCC1954 25 23.75 22 4 1 N - - N - SINE 0 1 1 4 0.757025304952183 0.428504889595575 0.757025304952183 0.428504889595575 2 - - 26664 Y Y 3.07630022095401 3.20976656280103 3.07630022095401 266 0 0.63599887209603 Y 0.658821711813781 0.986352868472551 N N 4968 172 ENSG00000104731 ENSG00000205047 + - 16 16 86357056 86292831 coding upstream KLHDC4 AC010536.8 86298920 86291389 - - 0 86299459 86294541 - + N 0.32922227298949 - N HCC1954 2 1.11111111111111 1 1 3 N - - Y - - 0 0 0 9 0.471355378555133 1.08554572030879 1.08554572030879 0.471355378555133 3 0 - 27756 N Y 3.57696143724454 3.50421730383029 3.50421730383029 0 0 0.19665977815347 N 0.713075060532688 0.713075060532688 N N 2048 45068 ENSG00000114107 ENSG00000205336 + + 3 16 139795819 56256445 intron upstream CEP70 GPR56 139695879 56220023 - + 0 139729603 56211295 - + Y 0.441139486407226 - N HCC1954 2 2 2 6 1 N - - N SINE - 1 0 1 6 0.235677689277566 0.749883556792257 0.749883556792257 0.235677689277566 1 0 - 34117 N Y 3.66848325143457 3.54144175291192 3.54144175291192 0 0 0.411790518239753 N 0 0.984060836501901 N N 0 0 ENSG00000204811 ENSG00000216334 - - 9 9 45060568 46224504 upstream upstream CR769775.11 RP11-34H11.6 45059822 46224288 + + 0.0277110266159697 45048339 46219391 - - N - - Y HCC1954 60 43.75 30 4 1 N 23 25.0978 N - SINE 0 0.970588235294118 0.970588235294118 4 0.914143764470561 0.692749571512847 0.914143764470561 0.692749571512847 1 - - 6194 N N 3.59528445727371 3.50272957331379 3.50272957331379 0 0 0.903795947537453 N 0.00290697674418605 0 N Y 982 103 ENSG00000173068 ENSG00000220804 - + 9 2 16860786 242729712 coding utr3p BNC2 AC134873.2 16399501 242679518 - + 0 16573083 242729712 + + Y - - N HCC1954 20 9.18181818181818 1 5 1 N - - N - - 0 0 0 11 0.757025304952183 1.5783263433437 1.5783263433437 0.757025304952183 4 - - 38099 Y Y 3.32423818963975 3.48593413659447 3.32423818963975 142 0 0.211130062430137 Y 0 0.98539768019884 N N 2793 27551 ENSG00000129472 ENSG00000100888 + - 14 14 21014972 20969237 downstream coding RAB2B CHD8 20997019 20923198 - - 0 20994048 20967249 - + N - 1.33346178016204 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 22 0.692749571512847 1.09268746846872 1.09268746846872 0.692749571512847 1 - 0 9576 Y Y 3.35935664638825 3.76951977068882 3.35935664638825 358 0 0.00266934057873869 Y 0 0.975069832402234 N N 265 752 ENSG00000161929 ENSG00000180626 + - 17 17 5078861 5035902 utr3p upstream C17orf87 ZNF594 5052980 5023554 - - 0 5057901 5036136 - + N 0.375874773949102 - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 1 0 1 6 0.671324327033068 0.607048593593732 0.671324327033068 0.607048593593732 1 0 - 12594 N N 3.2274272354209 3.59375687396386 3.2274272354209 10 0 0.117051287981449 N 0.384652163519005 0.0601960315562994 N N 1649619 8 ENSG00000141736 ENSG00000080573 + - 17 19 35138441 9982147 coding intron ERBB2 COL5A3 35104766 9931237 + - 0.0601960315562994 35122227 9964427 + + Y - 0.92955599235151 N HCC1954 11 4 1 13 1 N 516 16.9018 N - SINE 0 1 1 14 0.607048593593732 0.299953422716903 0.607048593593732 0.299953422716903 2 - 0 38341 Y Y 3.3828009725769 3.02754831752817 3.02754831752817 0 0 0.334274234067332 Y 0.994168707619 0.994168707619 N N 325 2660 ENSG00000133943 ENSG00000100784 - - 14 14 90761456 90596746 utr5p upstream C14orf159 RPS6KA5 90650110 90406925 + - 0 90693737 90596802 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 1.14982145374813 1.10697096478857 1.14982145374813 1.10697096478857 1 - - 30301 Y Y 3.47382827322697 3.38805025981237 3.38805025981237 203 0 0.652643832088868 Y 0.98842937335319 0.98842937335319 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 upstream intron STS HDHD1A 7147472 6976961 + - 0 7118922 7075644 - + N - 0.638327297478365 N HCC1954 1 1 1 0 5 N - - Y - DNA 0 0.278350515463918 0.278350515463918 5 0.964136001590045 0.692749571512847 0.964136001590045 0.692749571512847 1 - 0 20464 N Y 3.56807857436608 3.84271856484967 3.56807857436608 86 0 0.0775617218317901 N 0.95436940208182 0.95436940208182 N N 0 8888 ENSG00000208317 ENSG00000112159 - - 1 6 172101447 90586163 downstream intron SNORD78 MDN1 172101383 90409952 - - 0.511100736590933 172101309 90487833 + + Y - 1.96227421382155 N HCC1954 2 1.25 1 1 1 N - - N - - 0 0 0 4 0.678466075192994 0.785592297591888 0.785592297591888 0.678466075192994 1 - 0 38008 N Y 3.63825270713077 3.85425536676371 3.63825270713077 0 0 0.524036381688653 N 0.855510752688172 0.807347670250896 N N 0 2963 ENSG00000204817 ENSG00000133983 - + 9 14 46585552 69896147 upstream coding RP11-111F5.5 COX16 46584172 69680762 + - 0 46566138 69895989 - - Y - - N HCC1954 10 5 4 8 1 N - - N SINE - 1 0 1 8 0.357087407996313 0.714174815992626 0.714174815992626 0.357087407996313 4 - - 18603 Y Y 3.32167753656001 3.37548038812845 3.32167753656001 162 0 0.0213843447395737 Y 0 0.981930415263748 N N 0 0 ENSG00000213241 ENSG00000207106 + - 1 1 143075528 143022733 downstream downstream BX248398.9-1 U1 143075034 143022570 - - 0 143050952 143012808 - + N - - N HCC1954 25 16 6 11 1 N - - Y - - 0 0 0 11 0.87843502367093 0.871293275511003 0.87843502367093 0.871293275511003 2 - - 33003 N Y 2.98888957109253 3.43681151080804 2.98888957109253 480 0 0.000474765461313864 Y 0.0189258087201124 0.995789381153305 N N 59837 0 ENSG00000198695 ENSG00000210184 + + MT MT 14674 12266 coding intron MT-ND6 AF347015.1-20 14150 12208 - + 0 14320 12214 - + N 0.87601057384036 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.721316564152552 0.835584534711372 0.835584534711372 0.721316564152552 3 0 0 5629 N Y 3.7297745213208 3.35616415112274 3.35616415112274 1 0 0.0205254596583255 N 0 0.839971372338522 N N 20739 17179 ENSG00000143951 ENSG00000177189 - - 2 X 63669355 20194671 utr3p upstream C2orf86 RPS6KA3 63202041 20077951 - - 0.790731794596529 63309655 20205050 + + Y - - N HCC1954 640 575 420 4 1 N - - N LINE LINE 1 1 1 4 0.349945659836387 0.371370904316165 0.371370904316165 0.349945659836387 1 - - 18359 Y Y 3.0740755951147 3.05471950531564 3.05471950531564 373 0 0.00339046714588442 Y 0 0 N N 8 136 ENSG00000168148 ENSG00000162931 + - 1 1 226679649 226670988 upstream downstream HIST3H3 TRIM17 226679169 226662259 - - 0 226682444 226661889 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 4 0.799875793911741 0.707033067832699 0.799875793911741 0.707033067832699 4 - - 28837 N N 3.5010341561346 3.61257440753299 3.5010341561346 11 0 0.190975553828386 N 0 0.00336700336700346 N N 40617 4695 ENSG00000130164 ENSG00000091651 + + 19 16 11105490 45289806 utr3p utr3p LDLR ORC6L 11061132 45281059 + + 0.00336700336700346 11104135 45289294 + + Y - - N HCC1954 40 38.25 35 4 1 N - - N SINE SINE 0.567901234567901 0.207964601769911 0.567901234567901 4 0.578481600954027 0.792734045751814 0.792734045751814 0.578481600954027 3 - - 45891 N Y 3.57800808738356 3.1614158869593 3.1614158869593 0 0 0.392780000556528 N 0.0042372881355931 0 N N 17943 1063 ENSG00000105141 ENSG00000164603 + - 19 7 15027900 112367168 downstream intron CASP14 C7orf60 15024015 112246439 + - 0 15029502 112293243 + + Y - 0.792946737838266 N HCC1954 14 8.70731707317073 1 37 1 N - - N SINE SINE 0.201550387596899 1 1 41 0.914143764470561 0.28566992639705 0.914143764470561 0.28566992639705 3 - 0 34636 N Y 3.6533527266709 3.47129812537077 3.47129812537077 98 0.0183673469387755 0.595718779358688 Y 0 0.986734693877551 N N 2515 13277 ENSG00000137074 ENSG00000086061 - - 9 9 32991626 33029277 coding upstream APTX DNAJA1 32962609 33015242 - + 0 32979847 33015054 + - N - - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 53 0.964136001590045 0.914143764470561 0.964136001590045 0.914143764470561 3 - - 29931 N N 3.54768941479713 3.43937216388778 3.43937216388778 30 0.152450430228208 0.0793847582835643 N 0.152450430228208 0.152450430228208 N N 559 78560 ENSG00000102290 ENSG00000112493 - + X 6 91764885 33390114 utr3p utr3p PCDH11X TAPBP 90920960 33375449 + - 0.152450430228208 91025199 33375989 - - Y - 0.622657104455216 N HCC1954 38 37.25 36 4 1 N - - N SINE DNA 1 0.80952380952381 1 4 0.335662163516534 0.657040830713216 0.657040830713216 0.335662163516534 3 - 0 38241 Y Y 3.45400817511148 3.76951977068882 3.45400817511148 323 0 0.0251666104316822 Y 0 0.99330936896129 N N 2793 27551 ENSG00000129472 ENSG00000100888 + - 14 14 21014972 20969237 downstream upstream RAB2B CHD8 20997019 20923198 - - 0 20992881 20969861 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.771308801272036 0.835584534711372 0.835584534711372 0.771308801272036 1 - - 442 Y Y 3.4780843434859 3.54872248456702 3.4780843434859 119 0 0.993599584967625 Y 0.813294491525424 0.984441207627119 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 upstream coding C11orf66 C11orf79 61005168 60954173 + + 0 60992711 60962160 - + N - - N HCC1954 1 1 1 0 6 N - - Y SINE - 0.0227272727272727 0 0.0227272727272727 6 0.628473838073511 0.678466075192994 0.678466075192994 0.628473838073511 1 - - 4492 Y Y 3.56488607910057 3.61633596425197 3.56488607910057 0 0 0.963678340959382 Y 0 0.993355481727575 N N 8842 2897 ENSG00000006453 ENSG00000164713 + + 7 7 97868316 97758775 coding coding BAIAP2L1 BRI3P1 97760007 97748923 - + 0 97773728 97749698 - + N 0.425968770426943 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.165562913907285 0.165562913907285 10 1.04983697950916 1.07840397214886 1.07840397214886 1.04983697950916 2 0 - 13957 Y Y 3.77208042376856 3.49015970162987 3.49015970162987 133 0.00370370370370354 0.890292376256815 Y 0.988678451178451 0.988678451178451 N Y 855 4030 ENSG00000099910 ENSG00000185214 - + 22 22 19122146 19180122 coding coding SCARF2 KLHL22 19108874 19125806 - - 0 19114844 19130730 + - N - - N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 4 0.692749571512847 0.521347615674617 0.692749571512847 0.521347615674617 4 - - 45636 N N 3.63296356710195 3.58064844605001 3.58064844605001 0 0 0.24994164795303 N 0 0 N N 5408 107061 ENSG00000171466 ENSG00000198034 + + 19 X 9646734 71413866 upstream coding ZNF562 RPS4X 9620363 71409178 - - 0 9655156 71409859 - - Y - - N HCC1954 1 1 1 0 1 N 43 23.4015 N - - 0 0 0 4 0.421363141435649 0.671324327033068 0.671324327033068 0.421363141435649 1 - - 18269 Y Y 3.31588453542141 3.51207644450867 3.31588453542141 306 0 0.00117804865539517 Y 0 0 N N 0 0 ENSG00000219071 ENSG00000213353 + - 1 1 110155143 110111760 downstream upstream RP4-735C1.5 AL158847.22 110154789 110111549 - - 0 110136364 110132724 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.521347615674617 0.507064119354764 0.521347615674617 0.507064119354764 1 - - 31398 Y Y 3.35872480420248 3.52936639476796 3.35872480420248 2 0 0.999702337048202 Y 0.992561861743912 0.992561861743912 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 intron upstream LPP AC022498.18 189413415 189379637 + + 0 189606593 189354502 - + N 0.286981555487908 - N HCC1954 1 1 1 0 7 N - - Y - - 0 0 0 19 1.07126222398894 1.02126998686945 1.07126222398894 1.02126998686945 1 0 - 38113 Y Y 3.79362644428678 3.17979234015096 3.17979234015096 282 0 0.729644258857252 Y 0.957294832826748 0.985764944275583 N N 0 10336 ENSG00000221236 ENSG00000133961 - - 14 14 72985644 72892230 upstream utr5p AC005280.3 NUMB 72985548 72811671 + - 0 72946398 72892227 - + N - 19.4081672720134 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 98 1.06412047582901 1.07840397214886 1.07840397214886 1.06412047582901 4 - 0 47965 N N 3.27824527838653 3.64081336021051 3.27824527838653 0 0 0.366520332055473 N 0 0 N N 0 12549 ENSG00000212451 ENSG00000087206 - + 8 5 127753081 176366358 downstream coding U11 UIMC1 127752949 176264612 + - 0 128113124 176270998 - - Y - - N HCC1954 1 1 1 0 1 N - - N SINE Low_complexity 1 0.0163934426229508 1 4 0.614190341753658 0.871293275511003 0.871293275511003 0.614190341753658 4 - - 7410 Y Y 3.37758638046158 3.24847874239916 3.24847874239916 5 0.0387827977022202 0.799995829504099 Y 0.991181493556901 0.982362987113802 N N 5277 307 ENSG00000169756 ENSG00000214184 - - 2 2 108670134 108517107 coding upstream LIMS1 AC012487.12-1 108571199 108492643 + - 0 108642493 108517482 - + N - - N HCC1954 3 2.14285714285714 1 4 1 N - - Y - - 0 0 0 7 0.964136001590045 0.635615586233437 0.964136001590045 0.635615586233437 4 - - 10995 N Y 3.07101108092519 3.63296356710195 3.07101108092519 0 0 0.418131808263495 N 0.641927083333333 0.820963541666667 N N 1649619 0 ENSG00000141736 ENSG00000209924 - - 17 6 35138441 4991334 coding downstream ERBB2 AL359643.27 35104766 4991186 + - 0 35125066 4989507 - + Y - - N HCC1954 35 22.2352941176471 20 17 1 N - - N - SINE 0 1 1 17 0.899860268150708 0.349945659836387 0.899860268150708 0.349945659836387 1 - - 3777 N N 3.65231965690101 3.01080631397133 3.01080631397133 0 0 0.0943223915665302 N 0 0 N N 3825 21326 ENSG00000183762 ENSG00000182240 + + 22 21 27893094 41570378 intron upstream KREMEN1 BACE2 27799066 41461598 + + 0 27865930 41450669 + + Y 1.69479266640959 - N HCC1954 1 1 1 0 1 N 53 1.00658 N SINE SINE 0.566666666666667 0.407407407407407 0.566666666666667 8 0.642757334393363 0.771308801272036 0.771308801272036 0.642757334393363 2 0 - 320 Y N 3.50883846020528 2.61209605319877 2.61209605319877 0 0 0.326833942253777 Y 0 0.116143170197224 N N 410 109 ENSG00000120458 ENSG00000149564 + - 11 11 124175509 124137433 downstream upstream C11orf61 ESAM 124141604 124128229 - - 0.116143170197224 124140267 124137547 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.526785714285714 0.526785714285714 5 0.564198104634174 0.757025304952183 0.757025304952183 0.564198104634174 2 - - 7633 N Y 3.47233119514066 3.37126417066287 3.37126417066287 3 0 0.10233593118861 N 0 0.935889632785555 N N 20739 6 ENSG00000143951 ENSG00000101298 - + 2 20 63669355 1237972 utr3p upstream C2orf86 RAD21L1 63202041 1154700 - + 0 63309485 1148806 + + Y - - N HCC1954 620 480 400 4 1 N - - N LINE LINE 1 1 1 4 0.699891319672773 0.39993789695587 0.699891319672773 0.39993789695587 4 - - 39901 Y Y 3.43105836246279 2.9715114925506 2.9715114925506 257 0 0.673989054442517 Y 0.0177258971033289 0.972330306960657 N N 1136 38799 ENSG00000104147 ENSG00000187446 + + 15 15 39412111 39361377 downstream downstream OIP5 AC012652.1 39388762 39310729 - + 0 39388054 39364953 - + N - - N HCC1954 3 1.33333333333333 1 1 4 N - - Y LINE LTR 1 0.628571428571429 1 6 0.378512652476092 0.499922371194838 0.499922371194838 0.378512652476092 3 - - 41784 Y Y 3.49424793801946 3.09181081564808 3.09181081564808 0 0.283457955136151 0.827065868044558 Y 0.350633771842137 0.988804030549002 N N 6286 910 ENSG00000012232 ENSG00000104290 - + 8 8 28667116 28477878 utr5p downstream EXTL3 FZD3 28615050 28407692 + + 0 28615095 28536245 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.170212765957447 0.170212765957447 29 1.20695543902754 0.671324327033068 1.20695543902754 0.671324327033068 1 - - 27305 N Y 3.5816815158199 3.55401162459584 3.55401162459584 105 0.00289017341040465 0.97898289625829 Y 0.316446722652416 0.99372886901516 N N 69736 15881 ENSG00000181019 ENSG00000102908 + + 16 16 68318034 68296054 coding intron NQO1 NFAT5 68300808 68156498 - + 0 68304437 68278842 - + N - 0.911369880019537 N HCC1954 20 3.36363636363636 1 3 5 N - - N - SINE 0 1 1 11 1.02126998686945 0.742741808632331 1.02126998686945 0.742741808632331 2 - 0 19541 Y Y 3.41679307359967 3.56591914887046 3.41679307359967 0 0.00289017341040454 0.890186707307995 Y 0.00289017341040454 0.983381502890173 N N 27007 0 ENSG00000142973 ENSG00000217954 - + 1 1 47057605 46981401 coding downstream CYP4B1 RP11-8J9.5 47037257 46980453 + + 0 47049067 47005903 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.614173228346457 0.614173228346457 28 1.64974382494297 0.907002016310634 1.64974382494297 0.907002016310634 4 - - 3768 N N 3.15206901576442 3.44871903508266 3.15206901576442 0 0 0.112267635129853 N 0 0 N N 250 0 ENSG00000188681 ENSG00000217850 + - Y 21 11830682 30558070 downstream downstream AC134878.3-1 RPL8P2 11769481 30557569 - - 0.00427350427350426 11715038 30550215 - + Y - - N HCC1954 4 1.71428571428571 1 2 1 N 10 6.58713 N Satellite LTR 1 1 1 7 0.814159290231593 0.649899082553289 0.814159290231593 0.649899082553289 1 - - 1359 N Y 3.50000108636471 3.26824964015148 3.26824964015148 3 0 0.264719798247589 N 0.940423383461358 0.897868657362328 N N 15671 8014 ENSG00000115762 ENSG00000149084 - - 2 11 131827752 43834736 utr3p utr3p PLEKHB2 HSD17B12 131578890 43658719 + + 0.17443831367882 131621560 43834016 - - Y - 1.56799368003871 N HCC1954 99 64.2727272727273 58 11 1 N - - N SINE - 1 0 1 11 0.299953422716903 0.442788385915428 0.442788385915428 0.299953422716903 1 - 0 42892 N N 3.33424740824393 3.61104682422314 3.33424740824393 0 0 0.295397460929335 N 0.0324559108273588 0 N N 42670 0 ENSG00000128050 ENSG00000176366 + - 4 7 57022291 143085550 coding upstream PAICS AC106862.3 56996672 143083351 + - 0 57012844 143111891 + + Y - - N HCC1954 4 3 2 4 1 N - - N - - 0 0 0 4 0.435646637755502 0.221394192957714 0.435646637755502 0.221394192957714 2 - - 32913 N N 3.51935717616377 3.08086181322984 3.08086181322984 0 0.268131868131868 0.584497099570049 N 0.349450549450549 0 N N 551733 0 ENSG00000204628 ENSG00000198800 + - 5 3 180603512 110611583 utr3p upstream GNB2L1 AC092905.10 180596536 110611215 - - 0 180596558 110738671 - + Y - - N HCC1954 21 16.1666666666667 2 6 1 N - - N - SINE,SINE 0 0.8 0.8 6 0.471355378555133 0.28566992639705 0.471355378555133 0.28566992639705 2 - - 37208 N Y 3.50016892023405 3.45464001729725 3.45464001729725 7 0 0.215082666552876 N 0.895112781954887 0.912593984962406 N N 551733 110 ENSG00000204628 ENSG00000173262 - - 5 12 180603512 7916762 coding upstream GNB2L1 SLC2A14 180596536 7856383 - - 0 180601102 7927939 + + Y - - N HCC1954 40 24 20 5 1 N - - N - SINE,SINE 0 1 1 5 0.557056356474248 0.349945659836387 0.557056356474248 0.349945659836387 1 - - 36229 Y Y 3.40740634961144 3.38656252929588 3.38656252929588 321 0 0.162195436788722 Y 0.973937653981634 0.993484413495409 N N 10492 2365 ENSG00000211584 ENSG00000079337 - - 12 12 46461719 46439128 upstream upstream SLC48A1 RAPGEF3 46453258 46417296 + - 0 46452224 46440455 - + N - - N HCC1954 1 1 1 0 3 N - - Y - DNA 0 0.0635838150289017 0.0635838150289017 63 1.17124669822791 1.23552243166724 1.23552243166724 1.17124669822791 3 - - 40048 Y Y 3.57912086274016 3.48064499656564 3.48064499656564 321 0 0.00214032908339234 Y 0.953166488950218 0.99330949842146 N N 269689 3297 ENSG00000067225 ENSG00000137817 - + 15 15 70310738 70350682 utr5p downstream PKM2 PARP6 70278424 70320577 - - 0 70298504 70316785 + - N - - N HCC1954 2 1.30769230769231 1 12 1 N - - Y - - 0 0 0 39 1.10697096478857 1.12839620926835 1.12839620926835 1.10697096478857 1 - - 31538 Y N 3.53465553479678 3.67489874718912 3.53465553479678 0 0 0.521300207846593 N 0 0 N N 6846 41283 ENSG00000163755 ENSG00000047457 - + 3 3 150373995 150422519 intron coding HPS3 CP 150330061 150373220 + - 0 150366347 150376727 - - N 1.33045161304183 - Y HCC1954 2 1.16666666666667 1 1 1 N 124 24.4061 N - - 0 0 0 6 0.657040830713216 0.742741808632331 0.742741808632331 0.657040830713216 3 0 - 49273 Y Y 3.32423818963975 3.54296933622177 3.32423818963975 0 0 0.87679976727958 Y 0 0.965612235204712 N N 106385 55216 ENSG00000071539 ENSG00000028310 - - 5 5 971156 945915 coding intron TRIP13 BRD9 946004 916856 + - 0 946203 945025 - + N - 1.72203611175413 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 70 1.3069399132665 1.39978263934555 1.39978263934555 1.3069399132665 2 - 0 29052 N N 3.37655331069169 3.46448140203209 3.37655331069169 0 0 0.0841248072659027 N 0 0 N N 975 866 ENSG00000198487 ENSG00000154328 + + 6 8 42218335 11682263 intron intron AL512274.9 NEIL2 42183124 11664627 - + 0 42204322 11669178 - + Y 0.755947860259476 0.299393055803559 N HCC1954 23 21.2 20 5 1 N - - N - SINE 0 1 1 5 0.485638874874985 0.321378667196682 0.485638874874985 0.321378667196682 2 0 0 28768 N N 3.58271458558979 3.31422897103557 3.31422897103557 0 0 0.0771773341081093 N 0 0.0159245516388374 N N 18725 45068 ENSG00000130202 ENSG00000205336 + + 19 16 50084325 56256445 intron upstream PVRL2 GPR56 50041233 56220023 + + 0.0159245516388374 50047593 56211711 + + Y 0.513925569528207 - N HCC1954 2 1.46666666666667 1 7 1 N - - N SINE - 1 0 1 15 0.292811674556976 0.464213630395207 0.464213630395207 0.292811674556976 2 0 - 41985 N N 3.61464054707278 3.2793317813189 3.2793317813189 0 0 0.792637861028601 N 0 0 N N 86504 559 ENSG00000104408 ENSG00000102290 + + 8 X 109330135 91764885 coding upstream EIF3E PCDH11X 109283149 90920960 - + 0 109298865 90884375 - + Y - - N HCC1954 2 1.5 1 2 3 N - - N - LINE,LINE 0 1 1 4 0.771308801272036 0.799875793911741 0.799875793911741 0.771308801272036 1 - - 13748 Y Y 3.20128492750669 3.448886868952 3.20128492750669 262 0 0.304876086259042 Y 0 0 N N 0 18250 ENSG00000209587 ENSG00000077942 + + 22 22 44399175 44375678 upstream downstream Z95331.2 FBLN1 44399075 44277383 - + 0 44400817 44380057 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.93556900895034 0.635615586233437 0.93556900895034 0.635615586233437 4 - - 44192 N N 2.78544320277438 3.23999710710482 2.78544320277438 0 0 0.0465402188307329 N 0 0 N N 0 41507 ENSG00000095713 ENSG00000188846 + + 10 3 99780575 40478862 upstream coding CRTAC1 RPL14 99614748 40473834 - + 0 99794093 40478438 - + Y - - N HCC1954 6 3 1 3 1 N - - N LINE - 1 0 1 4 0.321378667196682 0.842726282871298 0.842726282871298 0.321378667196682 1 - - 40966 Y Y 3.40488554932505 3.329991337985 3.329991337985 220 0 0.0250130254126821 Y 0 0.990428321678322 N N 18886 0 ENSG00000125999 ENSG00000217037 - - 20 20 31361345 31324124 utr5p upstream C20orf114 RPL12P3 31334602 31323729 + - 0 31337513 31325083 - + N 0.927312502411046 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.871293275511003 0.749883556792257 0.871293275511003 0.749883556792257 1 0 - 41186 Y Y 3.47080361183081 3.62824348852659 3.47080361183081 0 0.156675766946576 0.959008268615884 Y 0.410224229171788 0.988976153816295 N Y 28646 2106 ENSG00000125835 ENSG00000088876 - + 20 20 2399499 2453165 coding coding SNRPB ZNF343 2390281 2410463 - - 0 2396404 2421345 + - N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 10 1.52119235806429 1.24266417982717 1.52119235806429 1.24266417982717 4 - - 27292 Y Y 3.68105312311849 3.12808613334584 3.12808613334584 0 0 0.296520148389648 Y 0 0 N N 16390 6535 ENSG00000140950 ENSG00000064270 + + 16 16 83095794 83055293 coding intron KIAA1609 ATP2C2 83068608 82959634 - + 0 83073700 83054107 - + N - 0.930794578192297 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.892718519990782 1.16410495006798 1.16410495006798 0.892718519990782 1 - 0 7038 Y Y 3.3478104969044 3.07317050642081 3.07317050642081 312 0 0.00340687040463294 Y 0 0.977849002849003 N N 0 3567 ENSG00000211215 ENSG00000011566 + - 2 2 39569088 39517797 downstream upstream AC007388.4 MAP4K3 39568835 39329930 - - 0 39555171 39534696 - + N - - N HCC1954 20 8.33333333333333 1 8 2 N - - Y DNA,DNA,LINE SINE,SINE 0.839080459770115 1 1 12 0.621332089913584 0.649899082553289 0.649899082553289 0.621332089913584 0 - - 45041 N Y 3.19872427442695 3.33780127830021 3.19872427442695 1 0 0.541690955779896 Y 0.602151627475964 0.994396501795436 N N 20790 0 ENSG00000099204 ENSG00000220318 - - 10 10 116434404 116560919 coding upstream ABLIM1 RP11-106M7.2 116180862 116559124 - + 0 116434040 116517812 + - N - - N HCC1954 1 1 1 0 1 N - - N - Low_complexity 0 0.327956989247312 0.327956989247312 47 1.53547585438415 1.32836515774628 1.53547585438415 1.32836515774628 2 - - 49027 Y Y 3.59105889223831 3.27465155553689 3.27465155553689 3 0 0.860804608760979 Y 0.00446428571428581 0.00446428571428581 N N 5 2781 ENSG00000215159 ENSG00000082196 - - 5 5 34232139 34160396 upstream intron AC138409.1-1 AMACR 34210910 34023069 + - 0.00446428571428581 34204890 34100578 - + N - 22.4681704598243 N HCC1954 4 2.375 1 5 3 N - - Y LTR LTR 1 1 1 8 0.885576771830856 0.857009779191151 0.885576771830856 0.857009779191151 1 - 0 5726 N N 3.28466077414108 3.39380340815762 3.28466077414108 0 0 0.0636267785314377 N 0 0 N N 131026 0 ENSG00000115053 ENSG00000213178 - + 2 3 232037449 170684502 coding intron NCL AC074033.18 232027706 170684153 - - 0 232035494 170684245 + - Y - 1 N HCC1954 6 3 2 4 1 N - - N Simple_repeat,Simple_repeat - 0.342657342657343 0 0.342657342657343 4 0.842726282871298 0.99270299422975 0.99270299422975 0.842726282871298 1 - 0 9457 N Y 3.33255199106474 3.44256465915329 3.33255199106474 0 0 0.0600369370453663 Y 0.676413043478261 0 N N 3045 252027 ENSG00000121058 ENSG00000141738 + + 17 17 52393410 35157070 intron intron COIL GRB7 52370562 35147713 - + 0 52385389 35153503 - + N 0.766117967365301 0.802196664093379 N HCC1954 13 5 1 3 1 N - - N SINE SINE 1 0.478260869565217 1 4 0.264244681917271 0.328520415356608 0.328520415356608 0.264244681917271 1 0 0 9534 Y Y 3.32333310094585 3.41423242051993 3.32333310094585 256 0.0171875 0.262548200932439 Y 0.0171875 0.98671875 N N 70 117 ENSG00000184361 ENSG00000184922 + + 17 17 40695262 40680464 coding downstream C17orf46 FMNL1 40687543 40655075 - + 0 40688282 40681150 - + N 0.733729562000239 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 12 1.18553019454776 0.564198104634174 1.18553019454776 0.564198104634174 1 0 - 17926 Y Y 3.5816815158199 3.43152237077921 3.43152237077921 152 0 0.170992985472395 Y 0 0 N N 15221 62 ENSG00000159592 ENSG00000159588 + - 1 1 45924795 45862260 coding utr5p GPBP1L1 CCDC17 45865563 45858304 - - 0 45866519 45862202 - + N - 2.65405552712215 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 7 1.17124669822791 1.20695543902754 1.20695543902754 1.17124669822791 4 - 0 34336 Y Y 3.49272035470961 2.77485557514691 2.77485557514691 148 0 0.323195672032376 Y 0.456820101351351 0.984480574324324 N N 364 1351 ENSG00000137070 ENSG00000213930 - + 9 9 34651883 34640571 coding downstream IL11RA GALT 34643932 34636635 + + 0 34645611 34642230 - + N 0.137447884219102 - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.858823529411765 0.858823529411765 6 0.521347615674617 0.599906845433805 0.599906845433805 0.521347615674617 3 0 - 3797 N N 3.53205502892369 3.3828009725769 3.3828009725769 0 0 0.0518237366697458 N 0 0 N N 551733 0 ENSG00000204628 ENSG00000218528 + - 5 21 180603512 34430241 coding intron GNB2L1 RPS5P2 180596536 34429602 - - 0 180597264 34429604 - + Y 0.559193797750339 1 N HCC1954 20 18.2 16 10 1 N - - N - Simple_repeat 0 0.722222222222222 0.722222222222222 10 0.521347615674617 0.257102933757345 0.521347615674617 0.257102933757345 1 0 0 28746 N N 3.40847927217468 3.11125084383316 3.11125084383316 0 0 0.0426127186031713 N 0 0 N N 6125 4096 ENSG00000090339 ENSG00000103121 - + 19 16 10258291 79597997 utr3p coding ICAM1 C16orf61 10242765 79567206 + - 0 10258144 79572941 - - Y - - N HCC1954 26 26 26 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.464213630395207 0.464213630395207 0.28566992639705 1 - - 19170 N Y 3.57489529770476 3.72146071989581 3.57489529770476 0 0 0.915710407348031 Y 0.452208835341365 0.966800535475234 N N 0 7600 ENSG00000203341 ENSG00000157978 - + 1 1 25784586 25767964 downstream coding AL606491.19-2 LDLRAP1 25784093 25742663 + + 0 25789246 25756344 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.614190341753658 0.735600060472404 0.735600060472404 0.614190341753658 1 - - 34212 Y Y 3.31951811106439 3.74593811585436 3.31951811106439 0 0 0.740460113969454 Y 0.126145572975839 0.993846095584337 N N 0 136 ENSG00000216459 ENSG00000176399 - + 9 9 22738227 22442472 upstream downstream RP11-370B11.1 DMRTA1 22737699 22436840 + + 0 22664440 22499038 - + N - - N HCC1954 2 1.28571428571429 1 2 1 N - - Y Low_complexity LINE,SINE 0.788235294117647 0.794117647058823 0.794117647058823 7 1.02841173502938 0.821301038391519 1.02841173502938 0.821301038391519 1 - - 30695 Y Y 3.3414348539432 3.30335451653084 3.30335451653084 0 0 0.831807762784545 Y 0.0113066666666667 0 N Y 19 3306 ENSG00000125931 ENSG00000147099 - + X X 71443762 71709623 utr5p coding CITED1 HDAC8 71438222 71466091 - - 0 71439509 71488308 + - N - - N HCC1954 1 1 1 0 1 N - - Y SINE SINE 0.0685714285714286 0.0305343511450382 0.0685714285714286 5 0.921285512630487 0.807017542071667 0.921285512630487 0.807017542071667 4 - - 10397 Y Y 3.23999710710482 3.30062602958175 3.23999710710482 0 0 0.996938624092295 Y 0 0.985954945358425 N N 23404 2826 ENSG00000181885 ENSG00000170291 + + 17 17 7106520 7103974 coding coding CLDN7 C17orf81 7103953 7096096 - + 0 7104685 7102730 - + N - 2.18829172514826 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 15 1.06412047582901 1.21409718718746 1.21409718718746 1.06412047582901 4 - 0 34549 Y Y 3.40951234194457 3.14574680596571 3.14574680596571 142 0.0274509803921568 0.0557465103022892 Y 0.156343019135365 0 N N 931 14115 ENSG00000106991 ENSG00000136877 + + 9 9 129656805 129616377 downstream coding ENG FPGS 129617115 129604975 - + 0 129616963 129615427 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.792734045751814 0.807017542071667 0.807017542071667 0.792734045751814 3 - - 47585 Y Y 3.48553290901035 3.707857778442 3.48553290901035 2 0 0.796237983271725 Y 0 0.988930041152264 N Y 78 5592 ENSG00000214456 ENSG00000171236 - + 19 19 4486208 4491092 utr5p coding AC011498.7-3 LRG1 4473546 4488237 - - 0 4485107 4490994 + - N - 0.487346481208276 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.728458312312478 0.642757334393363 0.728458312312478 0.642757334393363 4 - 0 13051 N Y 3.07101108092519 3.37548038812845 3.07101108092519 1 0 0.201827874231279 N 0.755656762813562 0.887226198221644 N N 1649619 272 ENSG00000141736 ENSG00000118322 - - 17 5 35138441 160211797 coding intron ERBB2 ATP10B 35104766 159922707 + - 0 35125066 160063205 - + Y - 2.26803544471748 N HCC1954 21 19.8 17 5 1 N - - N - SINE 0 1 1 5 0.599906845433805 0.364229156156239 0.599906845433805 0.364229156156239 1 - 0 9372 Y Y 3.40129182647542 3.70144228268745 3.40129182647542 249 0 0.998496109089357 N 0 0.986540757625095 Y N 317991 1482 ENSG00000171346 ENSG00000171345 + - 17 17 36932191 36938167 upstream intron KRT15 KRT19 36923523 36933396 - - 0 36946570 36935053 - + N - 5.9918222398681 N HCC1954 1 1 1 0 8 N - - N - - 0 0 0 7 0.892718519990782 0.478497126715059 0.892718519990782 0.478497126715059 2 - 0 14246 N Y 3.56232542602083 3.56591914887046 3.56232542602083 0 0 0.636413042073085 N 0 0 N N 3693 738 ENSG00000198125 ENSG00000197860 - + 22 5 34349347 65053697 utr5p utr3p MB SGTB 34332757 64997520 - - 0 34343258 65000199 + - Y - - N HCC1954 34 30.5 25 4 1 N - - N - SINE 0 1 1 4 0.685607823352921 0.378512652476092 0.685607823352921 0.378512652476092 3 - - 41275 Y Y 3.15212244892691 3.40591861909494 3.15212244892691 242 0.072812767170134 0.00467239743708125 Y 0.381875178113423 0 N N 23109 32008 ENSG00000196562 ENSG00000124151 + + 20 20 45848215 45719023 utr3p utr3p SULF2 NCOA3 45719063 45564053 - + 0 45719462 45717224 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.93556900895034 0.807017542071667 0.93556900895034 0.807017542071667 2 - - 29263 Y Y 3.65554265739006 3.67952553980864 3.65554265739006 257 0 0.123395835891728 Y 0.378770762729593 0.978578302163089 N N 3676 10523 ENSG00000111906 ENSG00000111907 + + 6 6 125664981 125627252 downstream downstream HDDC2 TPD52L1 125638195 125516684 - + 0.518011798669512 125633361 125631110 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR,LTR,LTR 1 0.883870967741936 1 5 0.621332089913584 0.778450549431962 0.778450549431962 0.621332089913584 4 - - 5481 N Y 3.40744620240479 3.44975210485255 3.40744620240479 3 0 0.0203698789894829 N 0.0232072406590855 0.951961011835693 N N 2636 4691 ENSG00000154642 ENSG00000152253 + + 21 2 18113574 169455190 downstream utr3p C21orf91 SPC25 18083156 169435648 - - 0.935948015780924 18066661 169435705 - - Y - - N HCC1954 640 595 500 4 1 N 526 22.9698 N LINE LINE 1 1 1 4 0.299953422716903 0.542772860154395 0.542772860154395 0.299953422716903 1 - - 26709 Y Y 2.81087912058931 3.42998543989955 2.81087912058931 135 0 0.0154779857950015 Y 0.0814814814814815 0.985185185185185 N N 0 17990 ENSG00000216095 ENSG00000205937 - - 16 16 2261842 2258115 intron upstream hsa-mir-940 RNPS1 2261749 2243125 + - 0 2261755 2258225 - + N 1 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.299953422716903 0.349945659836387 0.349945659836387 0.299953422716903 1 0 - 44349 N N 3.425274708894 3.21279122419719 3.21279122419719 14 0 0.141832197989522 N 0 0 N N 2591 3891 ENSG00000111696 ENSG00000166295 + + 12 10 102759064 73665622 utr3p intron NT5DC3 C10orf104 102690219 73645812 - + 0 102694263 73645955 - + Y - 0.744979490524871 N HCC1954 38 30.0322580645161 17 31 1 N - - N SINE - 1 0 1 31 0.378512652476092 1.0069864905496 1.0069864905496 0.378512652476092 1 - 0 32974 Y N 3.79465951405667 3.44615838200292 3.44615838200292 0 0 0.0947520429517623 N 0 0 N N 247001 59837 ENSG00000198786 ENSG00000198695 - + MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 12491 14268 - - N 0.721828659885003 0.830504532086389 Y HCC1954 3 1.25 1 1 1 N 269 5.56049 N - - 0 0 0 8 1.52119235806429 1.17124669822791 1.52119235806429 1.17124669822791 1 0 0 44969 Y Y 3.63296356710195 3.20079041396673 3.20079041396673 0 0 0.674532653166808 Y 0.923282599753188 0.950681671269907 N N 3919 0 ENSG00000150054 ENSG00000222374 - - 10 10 28611073 28639894 utr5p upstream MPP7 AC022021.10-3 28379928 28639788 - + 0 28583709 28631797 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 90 1.36407389854591 1.42834963198525 1.42834963198525 1.36407389854591 2 - - 31447 Y Y 3.45140766923839 3.4780843434859 3.45140766923839 306 0 0.0549452107764559 Y 0.979519204942251 0.993173068314084 N N 397 6473 ENSG00000180432 ENSG00000144648 + + 3 3 42892661 42883778 upstream coding CYP8B1 CCBP2 42888688 42836115 - + 0 42904035 42881356 - + N - 0.697700465296563 N HCC1954 1 1 1 0 3 N - - Y LINE - 0.861842105263158 0 0.861842105263158 14 1.08554572030879 1.10697096478857 1.10697096478857 1.08554572030879 1 - 0 17596 N Y 3.53296011761759 3.61720120015252 3.53296011761759 0 0.0342035060975608 0.608106999677629 Y 0.989615091463415 0.989615091463415 N N 104 3888 ENSG00000143248 ENSG00000143228 - - 1 1 161454008 161592178 coding upstream RGS5 NUF2 161378724 161558347 - + 0 161439206 161542648 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 1.02126998686945 0.735600060472404 1.02126998686945 0.735600060472404 2 - - 49285 Y Y 3.37188666527882 3.61720120015252 3.37188666527882 118 0 0.417678716808396 Y 0.914668367346939 0.97155612244898 N N 53 2006 ENSG00000006837 ENSG00000119048 - - 5 5 133730664 133755698 coding upstream CDKL3 UBE2B 133662010 133734769 - + 0 133685493 133734588 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.771308801272036 0.34280391167646 0.771308801272036 0.34280391167646 4 - - 36589 Y Y 3.52680574168822 3.40637327984155 3.40637327984155 0 0 0.995552172353682 Y 0 0.994097935032001 N N 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6321203 6327499 + - N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity 0 0.0258620689655172 0.0258620689655172 28 1.17124669822791 1.59975158782348 1.59975158782348 1.17124669822791 2 - - 46980 Y Y 3.59528445727371 3.44086924197409 3.44086924197409 318 0 0.011712430809812 Y 0 0 N N 4475 8665 ENSG00000129911 ENSG00000079313 + - 19 19 1814564 1799452 coding intron KLF16 REXO1 1803398 1766245 - - 0 1814049 1779635 - + N 2.15133320874377 6.309676292927 N HCC1954 1 1 1 0 1 N - - Y Low_complexity - 0.43859649122807 0 0.43859649122807 7 1.17838844638783 0.871293275511003 1.17838844638783 0.871293275511003 2 0 0 39886 Y Y 3.42783536197374 3.51849194026323 3.42783536197374 185 0 0.065032437779699 Y 0.383351351351352 0.980108108108108 N N 589 4202 ENSG00000074621 ENSG00000138614 - - 15 15 63735652 63690522 upstream upstream SLC24A1 C15orf44 63703472 63658173 + - 0 63703288 63691975 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.507064119354764 0.45707188223528 0.507064119354764 0.45707188223528 3 - - 612 Y Y 3.76848670091893 3.46977054206092 3.46977054206092 0 0 0.324100279434615 Y 0.989839339991316 0.989839339991316 N N 1899 8479 ENSG00000077458 ENSG00000166037 - - 11 11 95162429 95205502 coding upstream FAM76B CEP57 95141765 95163290 - + 0 95162205 95162970 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.442788385915428 0.578481600954027 0.578481600954027 0.442788385915428 1 - - 6547 Y Y 3.5587317031712 3.62977107183644 3.5587317031712 181 0 0.00823760280369756 Y 0 0 N N 321 11024 ENSG00000153208 ENSG00000153107 - - 2 2 112503415 112358212 coding upstream MERTK ANAPC1 112372662 112243113 + - 0 112403221 112358514 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.87843502367093 0.607048593593732 0.87843502367093 0.607048593593732 1 - - 38069 Y Y 3.77783357211381 3.4106386976703 3.4106386976703 396 0 0.0203315355280569 Y 0 0.986428915000343 N N 23086 2 ENSG00000155463 ENSG00000212930 - - 14 14 22310832 22303174 upstream upstream OXA1L AL135998.6-1 22305571 22303034 + - 0.986428915000343 22305473 22303731 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 24 1.23552243166724 0.871293275511003 1.23552243166724 0.871293275511003 4 - - 38640 N Y 3.377215658101 3.48656597878024 3.377215658101 2 0 0.422410253506943 N 0 0.776784447282532 N N 1991 0 ENSG00000125841 ENSG00000222619 - - 20 14 283512 49399317 downstream intron NRSN2 SRP_euk_arch 275668 49399021 + - 0 288545 49399287 - + Y - 1 N HCC1954 238 55.75 5 8 1 N - - N SINE srpRNA 1 1 1 8 0.328520415356608 0.371370904316165 0.371370904316165 0.328520415356608 2 - 0 34963 Y N 3.61360747730289 3.53039946453785 3.53039946453785 0 0 0.130364355105211 N 0 0 N N 6397 10000 ENSG00000160446 ENSG00000160445 - - 9 9 130526229 130574019 upstream intron ZDHHC12 ZER1 130522969 130531890 - - 0 130526735 130535262 + + N - 0.514073279329062 Y HCC1954 1 1 1 0 1 N - - N - LINE 0 1 1 5 0.292811674556976 0.692749571512847 0.692749571512847 0.292811674556976 2 - 0 27578 N N 3.63040291402221 3.54400240599166 3.54400240599166 0 0 0.0797763848986702 N 0 0 N N 441 975 ENSG00000103313 ENSG00000198487 - + 16 6 3246628 42218335 utr3p coding MEFV AL512274.9 3232029 42183124 - - 0 3232266 42183238 + - Y - - N HCC1954 32 28.5 24 4 1 N - - N SINE - 1 0 1 4 0.364229156156239 0.578481600954027 0.578481600954027 0.364229156156239 2 - - 5110 Y Y 3.72146071989581 3.28296535696188 3.28296535696188 0 0 0.934719166452032 N 0 0.98339973439575 N N 13708 570 ENSG00000050327 ENSG00000170356 + - 7 7 143708657 143683165 coding intron ARHGEF5 OR2A9P 143683366 143578263 + - 0 143705216 143597757 + + N - 5.60090302881915 Y HCC1954 2 1.75 1 3 1 N - - N - LINE 0 1 1 4 0.371370904316165 0.607048593593732 0.607048593593732 0.371370904316165 4 - 0 29445 N Y 2.81720133038802 3.56761456604966 2.81720133038802 0 0 0.949656900189442 Y 0 0.98966394501645 N Y 13029 17595 ENSG00000124664 ENSG00000196821 - + 6 6 34632069 34772603 utr5p coding SPDEF C6orf106 34613558 34663050 - - 0 34620239 34722356 + - N - 0.633272392020387 N HCC1954 2 1.056 1 21 1 N - - N - - 0 0 0 375 1.4140661356654 1.4140661356654 1.4140661356654 1.4140661356654 4 - 0 13006 N N 3.40951234194457 3.50848272165904 3.40951234194457 0 0 0.0451509622628586 N 0 0 N N 5189 551733 ENSG00000126858 ENSG00000204628 - + 17 5 27576859 180603512 downstream coding RHOT1 GNB2L1 27493586 180596536 + - 0 27588992 180599139 - - Y - - N HCC1954 21 20.75 20 4 1 N 533 25.4266 N SINE - 1 0 1 4 0.321378667196682 0.578481600954027 0.578481600954027 0.321378667196682 1 - - 48796 Y Y 3.48743121468078 3.43937216388778 3.43937216388778 292 0.0449486301369865 0.74445800623537 Y 0.0449486301369865 0.986158675799087 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 utr3p downstream TPPP CEP72 712978 665405 - + 0 715899 708635 - + N 0.670767120634175 - N HCC1954 2 1.29411764705882 1 15 6 N - - Y - - 0 0 0 51 1.22838068350732 0.942710757110266 1.22838068350732 0.942710757110266 1 0 - 44817 Y Y 3.32895826821511 3.68783934123363 3.32895826821511 322 0 0.0053777461441108 Y 0 0 N N 11 573 ENSG00000178363 ENSG00000205488 - - 10 10 5558225 5555140 downstream utr5p CALML3 AL732437.12 5556924 5546207 + - 0 5586031 5554035 - + N - 10.6978389127768 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.635615586233437 0.485638874874985 0.635615586233437 0.485638874874985 1 - 0 41225 Y Y 3.44409224246314 3.59321831773393 3.44409224246314 0 0 0.274410694215742 Y 0.992619431025228 0.992619431025228 N N 28931 18186 ENSG00000101224 ENSG00000125817 - - 20 20 3734757 3715337 coding upstream CDC25B CENPB 3724401 3712498 + - 0 3725376 3715783 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.737704918032787 0.737704918032787 4 0.578481600954027 0.742741808632331 0.742741808632331 0.578481600954027 1 - - 2539 N N 3.46977054206092 3.39231567764112 3.39231567764112 0 0 0.826953055428811 N 0.0214757010531658 0.129203146808781 N Y 597 1079 ENSG00000110799 ENSG00000149089 - + 12 11 6104097 34894472 coding coding VWF APIP 5928301 34860421 - - 0.129203146808781 6032210 34894351 + - Y - 1.77494074552898 N HCC1954 1 1 1 0 1 N 314 11.0358 N - - 0 0 0 4 0.549914608314322 0.385654400636018 0.549914608314322 0.385654400636018 4 - 0 9359 Y Y 3.43358851031899 3.38656252929588 3.38656252929588 319 0 0.992661659556733 Y 0 0.993526849326222 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 intron utr3p C17orf37 ERBB2 35138937 35104766 - + 0.993526849326222 35139800 35137899 - + N 1.35620378426741 1.67445378036653 N HCC1954 1 1 1 0 6 N - - Y SINE - 0.208588957055215 0 0.208588957055215 69 1.16410495006798 1.14982145374813 1.16410495006798 1.14982145374813 3 0 0 33040 N Y 3.51633251476761 3.22233643448495 3.22233643448495 375 0 0.929603021512322 Y 0 0.992557213930348 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0 11166 8840 - + N 0.783881048323133 0.584701791594024 N HCC1954 2 1.42857142857143 1 3 7 Y - - N - - 0 0 0 7 1.32122340958636 1.26408942430695 1.32122340958636 1.26408942430695 1 0 0 40085 Y Y 3.30744275292043 3.21232721588077 3.21232721588077 0 0 0.274880168508306 Y 0.994693952415889 0.989387904831779 N N 7644 2404 ENSG00000028528 ENSG00000166797 - - 15 15 62223486 62173260 coding upstream SNX1 FAM96A 62175230 62151818 + - 0 62191825 62173587 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 1.18553019454776 1.10697096478857 1.18553019454776 1.10697096478857 4 - - 47672 Y Y 3.4561676006071 3.45087846057827 3.45087846057827 0 0 0.370372843762011 N 0.00362318840579712 0.97627674258109 Y Y 7761 88 ENSG00000129455 ENSG00000213022 + - 19 19 56196770 56204649 coding downstream KLK8 KLK9 56191076 56195618 - - 0 56192952 56196166 - + N - - N HCC1954 11 3.125 2 8 1 N - - N - SINE 0 1 1 8 0.907002016310634 0.371370904316165 0.907002016310634 0.371370904316165 1 - - 38981 N N 3.72874145155091 3.27192306858781 3.27192306858781 0 0 0.845317276360929 N 0 0 N N 0 5111 ENSG00000184565 ENSG00000181827 + - Y 15 19698690 54322775 intron downstream TTTY14 RFX7 19553973 54170024 - - 0 19612924 54152570 - + Y 1 - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 4 0.771308801272036 0.621332089913584 0.771308801272036 0.621332089913584 1 0 - 30255 Y Y 3.54872248456702 3.3755202409218 3.3755202409218 314 0 0.743321581567252 Y 0.956022855001873 0.992670475833646 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 upstream coding STS HDHD1A 7147472 6976961 + - 0 7118920 7076123 - + N - 0.468896951399537 N HCC1954 2 1.05479452054795 1 4 5 N - - Y - - 0 0 0 73 1.02841173502938 1.3069399132665 1.3069399132665 1.02841173502938 1 - 0 36369 Y Y 3.45293525254824 3.34152813989903 3.34152813989903 238 0 0.116702768544063 Y 0.989406400858216 0.978812801716431 N N 742 16 ENSG00000173588 ENSG00000136040 + + 12 12 93377895 93223356 utr3p downstream CCDC41 PLXNC1 93226189 93066630 - + 0 93226690 93224532 - + N 0.369543039353605 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.692749571512847 0.842726282871298 0.842726282871298 0.692749571512847 4 0 - 7924 N N 3.52936639476796 3.27192306858781 3.27192306858781 0 0 0.800560984101244 N 0.051044878383008 0.0273210003425829 N Y 8425 3699 ENSG00000109586 ENSG00000115947 + - 4 2 174481692 148495606 coding coding GALNT7 ORC4L 174326479 148408202 + - 0.0273210003425829 174461844 148432905 + + Y - 0.832347802399413 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 33 1.16410495006798 0.592765097273879 1.16410495006798 0.592765097273879 4 - 0 47004 Y Y 3.23424395875957 3.4780843434859 3.23424395875957 295 0 0.0182436884550663 Y 0.746146466261593 0.990598017268948 N N 779 0 ENSG00000213096 ENSG00000201966 - - 19 19 24104483 23979149 upstream upstream ZNF254 5_8S_rRNA 24061816 23979000 + - 0 24024003 24008265 - + N - - N HCC1954 1 1 1 0 2 N - - Y Satellite - 0.708333333333333 0 0.708333333333333 5 0.678466075192994 0.692749571512847 0.692749571512847 0.678466075192994 2 - - 9334 Y Y 3.18032154881108 3.30272267434507 3.18032154881108 504 0 0.999882693925467 Y 0 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p intron ORMDL3 GSDMB 35330822 35314374 - - 0 35332223 35328227 - + N 3.33669963388877 9.44764878355004 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 9 1.20695543902754 0.535631111994469 1.20695543902754 0.535631111994469 2 0 0 4885 N N 3.21232721588077 3.60785432895764 3.21232721588077 0 0 0.0629050736952037 N 0 0 N N 0 165508 ENSG00000174495 ENSG00000196262 - + 7 7 28285855 44807754 intron utr3p AC005017.1 PPIA 28285354 44802805 - + 0 28285449 44807594 + + N 1 1.49258283646005 Y HCC1954 8 3.25 2 12 1 N - - N - - 0 0 0 12 0.28566992639705 0.364229156156239 0.364229156156239 0.28566992639705 1 0 0 6971 Y Y 3.71873223294673 3.04586198998753 3.04586198998753 313 0 0.166908699960241 Y 0.992980245691401 0.985960491382802 N N 126 0 ENSG00000186281 ENSG00000222119 + - 2 2 96064454 96034328 downstream upstream AC013272.5-2 SRP_euk_arch 96051422 96034040 - - 0.192728254511092 96050600 96040207 - + N - - N HCC1954 2 2 2 6 3 N - - Y - - 0 0 0 6 0.635615586233437 0.692749571512847 0.692749571512847 0.635615586233437 4 - - 46978 Y Y 3.42783536197374 3.24103017687471 3.24103017687471 234 0 0.0166262417169358 Y 0 0 N N 6 1 ENSG00000203404 ENSG00000179066 - + 19 19 40294870 40289174 downstream intron AC020907.6-3 AC020907.6-2 40293688 40263171 + + 0 40296087 40273831 - + N - 0.876390605686032 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.414221393275723 0.485638874874985 0.485638874874985 0.414221393275723 1 - 0 44081 N N 3.24575025545007 3.28808666312136 3.24575025545007 0 0 0.239426338876129 N 0 0 N N 0 53981 ENSG00000218987 ENSG00000138326 + + X 10 3041637 79470477 intron coding RP13-824C8.2 RPS24 3040941 79463580 - + 0 3041056 79465452 - + Y 1 1.93398522345441 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.257102933757345 0.328520415356608 0.328520415356608 0.257102933757345 2 0 0 26869 N N 3.61360747730289 3.36397409143795 3.36397409143795 0 0.00641025641025639 0.224401015265505 N 0.00641025641025639 0.00641025641025639 Y N 7487 45068 ENSG00000188603 ENSG00000205336 + + 16 16 28411124 56256445 downstream coding CLN3 GPR56 28396101 56220023 - + 0.00641025641025639 28395830 56242685 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.599906845433805 0.599906845433805 0.321378667196682 1 - - 25187 Y Y 3.42208221362849 3.49272035470961 3.42208221362849 205 0.0446829268292684 0.00392812062812942 Y 0.668292682926829 0.973463414634146 N N 61 1325 ENSG00000198553 ENSG00000204977 - + 13 13 49493059 49490604 downstream utr5p KCNRG TRIM13 49487391 49469144 + + 0 49499455 49469521 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.821301038391519 0.742741808632331 0.821301038391519 0.742741808632331 1 - - 338 Y Y 3.17255146128921 3.26932256271472 3.17255146128921 342 0 0.00238153618818993 Y 0 0.988669590643275 N N 5860 19757 ENSG00000177700 ENSG00000177697 + + 11 11 832529 828834 downstream utr3p POLR2L CD151 829754 822843 - + 0.988669590643275 829530 828317 - + N - 1.17345800264929 N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 4 0.45707188223528 0.842726282871298 0.842726282871298 0.45707188223528 1 - 0 42173 Y Y 3.50575423470996 3.29231222815676 3.29231222815676 294 0 0.355846490132309 Y 0.991763647607803 0.983527295215607 N N 10761 25208 ENSG00000138768 ENSG00000138757 - - 4 4 76954388 76817629 upstream utr5p USO1 G3BP2 76869028 76786991 + - 0 76868484 76806257 - + N - 2.02052559781598 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 127 1.08554572030879 0.914143764470561 1.08554572030879 0.914143764470561 4 - 0 38084 Y Y 3.54296933622177 3.76951977068882 3.54296933622177 189 0 0.204494602771206 Y 0.733810269021536 0.985990014159028 N N 2793 27551 ENSG00000129472 ENSG00000100888 + - 14 14 21014972 20969237 downstream upstream RAB2B CHD8 20997019 20923198 - - 0 20994035 20969861 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.864151527351077 0.664182578873142 0.864151527351077 0.664182578873142 1 - - 738 N Y 3.02805217863794 3.22273766206908 3.02805217863794 0 0 0.0241165568291005 N 0.946767631103074 0.698349909584087 N N 34 19 ENSG00000205867 ENSG00000204572 - + 11 11 1576056 70957628 upstream upstream KRTAP5-2 KRTAP5-10 1575523 70954257 - + 0.787070524412297 1576877 70953363 + + N - - Y HCC1954 5 2 1 1 1 N 265 7.64405 N LTR LTR 1 1 1 4 0.51420586751469 0.39993789695587 0.51420586751469 0.39993789695587 1 - - 3408 N N 3.40319013214585 3.42680229220385 3.40319013214585 0 0 0.95438903233084 N 0.0345528455284552 0 Y N 18589 9593 ENSG00000180530 ENSG00000205726 + + 21 21 15359192 34184448 downstream coding NRIP1 ITSN1 15255427 33936576 - + 0 15196760 34029379 - + N - 1.7594121493757 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.721316564152552 0.985561246069823 0.985561246069823 0.721316564152552 4 - 0 40829 N Y 3.09872082494259 3.684245618384 3.09872082494259 1 0 0.572258133462963 N 0.935028712059065 0 N N 6576 3393 ENSG00000106635 ENSG00000132623 - + 7 20 72609960 9985405 coding intron BCL7B ANKRD5 72588622 9963689 - + 0 72609753 9972448 + + Y - 1.64260588879815 N HCC1954 21 20.2 20 5 1 N - - N - SINE 0 1 1 5 0.5713398527941 0.335662163516534 0.5713398527941 0.335662163516534 3 - 0 22303 N Y 3.61360747730288 3.41848849077886 3.41848849077886 4 0 0.0490949931197132 N 0.00694444444444442 0.202546296296296 N N 49089 3297 ENSG00000117450 ENSG00000104613 - - 1 8 45760196 19753864 coding upstream PRDX1 INTS10 45749295 19719198 - + 0.232638888888889 45757256 19711048 + - Y - - N HCC1954 21 19.75 15 12 1 N - - N - SINE 0 1 1 12 0.407079645115797 0.321378667196682 0.407079645115797 0.321378667196682 1 - - 10138 Y Y 2.71788587159702 3.61720120015252 2.71788587159702 198 0 0.00892741651228701 Y 0.0241841491841492 0.942599067599068 N N 64784 120 ENSG00000170004 ENSG00000205498 - - 17 17 7756803 7717756 coding utr3p CHD3 AC104581.22-1 7728849 7711861 + - 0 7728899 7712411 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity LINE 1 1 1 4 0.428504889595575 0.314236919036755 0.428504889595575 0.314236919036755 2 - - 16229 N N 3.52407725473913 3.35356364524965 3.35356364524965 11 0 0.073491796186767 N 0 0 N N 5277 1302 ENSG00000169756 ENSG00000162585 - + 2 1 108670134 2122397 downstream coding LIMS1 C1orf86 108571199 2105777 + - 0.01654921213081 108674773 2114947 - - Y - - N HCC1954 9 3.8 1 2 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.492780623034912 0.492780623034912 0.314236919036755 2 - - 45248 N Y 3.39487633072086 3.45868840089349 3.39487633072086 2 0 0.133502523815842 N 0.0255668867789368 0 N N 5301 17943 ENSG00000107771 ENSG00000105141 - + 10 19 86268256 15027900 utr3p downstream KIAA1128 CASP14 86078322 15024015 + + 0 86265191 15029876 - + Y - - N HCC1954 138 56.2857142857143 10 7 1 N - - N SINE SINE 1 0.8515625 1 7 0.307095170876829 0.607048593593732 0.607048593593732 0.307095170876829 2 - - 623 Y N 3.77104735399867 3.69784855983781 3.69784855983781 0 0.420081967213115 0.361217631542 Y 0.803971369198799 0.420081967213115 N N 3781 308 ENSG00000110218 ENSG00000181333 - + 11 11 93554781 93487022 coding coding PANX1 HEPHL1 93501742 93394026 + + 0.420081967213115 93502143 93440558 - + N - 1.28296975539514 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 24 0.771308801272036 0.921285512630487 0.921285512630487 0.771308801272036 2 - 0 4091 Y Y 3.56488607910057 3.29652844562235 3.29652844562235 306 0 0.526736821138854 N 0.973242093257885 0.986621046628942 Y N 0 0 ENSG00000223189 ENSG00000208561 - + 7 7 128054565 128054565 downstream downstream U6 AC018638.5-1 128054462 128054463 + + 0 128066064 128059159 - + N - - N HCC1954 224 17.6153846153846 1 19 3 N - - N SINE SINE,LTR 1 0.51006711409396 1 26 0.985561246069823 1.06412047582901 1.06412047582901 0.985561246069823 4 - - 3885 N Y 1.52192809488736 3.17680753154815 1.52192809488736 0 0.0125000000000006 0.0100680024883054 N 0.835416666666667 0.0125000000000006 N N 0 32979 ENSG00000213706 ENSG00000106105 - - X 7 70489566 30640168 upstream utr5p AL590762.1 GARS 70488993 30600706 + + 0.0125000000000006 70472623 30600856 - - Y - 0.0020571973412267 N HCC1954 19 4.28571428571429 2 28 1 N - - N SINE - 1 0 1 28 0.299953422716903 0.45707188223528 0.45707188223528 0.299953422716903 1 - 0 17514 Y Y 3.3828009725769 3.36079094374226 3.36079094374226 150 0 0.0975416539529547 Y 0 0.994665481218049 N N 2732 0 ENSG00000168275 ENSG00000138396 - - 1 1 232586416 232559510 coding intron C1orf31 RP5-827C21.1 232575836 232559073 + - 0 232576625 232559408 - + N - 1 N HCC1954 4 2.35714285714286 1 20 2 N - - Y - - 0 0 0 28 1.28551466878673 1.02126998686945 1.28551466878673 1.02126998686945 2 - 0 23809 N Y 3.54077940550261 3.08977518133184 3.08977518133184 59 0 0.132508400523231 N 0 0.812878787878788 N N 1869 11413 ENSG00000173614 ENSG00000112877 - + 1 5 9968143 706664 coding intron NMNAT1 CEP72 9926073 665405 + + 0.812878787878788 9963902 665717 - + Y - 0.779055593662006 N HCC1954 24 23.25 22 4 1 Y - - N SINE - 1 0 1 4 0.549914608314322 0.785592297591888 0.785592297591888 0.549914608314322 0 - 0 9304 Y Y 3.38337003403037 3.36720643949681 3.36720643949681 403 0 0.00451584474816336 Y 0.261836228287841 0.995012406947891 N N 946 5297 ENSG00000159314 ENSG00000185602 + - 17 17 40866902 40858780 coding utr5p SH3D20 ARHGAP27 40862502 40827058 - - 0 40862770 40839230 - + N 0.25140773390113 6.30855367176587 N HCC1954 2 1.00636942675159 1 1 1 Y - - Y Low_complexity - 0.0301507537688442 0 0.0301507537688442 157 1.42120788382533 1.50690886174444 1.50690886174444 1.42120788382533 1 0 0 14094 Y Y 3.74913061111987 3.79040344379773 3.74913061111987 0 0 0.482355293424332 Y 0 0.975673772485756 N N 8351 35913 ENSG00000100138 ENSG00000196419 + + 22 22 40416454 40389998 coding downstream NHP2L1 XRCC6 40399886 40347241 - + 0 40401144 40393033 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 1.09268746846872 1.04269523134923 1.09268746846872 1.04269523134923 2 - - 44660 Y Y 3.35463656781289 3.44615838200292 3.35463656781289 223 0 0.0659474085303527 Y 0 0 N N 0 0 ENSG00000222071 ENSG00000199222 + + 10 10 21825576 21810752 downstream downstream hsa-mir-1915 Y_RNA 21825497 21810651 - + 0 21819376 21816808 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.471355378555133 0.664182578873142 0.664182578873142 0.471355378555133 4 - - 7525 N N 3.70512929149291 3.41315949795669 3.41315949795669 0 0 0.936289415273359 Y 0 0 N Y 8684 2286 ENSG00000055044 ENSG00000082146 - + 2 2 202876627 202053819 coding coding NOP58 STRADB 202838760 202024637 + + 0 202870347 202046044 - + N - - N HCC1954 2 1.63318777292576 1 145 1 Y 512 4.03905 N - - 0 0 0 229 1.32122340958636 1.46405837278488 1.46405837278488 1.32122340958636 4 - - 36961 N N 3.5059220685793 3.75744441254485 3.5059220685793 0 0 0.999806274508003 N 0 0.00395256916996045 N N 3 12084 ENSG00000179242 ENSG00000177119 + + 20 12 59945671 44112391 intron intron CDH4 ANO6 59260965 43896170 + + 0.00395256916996045 59560122 44047844 + + Y 0.929733246584255 3.80916331694549 N HCC1954 1 1 1 0 8 N - - N LINE - 1 0 1 4 0.799875793911741 0.664182578873142 0.799875793911741 0.664182578873142 1 0 0 46204 N Y 3.71041843152174 3.37232774565629 3.37232774565629 12 0.0145094426531551 0.215177325456823 N 0 0 N N 5530 3041 ENSG00000148154 ENSG00000167625 + + 9 19 113735168 47424193 coding intron UGCG ZNF526 113698867 47416332 + + 0.0324274527867343 113731620 47423853 + + Y - - N HCC1954 36 32.375 29 8 1 N - - N - SINE 0 1 1 8 0.464213630395207 0.549914608314322 0.549914608314322 0.464213630395207 2 - - 36603 Y Y 3.66592259835483 3.08421279479488 3.08421279479488 2 0 0.92619646329794 Y 0.966255778120185 0.983127889060093 N Y 7855 6150 ENSG00000078246 ENSG00000171792 - + 12 12 2920558 2868885 coding utr5p TULP3 C12orf32 2870294 2856650 + + 0 2888956 2856709 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 1.06412047582901 0.392796148795944 1.06412047582901 0.392796148795944 4 - - 37031 N Y 3.62295434849776 3.4439989565073 3.4439989565073 0 0 0.321105474516052 N 0 0 N N 871 0 ENSG00000084453 ENSG00000222231 + - 12 8 21439638 77340522 utr5p upstream SLCO1A2 U2 21311651 77340333 - - 0.963135228251507 21439558 77381259 - + Y - - N HCC1954 25 19.9166666666667 2 12 1 N - - N LINE LTR,LTR 1 1 1 12 0.435646637755502 0.971277749749971 0.971277749749971 0.435646637755502 2 - - 6249 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.740532282249917 N 0.256327438314095 0.957905326697024 N N 0 3966 ENSG00000222476 ENSG00000175772 - + 9 2 9432367 110111006 downstream upstream SRP_euk_arch AC013268.5-1 9432060 110103138 + + 0 9924789 110102056 - + Y - - N HCC1954 40 39.6875 30 32 1 N 448 23.8251 N LINE - 1 0 1 32 0.421363141435649 1.12839620926835 1.12839620926835 0.421363141435649 3 - - 44955 Y N 3.37192651807217 3.59057108125987 3.37192651807217 0 0 0.0620778305737987 Y 0 0 N N 1193 2679 ENSG00000176171 ENSG00000175470 + + 10 10 133645417 133620041 upstream coding BNIP3 PPP2R2D 133631859 133597950 - + 0.00595238095238082 133659745 133611185 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,LINE - 0.744 0 0.744 4 0.664182578873142 0.521347615674617 0.664182578873142 0.521347615674617 1 - - 44791 N Y 3.38912318237562 3.44359772892318 3.38912318237562 0 0 0.0420482669225152 Y 0.747597093068688 0.985152770180511 N N 40 0 ENSG00000165429 ENSG00000219443 - + 10 10 81600608 81435395 upstream downstream AL135925.10 RP11-773D16.3 81591094 81433020 + + 0 81554225 81442018 - + N - - N HCC1954 12 9.75 6 8 1 N - - N - LTR 0 0.174757281553398 0.174757281553398 8 0.428504889595575 0.735600060472404 0.735600060472404 0.428504889595575 1 - - 46657 N Y 3.47279520345708 3.48593413659447 3.47279520345708 1 0 0.125991392196418 N 0.61877311812461 0.717154248931162 N N 0 2530 ENSG00000205922 ENSG00000138744 - + 19 4 1726444 77081190 upstream utr3p ONECUT3 NAAA 1704662 77050833 + - 0 1663526 77051496 - - Y - - N HCC1954 20 20 20 6 1 N - - N SINE - 1 0 1 6 0.39993789695587 0.485638874874985 0.485638874874985 0.39993789695587 1 - - 47741 Y Y 3.31273189294925 3.46248981040582 3.31273189294925 289 0 0.00473304502235339 Y 0.881530234471411 0.993031190263024 N N 123 2307 ENSG00000176909 ENSG00000176920 + + 19 19 53914100 53901019 coding downstream AC008888.7-1 FUT2 53908065 53891040 - + 0 53908931 53902482 - + N - - N HCC1954 11 3.5 1 2 1 N - - Y Simple_repeat SINE,SINE 0.404255319148936 1 1 6 1.01412823870953 0.892718519990782 1.01412823870953 0.892718519990782 1 - - 11469 N Y 3.69784855983781 3.76273355257368 3.69784855983781 0 0 0.159098139285004 N 0.768889663452229 0.84812749312575 N N 12271 1649619 ENSG00000177479 ENSG00000141736 + + 3 17 48997971 35138441 utr5p upstream ARIH2 ERBB2 48931285 35104766 + + 0 48935246 35103535 + + Y - - N HCC1954 32 21.3 20 10 1 N - - N - SINE 0 1 1 10 1.26408942430695 0.364229156156239 1.26408942430695 0.364229156156239 1 - - 9605 Y Y 3.47080361183081 3.52357339362936 3.47080361183081 266 0 0.517959701054073 Y 0.00375939849624063 0 N N 679 0 ENSG00000183308 ENSG00000201849 - - 17 17 59895221 59817128 upstream downstream C17orf60 Y_RNA 59875702 59817023 + - 0 59851664 59812481 - + N - - N HCC1954 13 3.6 1 2 3 N - - Y SINE - 1 0 1 5 0.578481600954027 0.542772860154395 0.578481600954027 0.542772860154395 4 - - 40925 Y Y 3.20331121425312 3.25822684117816 3.20331121425312 273 0 0.0830184398694729 Y 0 0.975699097650317 N N 18886 0 ENSG00000125999 ENSG00000217037 - - 20 20 31361345 31324124 upstream upstream C20orf114 RPL12P3 31334602 31323729 + - 0 31334394 31325058 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.699891319672773 0.664182578873142 0.699891319672773 0.664182578873142 3 - - 38594 N N 3.46295381872224 3.2948728812365 3.2948728812365 3 0 0.177302803656092 N 0.00446428571428581 0.00446428571428581 N N 2128 21875 ENSG00000129480 ENSG00000185078 + + 14 15 30996431 80535839 upstream coding C14orf126 AC139425.3-2 30984996 80451514 - - 0.00446428571428581 31001863 80451699 - - Y - - N HCC1954 8 4.9 4 10 1 N - - N - - 0 0 0 10 0.307095170876829 0.471355378555133 0.471355378555133 0.307095170876829 1 - - 21918 N N 3.64809409186561 3.77104735399867 3.64809409186561 3 0 0.0272626485120178 N 0.081081081081081 0.081081081081081 N N 49089 0 ENSG00000117450 ENSG00000222575 - + 1 12 45760196 78443081 coding downstream PRDX1 SRP_euk_arch 45749295 78442788 - - 0.117117117117117 45757241 78436650 + - Y - - N HCC1954 4 2 1 2 1 N - - N - SINE 0 1 1 4 0.357087407996313 0.385654400636018 0.385654400636018 0.357087407996313 0 - - 13354 N Y 3.56911164413597 3.53039946453785 3.53039946453785 0 0 0.166334520071494 N 0.831463356409644 0.838485716559242 N N 100806 0 ENSG00000163931 ENSG00000216623 - + 3 22 53265078 29166305 coding downstream TKT RP4-539M6.18 53234715 29165824 - + 0 53249309 29169598 + + Y - - N HCC1954 35 23.8888888888889 20 9 1 N - - N - SINE 0 1 1 9 1.19981369086761 0.307095170876829 1.19981369086761 0.307095170876829 2 - - 35360 N Y 3.4718366816007 3.2274272354209 3.2274272354209 0 0.0204633204633206 0.655236248102167 N 0.900386100386101 0.900386100386101 N N 4077 1649619 ENSG00000120805 ENSG00000141736 + + 12 17 100325703 35138441 upstream coding ARL1 ERBB2 100311054 35104766 - + 0 100337978 35122227 - + Y - - N HCC1954 17 9.5 2 6 1 N - - N SINE - 1 0 1 6 0.28566992639705 0.357087407996313 0.357087407996313 0.28566992639705 3 - - 28585 N N 3.39487633072086 3.21808036422602 3.21808036422602 0 0 0.232806444276284 N 0 0 N N 42670 45068 ENSG00000128050 ENSG00000205336 + + 4 16 57022291 56256445 utr3p upstream PAICS GPR56 56996672 56220023 + + 0 57021824 56211249 + + Y - - N HCC1954 24 23.1428571428571 21 7 2 N - - N SINE - 1 0 1 7 0.299953422716903 0.699891319672773 0.699891319672773 0.299953422716903 2 - - 11778 N N 3.49065421516983 3.51423587000429 3.49065421516983 0 0 0.309111111142874 N 0 0 N N 3816 252027 ENSG00000107262 ENSG00000141738 + + 9 17 33254737 35157070 utr3p intron BAG1 GRB7 33244163 35147713 - + 0 33244240 35153499 - + Y - 0.802196664093379 N HCC1954 31 29.3333333333333 23 6 1 N - - N SINE SINE 1 0.478260869565217 1 6 0.278528178237124 0.328520415356608 0.328520415356608 0.278528178237124 1 - 0 44268 N N 3.18615440274303 3.39487633072086 3.18615440274303 0 0 0.246876340170399 N 0 0 N N 0 85100 ENSG00000218380 ENSG00000148303 + + 10 9 33387341 135208102 downstream coding RPL7AP53 RPL7A 33386549 135204890 - + 0 33386530 135208030 - + Y - - N HCC1954 11 4.66666666666667 3 15 1 N - - N - - 0 0 0 15 0.257102933757345 0.478497126715059 0.478497126715059 0.257102933757345 1 - - 7258 Y Y 3.62464976567696 3.66016945000958 3.62464976567696 0 0 0.0931773480642738 Y 0.979479161577173 0.979479161577173 N N 1872 2755 ENSG00000172965 ENSG00000153094 + + 2 2 111969088 111642493 downstream downstream AC068491.4 BCL2L11 111903370 111594962 - + 0 111818108 111714018 - + N - - N HCC1954 2 2 2 8 2 N - - Y LINE SINE 1 0.950819672131147 1 8 0.699891319672773 0.871293275511003 0.871293275511003 0.699891319672773 1 - - 7207 Y Y 3.6988816296077 3.61936062564813 3.61936062564813 267 0 0.0977937783715292 Y 0.731011235955056 0.990037453183521 N N 0 2365 ENSG00000201876 ENSG00000114956 + + 2 2 74048832 74039596 upstream intron 5S_rRNA DGUOK 74048741 74007461 - + 0 74061743 74028569 - + N - 0.693655441400304 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.635615586233437 0.671324327033068 0.671324327033068 0.635615586233437 1 - 0 29723 N N 3.59528445727371 3.78436848759686 3.59528445727371 0 0 0.348899535590259 Y 0 0 N N 3755 48732 ENSG00000204387 ENSG00000204389 - + 6 6 31915520 31893702 coding downstream C6orf48 HSPA1A 31910383 31891299 + + 0 31913014 31897985 - + N - - N HCC1954 1 1 1 0 2 N - - N SINE - 0.392156862745098 0 0.392156862745098 5 0.828442786551446 0.664182578873142 0.828442786551446 0.664182578873142 2 - - 3142 N Y 3.26824964015148 3.50000108636471 3.26824964015148 24 0 0.342017882759330 N 0.985559378584089 0.949457825044312 N N 8014 1814 ENSG00000149084 ENSG00000178229 - + 11 19 43834736 62533956 utr3p utr3p HSD17B12 ZNF543 43658719 62523689 + + 0.0324783651339797 43834016 62532991 - + Y - - N HCC1954 108 50.5135135135135 2 74 1 N - - N - SINE 0 1 1 74 0.985561246069823 0.899860268150708 0.985561246069823 0.899860268150708 2 - - 28975 N N 3.47336426491055 3.44040523365767 3.44040523365767 8 0.0215010141987828 0.109619398946765 N 0.445030425963489 0.649492900608519 N N 16390 3591 ENSG00000140950 ENSG00000145725 - + 16 5 83095794 102566806 utr5p downstream KIAA1609 HISPPD1 83068608 102483867 - + 0 83089218 102579128 + + Y - - N HCC1954 2 1.25 1 1 1 N - - N - SINE 0 1 1 4 0.392796148795944 0.299953422716903 0.392796148795944 0.299953422716903 2 - - 42478 Y Y 3.59524460448036 2.7614461108465 2.7614461108465 0 0 0.90637380543172 Y 0.994936676408758 0.989873352817515 N N 3011 0 ENSG00000018189 ENSG00000207058 - - 4 4 71891789 71787704 coding upstream RIPX U6 71806560 71787599 + - 0.746833820437881 71847100 71789875 - + N - - N HCC1954 2 1.01075268817204 1 1 2 N - - Y - Simple_repeat 0 0.142857142857143 0.142857142857143 93 1.42834963198525 1.44977487646503 1.44977487646503 1.42834963198525 4 - - 19153 Y Y 3.50529022639353 3.23892418454158 3.23892418454158 2 0.00411522633744865 0.907763694305548 Y 0.0315248990070601 0.990863442443463 N N 1166 27007 ENSG00000154198 ENSG00000142973 + + 1 1 47138734 47057605 intron coding CYP4Z2P CYP4B1 47096493 47037257 - + 0 47107089 47056417 - + N 0.197481874237702 - N HCC1954 3 1.28571428571429 1 1 4 N - - Y LINE - 1 0 1 7 0.771308801272036 1.04269523134923 1.04269523134923 0.771308801272036 2 0 - 30547 Y Y 3.68577320169385 3.61041498203738 3.61041498203738 0 0 0.473286731561678 Y 0 0 N N 0 10286 ENSG00000215197 ENSG00000130119 - + X X 54715796 54608698 upstream utr3p AL109854.10 GNL3L 54715144 54570464 + + 0 54663893 54603790 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 0.777142857142857 0 0.777142857142857 7 1.19267194270768 1.15696320190805 1.19267194270768 1.15696320190805 2 - - 18978 Y Y 3.55231620741665 2.78417194111826 2.78417194111826 325 0 0.0133815533332072 Y 0 0 N N 24548 0 ENSG00000134369 ENSG00000218820 - + 1 1 200062720 199756301 upstream downstream NAV1 RP11-134G8.6 199859224 199755807 + + 0 199858605 199775094 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 1.1426797055882 0.999844742389676 1.1426797055882 0.999844742389676 1 - - 26671 Y Y 3.42208221362849 3.2274272354209 3.2274272354209 248 0 0.0501639897593305 Y 0.0148579943899018 0 N N 2486 2586 ENSG00000121281 ENSG00000121274 - + 16 16 48909547 48826722 intron downstream ADCY7 PAPD5 48857979 48745280 + + 0 48879320 48837045 - + N 0.043160209968589 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.585623349113953 0.628473838073511 0.628473838073511 0.585623349113953 1 0 - 7293 Y Y 3.62464976567696 3.51679652308403 3.51679652308403 0 0 0.326965347104327 Y 0 0 N N 0 0 ENSG00000216666 ENSG00000176320 - + 2 2 220271180 220258976 downstream downstream AC009502.2 AC009502.4 220270765 220258486 + + 0 220367036 220261546 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.435646637755502 0.692749571512847 0.692749571512847 0.435646637755502 2 - - 29244 Y Y 3.58271458558979 3.2274272354209 3.2274272354209 157 0 0.0500158068300514 Y 0 0 N N 0 4260 ENSG00000218893 ENSG00000078401 - + 6 6 12427810 12404286 upstream downstream RP3-451B15.3 EDN1 12427671 12398599 + + 0 12419439 12404649 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.542772860154395 0.764167053112109 0.764167053112109 0.542772860154395 1 - - 14821 N N 3.36617336972692 3.54975555433691 3.36617336972692 2 0 0.135791154056141 N 0 0 N N 0 36874 ENSG00000212574 ENSG00000198830 - + 11 1 13596333 26675021 upstream utr3p 5S_rRNA HMGN2 13596227 26671533 + + 0 13587894 26674907 - + Y - - N HCC1954 14 12.25 9 4 1 N 539 24.7785 N - - 0 0 0 4 0.257102933757345 0.292811674556976 0.292811674556976 0.257102933757345 0 - - 42441 N N 3.61720120015252 3.64656650855576 3.61720120015252 0 0 0.44096190322431 N 0 0 Y N 3267 5930 ENSG00000145431 ENSG00000109572 + + 4 4 158111996 170878731 intron coding PDGFC CLCN3 157902214 170778297 - + 0 158038330 170848376 - + N 1.31966527208313 - N HCC1954 1 1 1 0 1 N 207 5.76162 N LINE - 0.23972602739726 0 0.23972602739726 17 1.02841173502938 1.10697096478857 1.10697096478857 1.02841173502938 1 0 - 30612 Y Y 3.34256120966892 3.14528279764928 3.14528279764928 0 0.0036496350364964 0.544381101884755 Y 0.0036496350364964 0.984184914841849 N N 294 1934 ENSG00000147003 ENSG00000186312 - - X X 15593075 15631393 utr5p intron TMEM27 CA5BP 15555372 15602976 - + 0 15592833 15603085 + - N - 0.0419537976485248 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.799875793911741 0.51420586751469 0.799875793911741 0.51420586751469 1 - 0 45418 N Y 3.3828009725769 3.27394935533424 3.27394935533424 0 0 0.345657119178785 N 0.566019197339581 0.901367999395359 N N 167 12443 ENSG00000197462 ENSG00000107798 - - 5 10 121842681 91164294 utr5p intron AC022101.4 LIPA 121800093 90963306 - - 0.901367999395359 121842610 91033626 + + Y - 218.56764930222 N HCC1954 22 21.5 21 6 1 N - - N LTR - 1 0 1 6 0.328520415356608 0.471355378555133 0.471355378555133 0.328520415356608 2 - 0 4690 Y Y 3.76273355257368 3.46704205511183 3.46704205511183 218 0.327044837834346 0.00466234442779567 Y 0.425184132316837 0.957940302364647 N N 3838 0 ENSG00000154710 ENSG00000203446 - - 7 7 65913881 65814279 utr5p upstream RABGEF1 AC027644.9 65843078 65814003 + - 0 65843214 65814611 - + N - - N HCC1954 2 2 2 5 1 N - - Y - LINE 0 1 1 5 0.628473838073511 0.685607823352921 0.685607823352921 0.628473838073511 1 - - 31182 Y Y 2.92342193653406 3.57489529770476 2.92342193653406 225 0 0.142868491892376 Y 0 0.988423772609819 N N 2481 3 ENSG00000158092 ENSG00000168917 - + 3 3 138150657 138057422 upstream intron NCK1 TMEM22 138063763 138020551 + + 0 138063292 138044139 - + N - 0.87027027027027 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 21 0.807017542071667 0.764167053112109 0.807017542071667 0.764167053112109 2 - 0 31302 Y Y 3.37295958784206 3.25141011783948 3.25141011783948 422 0 0.00143461629688124 Y 0 0.994395335214868 N N 1801 1178 ENSG00000113851 ENSG00000072756 + + 3 3 3196390 3165702 utr3p downstream CRBN TRNT1 3166698 3143600 - + 0.994395335214868 3167238 3166048 - + N 0.343971306520385 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.956994253430118 0.835584534711372 0.956994253430118 0.835584534711372 1 0 - 9379 Y Y 3.71041843152174 3.59697987445291 3.59697987445291 370 0 0.00261114781791916 Y 0 0.881056285643442 N N 2256 34343 ENSG00000011258 ENSG00000011052 + + 17 17 46692426 46604104 intron intron MBTD1 NME1-NME2 46609785 46585919 - + 0 46613442 46602561 - + N 0.635653353038152 0.422855616204492 N HCC1954 30 5.7 1 10 2 N - - Y SINE - 1 0 1 20 0.778450549431962 0.799875793911741 0.799875793911741 0.778450549431962 1 0 0 45601 N Y 2.25162916738782 3.17663969767881 2.25162916738782 58 0.157635467980296 0.0198534890581001 N 0.0172413793103446 0.578817733990148 N N 0 1582 ENSG00000182225 ENSG00000185917 + + 19 21 5527949 36373557 downstream utr5p AC011533.6 SETD4 5527671 36328709 - - 0.719211822660099 5518780 36353667 - - Y - - N HCC1954 38 36.5 36 4 1 N 216 22.531 N - SINE 0 1 1 4 0.371370904316165 0.271386430077198 0.371370904316165 0.271386430077198 1 - - 33087 N N 3.44719145177281 3.68953475841283 3.44719145177281 0 0 0.230820054132577 N 0 0 Y N 171855 59837 ENSG00000198886 ENSG00000198695 - - MT MT 12138 14674 coding coding MT-ND4 MT-ND6 10761 14150 + - 0 11115 14471 - + N 0.697581465041473 1.36591048969754 N HCC1954 1 1 1 0 2 N 189 4.09957 N - - 0 0 0 4 0.699891319672773 0.956994253430118 0.956994253430118 0.699891319672773 1 0 0 42072 N N 3.37192651807217 3.66745018166468 3.37192651807217 0 0 0.987095832664728 N 0 0 N N 29840 61 ENSG00000164830 ENSG00000038295 + + 8 4 107834093 167244443 coding upstream OXR1 TLL1 107739270 167013860 + + 0 107827193 166939322 + + Y - - N HCC1954 8 1.86363636363636 1 9 4 N - - N - LTR 0 1 1 22 1.28551466878673 1.21409718718746 1.28551466878673 1.21409718718746 1 - - 44433 N N 3.26720299001245 3.53209488171704 3.26720299001245 7 0.513353603418522 0.0581306655712582 N 0 0 N N 38799 1 ENSG00000187446 ENSG00000048740 + + 15 10 39361377 11509495 coding intron AC012652.1 CUGBP2 39310729 11099933 + + 0.0151203878708193 39350050 11499018 + + Y - 1.00975874220656 N HCC1954 40 36.2 21 5 1 N - - N - SINE 0 1 1 5 0.507064119354764 0.392796148795944 0.507064119354764 0.392796148795944 2 - 0 11904 N Y 2.99252314673551 3.43408302385895 2.99252314673551 5 0 0.238535411670003 N 0.893309222423146 0.928872814948764 N N 313916 0 ENSG00000131748 ENSG00000217982 - - 17 9 35073248 87937586 utr5p upstream STARD3 RP11-379P1.4 35046938 87937386 + + 0 35047008 87930932 - - Y - - N HCC1954 15 4.5 1 1 1 N - - N - SINE 0 1 1 4 0.849868031031224 0.264244681917271 0.849868031031224 0.264244681917271 2 - - 17357 Y Y 3.34785034969775 3.41592783769912 3.34785034969775 0 0 0.906915529316062 Y 0 0.99176327028676 N Y 95 4210 ENSG00000204219 ENSG00000088280 - + 1 1 23623848 23683285 coding coding TCEA3 ASAP3 23579510 23627643 - - 0 23618219 23630115 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 5 0.671324327033068 0.99270299422975 0.99270299422975 0.671324327033068 4 - - 42444 Y Y 2.94694081063622 3.39809933120991 2.94694081063622 227 0.0184277470993364 0.0825709616669812 Y 0.116584972389402 0.985977539244276 N N 95 7918 ENSG00000168993 ENSG00000185619 + + 4 4 809945 754428 downstream utr3p CPLX1 PCGF3 768746 689573 - + 0 765562 751405 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.392796148795944 0.871293275511003 0.871293275511003 0.392796148795944 1 - - 25498 N N 3.63552422018169 3.26194435520716 3.26194435520716 0 0 0.0685158563778258 N 0.00487804878048859 0 N N 551733 8733 ENSG00000204628 ENSG00000136153 + + 5 13 180603512 75343063 utr3p intron GNB2L1 LMO7 180596536 75092571 - + 0 180596563 75156660 - + Y - 0.0780802868329501 N HCC1954 20 12.1666666666667 2 6 1 N - - N - SINE,Low_complexity 0 0.611111111111111 0.611111111111111 6 0.714174815992626 0.257102933757345 0.714174815992626 0.257102933757345 1 - 0 34354 Y Y 3.27401971335113 3.62192127872787 3.27401971335113 239 0.0494484594903004 0.191111931171017 Y 0.932103461392164 0.988683910232028 N N 329 1173 ENSG00000218011 ENSG00000182150 - + 9 9 97774767 97770942 upstream coding AL159167.23-1 C9orf102 97772706 97677721 + + 0 97772677 97768815 - + N - 20.7840809184044 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 20 0.635615586233437 0.871293275511003 0.871293275511003 0.635615586233437 2 - 0 16625 N N 3.70256863841317 3.2948728812365 3.2948728812365 0 0 0.163113092617326 N 0 0 N N 42814 0 ENSG00000170315 ENSG00000212678 - - 17 1 16226779 560165 utr5p intron UBB RP5-857K21.11 16225092 559619 + + 0 16225941 559627 - - Y 0.424110856726413 1 N HCC1954 10 4 2 4 1 N 5 21.1711 N - - 0 0 0 4 0.742741808632331 0.278528178237124 0.742741808632331 0.278528178237124 2 0 0 34624 Y Y 3.19806192701765 3.63552422018169 3.19806192701765 322 0.408984028393966 0.390796590406355 Y 0.992879325643301 0.985758651286602 N N 11502 0 ENSG00000159921 ENSG00000222760 - - 9 9 36248450 36257919 utr5p downstream GNE U4 36204430 36257780 - + 0 36239394 36266891 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 453 1.29265641694665 1.03555348318931 1.29265641694665 1.03555348318931 4 - - 26597 Y N 3.68680627146374 3.47336426491055 3.47336426491055 0 0 0.778685365331522 N 0 0.00373134328358204 Y Y 9011 12607 ENSG00000157349 ENSG00000168872 - + 16 16 68925230 68964780 coding coding DDX19B DDX19A 68890573 68938322 + + 0.00373134328358204 68915989 68938452 - + N 0.692606555721075 0.40799316679032 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 64 0.764167053112109 0.914143764470561 0.914143764470561 0.764167053112109 4 0 0 31901 Y Y 3.56807857436608 3.17511211436895 3.17511211436895 99 0 0.295626547993516 Y 0 0.960114613180516 N N 8254 0 ENSG00000163812 ENSG00000188990 + - 3 3 44992618 44935005 coding intron ZDHHC3 AC098649.2-2 44941663 44934497 - - 0 44945926 44934641 - + N - 1 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.692749571512847 0.99270299422975 0.99270299422975 0.692749571512847 3 - 0 18692 N Y 3.60103760561896 3.57336771439491 3.57336771439491 0 0 0.0441327169480081 Y 0 0 N N 157 27007 ENSG00000186377 ENSG00000142973 - + 1 1 47289009 47057605 intron intron CYP4X1 CYP4B1 47261827 47037257 + + 0 47268193 47053530 - + N 0.138510119133056 1.33814267267642 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.964136001590045 0.99270299422975 0.99270299422975 0.964136001590045 0 0 0 32473 N Y 3.32423818963975 2.98511443400441 2.98511443400441 2 0 0.051588403965609 N 0.760210803689065 0.898550724637681 N N 4514 1 ENSG00000186329 ENSG00000132554 - - 3 8 173059802 101187520 utr3p intron TMEM212 RGS22 173043844 101042452 + - 0.870882740447958 173058907 101052824 - + Y - 0.980987589120676 N HCC1954 420 382.2 336 5 1 N - - N LINE,LINE LINE 1 1 1 5 0.349945659836387 0.292811674556976 0.349945659836387 0.292811674556976 1 - 0 31638 Y Y 3.24831090852981 3.1923087786724 3.1923087786724 0 0 0.966843989521294 Y 0.699636491557223 0.993609287054409 N Y 139 298 ENSG00000206552 ENSG00000182983 - + 3 3 42959283 42933958 utr5p coding C3orf41 ZNF662 42952856 42922406 + + 0 42955346 42925405 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 26 1.22123893534739 1.1426797055882 1.22123893534739 1.1426797055882 4 - - 6264 N N 3.12808613334584 2.95222995066504 2.95222995066504 0 0 0.558369235631781 N 0 0 N N 0 131026 ENSG00000213212 ENSG00000115053 + + 9 2 138829812 232037449 intron coding AL355987.31-1 NCL 138827058 232027706 - - 0 138829274 232033807 - - Y 1 - N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.685714285714286 0.685714285714286 14 0.264244681917271 0.749883556792257 0.749883556792257 0.264244681917271 3 0 - 29091 Y Y 3.16406982599488 3.43784458057793 3.16406982599488 106 0.00283286118980164 0.276653870228606 Y 0.624255860738186 0.985548302336084 N N 2056 0 ENSG00000203875 ENSG00000220563 + - 6 6 86445157 86427043 utr3p upstream AL355615.12-1 RP11-33E24.1 86443521 86426329 - - 0 86443530 86432584 - + N - - N HCC1954 7 3 1 3 1 N - - Y - SINE,DNA 0 0.736434108527132 0.736434108527132 4 1.01412823870953 0.699891319672773 1.01412823870953 0.699891319672773 4 - - 38159 Y Y 3.56228557322748 3.47080361183081 3.47080361183081 276 0 0.422165180314388 Y 0 0 N N 13117 13719 ENSG00000131981 ENSG00000168175 - + 14 14 54681874 54606665 upstream downstream LGALS3 MAPK1IP1L 54665574 54588110 + + 0 54639601 54631093 - + N - - N HCC1954 13 2.7 1 8 2 N - - Y - SINE,SINE 0 0.905172413793103 0.905172413793103 20 1.07126222398894 0.828442786551446 1.07126222398894 0.828442786551446 4 - - 36903 N Y 3.41741556821562 3.43142908482337 3.41741556821562 12 0 0.349898522744915 N 0.96015873015873 0.950198412698413 N N 319 871 ENSG00000166415 ENSG00000084453 - + 15 12 51842367 21439638 coding utr5p WDR72 SLCO1A2 51593230 21311651 - - 0 51602811 21439242 + - Y - - N HCC1954 24 22.75 21 4 1 N - - N - LINE,LINE 0 1 1 4 0.635615586233437 0.642757334393363 0.642757334393363 0.635615586233437 4 - - 20678 N Y 3.57336771439491 3.56385300933068 3.56385300933068 129 0 0.0494876772383502 N 0.761826086956522 0.761826086956522 N N 17904 8040 ENSG00000180198 ENSG00000147050 + + 1 X 28738194 44856787 intron intron RCC1 UTX 28705083 44617415 + + 0.761826086956522 28708488 44637063 + + Y 0.216232454679464 0.346702723102934 N HCC1954 2 2 2 7 1 N - - N - SINE 0 1 1 7 0.39993789695587 0.271386430077198 0.39993789695587 0.271386430077198 1 0 0 29924 N Y 3.48912663185998 3.4210491438586 3.4210491438586 2 0 0.0172217932776866 N 0 0.931433127366952 N N 6539 0 ENSG00000009413 ENSG00000183171 - - 6 X 111911125 149035415 coding upstream REV3L BX322650.2 111726927 149033269 - + 0.0914889376121187 111736102 149024054 + - Y - - N HCC1954 620 590 500 4 1 N - - N LINE LINE 1 1 1 4 0.335662163516534 0.321378667196682 0.335662163516534 0.321378667196682 1 - - 401 Y Y 2.97892020528169 3.53312795148693 2.97892020528169 121 0.0103664192949907 0.99906468896258 Y 0.0103664192949907 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.985760667903525 1816182 1814667 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 28 1.02841173502938 1.02126998686945 1.02841173502938 1.02126998686945 4 - - 36792 Y Y 3.59697987445291 3.36720643949681 3.36720643949681 0 0 0.276478099279869 Y 0 0.983417508417508 N N 408 9 ENSG00000134285 ENSG00000139537 + + 12 12 47605555 47611527 coding upstream FKBP11 CCDC65 47602019 47584187 - + 0 47604274 47583959 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.588607594936709 0.588607594936709 4 0.864151527351077 0.842726282871298 0.864151527351077 0.842726282871298 1 - - 40275 N Y 3.46720988898117 3.10910076590736 3.10910076590736 8 0 0.053909699695657 N 0 0.872988077496274 N N 86504 2684 ENSG00000104408 ENSG00000140199 + + 8 15 109330135 32417557 coding utr3p EIF3E SLC12A6 109283149 32309489 - - 0 109321447 32311167 - - Y - - N HCC1954 36 32.5 30 8 1 N - - N - SINE,SINE 0 1 1 8 0.385654400636018 0.385654400636018 0.385654400636018 0.385654400636018 1 - - 36191 Y Y 3.48015048302568 3.2557196212609 3.2557196212609 293 0 0.142543521245381 Y 0.967590665667749 0.991897666416937 N N 2401 16105 ENSG00000120647 ENSG00000073614 - - 12 12 422065 368881 coding upstream CCDC77 JARID1A 381084 259484 + - 0 391175 368955 - + N 0.792812670022485 - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 9 0.707033067832699 0.849868031031224 0.849868031031224 0.707033067832699 1 0 - 186 Y Y 3.38080938095063 3.61530289448208 3.38080938095063 229 0 0.0167002389230253 Y 0 0.98636118920859 N N 36582 1289 ENSG00000177600 ENSG00000177595 - - 11 11 802876 795245 upstream upstream RPLP2 LRDD 799936 789180 + - 0 799396 796025 - + N - - N HCC1954 20 11.875 2 8 2 N - - Y - SINE 0 1 1 8 0.742741808632331 0.828442786551446 0.828442786551446 0.742741808632331 1 - - 37030 N Y 3.63399663687184 3.60103760561896 3.60103760561896 0 0 0.831473685969074 N 0 0.946756409204082 N N 871 27 ENSG00000084453 ENSG00000164749 + + 12 8 21439638 76641600 utr5p upstream SLCO1A2 HNF4G 21311651 76482732 - + 0 21439215 76388528 - + Y - - N HCC1954 23 22.125 20 16 2 N - - N LINE,LINE LTR 1 1 1 16 0.664182578873142 1.12125446110842 1.12125446110842 0.664182578873142 0 - - 35359 N N 3.16775167712715 3.73233517440054 3.16775167712715 1 0 0.0746722785059636 N 0 0 N N 1123 1649619 ENSG00000111785 ENSG00000141736 - + 12 17 105807215 35138441 downstream coding RIC8B ERBB2 105692529 35104766 + + 0 105834192 35122165 - + Y - - N HCC1954 10 1.38888888888889 1 5 1 N 436 18.8518 N SINE - 1 0 1 36 0.328520415356608 0.799875793911741 0.799875793911741 0.328520415356608 2 - - 19604 N Y 3.73808832274579 3.24893340314576 3.24893340314576 2 0 0.884430418134587 N 0.449741147235452 0.975812797680679 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0.975812797680679 109336418 45272639 - - Y - - N HCC1954 8 5.23404255319149 3 94 2 N - - N - - 0 0 0 94 0.87843502367093 0.578481600954027 0.87843502367093 0.578481600954027 3 - - 36233 Y Y 3.46145674063593 3.2468138304435 3.2468138304435 275 0 0.0161828936721633 Y 0.971532467532468 0.990510822510822 N N 4116 4803 ENSG00000139579 ENSG00000181852 - - 12 12 54909905 54901971 utr5p upstream OBFC2B RNF41 54904410 54884555 + - 0 54904883 54902248 - + N 0.204000412823632 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.599906845433805 0.821301038391519 0.821301038391519 0.599906845433805 2 0 - 41693 Y Y 3.56232542602083 3.26001554431319 3.26001554431319 174 0 0.148630946776507 Y 0.0509404388714735 0 N N 1097 1486 ENSG00000221850 ENSG00000181638 - + 8 8 144430474 144416250 coding intron GLI4 ZFP41 144420982 144400484 + + 0 144428259 144404790 - + N 0.948611770571083 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.799875793911741 0.928427260790413 0.928427260790413 0.799875793911741 2 0 - 3000 N N 3.65384724021086 3.5010341561346 3.5010341561346 0 0 0.120861227372837 N 0 0 N N 3701 40617 ENSG00000132256 ENSG00000130164 - + 11 19 5850164 11105490 utr3p utr3p TRIM5 LDLR 5623164 11061132 - + 0 5641774 11104135 + + Y - 2.27267372255859 N HCC1954 40 38.5 35 4 1 N - - N SINE SINE 1 0.2 1 4 0.349945659836387 0.392796148795944 0.392796148795944 0.349945659836387 3 - 0 11708 N Y 3.54040868314203 3.03123532633363 3.03123532633363 0 0 0.169915312004809 N 0 0.601388888888889 N N 0 313916 ENSG00000217982 ENSG00000131748 + + 9 17 87937586 35073248 upstream intron RP11-379P1.4 STARD3 87937386 35046938 + + 0 87930953 35047120 + + Y - 1.09830374749134 N HCC1954 3 2.25 1 3 1 N - - N SINE - 1 0 1 4 0.257102933757345 0.614190341753658 0.614190341753658 0.257102933757345 2 - 0 31610 Y Y 3.61616813038263 2.7386201102425 2.7386201102425 117 0 0.423228401541008 Y 0.717544203771681 0.976462016980974 N N 20663 0 ENSG00000133657 ENSG00000198579 - + 3 3 195670257 195703392 utr5p downstream ATP13A3 AC108676.8 195604698 195700704 - - 0 195664253 195688585 + - N - - N HCC1954 2 1.00581395348837 1 1 4 N - - Y - Simple_repeat 0 0.870503597122302 0.870503597122302 172 1.09268746846872 0.99270299422975 1.09268746846872 0.99270299422975 2 - - 30618 N Y 3.65488030998075 3.60426060610801 3.60426060610801 5 0.0160994890581315 0.297292569465796 Y 0.0160994890581315 0.914971560782802 N N 650 0 ENSG00000170965 ENSG00000199920 - + X X 133620179 133722044 utr5p upstream PLAC1 U4 133527539 133721904 - - 0 133563758 133725942 + - N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 77 1.67831081758267 0.749883556792257 1.67831081758267 0.749883556792257 1 - - 6729 Y Y 2.93760751981047 3.39743698380061 2.93760751981047 0 0 0.930314053405287 Y 0.993484477124183 0.980453431372549 N N 676 2952 ENSG00000144401 ENSG00000118260 + + 2 2 208198276 208171806 coding intron FAM119A CREB1 208185086 208102917 - + 0 208186412 208155128 - + N - 3.86540137913076 N HCC1954 1 1 1 0 3 N - - Y - LINE 0 1 1 14 1.19267194270768 1.15696320190805 1.19267194270768 1.15696320190805 1 - 0 46932 Y Y 3.0218486023454 3.24421332457041 3.0218486023454 265 0 0.0653781518925508 Y 0 0 N N 2494 9856 ENSG00000142235 ENSG00000105443 + + 19 19 53708258 53674457 downstream downstream LMTK3 CYTH2 53680340 53664420 - + 0.991965916007304 53677490 53676315 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR LINE,LINE 1 1 1 7 0.792734045751814 0.749883556792257 0.792734045751814 0.749883556792257 2 - - 31294 Y Y 3.65913638023969 3.11854092305808 3.11854092305808 348 0 0.00244309765665429 Y 0 0 N N 46598 6318 ENSG00000118849 ENSG00000168827 + + 3 3 159932969 159893055 utr3p downstream RARRES1 GFM1 159897597 159845011 - + 0 159898161 159893123 - + N 0.383019800662145 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.1141127129485 0.635615586233437 1.1141127129485 0.635615586233437 1 0 - 2978 N Y 3.64759957832565 3.26001554431319 3.26001554431319 7 0 0.304955876175574 N 0.915815503709278 0.929846253091066 N N 290 3567 ENSG00000142405 ENSG00000177951 - - 19 11 59019460 197428 utr3p intron NALP12 BET1L 58988669 157784 - - 0 58988785 170412 + + Y - 2.87394543524002 N HCC1954 148 142 136 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.364229156156239 0.364229156156239 0.28566992639705 2 - 0 6492 N Y 3.57489529770476 3.42680229220385 3.42680229220385 0 0 0.0545824878031211 Y 0 0 N N 845 3 ENSG00000136689 ENSG00000136697 - + 2 2 113608063 113549896 utr5p downstream IL1RN IL1F10 113585164 113542018 + + 0 113585180 113552207 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE LINE 0.62406015037594 1 1 6 0.942710757110266 0.771308801272036 0.942710757110266 0.771308801272036 0 - - 37768 N Y 3.56658149627977 3.62088820895798 3.56658149627977 0 0 0.108469927332500 N 0 0.825932417956958 N N 46 0 ENSG00000214689 ENSG00000207444 - - 16 14 30219562 70934877 coding upstream AC106782.5-1 SNORD56 30202839 70934807 + + 0 30216682 70858063 - - Y - - N HCC1954 31 29.5 27 4 1 N 101 20.1562 N SINE - 1 0 1 4 0.264244681917271 0.385654400636018 0.385654400636018 0.264244681917271 2 - - 44519 N N 3.3828009725769 3.52783881145811 3.3828009725769 0 0 0.0716607013323046 N 0.00247524752475259 0 N N 906 86504 ENSG00000148814 ENSG00000104408 + + 10 8 134109058 109330135 utr3p coding LRRC27 EIF3E 133995648 109283149 + - 0 134041541 109321449 + - Y - - N HCC1954 40 36.25 35 4 1 N - - N SINE - 1 0 1 4 0.542772860154395 0.328520415356608 0.542772860154395 0.328520415356608 2 - - 31492 Y Y 3.33151892129485 3.25566618809842 3.25566618809842 270 0 0.00869605411455843 Y 0.932070707070707 0.992452300785634 N N 0 95 ENSG00000207650 ENSG00000215837 - + 3 3 196911548 196900773 upstream downstream hsa-mir-570 AC069513.28-2 196911452 196900191 + + 0 196911082 196900850 - + N - - N HCC1954 4 3 2 10 2 N - - Y LTR LINE 0.328467153284672 0.923076923076923 0.923076923076923 10 0.835584534711372 0.892718519990782 0.892718519990782 0.835584534711372 1 - - 41832 N Y 3.34256120966892 3.43039601505348 3.34256120966892 0 0 0.115285221863302 Y 0 0 N N 14395 418 ENSG00000104687 ENSG00000104691 - - 8 8 30704894 30744064 coding upstream GSR UBXN8 30655126 30721232 - + 0 30686892 30721152 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.807017542071667 0.421363141435649 0.807017542071667 0.421363141435649 2 - - 30804 N Y 3.70822850080258 2.71207657474418 2.71207657474418 270 0 0.077894470984584 N 0 0.873486184597296 N N 0 4873 ENSG00000218564 ENSG00000130021 + - Y X 16077348 7076189 upstream upstream AC006998.1 HDHD1A 15969936 6976961 - - 0 16099169 7076234 - + Y - - N HCC1954 2 1.57142857142857 1 4 2 N - - N - - 0 0 0 7 0.357087407996313 0.578481600954027 0.578481600954027 0.357087407996313 4 - - 47635 N N 2.2823895267752 3.84168549507978 2.2823895267752 0 0 0.733606296972629 N 0 0 N N 29248 1021 ENSG00000105738 ENSG00000028277 + - 19 19 43390849 47328470 intron upstream SIPA1L3 POU2F2 43089708 47284515 + - 0 43115295 47356353 + + N 0.361292069306371 - Y HCC1954 1 1 1 0 3 N 330 6.24336 N - - 0 0 0 4 0.528489363834543 0.34280391167646 0.528489363834543 0.34280391167646 3 0 - 30622 Y Y 3.4561676006071 3.11547640886856 3.11547640886856 0 0 0.648754958151285 Y 0 0 N N 1195 0 ENSG00000173681 ENSG00000206663 - + X X 19898337 19913198 utr5p upstream CXorf23 Y_RNA 19841403 19913097 - - 0 19898337 19918741 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.599906845433805 0.721316564152552 0.721316564152552 0.599906845433805 4 - - 3561 N N 3.45504124488137 3.54296933622177 3.45504124488137 0 0 0.992163432141556 N 0 0 N N 7284 5889 ENSG00000156299 ENSG00000198862 + + 21 21 31853161 29287141 coding coding TIAM1 RNF160 31412607 29222337 - - 0 31520035 29275313 - - N 0.626867192030515 - Y HCC1954 1 1 1 0 4 N 566 1.62267 N - - 0 0 0 4 0.871293275511003 0.714174815992626 0.871293275511003 0.714174815992626 1 0 - 33060 N Y 3.13999365762046 2.93868044237372 2.93868044237372 520 0.00624375624375628 0.864209295975502 Y 0.00192307692307703 0.995679320679321 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8502 5412 - + N 0.58925071454747 1.1781446307412 N HCC1954 4 2.33333333333333 1 5 9 Y - - N - - 0 0 0 6 0.956994253430118 1.06412047582901 1.06412047582901 0.956994253430118 1 0 0 4607 Y Y 3.33164690237084 3.0756913067072 3.0756913067072 274 0 0.0726001235205775 Y 0.00364963503649629 0 N N 650 4345 ENSG00000175873 ENSG00000136213 - + 7 7 2454008 2440740 utr5p intron AC004840.4 CHST12 2443924 2274908 + + 0 2443962 2440204 - + N 0.0730086443387476 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.721316564152552 1.22123893534739 1.22123893534739 0.721316564152552 2 0 - 26770 Y Y 3.50425715662364 3.58743466416515 3.50425715662364 255 0 0.0304126294320981 Y 0.989938601703308 0.979877203406615 N N 4108 441 ENSG00000006194 ENSG00000103313 - - 16 16 3281456 3246628 upstream upstream ZNF263 MEFV 3273488 3232029 + - 0 3272472 3253884 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.163461538461538 0.163461538461538 5 0.771308801272036 0.742741808632331 0.771308801272036 0.742741808632331 4 - - 27095 N Y 3.71976530271662 3.58424216889964 3.58424216889964 0 0.692054733439233 0.498041811509115 N 0 0.956887662681493 N Y 6304 4969 ENSG00000196696 ENSG00000183793 - + 16 16 68657352 14953402 utr3p utr3p PDXDC2 AC138932.4-1 68567713 14924160 - + 0.956887662681493 68569481 14952110 + + N - - Y HCC1954 9 7 3 4 1 N 537 25.4014 N - - 0 0 0 4 0.578481600954027 0.807017542071667 0.807017542071667 0.578481600954027 2 - - 3643 N N 3.62208911259722 3.34099377356572 3.34099377356572 0 0 0.261805917656253 Y 0 0 N N 5734 6113 ENSG00000160194 ENSG00000154640 - - 21 21 43202841 17907086 coding upstream NDUFV3 BTG3 43186447 17887844 + - 0 43196384 17984012 - + N - - N HCC1954 7 2.5 1 1 2 N - - N - LINE 0 1 1 4 0.592765097273879 0.657040830713216 0.657040830713216 0.592765097273879 1 - - 46934 Y Y 3.83489927696465 3.51100352194543 3.51100352194543 295 0 0.0618746021919182 Y 0 0.992830142665529 N N 22117 95 ENSG00000073008 ENSG00000216588 - + 19 19 49858690 49831921 upstream intron PVR AC138472.5 49839066 49808780 + + 0 49838869 49827763 - + N - 0.130281681124656 N HCC1954 4 1.94444444444444 1 7 1 N - - Y SINE LTR 0.133333333333333 1 1 18 0.921285512630487 0.899860268150708 0.921285512630487 0.899860268150708 2 - 0 14206 N Y 3.63552422018169 3.67526946954971 3.63552422018169 0 0 0.104918846941537 N 0.826740764955868 0.826740764955868 N N 1806 36111 ENSG00000164199 ENSG00000099917 - + 5 22 90495789 19271918 intron coding GPR98 MED15 89890373 19191886 + + 0 90394558 19221405 - + Y 0.950193893189114 - N HCC1954 40 24 20 5 1 N - - N SINE - 1 0 1 5 0.328520415356608 0.492780623034912 0.492780623034912 0.328520415356608 1 0 - 17430 Y Y 3.24165267149067 3.28466077414108 3.24165267149067 0 0 0.0763543827936564 Y 0.994750620005511 0.994750620005511 N N 2214 7996 ENSG00000116922 ENSG00000134690 - - 1 1 37928779 37947978 utr5p upstream C1orf109 CDCA8 37919837 37930677 - + 0 37928698 37930290 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.03555348318931 1.13553795742827 1.13553795742827 1.03555348318931 1 - - 45411 N N 3.79143651356762 3.60000453584907 3.60000453584907 0 0 0.201915285620707 N 0.0951178451178452 0 N N 11413 3919 ENSG00000112877 ENSG00000150054 - + 5 10 706664 28611073 coding utr3p CEP72 MPP7 665405 28379928 + - 0 672106 28380706 - - Y - - N HCC1954 21 20.75 20 4 1 N - - N - SINE 0 1 1 4 0.364229156156239 0.278528178237124 0.364229156156239 0.278528178237124 2 - - 42562 Y Y 3.23896403733493 3.57848902055439 3.23896403733493 85 0 0.978363596498452 Y 0 0.986881033945811 N N 1615 108 ENSG00000156219 ENSG00000169248 - - 4 4 77252964 77176376 utr5p upstream ART3 CXCL11 77214887 77173975 + - 0 77216058 77194451 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 26 0.99270299422975 0.99270299422975 0.99270299422975 0.99270299422975 4 - - 27243 Y Y 3.49272035470961 3.11444333909867 3.11444333909867 0 0 0.532318640894668 Y 0 0.956091930951425 N N 1962 1644 ENSG00000140939 ENSG00000102878 - + 16 16 65767125 65761349 utr5p downstream NOL3 HSF4 65765371 65754858 + + 0 65765372 65762910 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 7 1.09982921662864 1.09268746846872 1.09982921662864 1.09268746846872 2 - - 45403 N N 2.995317129762 2.42680847320244 2.42680847320244 0 0.150085579803166 0.231112759389856 N 0.417201540436457 0 N N 20790 5996 ENSG00000099204 ENSG00000187678 - - 10 5 116434404 141684750 utr3p utr3p ABLIM1 SPRY4 116180862 141670189 - - 0.150085579803166 116184048 141671703 + + Y - - N HCC1954 36 35.2 34 5 1 N - - N Simple_repeat - 1 0 1 5 0.299953422716903 0.321378667196682 0.321378667196682 0.299953422716903 1 - - 20634 N Y 3.21535187727693 3.52105259334297 3.21535187727693 0 0.678670360110803 0.0583882061701233 N 0.778393351800554 0.662049861495845 N N 78560 0 ENSG00000112493 ENSG00000217333 - - 6 1 33390114 169680726 utr3p upstream TAPBP RP1-81F6.1 33375449 169680447 - - 0.662049861495845 33376293 169691434 + + Y - - N HCC1954 195 35.0909090909091 1 41 1 N - - N DNA,SINE SINE 0.906382978723404 0.931818181818182 0.931818181818182 44 1.12125446110842 0.314236919036755 1.12125446110842 0.314236919036755 1 - - 26128 N Y 3.68680627146374 3.07101108092519 3.07101108092519 0 0 0.103498874958093 N 0 0.805901498238158 N N 2099 1649619 ENSG00000162076 ENSG00000141736 - - 16 17 2889359 35138441 upstream coding FLYWCH2 ERBB2 2873215 35104766 + + 0 2865541 35125066 - - Y - 0.990793461175642 N HCC1954 25 20.625 20 8 1 N 311 25.8457 N SINE - 1 0 1 8 0.264244681917271 0.664182578873142 0.664182578873142 0.264244681917271 1 - 0 16404 N Y 3.29756151539224 3.48639814491089 3.29756151539224 0 0.283112900134177 0.0589246221116134 N 0.388537473643857 0.936745255894192 N N 1186 0 ENSG00000137968 ENSG00000208202 - - 1 2 75849389 172729092 coding upstream SLC44A5 AC104801.4 75440404 172729005 - - 0.177688326624497 75538944 172766327 + + Y - - N HCC1954 20 20 20 4 1 N 493 26.2585 N - LINE 0 1 1 4 0.421363141435649 0.321378667196682 0.421363141435649 0.321378667196682 2 - - 48969 Y Y 3.45976132345673 3.15359659907427 3.15359659907427 176 0 0.966911264473586 Y 0.987724466891133 0.975448933782267 N N 26477 14691 ENSG00000161011 ENSG00000161013 - - 5 5 179197681 179166547 coding upstream SQSTM1 MGAT4B 179180503 179156711 + - 0 179182564 179166729 - + N 0.46945296621819 - N HCC1954 1 1 1 0 5 N - - Y - Low_complexity 0 0.22972972972973 0.22972972972973 8 0.678466075192994 0.528489363834543 0.678466075192994 0.528489363834543 4 0 - 5087 Y Y 3.09083117904067 3.49697642496854 3.09083117904067 303 0 0.0175030185108024 Y 0.955371656568642 0.99256194276144 N N 273 0 ENSG00000214765 ENSG00000203462 + - 7 7 45771955 45731691 coding upstream AC091439.5-3 AC091439.5-2 45734299 45731307 - - 0.99256194276144 45734304 45732987 - + N - - N HCC1954 12 4.05882352941176 2 17 1 N - - Y - LTR,LTR 0 0.566265060240964 0.566265060240964 17 0.99270299422975 1.18553019454776 1.18553019454776 0.99270299422975 2 - - 49369 Y Y 3.51360402781852 3.40591861909494 3.40591861909494 0 0.0256251853316201 0.894636458467867 Y 0.992562024315509 0.992562024315509 N Y 4089 39024 ENSG00000213347 ENSG00000169223 - + 5 5 176671502 176711254 coding coding MXD3 LMAN2 176666821 176691357 - - 0 176671091 176693891 + - N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.0357142857142857 0 0.0357142857142857 4 0.792734045751814 0.749883556792257 0.792734045751814 0.749883556792257 4 - - 48533 N Y 3.46128890676658 3.45144752203174 3.45144752203174 0 0 0.301340365407395 N 0 0.868260161602507 N N 551733 2071 ENSG00000204628 ENSG00000136197 + - 5 7 180603512 42918182 coding downstream GNB2L1 C7orf25 180596536 42915399 - - 0.868260161602507 180601100 42712740 - + Y 0.953258765677636 - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.692749571512847 0.314236919036755 0.692749571512847 0.314236919036755 1 0 - 37860 N N 3.3085292558528 3.51001030496889 3.3085292558528 0 0 0.0804189762092506 N 0 0 N N 10336 8888 ENSG00000133961 ENSG00000112159 - - 14 6 72892230 90586163 utr5p intron NUMB MDN1 72811671 90409952 - - 0 72892230 90436300 + + Y - 1.91573150519183 N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 4 0.507064119354764 0.278528178237124 0.507064119354764 0.278528178237124 2 - 0 6707 N N 3.3755202409218 3.08507803069543 3.08507803069543 11 0 0.0669356488116087 N 0 0 N N 15671 4140 ENSG00000115762 ENSG00000152117 + + 2 2 131827752 131995615 utr5p utr5p PLEKHB2 AC093838.3-2 131578890 131967133 + + 0 131594352 131975535 + + N - 1.05981300116657 Y HCC1954 30 25.5714285714286 21 7 1 N - - N SINE - 1 0 1 7 0.378512652476092 0.471355378555133 0.471355378555133 0.378512652476092 2 - 0 45622 N N 3.83593234673454 3.39959640929622 3.39959640929622 6 0 0.113329584267718 N 0.56127193640318 0.37565621718914 N N 3640 350 ENSG00000197961 ENSG00000133134 + + 19 X 9556209 102452601 downstream upstream ZNF121 BEX2 9537292 102450938 - - 0 9537213 102458257 - - Y - - N HCC1954 20 14.25 3 4 1 N - - N SINE SINE 1 1 1 4 0.321378667196682 0.299953422716903 0.321378667196682 0.299953422716903 2 - - 47232 N N 3.15988830364945 3.18615440274303 3.15988830364945 9 0.127559267241379 0.115271018073171 N 0.127559267241379 0 N N 0 40756 ENSG00000167769 ENSG00000065000 + + 19 19 6284640 2102556 intron coding ACER1 AP3D1 6257627 2051993 - - 0 6261912 2065235 - - N 1 - Y HCC1954 1 1 1 0 1 N - - N SINE - 0.4 0 0.4 6 0.249961185597419 0.421363141435649 0.421363141435649 0.249961185597419 3 0 - 6340 N Y 3.47233119514066 3.58424216889964 3.47233119514066 2 0 0.0906752598294565 N 0 0.907487860976233 N N 20739 12076 ENSG00000143951 ENSG00000148219 - - 2 9 63669355 119217138 utr3p utr3p C2orf86 ASTN2 63202041 118227328 - - 0 63309485 118415266 + + Y - - N HCC1954 651 542.5 441 6 1 N - - N LINE LINE 1 1 1 6 0.385654400636018 0.299953422716903 0.385654400636018 0.299953422716903 4 - - 27805 N Y 3.56146019012029 3.19503726562149 3.19503726562149 0 0 0.0548347279427849 N 0 0.841991869918699 N N 76 0 ENSG00000166676 ENSG00000213113 - + 16 3 10820122 199332046 utr3p downstream FAM18A AC073135.3-1 10768034 199330983 - + 0.00333333333333341 10769908 199368996 + + Y - - N HCC1954 160 147.052631578947 114 19 1 N - - N SINE - 1 0 1 19 0.392796148795944 0.735600060472404 0.735600060472404 0.392796148795944 1 - - 36950 N Y 3.12804628055249 3.55334927718654 3.12804628055249 0 0 0.115727604508572 N 0 0 N N 0 0 ENSG00000149617 ENSG00000136011 + - 20 12 51925503 102684635 downstream intron AC005220.1 STAB2 51925198 102505181 - + 0 51897834 102600778 - - Y - 1 N HCC1954 20 20 20 7 1 N - - N SINE SINE 0.705128205128205 1 1 7 0.557056356474248 0.307095170876829 0.557056356474248 0.307095170876829 3 - 0 29012 N N 3.12747721909902 3.25103939547889 3.12747721909902 0 0 0.253186747792597 N 0 0 N N 551733 3 ENSG00000204628 ENSG00000175267 + + 5 16 180603512 22075775 utr3p intron GNB2L1 VWA3A 180596536 22011363 - + 0 180596544 22013356 - + Y - 0.955837252095686 N HCC1954 8 2.75 1 1 1 N - - N - - 0 0 0 4 0.714174815992626 0.271386430077198 0.714174815992626 0.271386430077198 4 - 0 2031 N Y 3.26824964015148 3.50000108636471 3.26824964015148 24 0 0.308841210320022 N 0.992830477885733 0.956982867314396 N N 8014 2601 ENSG00000149084 ENSG00000172197 - + 11 6 43834736 20320649 utr3p utr3p HSD17B12 MBOAT1 43658719 20208914 + - 0.175504956859255 43834016 20210044 - - Y 1.56799368003871 - N HCC1954 117 54.2258064516129 23 93 1 N 419 19.7725 N - SINE 0 1 1 93 1.01412823870953 1.05697872766909 1.05697872766909 1.01412823870953 2 0 - 30317 N N 3.13383928169109 3.5465630590714 3.13383928169109 0 0 0.932208714675616 Y 0.0249784048373165 0 N N 8617 441 ENSG00000221867 ENSG00000147402 - + X X 151621480 151576655 upstream upstream MAGEA6 GABRQ 151617901 151557293 + + 0 151616673 151494062 - + N - - N HCC1954 2 2 2 8 4 N - - N - LTR 0 1 1 8 0.39993789695587 1.22123893534739 1.22123893534739 0.39993789695587 2 - - 39951 Y N 3.12892803184602 3.43354865752564 3.12892803184602 0 0 0.542056549348278 Y 0 0 N N 3057 178 ENSG00000140400 ENSG00000140398 + + 15 15 73447994 73434639 downstream intron MAN2C1 NEIL1 73435186 73426463 - + 0 73435032 73430087 - + N - 0.524669707898294 N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.541463414634146 0.541463414634146 5 0.649899082553289 0.899860268150708 0.899860268150708 0.649899082553289 3 - 0 19738 N Y 3.40744620240479 3.4676111165653 3.40744620240479 0 0.641996660305344 0.0958689912187203 N 0.517473759541985 0 N N 9809 1136 ENSG00000072864 ENSG00000116678 - - 16 1 15727711 65875410 utr5p intron NDE1 LEPR 15644625 65658906 + + 0 15650756 65807925 - - Y - 0.760847506704334 N HCC1954 3 2.8 2 5 1 N - - N - SINE 0 1 1 5 0.842726282871298 0.264244681917271 0.842726282871298 0.264244681917271 2 - 0 14179 N N 3.46973068926756 3.55297855482595 3.46973068926756 0 0 0.376012677668499 N 0 0 N N 3693 28 ENSG00000198125 ENSG00000186479 + + 22 5 34349347 63943875 intron downstream MB RGS7BP 34332757 63838208 - + 0 34349155 63973774 - + Y 2.35446170667624 - N HCC1954 16 3.9375 1 15 2 N 200 25.2949 N SINE SINE 0.618556701030928 1 1 16 0.692749571512847 0.278528178237124 0.692749571512847 0.278528178237124 3 0 - 13474 N N 3.6272104187567 3.32064446679012 3.32064446679012 252 0.765639589169001 0.0117248275438026 N 0.765639589169001 0.492219109866169 N N 1157 81 ENSG00000127993 ENSG00000133424 + - 7 22 92004758 32646410 utr3p intron C7orf64 LARGE 91996023 31998847 + - 0.492219109866169 92004474 32087074 + + Y - 0.692052643815131 N HCC1954 1 1 1 0 1 N - - N SINE SINE 0.364864864864865 1 1 4 0.528489363834543 0.357087407996313 0.528489363834543 0.357087407996313 1 - 0 23292 N Y 3.36361271664718 3.61360747730289 3.36361271664718 14 0 0.0504769848402062 N 0.116071428571428 0.87593984962406 N N 14 49089 ENSG00000105641 ENSG00000117450 - - 19 1 17865897 45760196 upstream coding SLC5A5 PRDX1 17843782 45749295 + - 0.116071428571428 17841755 45757256 - + Y - 3.16366837851847 N HCC1954 21 5.64367816091954 2 87 1 N - - N SINE - 1 0 1 87 0.364229156156239 0.671324327033068 0.671324327033068 0.364229156156239 1 - 0 1651 N Y 3.17101453040955 3.38337003403037 3.17101453040955 0 0 0.650179771553722 N 0.833967046894804 0.889311364596536 N N 1649619 5698 ENSG00000141736 ENSG00000162105 - - 17 11 35138441 70536020 coding intron ERBB2 SHANK2 35104766 69991609 + - 0 35125065 70080311 - + Y - 1.10811161086291 N HCC1954 21 5.57142857142857 1 5 1 N - - N - SINE 0 1 1 7 0.564198104634174 0.249961185597419 0.564198104634174 0.249961185597419 3 - 0 13643 Y Y 3.37089344830228 3.59169073442408 3.37089344830228 283 0 0.196368954312913 Y 0.980070671378092 0.990035335689046 N N 8168 388 ENSG00000100099 ENSG00000128203 + + 22 22 25209820 25169557 coding downstream HPS4 ASPHD2 25177446 25155239 - + 0 25183827 25170662 - + N 0.321639387031053 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 29 0.799875793911741 1.29265641694665 1.29265641694665 0.799875793911741 3 0 - 34717 Y Y 3.50120199000394 3.21336028565066 3.21336028565066 236 0.00423728813559343 0.0355363828627779 Y 0.0180673258003767 0.986169962335217 N N 1561 949 ENSG00000106948 ENSG00000095397 - + 9 9 116196506 116307557 utr5p downstream AKNA DFNB31 116136257 116204181 - - 0 116183546 116200540 + - N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.0466321243523316 0 0.0466321243523316 6 0.93556900895034 0.328520415356608 0.93556900895034 0.328520415356608 1 - - 17711 N N 3.25256697878875 3.48912663185998 3.25256697878875 0 0 0.244266912781657 N 0 0 N N 49089 2080 ENSG00000117450 ENSG00000067208 - - 1 1 45760196 93030549 coding intron PRDX1 EVI5 45749295 92746841 - - 0 45757275 92875473 + + N 3.11556065904221 0.589774829039507 Y HCC1954 8 2.51428571428571 1 69 2 N - - N - SINE 0 1 1 70 0.785592297591888 0.328520415356608 0.785592297591888 0.328520415356608 2 0 0 35135 N Y 3.03589262417669 3.49744043328497 3.03589262417669 0 0 0.778511130410142 N 0.0647745358090186 0.969336870026525 N N 0 542 ENSG00000157680 ENSG00000135482 + + 7 12 137182149 54802545 intron upstream DGKI ZC3H10 136724925 54798297 - + 0.969336870026525 136849157 54796850 - + Y 1 - N HCC1954 9 7.184 2 250 1 N - - N - - 0 0 0 250 0.642757334393363 1.37835739486577 1.37835739486577 0.642757334393363 4 0 - 38448 Y Y 3.54872248456702 3.61360747730288 3.54872248456702 82 0 0.350120798095933 Y 0.628999133984906 0.985450946430781 N N 435 13440 ENSG00000133962 ENSG00000165929 - + 14 14 91268166 91372436 coding utr3p CATSPERB TC2N 91116871 91316281 - - 0 91265576 91316673 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.956994253430118 1.03555348318931 1.03555348318931 0.956994253430118 4 - - 37858 N Y 3.30128837699106 3.46977054206091 3.30128837699106 0 0 0.0853940028129536 N 0 0.716129032258064 N N 2697 1800 ENSG00000111911 ENSG00000127150 - - 6 14 126343056 103128261 utr3p coding HINT3 C14orf153 126319564 103099052 + + 0 126342561 103110260 - - Y - - N HCC1954 35 29.75 25 4 1 N - - N SINE - 1 0 1 4 0.349945659836387 0.314236919036755 0.349945659836387 0.314236919036755 1 - - 31338 N Y 3.0881772400051 3.50785087947327 3.0881772400051 311 0 0.00368721157857232 Y 0.80064308681672 0.991693461950697 N N 12648 12648 ENSG00000163939 ENSG00000163939 + - 3 3 52694892 52694892 utr5p intron PBRM1 PBRM1 52554423 52554423 - - 0 52694806 52691290 - + N 11.9163786887087 11.5398153430346 N HCC1954 1 1 1 0 1 N - - N Simple_repeat - 0.686274509803922 0 0.686274509803922 12 0.728458312312478 0.771308801272036 0.771308801272036 0.728458312312478 1 0 0 31206 Y Y 3.24103017687471 3.31166831795583 3.24103017687471 2 0 0.584186823815589 Y 0 0.984188988095238 N N 0 0 ENSG00000184531 ENSG00000213178 - - 3 3 170910252 170684502 upstream intron AC007849.24-1 AC074033.18 170909777 170684153 + - 0 170863818 170684444 - + N - 1 N HCC1954 8 3.86666666666667 2 15 1 N - - Y Low_complexity - 0.0636363636363636 0 0.0636363636363636 15 0.764167053112109 0.914143764470561 0.914143764470561 0.764167053112109 4 - 0 9403 N Y 3.05525806154557 3.54768941479713 3.05525806154557 355 0.00281690140845059 0.00155658720747431 Y 0.00281690140845059 0 N N 7610 7610 ENSG00000005156 ENSG00000005156 - + 17 17 30356201 30356201 downstream coding LIG3 LIG3 30331651 30331651 + + 0 30358204 30355622 - + N - 1.9744570736236 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 7 0.842726282871298 1.48548361726466 1.48548361726466 0.842726282871298 1 - 0 12350 N N 3.27505278312102 2.71123698212769 2.71123698212769 0 0 0.174298303173618 N 0 0 N N 1649619 24465 ENSG00000141736 ENSG00000164104 - + 17 4 35138441 174492167 utr5p coding ERBB2 HMGB2 35104766 174489363 + - 0 35109800 174489853 - - Y 0.0386152290119025 - N HCC1954 1 1 1 0 1 N 577 18.2422 N Low_complexity Low_complexity 0.184210526315789 0.285714285714286 0.285714285714286 4 0.735600060472404 0.757025304952183 0.757025304952183 0.735600060472404 1 0 - 44996 Y Y 3.63825270713077 3.48743121468078 3.48743121468078 271 0 0.447388579649195 Y 0 0 N N 828 4690 ENSG00000138347 ENSG00000148634 - - 10 10 69641464 69505109 utr5p upstream MYPN HERC4 69535918 69351663 + - 0 69539485 69517753 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 1.25694767614702 0.799875793911741 1.25694767614702 0.799875793911741 2 - - 31499 Y Y 3.3984700535705 3.2280098772435 3.2280098772435 272 0 0.105970760758535 Y 0.991627533366288 0.991627533366288 N N 0 8002 ENSG00000210957 ENSG00000172340 + - 3 3 67967650 67787728 downstream upstream AC113171.3 SUCLG2 67967527 67507835 - - 0 67879881 67804114 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LINE,LINE 0 1 1 6 0.735600060472404 0.921285512630487 0.921285512630487 0.735600060472404 1 - - 31372 N Y 3.56335849579072 3.40591861909494 3.40591861909494 223 0 0.0451316041920785 Y 0.269115059317705 0.949594142021911 N N 298 7313 ENSG00000182983 ENSG00000181061 - - 3 3 42933958 42820986 intron upstream ZNF662 HIGD1D 42922406 42800797 + - 0 42924501 42826018 - + N 0.175276779295471 - N HCC1954 1 1 1 0 3 N - - N - LTR 0 1 1 5 0.771308801272036 0.507064119354764 0.771308801272036 0.507064119354764 1 0 - 24725 Y Y 2.91398177938334 3.58743466416515 2.91398177938334 244 0 0.160765222634767 Y 0 0.975102459016393 N N 4614 2590 ENSG00000134490 ENSG00000134508 + + 18 18 19271923 19092614 intron utr3p C18orf45 CABLES1 19129975 18969725 - + 0 19165009 19091470 - + N 2.38472514413486 1.16872234083898 N HCC1954 1 1 1 0 3 N - - Y SINE - 0.681159420289855 0 0.681159420289855 5 0.492780623034912 0.5713398527941 0.5713398527941 0.492780623034912 1 0 0 42275 Y N 2.94268474037728 3.60000453584907 2.94268474037728 0 0 0.7561570137313 Y 0 0 N N 1 5644 ENSG00000189099 ENSG00000109686 - - 4 4 152432055 152367022 downstream intron AC104819.4 SH3D19 152417775 152260886 + - 0 152465843 152328177 - + N - 11.435089056451 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 11 0.799875793911741 0.407079645115797 0.799875793911741 0.407079645115797 3 - 0 16600 N Y 3.33680806132368 3.52680574168822 3.33680806132368 83 0.668421052631579 0.0111876140808574 N 0.701578947368421 0.0881578947368421 N N 409 0 ENSG00000070731 ENSG00000213025 + + 17 1 72093524 243073163 upstream intron ST6GALNAC2 BX323046.3-1 72073056 243072961 - - 0.734736842105263 72103371 243073047 - - Y - 1 N HCC1954 2 1.54545454545455 1 6 1 N - - N - - 0 0 0 11 0.349945659836387 0.45707188223528 0.45707188223528 0.349945659836387 2 - 0 3701 N Y 3.375 3.29553522864581 3.29553522864581 0 0 0.197583298628151 N 0.23819073083779 0.23819073083779 N N 2470 7736 ENSG00000121864 ENSG00000154639 + + 3 21 180536017 17887768 utr5p intron ZNF639 CXADR 180524245 17807201 + + 0.23819073083779 180525747 17862853 + + Y - 7.36190083851724 N HCC1954 27 22.5 17 8 1 N 52 24.5122 N SINE SINE 0.905660377358491 0.0775862068965517 0.905660377358491 8 0.378512652476092 0.814159290231593 0.814159290231593 0.378512652476092 1 - 0 42018 N Y 3.50744965188915 3.17717825390873 3.17717825390873 0 0 0.344389649671187 N 0.854811946902655 0.792588495575221 N N 22644 0 ENSG00000167110 ENSG00000170289 + - 9 8 130078089 87825017 coding intron GOLGA2 CNGB3 130057932 87655277 - - 0.792588495575221 130069560 87741191 - + Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 14 0.871293275511003 0.464213630395207 0.871293275511003 0.464213630395207 1 - 0 470 Y Y 2.97680063257943 3.27188321579446 2.97680063257943 0 0 0.566480091949665 Y 0 0 N N 317 5071 ENSG00000133808 ENSG00000133816 - + 11 11 12337267 12241903 upstream coding MICALCL MICAL2 12265023 12088714 + + 0 12254086 12238018 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 0.899860268150708 0.828442786551446 0.899860268150708 0.828442786551446 1 - - 9320 Y Y 3.22167408707565 3.06525793257994 3.06525793257994 264 0.0615393061045235 0.022779202216338 Y 0 0.985562143170839 N N 3576 1877 ENSG00000108963 ENSG00000185924 - - 17 17 1893474 1787865 upstream coding DPH1 RTN4RL1 1880181 1786540 + - 0 1864275 1787845 - + N - 11.7660452222859 N HCC1954 1 1 1 0 2 N - - Y LINE - 0.378378378378378 0 0.378378378378378 21 1.05697872766909 1.37835739486577 1.37835739486577 1.05697872766909 2 - 0 36773 Y Y 3.65231965690101 3.46977054206092 3.46977054206092 0 0 0.473859436114113 Y 0.994301631516116 0.965809789096697 N N 3178 616 ENSG00000205323 ENSG00000135414 + + 12 12 54497773 54430332 utr3p downstream AC073487.34 GDF11 54437325 54423331 - + 0 54437437 54432894 - + N - - N HCC1954 2 1.04444444444444 1 2 1 N - - Y - - 0 0 0 45 1.31408166142643 1.36407389854591 1.36407389854591 1.31408166142643 1 - - 26553 Y Y 2.92192809488736 3.36613351693357 2.92192809488736 0 0 0.180182179000060 Y 0.551435406698565 0.551435406698565 N N 3336 101 ENSG00000090447 ENSG00000185739 + - 16 16 4263002 4232077 downstream upstream TFAP4 SRL 4247189 4179378 - - 0.551435406698565 4243800 4237030 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.649899082553289 0.599906845433805 0.649899082553289 0.599906845433805 3 - - 15279 N Y 3.57696143724454 3.50529022639353 3.50529022639353 2 0 0.478497958471416 N 0.951012536162006 0.934683381549341 N N 40 3826 ENSG00000174945 ENSG00000160072 - + 7 1 2721587 1421444 intron coding AMZ1 ATAD3B 2685689 1397006 + + 0 2703308 1402593 - + Y 0.587708419457076 - N HCC1954 40 13 4 4 1 N - - N SINE - 1 0 1 4 0.335662163516534 0.385654400636018 0.385654400636018 0.335662163516534 3 0 - 48698 N N 3.43937216388778 3.4185747493504 3.4185747493504 0 0.00884955752212357 0.026818460544046 N 0.107964601769911 0.207079646017699 N N 5148 12076 ENSG00000172262 ENSG00000148219 - + 5 9 43211578 119217138 upstream utr3p ZNF131 ASTN2 43157399 118227328 + - 0.207079646017699 43122743 118415234 - - Y - - N HCC1954 588 462 420 5 1 N - - N Other LINE 1 1 1 5 0.692749571512847 0.364229156156239 0.692749571512847 0.364229156156239 2 - - 27149 Y Y 3.62977107183644 3.36551102231762 3.36551102231762 0 0 0.775938016758976 Y 0 0.992775062173055 N N 4369 211 ENSG00000140743 ENSG00000157341 - - 16 16 22293439 22385434 coding upstream CDR2 AC106788.3-1 22264758 22370389 - + 0 22283821 22344995 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.614190341753658 0.764167053112109 0.764167053112109 0.614190341753658 3 - - 45281 N N 3.41592783769912 3.09087103183403 3.09087103183403 7 0 0.152521876829345 N 0 0 N N 779 3891 ENSG00000213096 ENSG00000166295 + + 19 10 24104483 73665622 upstream intron ZNF254 C10orf104 24061816 73645812 + + 0 24022549 73645953 + + Y - 0.744979490524871 N HCC1954 21 17.25 8 4 1 N 99 22.2581 N SINE - 1 0 1 4 0.314236919036755 0.299953422716903 0.314236919036755 0.299953422716903 1 - 0 28770 N N 3.73233517440054 3.48809356209009 3.48809356209009 0 0 0.0845321513769723 N 0 0 N N 7111 45068 ENSG00000129933 ENSG00000205336 + + 19 16 19339989 56256445 intron upstream KIAA0892 GPR56 19292614 56220023 + + 0 19322021 56211646 + + Y 1.45323377803116 - N HCC1954 20 20 20 7 1 N - - N SINE - 1 0 1 7 0.28566992639705 0.28566992639705 0.28566992639705 0.28566992639705 1 0 - 13729 N Y 3.18036140160443 3.27658036643087 3.18036140160443 1 0 0.555830848055222 Y 0 0 N N 91 14981 ENSG00000213784 ENSG00000100207 + - 22 22 41158345 40941389 downstream utr5p NFAM1 TCF20 41106357 40885963 - - 0 41069430 40941292 - + N - 82.384087295852 N HCC1954 1 1 1 0 1 N - - N Low_complexity Simple_repeat 0.597938144329897 0.0099009900990099 0.597938144329897 11 0.692749571512847 0.721316564152552 0.721316564152552 0.692749571512847 1 - 0 283 Y Y 3.61253455473964 3.34984194132402 3.34984194132402 298 0 0.0352891077352366 Y 0 0.99322010683468 N N 1658 129 ENSG00000149743 ENSG00000149781 + + 11 11 63750257 63747930 coding intron TRPT1 FERMT3 63747848 63730782 - + 0.99322010683468 63748337 63746793 - + N 0.861928204464055 0.439096559465417 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.799875793911741 0.849868031031224 0.849868031031224 0.799875793911741 2 0 0 13948 Y Y 3.32163768376666 3.47336426491055 3.32163768376666 0 0 0.996586794589178 Y 0 0.98860353130016 N Y 855 4030 ENSG00000099910 ENSG00000185214 - + 22 22 19122146 19180122 coding coding SCARF2 KLHL22 19108874 19125806 - - 0 19116275 19130730 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 27 1.33550690590621 1.27123117246687 1.33550690590621 1.27123117246687 4 - - 39386 N Y 3.40591861909494 3.66592259835483 3.40591861909494 1 0 0.499262399913836 N 0.887384716732543 0.878722002635046 N N 273 36111 ENSG00000182405 ENSG00000099917 - + 15 22 32183883 19271918 downstream coding PGBD4 MED15 32181566 19191886 + + 0 32200855 19192033 - + Y - - N HCC1954 40 22.625 20 8 1 N - - N SINE - 1 0 1 8 0.314236919036755 0.535631111994469 0.535631111994469 0.314236919036755 4 - - 35568 N Y 3.31063524818594 3.48337348351473 3.31063524818594 0 0.0137015937116896 0.297195890540868 N 0.908487776736136 0.908487776736136 N N 1649619 1721 ENSG00000141736 ENSG00000168778 + + 17 12 35138441 122758901 coding intron ERBB2 TCTN2 35104766 122721615 + + 0.908487776736136 35122222 122733720 + + Y - 1.10344256044627 N HCC1954 24 20.5526315789474 20 38 1 N - - N - SINE 0 1 1 38 0.842726282871298 0.378512652476092 0.842726282871298 0.378512652476092 1 - 0 18717 Y N 3.45050886381334 3.2496867133392 3.2496867133392 0 0 0.182556202738915 Y 0 0 N N 188 9050 ENSG00000163462 ENSG00000163463 - - 1 1 153424069 153412428 coding upstream TRIM46 KRTCAP2 153412970 153408509 + - 0 153416349 153412489 - + N 0.36068595299472 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.635615586233437 0.599906845433805 0.635615586233437 0.599906845433805 3 0 - 38456 Y N 3.43681151080804 2.98723400670668 2.98723400670668 13 0.0856540084388185 0.55063354482017 Y 0.0856540084388185 0 N N 7970 10628 ENSG00000029364 ENSG00000100632 - - 14 14 68997021 68934774 coding upstream SLC39A9 ERH 68935162 68916601 + - 0 68960662 68934950 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.45707188223528 0.34280391167646 0.45707188223528 0.34280391167646 2 - - 9494 Y Y 3.38127338926705 3.16419780707087 3.16419780707087 252 0 0.654373267443953 Y 0 0 N N 9613 185 ENSG00000132510 ENSG00000183914 - + 17 17 7698831 7677783 upstream downstream JMJD3 DNAH2 7683947 7562746 + + 0 7683946 7680619 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 6 0.864151527351077 0.692749571512847 0.864151527351077 0.692749571512847 1 - - 30443 N Y 3.60103760561896 3.27824527838653 3.27824527838653 256 0 0.0352758096583748 Y 0 0 N N 1071 0 ENSG00000204019 ENSG00000207033 + - X X 115508165 115446141 intron upstream CXorf61 U6 115506878 115446035 - - 0 115507970 115450007 - + N 0.600829561404892 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.785592297591888 0.685607823352921 0.785592297591888 0.685607823352921 1 0 - 30282 Y Y 3.23636353146184 3.21063179870157 3.21063179870157 345 0 0.00755709596380916 Y 0 0.966199950872022 N N 0 0 ENSG00000220528 ENSG00000213468 + - X X 130765450 130757838 upstream downstream RP1-197O17.2 AL121572.14 130765021 130757360 - - 0 130766707 130756316 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE SINE 0.279411764705882 0.746478873239437 0.746478873239437 4 0.485638874874985 0.507064119354764 0.507064119354764 0.485638874874985 2 - - 7683 N Y 3.8333716936548 3.24996647291565 3.24996647291565 20 0.103030303030303 0.646976157613401 N 0.0698092031425366 0.966778900112233 N N 0 11 ENSG00000183846 ENSG00000176406 + + 2 8 110575338 105333263 upstream intron AC112229.4-1 RIMS2 110574935 104582291 - + 0 110576429 104686854 - + Y - 1.06909912995821 N HCC1954 60 40.1935483870968 6 31 1 N - - N - LINE,LINE 0 1 1 31 1.07840397214886 0.628473838073511 1.07840397214886 0.628473838073511 3 - 0 41655 Y Y 3.19442835137467 3.44615838200292 3.19442835137467 275 0 0.215958117832074 Y 0 0.985017088174983 N N 0 4 ENSG00000221771 ENSG00000184090 - - 8 8 129042123 129029462 downstream downstream hsa-mir-1205 TMEM75 129042061 129029046 + - 0 129050844 129021104 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.215384615384615 0.215384615384615 4 0.664182578873142 0.785592297591888 0.785592297591888 0.664182578873142 4 - - 33732 N Y 3.07933422991999 3.45400817511148 3.07933422991999 329 0 0.00461097975749480 Y 0 0.993526230608298 N N 339915 59837 ENSG00000198727 ENSG00000198695 - - MT MT 15882 14674 coding coding MT-CYB MT-ND6 14748 14150 + - 0.993526230608298 15522 14234 - + N - 0.742053250532238 N HCC1954 2 1.25 1 1 2 N - - N - - 0 0 0 4 0.635615586233437 0.864151527351077 0.864151527351077 0.635615586233437 0 - 0 18813 Y Y 3.47804449069255 3.6314359837921 3.47804449069255 331 0 0.00307582321392574 Y 0 0.993807584770412 N N 1964 34471 ENSG00000158286 ENSG00000116251 - - 1 1 6203946 6182266 upstream upstream C1orf188 RPL22 6188477 6167668 + - 0 6188402 6183398 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 8 1.06412047582901 1.02841173502938 1.06412047582901 1.02841173502938 1 - - 42083 N N 3.35935664638825 3.54144175291192 3.35935664638825 0 0.0387244430881906 0.974670076011919 N 0.0387244430881906 0 N N 29840 61 ENSG00000164830 ENSG00000038295 + + 8 4 107834093 167244443 coding upstream OXR1 TLL1 107739270 167013860 + + 0 107827194 166908716 + + Y - - N HCC1954 1 1 1 0 4 N - - N - LINE 0 0.529411764705882 0.529411764705882 5 0.842726282871298 0.828442786551446 0.842726282871298 0.828442786551446 2 - - 46820 Y Y 3.33102440775489 3.37824872787089 3.33102440775489 219 0 0.0127535093575720 Y 0 0.944698122780315 N N 345 302 ENSG00000185869 ENSG00000167637 + + 19 19 42099030 42062306 intron intron ZNF829 ZNF345 42074093 42033103 - + 0 42075556 42033757 - + N 1.04000939341478 0.191267882868105 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.392796148795944 0.51420586751469 0.51420586751469 0.392796148795944 1 0 0 30477 Y Y 3.49015970162987 3.36464578641707 3.36464578641707 290 0 0.0770708728272692 Y 0.96563614744352 0.99140903686088 N N 51 1011 ENSG00000205662 ENSG00000205663 + - X X 3848751 3810322 downstream downstream BX890604.9-2 BX890604.9-1 3834245 3792439 - - 0 3833388 3782967 - + N - - N HCC1954 9 6 3 15 2 N - - Y LTR - 0.0900900900900901 0 0.0900900900900901 15 1.44977487646503 0.578481600954027 1.44977487646503 0.578481600954027 1 - - 48221 N Y 3.20487865035633 3.18036140160443 3.18036140160443 0 0 0.075522348230957 N 0 0 N N 26 38037 ENSG00000152954 ENSG00000131446 - - 6 5 24255609 180175147 utr3p upstream NRSN1 MGAT1 24234329 180150147 + - 0 24254804 180191498 - + Y - - N HCC1954 25 22 21 4 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.51420586751469 0.51420586751469 0.271386430077198 2 - - 35752 N N 3.65488030998075 3.58424216889964 3.58424216889964 0 0 0.247647696888528 N 0 0.0641779006798018 N N 12314 45068 ENSG00000011105 ENSG00000205336 - + 12 16 3265990 56256445 intron upstream TSPAN9 GPR56 3056818 56220023 + + 0.0641779006798018 3074078 56211650 - + Y 0.458286817795374 - N HCC1954 21 13.8333333333333 5 6 1 N - - N SINE - 1 0 1 6 0.28566992639705 0.492780623034912 0.492780623034912 0.28566992639705 3 0 - 16770 N Y 3.12804628055249 3.684245618384 3.12804628055249 1 0 0.248810974161163 N 0.828992403372569 0.90946656649136 N N 1649619 36 ENSG00000141736 ENSG00000186409 - - 17 1 35138441 42892444 coding intron ERBB2 RP5-994D16.1 35104766 42701612 + + 0 35122227 42807077 - - Y - 1.19972687185668 N HCC1954 25 21.8571428571429 20 7 1 N - - N - SINE 0 1 1 7 0.885576771830856 0.357087407996313 0.885576771830856 0.357087407996313 2 - 0 36201 N Y 3.5319270478477 3.59528445727371 3.5319270478477 351 0 0.0080282986473339 Y 0.0294396961063628 0.98670465337132 N N 44572 44572 ENSG00000092841 ENSG00000092841 - + 12 12 54841633 54841633 downstream coding MYL6 MYL6 54838367 54838367 + + 0.98670465337132 54842314 54840370 - + N - 3.08267093796757 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 8 0.421363141435649 0.692749571512847 0.692749571512847 0.421363141435649 1 - 0 16094 N N 3.53039946453785 3.55657227767559 3.53039946453785 0 0 0.0632143063473554 N 0 0 N N 0 131026 ENSG00000212679 ENSG00000115053 - - 1 2 559619 232037449 intron coding RP5-857K21.10 NCL 558939 232027706 + - 0 559164 232034775 - + Y 1 0.862915057278469 N HCC1954 2 2 2 4 1 N - - N - Simple_repeat,Simple_repeat 0 0.365482233502538 0.365482233502538 4 0.907002016310634 0.864151527351077 0.907002016310634 0.864151527351077 1 0 0 45901 N N 3.57800808738356 3.21488786896051 3.21488786896051 0 0 0.388576501091042 N 0 0 N N 17943 2252 ENSG00000105141 ENSG00000178397 + - 19 7 15027900 6355115 downstream intron CASP14 AC009412.5 15024015 6335568 + - 0.0198001925854596 15029502 6342019 + + Y - 2.56390298001684 N HCC1954 20 20 20 19 1 N 334 24.9586 N - SINE,SINE 0 1 1 19 0.785592297591888 0.278528178237124 0.785592297591888 0.278528178237124 3 - 0 31530 Y Y 3.45140766923839 3.72824693801095 3.45140766923839 250 0 0.447586184352572 Y 0 0.990423076923077 N N 397 6473 ENSG00000180432 ENSG00000144648 + + 3 3 42892661 42883778 upstream coding CYP8B1 CCBP2 42888688 42836115 - + 0 42904035 42881884 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE - 0.9875 0 0.9875 4 0.5713398527941 0.771308801272036 0.771308801272036 0.5713398527941 1 - - 18458 Y Y 3.51423587000429 3.78105657260285 3.51423587000429 322 0 0.162153350849519 Y 0 0 N N 17101 0 ENSG00000162407 ENSG00000219539 + - 1 1 56817845 56446716 downstream upstream PPAP2B RP4-710M16.1 56733023 56445827 - - 0 56613665 56556838 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LINE 0 0.61046511627907 0.61046511627907 10 0.907002016310634 1.1141127129485 1.1141127129485 0.907002016310634 1 - - 7693 N Y 3.14574680596571 3.3846622288154 3.14574680596571 0 0.00353356890459355 0.0965150749421303 N 0 0.00353356890459355 N N 30801 26 ENSG00000144063 ENSG00000186530 + + 2 8 110231432 6680576 utr3p utr3p MALL XKR5 110198738 6653448 - - 0.00353356890459355 110199534 6654806 - - Y 0.875583720369174 - N HCC1954 37 35.5 35 4 1 N - - N Low_complexity SINE 0.178947368421053 1 1 4 0.557056356474248 0.271386430077198 0.557056356474248 0.271386430077198 1 0 - 16039 N N 3.47548383761281 3.49744043328497 3.47548383761281 0 0 0.825878541600108 N 0 0.0361916264090177 N N 154774 0 ENSG00000122566 ENSG00000220375 - - 7 1 26206942 558984 coding intron HNRPA2B1 RP5-857K21.14 26196081 558778 - + 0.0361916264090177 26202961 558961 + - Y - 1 N HCC1954 3 2.25 2 4 3 N - - N - - 0 0 0 4 0.87843502367093 0.692749571512847 0.87843502367093 0.692749571512847 2 - 0 46859 Y Y 3.54296933622177 3.4780843434859 3.4780843434859 298 0 0.122154396498076 Y 0.743288590604027 0.99244966442953 N N 779 0 ENSG00000213096 ENSG00000201966 - - 19 19 24104483 23979149 upstream upstream ZNF254 5_8S_rRNA 24061816 23979000 + - 0.222315436241611 24020828 24008265 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 50 1.0069864905496 1.07840397214886 1.07840397214886 1.0069864905496 2 - - 19565 Y Y 3.62617734898681 3.59784511035345 3.59784511035345 375 0 0.0162625894715406 Y 0 0.987911111111111 N N 40092 16599 ENSG00000163435 ENSG00000176393 - + 1 1 200251760 200241898 utr5p intron ELF3 RNPEP 200243696 200218389 + + 0 200245551 200237059 - + N - 1.10685247315652 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 1.02126998686945 1.21409718718746 1.21409718718746 1.02126998686945 4 - 0 4143 N N 2.71719788090366 3.64400585547602 2.71719788090366 0 0 0.969319560102168 N 0.00317460317460339 0 Y Y 4358 1830 ENSG00000091127 ENSG00000146776 + - 7 7 104949921 105310263 utr5p intron PUS7 ATXN7L1 104884194 105032750 - - 0 104949735 105092971 - + N 1.93851919872122 2.79788483023414 N HCC1954 1 1 1 0 2 N 12 15.1376 N - - 0 0 0 22 1.17124669822791 1.08554572030879 1.17124669822791 1.08554572030879 4 0 0 118 Y Y 3.71720464963688 3.35975787397237 3.35975787397237 245 0 0.439173635539833 Y 0.413618157543391 0.981384703414076 N N 410 109 ENSG00000120458 ENSG00000149564 + - 11 11 124175509 124137433 downstream upstream C11orf61 ESAM 124141604 124128229 - - 0 124139835 124137581 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.504273504273504 0.504273504273504 9 0.814159290231593 0.835584534711372 0.835584534711372 0.814159290231593 4 - - 8516 N Y 3.58953130892846 3.64231043829683 3.58953130892846 244 0.847566075610572 0.00995235917378157 N 0.847566075610572 0.847566075610572 N N 0 850768 ENSG00000204458 ENSG00000075624 - + 17 7 17086925 5536758 intron coding AC055811.5 ACTB 17086049 5533313 + - 0.847566075610572 17086633 5534314 - - Y 1 - N HCC1954 2 1.5 1 4 1 N - - N - - 0 0 0 8 0.521347615674617 0.778450549431962 0.778450549431962 0.521347615674617 2 0 - 27249 N N 3.48809356209009 3.85425536676371 3.48809356209009 0 0 0.101900325686014 N 0 0 N N 45068 0 ENSG00000205336 ENSG00000168418 + - 16 16 56256445 82830857 upstream intron GPR56 KCNG4 56220023 82813324 + - 0 56211646 82820321 + + N - 1 Y HCC1954 20 20 20 6 1 N - - N - SINE 0 1 1 6 0.499922371194838 0.264244681917271 0.499922371194838 0.264244681917271 1 - 0 35491 N Y 3.73912139251568 3.07101108092519 3.07101108092519 0 0.00352112676056326 0.436082175949521 N 0.757864946689483 0.860306700013163 N N 1681 1649619 ENSG00000111358 ENSG00000141736 - - 12 17 122712140 35138441 utr3p coding GTF2H3 ERBB2 122684360 35104766 + + 0 122712015 35125066 - - Y - - N HCC1954 28 22.453125 20 64 1 N - - N SINE - 1 0 1 64 0.328520415356608 1.17838844638783 1.17838844638783 0.328520415356608 1 - - 45876 N N 3.62617734898681 3.59169073442408 3.59169073442408 0 0.138076923076923 0.546975550481538 N 0.502 0.195538461538461 N N 2469 0 ENSG00000142252 ENSG00000185037 - - 19 7 50286622 62401869 utr5p downstream GEMIN7 AC006455.2 50274370 62389140 + - 0.367923076923077 50285212 62360876 - + Y - - N HCC1954 2 1.16666666666667 1 1 1 N - - N - - 0 0 0 6 0.428504889595575 0.299953422716903 0.428504889595575 0.299953422716903 3 - - 17293 Y Y 3.31319590126568 3.43784458057793 3.31319590126568 43 0 0.816603120356716 Y 0 0 N N 2003 24302 ENSG00000160781 ENSG00000198952 - + 1 1 154484471 154519240 coding utr3p PAQR6 SMG5 154479831 154485641 - - 0 154483134 154486069 + - N - 0.511016429515623 N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 5 0.721316564152552 0.671324327033068 0.721316564152552 0.671324327033068 2 - 0 30348 Y Y 3.62295434849776 3.55401162459584 3.55401162459584 325 0 0.00574873211473759 Y 0.948545905707196 0.993568238213399 N N 0 0 ENSG00000199168 ENSG00000207820 + - X X 73423917 73423769 upstream downstream hsa-mir-374a hsa-mir-545 73423846 73423664 - - 0 73428730 73418409 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.785592297591888 1.09982921662864 1.09982921662864 0.785592297591888 1 - - 36836 N Y 3.70040921291755 3.49263037034389 3.49263037034389 103 0.854368932038835 0.0443657128046026 N 0.883495145631068 0.854368932038835 N N 3 6971 ENSG00000165496 ENSG00000127314 + + 14 12 46190689 67340554 coding intron RPL10L RAP1B 46190045 67290955 - + 0.854368932038835 46190361 67307069 - + Y 0.915382714014995 1.60406068448132 N HCC1954 8 6.5 6 4 1 N 39 27.345 N - - 0 0 0 4 0.34280391167646 0.257102933757345 0.34280391167646 0.257102933757345 3 0 0 34148 Y Y 3.63552422018169 3.19806192701765 3.19806192701765 322 0.408984028393966 0.390134492587408 Y 0.992879325643301 0.985758651286602 N N 0 11502 ENSG00000222760 ENSG00000159921 - - 9 9 36257919 36248450 downstream utr5p U4 GNE 36257780 36204430 + - 0 36266891 36239394 - + N - 135.879330455301 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 461 1.03555348318931 1.33550690590621 1.33550690590621 1.03555348318931 4 - 0 4068 Y Y 3.61360747730289 3.78784279071799 3.61360747730289 274 0 0.0760178735101533 N 0.814239762464432 0.991556352839292 Y N 0 0 ENSG00000201515 ENSG00000177418 + - 7 7 65653116 65659784 upstream downstream 5S_rRNA AC006001.2-1 65652992 65659267 - - 0 65663002 65657260 - + N - - N HCC1954 36 10.9 2 10 2 N - - N SINE - 1 0 1 10 0.835584534711372 0.792734045751814 0.835584534711372 0.792734045751814 1 - - 39789 Y Y 3.02336260528612 3.44193281696752 3.02336260528612 0 0 0.980312712168423 Y 0.993690065209053 0.993690065209053 N Y 4995 856 ENSG00000128973 ENSG00000129007 + - 15 15 66309079 66285502 coding intron CLN6 CALML4 66286386 66270098 - - 0 66308894 66277020 - + N 2.03850624211521 1.03253134759672 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 17 1.24980592798709 0.907002016310634 1.24980592798709 0.907002016310634 4 0 0 34073 N N 3.06380821146206 2.6718368118362 2.6718368118362 0 0.208645336963921 0.196064151404067 N 0.489448604492852 0.208645336963921 N N 1 11502 ENSG00000101958 ENSG00000159921 + - X 9 14659852 36248450 utr3p utr3p GLRA2 GNE 14457565 36204430 + - 0.208645336963921 14658953 36206342 + + Y - 0.659918255598569 N HCC1954 39 36.4 34 5 1 N 190 25.3415 N Simple_repeat LINE 1 0.514563106796116 1 5 0.414221393275723 0.735600060472404 0.735600060472404 0.414221393275723 1 - 0 46771 Y Y 3.25360004855864 3.34252135687557 3.25360004855864 339 0 0.0486466880570449 Y 0.842889067667829 0.993957271833378 N N 6 14186 ENSG00000213052 ENSG00000171570 + + 19 19 46048180 46006176 downstream coding CYP2A6 EGLN2 46041284 45996959 - + 0 46024307 45999158 - + N - 0.880817265657256 N HCC1954 2 1.73949579831933 1 88 3 N - - Y - - 0 0 0 119 1.28551466878673 1.24266417982717 1.28551466878673 1.24266417982717 1 - 0 47948 N N 3.58527523866953 3.00659009650574 3.00659009650574 0 0 0.401168857199027 N 0 0 N N 249 20017 ENSG00000155897 ENSG00000160867 + + 8 5 132123854 176457749 intron downstream ADCY8 FGFR4 131861736 176446521 - + 0 131950752 176458417 - + Y 0.18342889971829 - N HCC1954 1 1 1 0 1 N 278 7.1 N Low_complexity - 0.0223463687150838 0 0.0223463687150838 125 1.2783729206268 1.36407389854591 1.36407389854591 1.2783729206268 1 0 - 34449 N Y 3.73656073943594 2.84492465477456 2.84492465477456 202 0.00495049504950495 0.00736200394555109 Y 0.00495049504950495 0.985985218240134 N N 0 7080 ENSG00000218423 ENSG00000148296 - - 9 9 135196116 135192868 intron coding RP11-244N20.7 SURF6 135195648 135187390 + - 0 135196085 135191245 - + N 1 0.803794621945098 N HCC1954 4 1.85714285714286 1 2 1 N - - N - - 0 0 0 7 0.899860268150708 0.93556900895034 0.93556900895034 0.899860268150708 1 0 0 6325 N N 3.44296588673741 2.77339348791447 2.77339348791447 0 0 0.161638911513020 N 0 0 N N 122511 29655 ENSG00000187514 ENSG00000136938 - + 2 9 232286495 99818046 coding coding PTMA ANP32B 232280638 99785310 + + 0 232285428 99814564 - + Y - - N HCC1954 4 2 1 2 1 N - - N - Low_complexity,Low_complexity 0 0.366101694915254 0.366101694915254 5 0.821301038391519 1.19267194270768 1.19267194270768 0.821301038391519 0 - - 46870 Y Y 3.61513506061274 3.11188268601893 3.11188268601893 331 0 0.00234922451031727 Y 0.386474552637695 0.900302114803625 N N 1660 0 ENSG00000221849 ENSG00000196977 - - 19 19 63648682 63610475 intron downstream ZNF584 AC012313.7-1 63611875 63607435 + - 0 63618698 63604913 - + N 0.458460350033243 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.535631111994469 0.51420586751469 0.535631111994469 0.51420586751469 2 0 - 18172 Y Y 3.34884356667429 3.28126993978269 3.28126993978269 294 0 0.0447385810654717 Y 0.299095462360768 0.978096733198774 N N 16110 1110 ENSG00000163374 ENSG00000198358 + - 1 1 153925415 153865810 downstream upstream YY1AP1 ERVK5 153895858 153863173 - - 0 153884821 153873907 - + N - - N HCC1954 2 1.04347826086957 1 1 1 N - - Y Simple_repeat LTR,LTR 0.311111111111111 0.504950495049505 0.504950495049505 23 0.642757334393363 0.721316564152552 0.721316564152552 0.642757334393363 4 - - 21800 N N 3.61360747730288 2.96957333408681 2.96957333408681 9 0 0.0210143181556302 N 0.916008244589488 0 N N 6330 23800 ENSG00000143190 ENSG00000067182 + - 1 12 165663206 6321522 utr3p coding POU2F1 TNFRSF1A 165456744 6308185 + - 0 165656166 6310128 + + Y - 0.593726962781154 N HCC1954 23 22 21 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.564198104634174 0.564198104634174 0.278528178237124 2 - 0 9420 Y Y 3.47961192679575 3.19236221183489 3.19236221183489 349 0 0.00292643550831417 Y 0.00286532951289398 0.991404011461318 N N 18 267 ENSG00000167159 ENSG00000204650 - + 17 17 41075005 41069945 upstream upstream C17orf69 AC126544.5-3 41073731 41069421 + + 0 41072524 41063413 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 5 0.764167053112109 0.714174815992626 0.764167053112109 0.714174815992626 3 - - 36991 N N 3.53039946453785 3.42424163912411 3.42424163912411 0 0 0.985775428827933 N 0.0383917353064358 0.00404858299595146 N N 2 20154 ENSG00000185610 ENSG00000168575 + + 12 8 43731149 42516225 intron intron DBX2 SLC20A2 43694806 42393173 - - 0.00404858299595146 43723519 42515841 - - Y 0.918684047175667 36.1317356738638 N HCC1954 1 1 1 0 4 N 141 0.300921 N LTR - 1 0 1 8 0.664182578873142 0.821301038391519 0.821301038391519 0.664182578873142 1 0 0 40768 N Y 3.51100352194543 3.69784855983781 3.51100352194543 0 0 0.0436374842695786 N 0.717789757412399 0.862030548068284 N N 16861 12271 ENSG00000088367 ENSG00000177479 - + 20 3 34284135 48997971 intron utr5p EPB41L1 ARIH2 34142840 48931285 + + 0 34223956 48935246 - + Y 0.0729128935569135 - N HCC1954 20 20 20 7 1 N 91 24.3607 N SINE - 1 0 1 7 0.264244681917271 1.01412823870953 1.01412823870953 0.264244681917271 1 0 - 14346 N Y 3.63296356710195 3.52105259334297 3.52105259334297 0 0 0.0838948870872743 N 0.802871845949535 0 N N 11860 14402 ENSG00000143374 ENSG00000156689 - - 1 11 148746702 58368833 utr3p utr5p TARS2 GLYATL2 148726517 58358118 + - 0 148746526 58368484 - + Y - - N HCC1954 36 35 34 6 1 N - - N SINE - 1 0 1 6 0.28566992639705 0.578481600954027 0.578481600954027 0.28566992639705 1 - - 47567 Y Y 2.91394192658999 2.97470398781611 2.91394192658999 231 0 0.0326964550433128 Y 0 0 N N 49782 15 ENSG00000089327 ENSG00000221946 - + 19 19 40352625 40337045 utr5p intron FXYD5 FXYD7 40337467 40325994 + + 0 40337847 40326515 - + N - 0.350908025776216 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.45707188223528 0.628473838073511 0.628473838073511 0.45707188223528 1 - 0 36701 Y Y 3.57489529770476 3.38656252929588 3.38656252929588 0 0 0.974652128483821 Y 0.623675293778386 0.993031023958859 N Y 119 1870 ENSG00000111275 ENSG00000111271 - + 12 12 110732165 110679284 coding coding ALDH2 ACAD10 110688729 110608285 + + 0 110704105 110677932 - + N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 5 1.04269523134923 0.828442786551446 1.04269523134923 0.828442786551446 4 - - 21755 N N 3.25000632570901 3.45612774781375 3.25000632570901 5 0 0.0509996901099581 N 0 0 N N 22666 28881 ENSG00000111684 ENSG00000127483 - + 12 1 6996103 20985768 coding utr3p LPCAT3 HP1BP3 6955608 20941758 - - 0 6995948 20942901 + - Y - - N HCC1954 28 28 28 4 1 N - - N - SINE 0 1 1 4 0.678466075192994 0.271386430077198 0.678466075192994 0.271386430077198 1 - - 47955 N N 3.70040921291755 3.65657572715995 3.65657572715995 0 0 0.999999896766266 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117948008 2596256 - + Y 1.55093916602555 - N HCC1954 1 1 1 0 12 N 282 1.61558 N - - 0 0 0 19 1.10697096478857 1.22838068350732 1.22838068350732 1.10697096478857 2 0 - 32254 N Y 3.64759957832565 3.1352735790451 3.1352735790451 16 0.0353174603174604 0.0384672875090656 N 0.0778769841269843 0.92906746031746 N N 82 0 ENSG00000106069 ENSG00000213113 + + 7 3 29520469 199332046 intron downstream CHN2 AC073135.3-1 29200646 199330983 + + 0.0778769841269843 29385027 199368886 + + Y 0.487162608745248 - N HCC1954 148 97 80 4 1 N - - N SINE - 1 0 1 4 0.292811674556976 0.39993789695587 0.39993789695587 0.292811674556976 1 0 - 33963 Y Y 3.36551102231762 3.28126993978269 3.28126993978269 356 0.202247191011236 0.999111027333863 Y 0.254274548119199 0.774548119198828 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.774548119198828 14415 12463 - + N - 0.765602338255227 N HCC1954 4 2 1 4 10 N - - Y - - 0 0 0 8 1.24266417982717 0.785592297591888 1.24266417982717 0.785592297591888 2 - 0 42116 N N 3.26936241550807 3.31319590126568 3.26936241550807 12 0 0.0423422226016861 N 0.453610416615095 0.378419189543778 N N 78560 1 ENSG00000112493 ENSG00000163116 - - 6 4 33390114 99283414 utr3p intron TAPBP C4orf37 33375449 98699050 - - 0 33376426 99124498 + + Y - 0.907096774193548 N HCC1954 147 28.5454545454545 1 40 1 N - - N SINE LINE,SINE 1 0.875 1 44 0.835584534711372 0.28566992639705 0.835584534711372 0.28566992639705 1 - 0 33122 N N 3.14484171727181 3.779528989293 3.14484171727181 1 0 0.891775071843822 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 14052 15834 - + N 1.73382696856726 2.74556537998934 N HCC1954 2 1.2 1 1 4 N - - N - - 0 0 0 5 0.999844742389676 0.835584534711372 0.999844742389676 0.835584534711372 1 0 0 35735 N N 3.48383749183115 3.64553343878587 3.48383749183115 0 0 0.768337881857856 N 0 0 N N 17333 712661 ENSG00000169180 ENSG00000111640 + + 16 12 28130691 6517797 upstream coding XPO6 GAPDH 28016817 6513918 - + 0 28159152 6516539 - + Y - - N HCC1954 5 3.83333333333333 2 6 2 N - - N - - 0 0 0 6 0.34280391167646 0.535631111994469 0.535631111994469 0.34280391167646 3 - - 39406 N N 3.68953475841283 3.60785432895764 3.60785432895764 11 0 0.0834819003698223 N 0 0.0447596749758987 N N 5846 524 ENSG00000100281 ENSG00000203289 + + 22 15 34021799 28848794 upstream intron HMGXB4 AC004460.1-2 33983489 28795810 + + 0.0822200798788045 33958855 28815206 + + Y - 0.160431692550671 N HCC1954 20 14.5 9 4 1 N 564 28.3373 N LINE LINE 1 1 1 4 0.385654400636018 0.357087407996313 0.385654400636018 0.357087407996313 2 - 0 527 Y Y 3.47695798776018 3.08086181322984 3.08086181322984 0 0 0.663082778499254 Y 0 0.990130541716592 N N 7926 0 ENSG00000011405 ENSG00000213779 - - 11 11 17147930 17172431 coding downstream PIK3C2A RPL29P21 17064705 17171612 - + 0 17133714 17185883 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.771308801272036 0.535631111994469 0.771308801272036 0.535631111994469 3 - - 46722 N N 3.5010341561346 3.02758817032152 3.02758817032152 0 0 0.0718738795666733 N 0 0 N N 556 9 ENSG00000090920 ENSG00000168995 + - 19 19 45132373 56348595 coding intron FCGBP SIGLEC7 45045804 56337370 - + 0 45132340 56348069 - - N 0.946883165551831 0.397775876817793 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 10 0.392796148795944 0.892718519990782 0.892718519990782 0.392796148795944 1 0 0 32376 N N 3.28764558274389 3.56591914887046 3.28764558274389 0 0 0.0701862264285298 N 0 0 N N 310 5530 ENSG00000053524 ENSG00000148154 - + 3 9 184628549 113735168 utr3p coding MCF2L2 UGCG 184378525 113698867 - + 0 184379011 113731642 + + Y - - N HCC1954 37 35.5 34 4 1 N - - N SINE - 1 0 1 4 0.364229156156239 0.714174815992626 0.714174815992626 0.364229156156239 1 - - 24336 N Y 3.52105259334297 3.46128890676658 3.46128890676658 147 0 0.00553970977580964 N 0.931027966742252 0.889644746787604 N N 0 1775 ENSG00000209924 ENSG00000168234 + + 6 18 4991334 19966989 downstream intron AL359643.27 TTC39C 4991186 19826735 - + 0.0757747543461831 4987875 19840239 - + Y - 0.0183643553533472 N HCC1954 4 3 2 6 1 N - - N LTR,LTR SINE 1 1 1 6 0.814159290231593 0.335662163516534 0.814159290231593 0.335662163516534 2 - 0 37179 N N 3.6026931700048 2.46663405879449 2.46663405879449 0 0 0.07152418262408 N 0 0 N N 551733 0 ENSG00000204628 ENSG00000151952 + - 5 12 180603512 128953837 coding intron GNB2L1 TMEM132D 180596536 128122226 - - 0.0260821309655938 180597262 128575777 - + Y 0.55215727026097 1 N HCC1954 20 16.5454545454545 2 11 1 N - - N - SINE,Simple_repeat 0 0.568627450980392 0.568627450980392 11 0.642757334393363 0.364229156156239 0.642757334393363 0.364229156156239 2 0 0 5214 N Y 3.60632674564779 3.47233119514066 3.47233119514066 0 0 0.0989404786285728 N 0 0.92244722102542 N N 101048 17935 ENSG00000127954 ENSG00000148180 - + 7 9 87774145 123134942 utr3p utr5p STEAP4 GSN 87743687 123009896 - + 0 87745085 123083632 + + Y - - N HCC1954 36 24.5 4 4 1 N - - N SINE Low_complexity 1 0.0133333333333333 1 4 0.39993789695587 0.535631111994469 0.535631111994469 0.39993789695587 1 - - 6749 Y Y 3.24528624713365 3.55504469436574 3.24528624713365 342 0 0.0135433602629234 Y 0 0 N N 5567 0 ENSG00000123992 ENSG00000219903 + - 2 2 219961842 219931949 coding upstream DNPEP AC053503.2 219946424 219931836 - - 0 219947822 219935775 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 5 1.1141127129485 1.04269523134923 1.1141127129485 1.04269523134923 1 - - 7427 Y Y 3.47382827322697 3.62464976567696 3.47382827322697 0 0 0.652973978334427 N 0.96536231884058 0.922065217391304 Y N 11024 1872 ENSG00000153107 ENSG00000172965 - + 2 2 112358212 111969088 coding downstream ANAPC1 AC068491.4 112243113 111903370 - - 0 112312560 111818109 + - N - - N HCC1954 2 2 2 6 1 N - - N - LINE 0 1 1 6 0.421363141435649 0.499922371194838 0.499922371194838 0.421363141435649 4 - - 18153 Y Y 3.37085359550893 3.51360402781852 3.37085359550893 288 0 0.00232930663611208 Y 0 0 N N 2873 4314 ENSG00000127124 ENSG00000127129 + - 1 1 42156965 41722884 downstream upstream HIVEP3 EDN2 41744623 41717036 - - 0 41738530 41724425 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.699891319672773 0.671324327033068 0.699891319672773 0.671324327033068 1 - - 19103 N Y 3.54036883034868 3.36447795254773 3.36447795254773 238 0 0.0375305226299991 Y 0 0.989838792659921 N N 16479 29989 ENSG00000132698 ENSG00000160803 - - 1 1 154306917 154290140 upstream intron RAB25 UBQLN4 154297590 154271717 + - 0 154297080 154288273 - + N - 2.42737065328364 N HCC1954 38 12.5 1 3 1 N - - N SINE - 1 0 1 4 0.521347615674617 0.607048593593732 0.607048593593732 0.521347615674617 1 - 0 41549 N N 3.65657572715995 3.52208566311286 3.52208566311286 0 0 0.996052014461065 Y 0 0 N N 0 0 ENSG00000208525 ENSG00000222501 - - 8 8 130372654 129092039 downstream upstream AC103833.2-1 U4 130372411 129091912 + - 0 130412707 129102147 - + N - - N HCC1954 1 1 1 0 4 N 575 2.9574 N LTR LTR 1 1 1 6 0.885576771830856 0.871293275511003 0.885576771830856 0.871293275511003 4 - - 18387 Y Y 3.66951632120446 3.23995725431147 3.23995725431147 441 0 0.00247120911001086 Y 0.0431104215565367 0.994165307448515 N N 19525 86 ENSG00000117399 ENSG00000117400 - + 1 1 43601461 43592722 upstream downstream CDC20 MPL 43597213 43576062 + + 0 43596062 43593265 - + N - - N HCC1954 15 4.47058823529412 1 12 1 N - - Y SINE,SINE,SINE LTR 0.3690036900369 1 1 17 0.985561246069823 1.09982921662864 1.09982921662864 0.985561246069823 1 - - 3450 Y Y 3.63552422018169 3.3414348539432 3.3414348539432 207 0 0.0338178837226136 Y 0 0.961227178618483 N N 3641 6040 ENSG00000142188 ENSG00000159128 + + 21 21 33774151 33731698 downstream coding TMEM50B IFNGR2 33743321 33697072 - + 0 33742950 33726983 - + N - 1.0563592055608 N HCC1954 21 4.66666666666667 1 2 2 N - - Y SINE - 1 0 1 9 0.657040830713216 0.442788385915428 0.657040830713216 0.442788385915428 2 - 0 18629 N Y 3.30591516961058 3.53768019619294 3.30591516961058 0 0 0.257876011337530 Y 0 0.926700367647059 N N 0 0 ENSG00000220674 ENSG00000207106 - - 1 1 146560480 143022733 upstream downstream RP11-289I10.2 U1 146559962 143022570 + - 0 146542916 143013069 - + N - - N HCC1954 6 6 6 4 1 N 475 26.8882 N - - 0 0 0 4 0.335662163516534 0.485638874874985 0.485638874874985 0.335662163516534 3 - - 36790 Y Y 3.52105259334297 3.50744965188915 3.50744965188915 10 0.0241163475699557 0.556771169722705 Y 0.0138438880706921 0 N N 10865 84 ENSG00000179912 ENSG00000185482 + - 12 12 56111055 55931236 coding upstream R3HDM2 STAC3 55933814 55923509 - - 0 55936040 55931243 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.914143764470561 0.728458312312478 0.914143764470561 0.728458312312478 4 - - 6494 Y Y 3.23697244570866 3.55504469436573 3.23697244570866 340 0.00294117647058822 0.0148531197266517 Y 0.00294117647058822 0.99339696143358 N N 134 29 ENSG00000168505 ENSG00000182177 - + 2 2 236741391 236837727 coding intron GBX2 ASB18 236739046 236766834 - - 0 236741052 236794290 + - N - 1.98831985624438 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.785592297591888 0.807017542071667 0.807017542071667 0.785592297591888 1 - 0 36805 N Y 3.73233517440054 3.42254622194492 3.42254622194492 16 0.0403778040141677 0.6123759000819 Y 0.92443919716647 0.992443919716647 N N 68 0 ENSG00000212127 ENSG00000212128 + - 12 12 11215465 10953164 coding downstream TAS2R14 TAS2R13 10982120 10952253 - - 0 11017521 10928141 - + N - - N HCC1954 2 1.25 1 1 1 N - - N LINE,SINE,LTR - 0.407407407407407 0 0.407407407407407 4 0.828442786551446 0.628473838073511 0.828442786551446 0.628473838073511 4 - - 33021 N N 3.50272957331379 3.23267652265637 3.23267652265637 0 0 0.999999460339879 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8758 11117 - + N 0.561836870404971 0.700997169053331 N HCC1954 4 2.4 2 5 12 N 189 4.09957 N - - 0 0 0 5 0.857009779191151 1.25694767614702 1.25694767614702 0.857009779191151 3 0 0 34484 N Y 3.46807512488172 3.29383981146661 3.29383981146661 0 0 0.871915986921713 Y 0.171183079973562 0.98325622383785 N N 50 0 ENSG00000107018 ENSG00000214195 + + 9 9 5329873 5301716 coding upstream RLN1 AL135786.17-1 5324969 5301445 - + 0.380480282000441 5329262 5298268 - + N 1.59184834263519 - N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.685607823352921 0.849868031031224 0.849868031031224 0.685607823352921 4 0 - 14366 N N 3.50272957331379 3.20703807585194 3.20703807585194 0 0.0188704318936875 0.171070105777172 N 0 0.232159468438538 N N 12635 0 ENSG00000109919 ENSG00000209237 - + 11 1 47620640 107148612 utr5p upstream MTCH2 AL627169.8-3 47595444 107148546 - + 0 47620596 106824724 + + Y - - N HCC1954 3 1.5 1 1 1 N - - N - LTR 0 1 1 4 0.371370904316165 0.292811674556976 0.371370904316165 0.292811674556976 3 - - 48873 N N 3.59681204058356 3.43784458057793 3.43784458057793 0 0 0.97928133898689 N 0 0 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 intron intron TICAM2 AC034236.1 114942238 115326170 - + 0 114989196 115383748 - + N 0.297252844097792 0.505191337881934 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 9 0.578481600954027 0.978419497909897 0.978419497909897 0.578481600954027 2 0 0 47735 N N 3.63978029044062 3.09815176348912 3.09815176348912 0 0 0.992825997874338 N 0.0996234863132186 0.00315457413249232 Y N 8665 5583 ENSG00000079313 ENSG00000104885 + + 19 19 1799452 2181007 coding coding REXO1 DOT1L 1766245 2115148 - + 0.00315457413249232 1767327 2161400 - + N - - N HCC1954 1 1 1 0 5 N 279 3.37031 N - - 0 0 0 4 0.835584534711372 0.542772860154395 0.835584534711372 0.542772860154395 2 - - 19698 N N 3.59425138750382 3.37295958784206 3.37295958784206 0 0 0.074950829770579 N 0 0 N N 230 1924 ENSG00000180730 ENSG00000162604 + - 13 1 25523198 61963683 utr3p intron TMEM46 TM2D1 25516735 61919305 - - 0 25518182 61921985 - + Y - 0.459842311393412 N HCC1954 28 25.75 25 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.385654400636018 0.385654400636018 0.28566992639705 2 - 0 1152 N N 3.54296933622177 1.14851232086445 1.14851232086445 0 0 0.19088280653579 N 0 0 N N 74637 0 ENSG00000089597 ENSG00000206951 - - 11 2 62170680 33024022 coding downstream GANAB Y_RNA 62148876 33023910 - - 0 62163732 32995158 + + Y - - N HCC1954 4 1.85714285714286 1 3 2 N 604 19.3493 N - Simple_repeat 0 1 1 7 0.764167053112109 0.857009779191151 0.857009779191151 0.764167053112109 1 - - 49 Y Y 2.97892020528169 3.50376264308368 2.97892020528169 331 0 0.949622828732558 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream intron TNNI2 SYT8 1816795 1809259 + + 0.993807584770412 1816183 1814668 - + N - 0.680623103938333 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 20 1.13553795742827 1.17838844638783 1.17838844638783 1.13553795742827 1 - 0 18386 N Y 3.1394991440805 2.37463131143364 2.37463131143364 227 0 0.0247561068414951 Y 0 0.987555066079295 N N 0 582 ENSG00000213037 ENSG00000153363 - + 1 1 209682923 209638102 upstream intron AL590101.9 C1orf97 209682219 209622768 + + 0 209672234 209636797 - + N - 14.0855049024855 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 13 0.692749571512847 0.442788385915428 0.692749571512847 0.442788385915428 1 - 0 17969 Y Y 3.51463709758841 3.64024429875705 3.51463709758841 173 0 0.0449544531400941 Y 0 0.992206554878049 N N 7439 3091 ENSG00000054277 ENSG00000117009 + + 1 1 239870324 239825566 coding coding OPN3 KMO 239823075 239762057 - + 0 239827673 239822047 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.678466075192994 0.735600060472404 0.735600060472404 0.678466075192994 1 - - 18908 Y Y 3.31745197152461 3.4342508577283 3.31745197152461 280 0 0.00522321838286577 Y 0 0.957295918367347 N N 2748 198 ENSG00000135845 ENSG00000212919 + - 1 1 170679853 170679811 intron intron PIGC Z97195.1-1 170677220 170629356 - - 0 170679694 170651121 - + N 1.4954103367001 1.98384233051846 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.592765097273879 0.471355378555133 0.592765097273879 0.471355378555133 1 0 0 30568 N N 3.70040921291755 3.61207989399303 3.61207989399303 0 0 0.189897207234225 Y 0 0 N N 1 62436 ENSG00000122824 ENSG00000102225 - + X X 51097117 46974336 upstream coding NUDT10 PCTK1 51091823 46962576 + + 0 51055691 46971407 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.657040830713216 0.799875793911741 0.799875793911741 0.657040830713216 2 - - 40936 Y Y 3.49168728493972 3.32952732966858 3.32952732966858 194 0 0.0770005396764453 Y 0 0 N N 6319 0 ENSG00000197818 ENSG00000217373 - - 20 20 47942179 47779786 upstream upstream SLC9A8 SNRPFP1 47862657 47779535 + - 0 47825275 47821056 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.535631111994469 0.528489363834543 0.535631111994469 0.528489363834543 1 - - 4398 N Y 3.62617734898681 3.37654396312188 3.37654396312188 271 0 0.0371544016071008 Y 0.796031031176453 0.992155039660633 N N 12405 124 ENSG00000160862 ENSG00000176402 + - 7 7 99411623 99365260 intron coding AZGP1 GJC3 99402290 99358828 - - 0 99407304 99365179 - + N 0.739902791142458 9.36884512085945 N HCC1954 2 1.14285714285714 1 1 2 N - - N - - 0 0 0 7 0.885576771830856 0.914143764470561 0.914143764470561 0.885576771830856 1 0 0 36308 Y Y 3.56016600052522 3.44143830342756 3.44143830342756 285 0 0.00783461211860992 Y 0 0.945645933014354 N N 11278 208 ENSG00000161800 ENSG00000086159 + + 12 12 48705493 48657189 coding downstream RACGAP1P AQP6 48669214 48652887 - + 0 48672126 48657226 - + N 0.508499971535962 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.49 0.49 7 0.685607823352921 0.714174815992626 0.714174815992626 0.685607823352921 3 0 - 41042 N N 3.49268050191626 3.74487454086093 3.49268050191626 0 0 0.897478553514943 N 0 0 Y N 9407 7469 ENSG00000101346 ENSG00000126001 - + 20 20 30290125 33563218 downstream coding POFUT1 CEP250 30259357 33506564 + + 0 30301958 33527832 - + N - - N HCC1954 17 2.45454545454545 1 5 2 N - - N SINE - 1 0 1 22 1.04983697950916 1.14982145374813 1.14982145374813 1.04983697950916 1 - - 19239 Y Y 3.42783536197374 3.42464286670823 3.42464286670823 0 0 0.683291399877476 Y 0 0 N N 556 113 ENSG00000069712 ENSG00000189195 - + 1 1 92422870 92385983 upstream coding KIAA1107 BTBD8 92405130 92318450 + + 0 92405103 92385931 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 16 0.985561246069823 0.907002016310634 0.985561246069823 0.907002016310634 4 - - 22774 N Y 3.32523140661629 3.78465029545248 3.32523140661629 0 0 0.0230159106276642 N 0.851599147121535 0.851599147121535 N N 73 5169 ENSG00000109743 ENSG00000189337 - - 4 1 15343508 15317130 upstream intron BST1 RP1-21O18.1 15313739 14797787 + + 0 15292111 14989133 - - Y - 0.0438387320020192 N HCC1954 23 6.97560975609756 2 41 1 N - - N - SINE 0 1 1 41 1.12839620926835 0.414221393275723 1.12839620926835 0.414221393275723 1 - 0 16108 N Y 3.62039369541802 3.7297745213208 3.62039369541802 21 0 0.0872733678679467 N 0.51533556027938 0.694840908324054 N N 2251 0 ENSG00000186275 ENSG00000172554 - + 1 2 143541658 1350392 upstream upstream NBPF8 SNTG2 143326471 936552 + + 0 143307638 909199 - + Y - - N HCC1954 6 3.5 2 4 1 N 468 14.5195 N SINE SINE 1 1 1 4 0.607048593593732 0.257102933757345 0.607048593593732 0.257102933757345 1 - - 18132 Y Y 3.53039946453785 3.45041445226185 3.45041445226185 282 0 0.0122095774217214 Y 0 0 N N 13757 568 ENSG00000135823 ENSG00000215828 + - 1 1 179258669 179212241 coding intron STX6 AL162431.17-1 179208801 179179798 - - 0 179220437 179186678 - + N 0.398128622532935 0.0731551073274452 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 24 0.714174815992626 1.19267194270768 1.19267194270768 0.714174815992626 1 0 0 30759 Y Y 3.44512531223303 3.38337003403037 3.38337003403037 187 0 0.030737536596962 Y 0 0 N N 4574 0 ENSG00000188917 ENSG00000174225 + + X X 100193758 100132349 utr3p coding TRMT2B ARL13A 100150992 100111356 - + 0 100152167 100115366 - + N - 1 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 1.72830305470215 1.07840397214886 1.72830305470215 1.07840397214886 2 - 0 34141 Y Y 3.46335504630636 3.4780843434859 3.46335504630636 284 0 0.0106741840175968 Y 0 0 N N 108 0 ENSG00000106772 ENSG00000211139 + + 9 9 78518458 78376770 downstream upstream PRUNE2 AL161626.20-2 78416112 78376469 - + 0 78410585 78370550 - + N - - N HCC1954 3 1.27272727272727 1 2 1 N - - Y LTR SINE,LINE 0.91156462585034 0.834710743801653 0.91156462585034 11 1.04983697950916 0.864151527351077 1.04983697950916 0.864151527351077 1 - - 12686 N N 3.51849194026323 3.16360581767846 3.16360581767846 0 0 0.0737256329286041 N 0 0 N N 1673 37605 ENSG00000130517 ENSG00000131771 - - 19 17 18526861 35046404 intron downstream PGPEP1 PPP1R1B 18312397 35036705 + + 0 18313981 35046596 - - Y 1.02178852495778 - N HCC1954 22 18.5 12 4 1 N 102 21.7016 N SINE,SINE - 0.977777777777778 0 0.977777777777778 4 0.321378667196682 0.628473838073511 0.628473838073511 0.321378667196682 2 0 - 36866 N Y 3.09715338883939 3.67320333000993 3.09715338883939 261 0.959340057862226 0.00523832223630272 N 0.959340057862226 0.593400578622254 N N 17109 7808 ENSG00000187109 ENSG00000015133 + - 12 14 74764717 90953886 utr3p intron NAP1L1 CCDC88C 74726227 90807422 - - 0.593400578622254 74728467 90920507 - + Y - 2.11770474633426 N HCC1954 2 1.83333333333333 1 15 1 N - - N - - 0 0 0 18 0.714174815992626 0.378512652476092 0.714174815992626 0.378512652476092 1 - 0 33216 Y Y 3.45360694752736 3.52105259334297 3.45360694752736 491 0 0.993260397440032 Y 0 0.995603685726334 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.995603685726334 14455 13503 - + N 1.36431549640773 - N HCC1954 2 1.75 1 3 10 N - - Y - - 0 0 0 4 0.607048593593732 0.721316564152552 0.721316564152552 0.607048593593732 3 0 - 31466 Y Y 3.59524460448036 3.78208964237274 3.59524460448036 240 0 0.93042894548104 Y 0 0.989056776556777 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 intron upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42867020 42826031 - + N 0.0692123342775211 - N HCC1954 1 1 1 0 6 N - - Y LINE LTR 0.216867469879518 1 1 6 1.10697096478857 0.51420586751469 1.10697096478857 0.51420586751469 1 0 - 11574 N Y 3.12804628055249 3.60422075331465 3.12804628055249 1 0 0.231161844866084 N 0.87350997467729 0.87350997467729 N N 1649619 6307 ENSG00000141736 ENSG00000189221 - - 17 X 35138441 43491011 coding upstream ERBB2 MAOA 35104766 43400353 + + 0 35122227 43340809 - - Y - - N HCC1954 22 9.25 3 8 1 N - - N - SINE 0 1 1 8 0.542772860154395 0.335662163516534 0.542772860154395 0.335662163516534 2 - - 33026 N N 3.5744007841648 3.17784060131804 3.17784060131804 4 0 0.999997644655495 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8999 12012 - + N 0.568408982197195 2.40241012810684 N HCC1954 2 1.8 1 4 12 N 189 4.09957 N - - 0 0 0 5 0.892718519990782 0.714174815992626 0.892718519990782 0.714174815992626 2 0 0 29606 Y Y 3.0888395874144 3.25463311832853 3.0888395874144 6 0 0.323022577657121 Y 0 0.982541720154044 N N 6925 32702 ENSG00000135317 ENSG00000135316 - + 6 6 86360348 86409746 coding coding SNX14 SYNCRIP 86271933 86379319 - - 0 86360073 86381420 + - N - - N HCC1954 2 1.75 1 3 1 Y - - Y - - 0 0 0 4 0.364229156156239 0.5713398527941 0.5713398527941 0.364229156156239 2 - - 8291 N N 3.30587531681723 3.7061623612628 3.30587531681723 0 0 0.0902400737926355 N 0 0 N N 551733 0 ENSG00000204628 ENSG00000213048 + + 5 2 180603512 240698142 coding upstream GNB2L1 AC013469.8-1 180596536 240697192 - + 0.0374101338843688 180597248 240694781 - + Y 0.533804592371237 - N HCC1954 20 19.25 18 8 1 N - - N - Simple_repeat 0 0.594594594594595 0.594594594594595 8 0.392796148795944 0.264244681917271 0.392796148795944 0.264244681917271 0 0 - 42912 N N 3.45400817511148 3.6272104187567 3.45400817511148 0 0 0.866917796780608 N 0.154707016514377 0.331335401123313 N N 21519 11640 ENSG00000164111 ENSG00000137038 + + 4 9 122837585 7789799 intron upstream ANXA5 C9orf123 122808598 7786490 - - 0.331335401123313 122837373 7813348 - - Y 1.18878777625704 - N HCC1954 1 1 1 0 4 N - - N - LTR,LTR 0 1 1 17 0.599906845433805 0.692749571512847 0.692749571512847 0.599906845433805 2 0 - 30409 N N 3.44529314610237 3.46397754092232 3.44529314610237 0 0 0.102981426273765 Y 0 0 N N 0 1830 ENSG00000217686 ENSG00000147124 + - X X 47257316 47227289 downstream upstream Z84466.2 ZNF41 47257106 47191352 - - 0.127906976744186 47242543 47241440 - + N - - N HCC1954 21 4.33333333333333 1 8 1 N - - N SINE LTR 1 1 1 18 0.864151527351077 0.742741808632331 0.864151527351077 0.742741808632331 2 - - 10109 N N 3.46807512488172 3.40744620240479 3.40744620240479 0 0 0.748245952174333 N 0.814401622718053 0 Y Y 1572 8390 ENSG00000136447 ENSG00000120071 - + 17 17 42012364 41625943 coding coding ARL17P1 KIAA1267 41949797 41463181 - - 0 42003551 41527743 + - N - - N HCC1954 5 2.27906976744186 2 43 1 Y 498 1.79514 N - - 0 0 0 43 1.09268746846872 1.07840397214886 1.09268746846872 1.07840397214886 4 - - 49087 Y Y 2.97635955220195 3.59528445727371 2.97635955220195 250 0 0.00880824832061733 Y 0.268759493670886 0.962177215189873 N N 81 5638 ENSG00000152380 ENSG00000039319 - + 5 5 79873962 79811254 upstream downstream FAM151B ZFYVE16 79819556 79739594 + + 0 79819311 79814743 - + N - - N HCC1954 21 12 2 7 2 N - - Y - SINE 0 1 1 7 0.678466075192994 0.321378667196682 0.678466075192994 0.321378667196682 1 - - 44310 N N 3.25195669441967 3.3038490300708 3.25195669441967 1 0 0.242603514662394 N 0 0 N N 41134 0 ENSG00000035403 ENSG00000220830 + + 10 9 75549916 11003096 intron upstream VCL RP11-109M17.1 75427878 11001748 + + 0.0111111111111112 75455903 10938426 + + Y 0.725776949372927 - N HCC1954 11 10 9 4 2 N - - N LTR - 1 0 1 4 0.307095170876829 0.735600060472404 0.735600060472404 0.307095170876829 2 0 - 20736 N Y 3.61257440753299 3.52936639476796 3.52936639476796 16 0 0.317833801927178 N 0.0704761904761906 0.814095238095238 N N 3703 5599 ENSG00000102393 ENSG00000137992 + + X 1 100549657 100487997 intron utr3p GLA DBT 100539435 100425072 - - 0.814095238095238 100542715 100432673 - - Y 0.668716697338045 - N HCC1954 26 22.5714285714286 21 7 1 N - - N - SINE 0 1 1 7 0.5713398527941 0.328520415356608 0.5713398527941 0.328520415356608 1 0 - 42492 Y Y 3.63296356710195 3.33680806132368 3.33680806132368 137 0.0394230769230769 0.935603410986856 Y 0.833974358974359 0.988141025641026 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 coding downstream AFF1 AC093827.3 88147177 88089842 + - 0 88186337 88088742 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 49 1.25694767614702 0.635615586233437 1.25694767614702 0.635615586233437 1 - - 46416 N Y 3.47552369040616 3.39950312334039 3.39950312334039 5 0 0.544962301115696 N 0.895548149029877 0.919652422330675 N N 1992 246 ENSG00000003436 ENSG00000197013 - + 2 19 188127464 21512919 utr5p intron TFPI ZNF429 188037202 21480277 - + 0.919652422330675 188127364 21486704 + + Y - 0.268803173058492 N HCC1954 24 20.1 17 10 2 N - - N - Other 0 1 1 10 0.821301038391519 0.721316564152552 0.821301038391519 0.721316564152552 2 - 0 22526 N N 3.34528969661801 3.4722913423473 3.34528969661801 1 0 0.0436028232887744 N 0 0 N N 5103 413 ENSG00000164933 ENSG00000179743 - + 8 1 104496447 16047229 utr3p utr3p SLC25A32 AL450998.19 104480045 16033561 - - 0 104481262 16033887 + - Y - - N HCC1954 26 24 22 4 1 N 268 27.3228 N SINE - 1 0 1 4 0.271386430077198 0.449930134075354 0.449930134075354 0.271386430077198 1 - - 48893 Y Y 3.60103760561896 3.60888739872753 3.60103760561896 358 0 0.00855499674169968 Y 0 0 N N 8953 6369 ENSG00000154122 ENSG00000154124 + + 5 5 14924876 14752842 intron utr3p ANKH FAM105B 14762019 14717783 - + 0 14765829 14746201 - + N 0.532449441058688 2.83458568583105 N HCC1954 1 1 1 0 1 N - - Y LINE - 0.291208791208791 0 0.291208791208791 28 1.29979816510658 1.28551466878673 1.29979816510658 1.28551466878673 1 0 0 44250 N Y 3.48759904855013 3.27973300890302 3.27973300890302 0 0 0.0431068114238319 N 0.0663299663299661 0.0979797979797979 N N 0 401 ENSG00000218767 ENSG00000172650 - + 9 10 29626851 75127645 upstream coding RP11-48L13.1 AGAP5 29626484 75104049 + - 0 29508063 75105744 - - Y - - N HCC1954 36 22.25 2 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.749883556792257 0.749883556792257 0.278528178237124 1 - - 720 Y Y 3.33953654827276 3.60785432895764 3.33953654827276 276 0 0.0216919242436970 Y 0.078821438337435 0.98120043751709 N N 0 27894 ENSG00000205177 ENSG00000085063 - + 11 11 33678862 33714600 coding utr3p C11orf91 CD59 33676484 33681134 - - 0 33676559 33688232 + - N - 0.143421753737198 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.842726282871298 0.721316564152552 0.842726282871298 0.721316564152552 2 - 0 21216 N N 2.99376390316809 3.0904070235176 2.99376390316809 6 0 0.212569888450349 N 0 0 N N 0 0 ENSG00000220375 ENSG00000222549 - + 1 3 558984 75314889 intron upstream RP5-857K21.14 SRP_euk_arch 558778 75314597 + - 0 558810 75347301 - - Y 1 - N HCC1954 14 9 4 4 1 N - - N - Simple_repeat 0 0.350961538461538 0.350961538461538 4 0.821301038391519 0.649899082553289 0.821301038391519 0.649899082553289 2 0 - 4430 N Y 3.234707967076 3.57336771439491 3.234707967076 0 0 0.304700665820528 N 0 0.872604651162791 Y N 0 5103 ENSG00000209951 ENSG00000196683 + - 7 7 86960 22828989 upstream intron AC097646.2-1 TOMM7 86858 22816536 - - 0 126103 22820436 - + N - 1.03110394785917 N HCC1954 148 98 80 4 1 N - - N - SINE 0 1 1 4 0.371370904316165 0.39993789695587 0.39993789695587 0.371370904316165 2 - 0 15754 N Y 3.39384326095097 3.82911562339586 3.39384326095097 2 0 0.400564592961012 N 0 0.775945793337098 N N 950 0 ENSG00000185436 ENSG00000177418 + - 1 7 24387036 65659784 intron downstream IL28RA AC006001.2-1 24353234 65659267 - - 0 24383836 65657259 - + Y 7.29859252223469 - N HCC1954 2 1.25 1 1 1 N - - N SINE - 1 0 1 4 0.299953422716903 0.385654400636018 0.385654400636018 0.299953422716903 3 0 - 47984 N N 3.38014703354132 3.45504124488137 3.38014703354132 0 0.166630192147766 0.184751888833994 N 0.181511795859413 0.151748588436119 N N 0 6627 ENSG00000223281 ENSG00000113269 + + 8 5 100002954 179431719 downstream coding 7SK RNF130 100002637 179315111 - - 0 99996157 179337828 - - Y - - N HCC1954 1 1 1 0 2 N 272 23.0717 N - - 0 0 0 6 0.942710757110266 0.735600060472404 0.942710757110266 0.735600060472404 0 - - 47993 N N 3.7297745213208 2.46144997190271 2.46144997190271 0 0 0.999903144213147 N 0 0.0128443526170799 N N 86504 0 ENSG00000104408 ENSG00000182152 + + 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0.0128443526170799 109296012 116890300 - - Y 0.543515163097469 - N HCC1954 2 1.23762376237624 1 24 7 N 241 0.00319582 N - LINE 0 1 1 101 0.842726282871298 1.16410495006798 1.16410495006798 0.842726282871298 4 0 - 34306 N Y 3.45447218342791 3.39489713955974 3.39489713955974 0 0 0.0906520166809333 Y 0.597026209677419 0 N N 0 545 ENSG00000218062 ENSG00000196597 - - 9 9 98721421 98655175 upstream upstream RP11-330M2.3 ZNF782 98721031 98619094 + - 0 98720761 98662441 - + N - - N HCC1954 2 1.71428571428571 1 5 2 N - - N - LINE 0 1 1 7 0.657040830713216 0.814159290231593 0.814159290231593 0.657040830713216 1 - - 39994 Y Y 3.47080361183081 3.65128658713112 3.47080361183081 0 0 0.974459842742235 Y 0.960761154855643 0.984304461942257 N N 524 1874 ENSG00000203289 ENSG00000187951 - + 15 15 28848794 28765101 upstream utr3p AC004460.1-2 ARHGAP11B 28795810 28705695 + + 0 28795715 28727209 - + N - - N HCC1954 5 2.02857142857143 1 30 3 N - - Y - - 0 0 0 35 0.93556900895034 1.22123893534739 1.22123893534739 0.93556900895034 4 - - 33637 N Y 3.50529022639353 3.57742544556096 3.50529022639353 157 0 0.0167550362410341 Y 0 0.979721825035747 N N 336285 151141 ENSG00000198868 ENSG00000198888 - + MT MT 12138 4264 coding coding MT-ND4 MT-ND1 10471 3308 + + 0 10974 4148 - + N - - N HCC1954 4 2 1 3 1 Y - - N - - 0 0 0 5 0.799875793911741 0.835584534711372 0.835584534711372 0.799875793911741 1 - - 6297 N Y 3.50848272165904 3.13636008197748 3.13636008197748 0 0 0.0725768949788736 N 0 0 N N 6863 0 ENSG00000068724 ENSG00000214121 - - 2 9 47156780 12963437 intron intron TTC7A AL161449.7 46996800 12962842 + - 0 47050700 12963410 - + Y 0.526115286317017 1 N HCC1954 16 7.6 2 5 1 N - - N SINE - 1 0 1 5 0.264244681917271 0.307095170876829 0.307095170876829 0.264244681917271 2 0 0 26461 N Y 3.45976132345673 3.51935717616377 3.45976132345673 157 0 0.0154074169795297 N 0 0.97419141368186 N N 0 0 ENSG00000169575 ENSG00000221580 + + 22 16 20929926 34993954 downstream downstream VPREB1 AC116553.2 20929192 34993845 + + 0 20952003 35120549 + + Y - - N HCC1954 240 240 240 4 1 N 119 23.2315 N - LINE 0 1 1 4 0.335662163516534 0.542772860154395 0.542772860154395 0.335662163516534 3 - - 23074 N Y 3.684245618384 3.33255199106474 3.33255199106474 0 0.647290809327846 0.670894430588897 N 0.647290809327846 0.626543209876543 N N 28881 324 ENSG00000127483 ENSG00000119946 + + 1 10 20985768 101144075 utr3p upstream HP1BP3 CNNM1 20941758 101078846 - + 0.626543209876543 20943024 101044577 - + Y - - N HCC1954 2 1.08333333333333 1 1 1 N - - N SINE,Simple_repeat SINE 0.318681318681319 1 1 12 0.649899082553289 0.34280391167646 0.649899082553289 0.34280391167646 4 - - 7664 N N 3.41175185377494 3.62361669590707 3.41175185377494 0 0 0.492278538695126 N 0 0 N N 462279 130 ENSG00000070756 ENSG00000198526 + + 8 2 101803491 147065027 coding intron PABPCP5 PABPCP2 101784320 147061731 - + 0 101786406 147063222 - + Y 0.583418240080683 - N HCC1954 2 1.75 1 3 1 N 233 11.1564 N - - 0 0 0 4 0.278528178237124 0.257102933757345 0.278528178237124 0.257102933757345 2 0 - 16998 N Y 3.53768019619294 3.26191384998362 3.26191384998362 5 0 0.785442903884055 N 0 0.944054307116105 N N 7935 9789 ENSG00000188529 ENSG00000159842 - + 1 17 24179408 1029881 utr3p coding FUSIP1 ABR 24163881 853510 - - 0 24169731 958925 + - Y - - N HCC1954 36 34.5 32 4 1 N - - N SINE - 1 0 1 4 0.364229156156239 0.45707188223528 0.45707188223528 0.364229156156239 2 - - 10431 Y Y 3.35872480420248 3.49744043328497 3.35872480420248 78 0.0295548961424333 0.187785683840203 Y 0.0295548961424333 0 N N 708 5401 ENSG00000108641 ENSG00000072134 + + 17 17 19206639 19180621 coding downstream B9D1 EPN2 19187076 19081283 - + 0 19187698 19181656 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.465277777777778 0.465277777777778 12 1.19267194270768 1.02841173502938 1.19267194270768 1.02841173502938 2 - - 19519 N Y 3.5920919620082 3.36079094374226 3.36079094374226 303 0.873434962543874 0.0265189338913452 N 0.936717481271937 0.976269055476976 N N 29204 3863 ENSG00000203832 ENSG00000219481 - + 1 1 146713675 146862781 utr5p intron NBPF10 NBPF15 146616873 146827614 - + 0 146713672 146836049 + + N - 1.38806547948372 Y HCC1954 20 12.8571428571429 8 7 1 N - - N - SINE 0 0.234782608695652 0.234782608695652 7 0.599906845433805 0.792734045751814 0.792734045751814 0.599906845433805 4 - 0 19955 N N 3.54144175291192 3.53039946453785 3.53039946453785 0 0 0.0603149851276544 N 0 0 N N 4626 0 ENSG00000133059 ENSG00000221151 + - 1 16 203447322 88689322 utr3p upstream DSTYK AC133919.3-4 203378255 88689218 - - 0 203382380 88700748 - + Y - - N HCC1954 152 132.655737704918 24 61 1 N - - N SINE - 1 0 1 61 0.485638874874985 1.0069864905496 1.0069864905496 0.485638874874985 2 - - 43033 N N 3.41952156054875 3.50848272165904 3.41952156054875 1 0 0.0673114150057604 N 0 0.596638655462185 N N 0 551733 ENSG00000212191 ENSG00000204628 + + 4 5 179844104 180603512 upstream coding SNORD65 GNB2L1 179844034 180596536 - - 0.596638655462185 180347017 180599139 - - Y - - N HCC1954 20 20 20 6 1 N - - N SINE - 1 0 1 6 0.335662163516534 0.899860268150708 0.899860268150708 0.335662163516534 1 - - 41638 N N 3.25512763186849 3.55334927718654 3.25512763186849 0 0 0.654736264228869 Y 0 0 N N 20899 35 ENSG00000164944 ENSG00000079112 + - 8 8 95634864 95289986 coding downstream KIAA1429 CDH17 95569776 95208566 - - 0 95587906 95113903 - + N 0.664204407523352 - N HCC1954 1 1 1 0 1 N 135 5.60697 N - - 0 0 0 4 0.87843502367093 0.685607823352921 0.87843502367093 0.685607823352921 2 0 - 46777 Y Y 3.06423421037986 3.81145495077599 3.06423421037986 285 0 0.0106799122811847 Y 0 0.98555809814391 N N 38635 288 ENSG00000083845 ENSG00000152475 - - 19 19 63597982 63573051 upstream upstream RPS5 ZNF837 63590448 63570805 + - 0 63584188 63573208 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.464213630395207 0.599906845433805 0.599906845433805 0.464213630395207 1 - - 33193 N N 3.67849247003875 3.63399663687184 3.63399663687184 1 0 0.0731140371896208 N 0 0 Y N 275222 240508 ENSG00000198763 ENSG00000198899 - + MT MT 5512 9208 coding coding MT-ND2 MT-ATP6 4471 8528 + + 0 5019 9078 - + N 0.971423063735393 - N HCC1954 4 2.5 2 4 1 N 563 8.20203 N - - 0 0 0 4 1.22838068350732 0.685607823352921 1.22838068350732 0.685607823352921 1 0 - 49520 N N 3.49424793801946 3.31063524818594 3.31063524818594 3 0 0.829810757240904 N 0 0 N N 3984 848 ENSG00000177879 ENSG00000112874 + - 5 5 115277675 102926389 coding upstream AP3S1 NUDT12 115205518 102912456 + - 0 115233724 103156551 + + N - - Y HCC1954 2 1.33333333333333 1 2 1 N 276 10.0817 N - LTR 0 0.889830508474576 0.889830508474576 6 0.892718519990782 0.842726282871298 0.892718519990782 0.842726282871298 4 - - 39943 Y N 3.15563906222957 3.68354236243323 3.15563906222957 0 0.249197860962567 0.0471447041981026 Y 0.249197860962567 0.249197860962567 N N 2124 2509 ENSG00000169612 ENSG00000103942 - - 15 15 81450795 81412481 upstream coding FAM103A1 HOMER2 81445975 81314792 + - 0.249197860962567 81445925 81352481 - + N - 1.80309713665875 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.528489363834543 0.621332089913584 0.621332089913584 0.528489363834543 1 - 0 12342 N N 3.49528100778935 3.39487633072086 3.39487633072086 0 0 0.0446682164895441 N 0 0 N N 7525 20636 ENSG00000173894 ENSG00000196526 - - 17 4 75375973 7992553 upstream intron CBX2 AFAP 75366588 7811341 + - 0 75358159 7879967 - + Y - 1.20478346788234 N HCC1954 21 20.5 20 4 1 N - - N LTR SINE 1 1 1 4 0.492780623034912 0.307095170876829 0.492780623034912 0.307095170876829 1 - 0 47032 N Y 3.14376879470857 3.33784113109357 3.14376879470857 217 0 0.122319249832754 Y 0.00460829493087567 0 N N 0 41760 ENSG00000177051 ENSG00000125743 + - 19 19 50906933 50887282 upstream intron FBXO46 SNRPD2 50906323 50882559 - - 0 50925948 50883665 - + N - 1.41403723103748 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 0.507064119354764 0.685607823352921 0.685607823352921 0.507064119354764 1 - 0 24523 N Y 3.47233119514066 3.37126417066287 3.37126417066287 5 0 0.104076166028897 N 0 0.902273929138022 N N 20739 0 ENSG00000143951 ENSG00000221471 - + 2 18 63669355 55567969 utr3p downstream C2orf86 AC098847.4 63202041 55567889 - + 0.902273929138022 63309485 55592955 + + Y - - N HCC1954 620 551.428571428571 400 7 1 N 471 22.5905 N LINE LINE 1 1 1 7 0.657040830713216 0.392796148795944 0.657040830713216 0.392796148795944 4 - - 40450 N N 3.25679254382414 3.57952209032428 3.25679254382414 8 0 0.0387329060732157 N 0 0 N N 4159 136 ENSG00000012061 ENSG00000188089 - + 19 15 50619017 40130680 utr5p utr3p ERCC1 PLA2G4E 50604712 40061072 - - 0 50618890 40062682 + - Y - - N HCC1954 32 24.4761904761905 21 21 1 N - - N - SINE,SINE 0 1 1 21 0.942710757110266 0.357087407996313 0.942710757110266 0.357087407996313 1 - - 41466 N N 3.65657572715995 3.58320909912975 3.58320909912975 0 0 0.892459278608423 Y 0 0 N N 0 0 ENSG00000208525 ENSG00000222501 - - 8 8 130372654 129092039 downstream downstream AC103833.2-1 U4 130372411 129091912 + - 0 130412706 129091871 - + N - - N HCC1954 1 1 1 0 4 N 575 2.9574 N LTR - 1 0 1 9 0.857009779191151 0.592765097273879 0.857009779191151 0.592765097273879 1 - - 40926 Y Y 3.70463477795295 3.29590595100639 3.29590595100639 249 0 0.0271715965704759 Y 0.820002903178981 0.988000193545265 N N 2 103 ENSG00000124249 ENSG00000064205 - + 20 20 42813078 42790564 upstream intron KCNK15 WISP2 42807902 42776899 + + 0 42800873 42778846 - + N - 1.12629834122864 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 7 0.39993789695587 0.528489363834543 0.528489363834543 0.39993789695587 1 - 0 26673 Y Y 3.69937614314766 3.39271690522525 3.39271690522525 163 0 0.0515842911052166 Y 0 0.985384337784194 N N 0 0 ENSG00000221286 ENSG00000207514 + + 16 16 71171037 70968219 downstream downstream AC092289.3 U6 71170942 70968104 - + 0 71114757 71018832 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR - 0.178947368421053 0 0.178947368421053 5 0.678466075192994 0.835584534711372 0.835584534711372 0.678466075192994 1 - - 26298 N Y 3.54144175291192 3.29549537585246 3.29549537585246 32 0.167548775425488 0.473108366367541 N 0.167548775425488 0.931766293067663 N N 66 7425 ENSG00000175311 ENSG00000068489 - + 16 17 21171251 54634706 utr3p utr3p ANKS4B PRR11 21152517 54587883 + + 0 21170951 54633911 - + Y - 2.28419318010561 N HCC1954 36 29.2 11 5 1 N - - N SINE - 1 0 1 5 0.442788385915428 0.428504889595575 0.442788385915428 0.428504889595575 2 - 0 14899 N N 3.49740058049162 3.69784855983781 3.49740058049162 20 0 0.0532784124550894 N 0 0 N N 29439 0 ENSG00000160752 ENSG00000219241 - + 1 21 153557080 20683028 coding intron FDPS FDPSP 153545331 20682517 + + 0.0453505796987144 153546478 20682667 - + Y - 1 N HCC1954 4 1.08928571428571 1 2 1 N - - N - - 0 0 0 56 0.999844742389676 0.292811674556976 0.999844742389676 0.292811674556976 1 - 0 29433 Y Y 3.43681151080804 3.21232721588077 3.21232721588077 0 0 0.463232104853904 Y 0 0 N N 161 3458 ENSG00000112293 ENSG00000124532 + + 6 6 24597829 24533788 intron coding GPLD1 MRS2L 24536384 24511132 - + 0 24538468 24526783 - + N 0.956991176811284 - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.0579710144927536 0 0.0579710144927536 6 0.871293275511003 0.742741808632331 0.871293275511003 0.742741808632331 2 0 - 31873 N N 3.6491271616355 3.63552422018169 3.63552422018169 0 0 0.0422527556163508 N 0.791445182724253 0 N N 12271 17644 ENSG00000177479 ENSG00000154174 + - 3 3 48997971 101602915 utr5p intron ARIH2 TOMM70A 48931285 101564999 + - 0 48939899 101599919 + + N - 1.48028694627654 Y HCC1954 28 23.25 20 4 1 N - - N - SINE 0 1 1 4 0.564198104634174 0.335662163516534 0.564198104634174 0.335662163516534 1 - 0 41613 Y Y 3.50272957331379 3.58527523866953 3.50272957331379 181 0 0.00533805673189513 Y 0.910608976348625 0.988826122043578 N N 0 34856 ENSG00000201216 ENSG00000155096 + - 8 8 104031968 103945573 downstream upstream Y_RNA AZIN1 104031870 103907712 - - 0 104019077 103961432 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE LTR 0.0208333333333333 1 1 4 0.914143764470561 0.478497126715059 0.914143764470561 0.478497126715059 2 - - 33190 N Y 3.45976132345673 3.15099609320118 3.15099609320118 289 0 0.00329916035129962 Y 0.129886897691474 0.992563135877705 N N 247001 240508 ENSG00000198786 ENSG00000198899 - + MT MT 14149 9208 coding coding MT-ND5 MT-ATP6 12338 8528 + + 0 13384 8949 - + N 0.889638996628838 - N HCC1954 6 4.25 3 4 1 N - - N - - 0 0 0 4 0.871293275511003 0.635615586233437 0.871293275511003 0.635615586233437 2 0 - 9575 Y Y 2.96419090810215 3.23164345288648 2.96419090810215 276 0 0.00243348121849718 Y 0.702694015895278 0.991964703132305 N N 4728 10313 ENSG00000129219 ENSG00000142507 - + 17 17 4673694 4648744 upstream downstream PLD2 PSMB6 4657378 4646415 + + 0 4657178 4651707 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity - 0.36986301369863 0 0.36986301369863 4 0.521347615674617 0.642757334393363 0.642757334393363 0.521347615674617 1 - - 39921 Y Y 3.37080016234644 3.46977054206092 3.37080016234644 172 0.0811310782241016 0.0158462979254455 Y 0.0811310782241016 0.984936575052854 N N 52 44 ENSG00000188095 ENSG00000166823 - - 15 15 88122979 88095547 coding upstream MESP2 MESP1 88120593 88094111 + - 0 88122401 88104850 - + N 0.194642777437044 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 1.19981369086761 0.585623349113953 1.19981369086761 0.585623349113953 2 0 - 13863 N Y 3.39168383545536 3.19396434305824 3.19396434305824 130 0.76445637705029 0.0877767233342271 N 0.85082237213185 0.952891275410058 Y Y 523 1381 ENSG00000100058 ENSG00000206062 - + 22 22 23957836 24187186 coding upstream CRYBB2 CRYBB2P1 23945612 24183283 + + 0 23955545 24185383 - + N - - N HCC1954 2 1.94642857142857 1 53 3 Y - - N - - 0 0 0 56 1.32122340958636 0.971277749749971 1.32122340958636 0.971277749749971 0 - - 49056 Y Y 3.36191729946799 3.46128890676658 3.36191729946799 341 0 0.364730056480805 Y 0.0195503421309873 0.983382209188661 N N 55216 1458 ENSG00000028310 ENSG00000188818 + - 5 5 945915 904101 downstream coding BRD9 ZDHHC11 916856 848722 - - 0 913659 903717 - + N - 3.56801771905363 N HCC1954 2 1.25 1 2 2 N - - Y LTR - 1 0 1 8 0.764167053112109 0.87843502367093 0.87843502367093 0.764167053112109 4 - 0 41493 Y Y 3.37824872787089 3.23999710710482 3.23999710710482 328 0.0434657218193802 0.0125380965452515 Y 0.986527686222808 0.993263843111404 N N 1458 0 ENSG00000158856 ENSG00000158815 - + 8 8 21995982 21962263 intron downstream EPB49 FGF17 21971322 21956374 + + 0 21980161 21962680 - + N 0.0226533324553753 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity,Low_complexity,Low_complexity 0 0.525641025641026 0.525641025641026 20 1.12125446110842 1.1141127129485 1.12125446110842 1.1141127129485 1 0 - 36296 N Y 3.37023110089298 3.57592836747465 3.37023110089298 351 0 0.201061079541834 Y 0 0 N Y 278 5028 ENSG00000198353 ENSG00000180818 - + 12 12 52736081 52670327 intron coding HOXC4 HOXC10 52696909 52665213 + + 0 52733211 52666061 - + N 0.314022379653777 0.593432355775348 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 11 1.04269523134923 1.1426797055882 1.1426797055882 1.04269523134923 4 0 0 6473 Y Y 3.57485544491141 3.13590542123087 3.13590542123087 112 0 0.0448180516123029 Y 0 0 N N 14117 0 ENSG00000068697 ENSG00000213729 - + 2 2 20114926 20219305 coding downstream LAPTM4A AC098828.3 20095894 20218875 - - 0 20104241 20170052 + - N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 5 0.807017542071667 0.535631111994469 0.807017542071667 0.535631111994469 1 - - 2722 N Y 3.39231567764112 3.41844863798551 3.39231567764112 332 0 0.00819370079049642 N 0 0.868322345987724 N N 4153 36780 ENSG00000120533 ENSG00000156599 - + 8 11 110425074 57225235 intron upstream ENY2 ZDHHC5 110415764 57191944 + + 0 110420525 57189369 - + Y 2.15856704737767 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 37 0.642757334393363 0.371370904316165 0.642757334393363 0.371370904316165 2 0 - 47474 N Y 3.44611852920956 3.46973068926756 3.44611852920956 0 0.72867280398926 0.194629791115369 N 0.955830456463368 0.955830456463368 N Y 232 2375 ENSG00000204514 ENSG00000178935 - - 19 19 63092182 63018093 coding upstream AC010326.7-2 ZNF552 63076002 63010262 - - 0 63080096 63012283 + + N - - Y HCC1954 3 2.5 1 5 1 Y - - N - - 0 0 0 6 0.899860268150708 0.928427260790413 0.928427260790413 0.899860268150708 2 - - 44104 N N 3.44512531223303 3.43408302385895 3.43408302385895 8 0 0.0446027327927745 N 0 0 N N 3891 3 ENSG00000166295 ENSG00000188937 - - 10 X 73665622 41219907 coding upstream C10orf104 NYX 73645812 41191631 + + 0.00214592274678105 73653742 41142397 - - Y - - N HCC1954 21 20.375 20 8 1 N 258 24.3085 N - SINE 0 1 1 8 1.17124669822791 0.328520415356608 1.17124669822791 0.328520415356608 1 - - 14892 N N 3.54503547576155 2.93343896987973 2.93343896987973 0 0.388529411764706 0.0210965840089604 N 0.563235294117647 0.621470588235294 N N 0 49 ENSG00000201183 ENSG00000186842 - - 1 21 146341653 32870062 upstream intron U1 C21orf77 146341492 32866420 + - 0.592352941176471 146337135 32868363 - + Y - 3.7798074459128 N HCC1954 23 20.75 20 4 1 N 332 22.7871 N SINE - 1 0 1 4 0.292811674556976 0.364229156156239 0.364229156156239 0.292811674556976 1 - 0 39827 Y Y 3.21804051143267 2.95591695947051 2.95591695947051 289 0 0.069267120497651 Y 0.466139396935245 0.976272862086011 N N 1304 0 ENSG00000186073 ENSG00000210354 - - 15 15 34889724 34649513 upstream upstream C15orf41 AC103988.7 34770651 34649295 + - 0 34724714 34659506 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 55 0.599906845433805 1.1426797055882 1.1426797055882 0.599906845433805 1 - - 17919 Y Y 3.33168675516419 3.64656650855576 3.33168675516419 288 0 0.084374628065163 Y 0.0449942129629631 0 N Y 2458 4504 ENSG00000158715 ENSG00000158711 + - 1 1 203916253 203868623 coding utr5p SLC45A3 ELK4 203893604 203851860 - - 0 203897612 203859642 - + N - 9.50758372018032 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 6 1.1426797055882 0.692749571512847 1.1426797055882 0.692749571512847 4 - 0 44390 N Y 3.3984700535705 3.63296356710195 3.3984700535705 0 0.692773813568921 0.0350361130532457 N 0.72964095594065 0.754219050855136 N N 8304 249 ENSG00000087299 ENSG00000150076 + + 14 10 49848697 33211797 utr3p intron L2HGDH C10orf68 49774064 32896657 - + 0.754219050855136 49780478 33113488 - + Y - 13.7178929359707 N HCC1954 32 27.5 21 12 1 N - - N LINE,LINE LINE 1 1 1 12 0.628473838073511 0.264244681917271 0.628473838073511 0.264244681917271 0 - 0 32502 N Y 3.24575025545007 3.48639814491089 3.24575025545007 220 0.184965034965035 0.00384567077062659 N 0.611888111888112 0.314335664335664 N N 56 0 ENSG00000181092 ENSG00000216027 - - 3 4 188058944 61212351 downstream downstream ADIPOQ AC095061.3 188043157 61212262 + - 0.443706293706294 188068649 60902269 - + Y - - N HCC1954 49 15.1333333333333 4 15 1 N 348 20.5716 N SINE SINE,SINE 1 0.842105263157895 1 15 0.321378667196682 0.271386430077198 0.321378667196682 0.271386430077198 1 - - 35944 N Y 3.47382827322697 3.6035982586987 3.47382827322697 0 0 0.313717947384145 N 0 0.713001575386896 N N 10259 430 ENSG00000049130 ENSG00000057657 - + 12 6 87498369 106664507 upstream upstream KITLG PRDM1 87410697 106640888 - + 0.713001575386896 87498695 106625732 + + Y - - N HCC1954 21 10 5 5 1 N 303 26.7224 N - SINE 0 1 1 5 0.464213630395207 0.271386430077198 0.464213630395207 0.271386430077198 4 - - 36526 Y Y 3.23892418454158 3.46910819465161 3.23892418454158 0 0 0.93317926621783 Y 0.936537050623624 0.978845683541208 N N 2401 16105 ENSG00000120647 ENSG00000073614 - - 12 12 422065 368881 utr5p upstream CCDC77 JARID1A 381084 259484 + - 0 384991 368912 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 6 0.535631111994469 0.685607823352921 0.685607823352921 0.535631111994469 1 - - 36689 N Y 3.41315949795669 3.47233119514066 3.41315949795669 0 0 0.98471602797829 Y 0 0.963358665613896 N N 9765 351 ENSG00000139182 ENSG00000205885 - + 12 12 7202793 7165701 utr5p coding CLSTN3 AC018653.29-1 7174234 7152443 + + 0 7174443 7164497 - + N - - N HCC1954 1 1 1 0 3 Y - - N - - 0 0 0 4 0.942710757110266 0.892718519990782 0.942710757110266 0.892718519990782 4 - - 13773 Y Y 3.28399842673177 3.51001030496889 3.28399842673177 257 0 0.279277356611335 Y 0 0.982972496591174 N N 3693 721 ENSG00000198125 ENSG00000100302 + + 22 22 34349347 34279987 downstream downstream MB RASD2 34332757 34267296 - + 0 34306893 34282904 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE LTR 0.66 1 1 6 0.714174815992626 0.914143764470561 0.914143764470561 0.714174815992626 4 - - 496 Y Y 3.02647539496492 3.63399663687184 3.02647539496492 44 0.094359259624788 0.447429001142212 Y 0.0591887454354593 0.995603685726334 N N 95337 3156 ENSG00000172757 ENSG00000172732 - - 11 11 65382380 65390485 utr5p intron CFL1 MUS81 65378884 65384801 - + 0 65382206 65385350 + - N - 0.555188948980558 N HCC1954 2 1.07142857142857 1 1 3 N - - Y - SINE 0 0.136363636363636 0.136363636363636 14 1.27123117246687 1.47834186910473 1.47834186910473 1.27123117246687 1 - 0 5289 N Y 3.58743466416515 3.48337348351473 3.48337348351473 22 0.0274174388215727 0.0281995336398011 N 0.762984081729627 0.79567593252554 N N 153380 420 ENSG00000185275 ENSG00000122641 + - Y 7 19614093 41709231 utr3p upstream CD24L4 INHBA 19611898 41695126 - - 0 19612795 41762360 - + Y - - N HCC1954 5 3.16666666666667 1 5 1 N - - N - SINE 0 1 1 6 0.485638874874985 0.278528178237124 0.485638874874985 0.278528178237124 1 - - 4760 N Y 3.22912265260009 3.38296880644625 3.22912265260009 0 0 0.702691201874492 Y 0.012025669642857 0.973297991071429 N N 497 0 ENSG00000135205 ENSG00000201959 - + 7 7 76762457 76509001 utr5p downstream CCDC146 Y_RNA 76589870 76508900 + + 0 76634911 76514170 - + N - - N HCC1954 20 10 2 5 1 N - - N - LTR 0 1 1 5 1.05697872766909 0.621332089913584 1.05697872766909 0.621332089913584 4 - - 36997 N N 3.6035982586987 3.44296588673741 3.44296588673741 0 0 0.988863995890922 N 0.00352112676056349 0 N N 2 20154 ENSG00000185610 ENSG00000168575 + + 12 8 43731149 42516225 intron intron DBX2 SLC20A2 43694806 42393173 - - 0 43723522 42477706 - - Y 0.918684047175667 36.1317356738638 N HCC1954 1 1 1 0 4 N 141 0.300921 N LTR - 1 0 1 33 0.928427260790413 1.18553019454776 1.18553019454776 0.928427260790413 4 0 0 759 N Y 3.46657804679541 3.2720510496638 3.2720510496638 0 0.0934235976789169 0.0253295785130158 Y 0.683752417794971 0.915667311411992 N N 2001 12566 ENSG00000178202 ENSG00000173039 + - 11 11 107874369 65186959 utr3p upstream KDELC2 RELA 107848062 65177649 - - 0.0934235976789169 107849074 65187086 - + N - - N HCC1954 35 33.8 33 10 1 N - - N SINE Low_complexity 1 0.0121951219512195 1 10 0.307095170876829 0.585623349113953 0.585623349113953 0.307095170876829 1 - - 10399 Y Y 3.54569782317086 3.61001375445325 3.54569782317086 6 0 0.799014723534001 Y 0 0.98288265938973 N N 23404 2826 ENSG00000181885 ENSG00000170291 + + 17 17 7106520 7103974 coding intron CLDN7 C17orf81 7103953 7096096 - + 0 7104742 7099355 - + N - 2.67555365111925 N HCC1954 20 13.8 4 5 3 N - - Y - SINE 0 0.975308641975309 0.975308641975309 5 0.607048593593732 0.578481600954027 0.607048593593732 0.578481600954027 3 - 0 48880 N N 3.19396434305824 3.70889084821189 3.19396434305824 0 0 0.514107299952212 Y 0 0 N N 0 21549 ENSG00000201910 ENSG00000063438 - + 5 5 103462638 491392 downstream intron U1 PDCD6 103462474 324736 + + 0 103467776 325889 - + N - 11.2085024156116 N HCC1954 4 2.66666666666667 2 6 2 N 312 11.8566 N LINE,LTR - 0.666666666666667 0 0.666666666666667 6 0.857009779191151 0.671324327033068 0.857009779191151 0.671324327033068 2 - 0 26708 Y Y 3.48487056160104 2.9406186008375 2.9406186008375 215 0 0.0275667737703367 Y 0.990520487264673 0.981040974529347 N Y 7869 284 ENSG00000140905 ENSG00000166455 + - 16 16 79687481 79668373 coding coding GCSH C16orf46 79673430 79644603 - - 0 79675569 79645200 - + N 0.313762603761554 1.00069041265138 N HCC1954 5 3.57142857142857 2 7 1 N - - Y - - 0 0 0 7 0.764167053112109 0.749883556792257 0.764167053112109 0.749883556792257 4 0 0 40552 N N 3.25000632570901 3.46657804679541 3.25000632570901 1 0 0.346578365202968 N 0 0 N N 106385 21198 ENSG00000071539 ENSG00000137815 - - 5 15 971156 39563053 coding intron TRIP13 RTF1 946004 39496594 + + 0 947903 39506008 - - Y - 0.624287980678544 N HCC1954 1 1 1 0 1 N 450 18.3692 N - SINE 0 1 1 4 0.428504889595575 0.271386430077198 0.428504889595575 0.271386430077198 3 - 0 235 Y Y 3.69784855983781 3.46873266376303 3.46873266376303 0 0 0.152974715619366 Y 0.233246753246753 0.971601731601731 N N 3202 1747 ENSG00000166575 ENSG00000174804 - - 11 11 86712215 86344081 upstream upstream TMEM135 FZD4 86426548 86334370 + - 0 86388567 86344863 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.94488188976378 0 0.94488188976378 5 0.649899082553289 0.671324327033068 0.671324327033068 0.649899082553289 2 - - 14227 N Y 3.64231043829683 3.20600500608205 3.20600500608205 5 0 0.192283097718988 N 0 0.325784615384615 N N 85 18603 ENSG00000178722 ENSG00000099940 - + 5 22 61038108 19574109 utr3p downstream AC094086.2 SNAP29 61018466 19543292 + + 0.325784615384615 61036485 19575218 - + Y - - N HCC1954 33 32.4 31 5 1 N 98 26.4182 N SINE SINE,SINE 1 0.5625 1 5 0.328520415356608 0.34280391167646 0.34280391167646 0.328520415356608 1 - - 5788 N Y 3.43937216388778 3.49015970162987 3.43937216388778 144 0 0.0309681576571744 N 0.932268518518519 0.864537037037037 N N 1031 10473 ENSG00000175105 ENSG00000134318 - - 3 2 88276504 11402162 upstream intron ZNF654 ROCK2 88270952 11237338 + - 0.00865740740740739 88260646 11315324 - + Y - 1.8670296210948 N HCC1954 2 1.8 1 16 1 N - - N - - 0 0 0 20 1.15696320190805 1.40692438750547 1.40692438750547 1.15696320190805 0 - 0 38215 Y Y 3.55401162459584 3.65760879692984 3.55401162459584 201 0 0.0530338019602845 Y 0 0 N N 13117 13719 ENSG00000131981 ENSG00000168175 - + 14 14 54681874 54606665 upstream downstream LGALS3 MAPK1IP1L 54665574 54588110 + + 0 54639599 54623476 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 8 0.492780623034912 0.764167053112109 0.764167053112109 0.492780623034912 1 - - 694 N Y 3.41207299502431 2.80146189137754 2.80146189137754 10 0 0.659684624256731 Y 0.520275750202758 0.981549067315491 N N 8913 0 ENSG00000134909 ENSG00000209294 - - 11 11 128567303 128665093 coding upstream AP000751.4-1 AP002886.3-1 128343052 128665009 - + 0 128567204 128654599 + - N - - N HCC1954 1 1 1 0 2 N - - N - Low_complexity 0 0.530769230769231 0.530769230769231 4 0.807017542071667 0.671324327033068 0.807017542071667 0.671324327033068 2 - - 37203 N N 3.56488607910057 3.49640736351508 3.49640736351508 20 0.0231971153846153 0.0491112737645193 N 0.0231971153846153 0.7984375 N N 11413 3189 ENSG00000112877 ENSG00000135679 - + 5 12 706664 67520481 coding utr3p CEP72 MDM2 665405 67488247 + + 0.178245192307692 672182 67520464 - + Y - - N HCC1954 34 31.2857142857143 29 7 1 N 114 24.8792 N - SINE 0 1 1 7 0.485638874874985 0.328520415356608 0.485638874874985 0.328520415356608 1 - - 14973 N Y 3.66592259835483 3.50575423470996 3.50575423470996 0 0 0.97280498488496 N 0 0.898367346938775 N N 3 0 ENSG00000185177 ENSG00000218362 - + 7 1 57211513 245439418 coding intron ZNF733 RP11-488L18.4 57191270 245419776 - - 0.898367346938775 57198242 245429994 + - Y - 1 N HCC1954 3 3 3 4 2 N 199 24.7532 N - - 0 0 0 4 0.335662163516534 0.357087407996313 0.357087407996313 0.335662163516534 2 - 0 5371 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.790327275353928 N 0.114775 0.98405 N N 2799 3966 ENSG00000111816 ENSG00000175772 + + 6 2 116488614 110111006 intron upstream FRK AC013268.5-1 116369389 110103138 - + 0 116391466 110102056 - + Y 0.65625334462359 - N HCC1954 40 39.7241379310345 34 29 1 N - - N LINE - 1 0 1 29 0.685607823352921 1.29979816510658 1.29979816510658 0.685607823352921 3 0 - 46755 Y Y 3.25822684117816 3.45823374014688 3.25822684117816 385 0 0.00277648324143343 Y 0.0025974025974026 0.983376623376623 N N 65965 17 ENSG00000108107 ENSG00000160472 - + 19 19 60595261 60581424 upstream downstream RPL28 TMEM190 60589112 60580016 + + 0 60587113 60582549 - + N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.230769230769231 0 0.230769230769231 7 1.02126998686945 0.442788385915428 1.02126998686945 0.442788385915428 1 - - 3788 N N 3.11129069662652 3.29006956921008 3.11129069662652 2 0 0.117933768105663 N 0 0 N N 0 5 ENSG00000221415 ENSG00000183844 - + 4 21 48895063 41651524 downstream intron AC118282.4-1 FAM3B 48894981 41610526 + + 0 49001703 41632350 - + Y - 0.768768578837518 N HCC1954 13 11.75 11 4 1 N - - N Satellite - 1 0 1 4 0.307095170876829 0.507064119354764 0.507064119354764 0.307095170876829 3 - 0 33361 N N 3.51104337473878 3.30232144676095 3.30232144676095 0 0 0.0667952455347178 N 0 0.00772380772380765 Y N 544065 0 ENSG00000198744 ENSG00000210194 - - MT MT 9988 14743 coding intron MT-CO3 AF347015.1-22 8367 14675 + - 0.00772380772380765 8752 14730 - + N - 1 N HCC1954 2 2 2 4 1 N 189 4.09957 N - - 0 0 0 4 0.849868031031224 0.614190341753658 0.849868031031224 0.614190341753658 1 - 0 17442 N Y 3.32320511986986 3.80041266240192 3.32320511986986 34 0.0779344967726512 0.461100684400192 Y 0.989401545939915 0.978803091879831 N Y 13331 66911 ENSG00000011007 ENSG00000142676 - + 1 1 23958974 23895502 coding coding TCEB3 RPL11 23942549 23890881 + + 0 23948098 23893868 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.849868031031224 0.764167053112109 0.849868031031224 0.764167053112109 4 - - 14330 N N 3.53039946453785 3.51679652308403 3.51679652308403 12 0.0419620943550586 0.0895501690258635 N 0.0944573220616306 0.704714344150532 N N 14402 13788 ENSG00000156689 ENSG00000116237 - + 11 1 58368833 6218631 utr5p utr3p GLYATL2 ICMT 58358118 6203840 - - 0.0944573220616306 58363701 6204788 + - Y - - N HCC1954 40 39 38 4 1 N 281 24.8498 N - SINE 0 1 1 4 0.385654400636018 0.292811674556976 0.385654400636018 0.292811674556976 2 - - 21950 N N 3.71873223294673 3.58999531724489 3.58999531724489 6 0 0.0864366648855037 N 0 0.313072146218843 N N 0 70 ENSG00000212875 ENSG00000198732 + + 1 14 557859 69568836 intron intron RP5-857K21.6 SMOC1 556317 69415896 + + 0 556712 69506151 + + Y 1 1.15442562035188 N HCC1954 3 2.2 2 5 1 N - - N - LTR 0 1 1 5 0.714174815992626 0.249961185597419 0.714174815992626 0.249961185597419 2 0 0 10398 Y Y 3.23999710710482 3.72079837248651 3.23999710710482 0 0 0.988413611967062 Y 0 0.983191866145579 N N 23404 2826 ENSG00000181885 ENSG00000170291 + + 17 17 7106520 7103974 coding intron CLDN7 C17orf81 7103953 7096096 - + 0 7104685 7100668 - + N - 2.67555365111925 N HCC1954 1 1 1 0 3 N - - Y - SINE 0 0.264248704663212 0.264248704663212 10 1.1141127129485 1.31408166142643 1.31408166142643 1.1141127129485 4 - 0 18996 Y Y 3.62039369541802 3.61038447681384 3.61038447681384 0 0 0.626719586712966 Y 0.993172637864419 0.993172637864419 N N 2211 0 ENSG00000143036 ENSG00000217711 - - 1 1 95133389 94912305 upstream upstream SLC44A3 RP11-86H7.2 95058523 94911066 + - 0 95058103 94917754 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.342105263157895 0.342105263157895 6 1.08554572030879 1.08554572030879 1.08554572030879 1.08554572030879 2 - - 44219 N N 3.21279122419719 3.425274708894 3.21279122419719 0 0 0.0835159657437814 N 0 0 N N 3891 24641 ENSG00000166295 ENSG00000144674 + + 10 3 73665622 37383240 intron intron C10orf104 GOLGA4 73645812 37259742 + + 0 73645955 37359834 + + Y 0.744979490524871 3.47477375505331 N HCC1954 21 19.3333333333333 17 6 1 N - - N - SINE 0 1 1 6 0.814159290231593 0.407079645115797 0.814159290231593 0.407079645115797 1 0 0 5449 N Y 3.47552369040616 3.57229479183167 3.47552369040616 4 0 0.229878207792559 N 0.901277703559072 0.89230294933717 N N 1992 0 ENSG00000003436 ENSG00000211421 - + 2 6 188127464 88487454 utr5p downstream TFPI AL133211.9 188037202 88487352 - + 0.89230294933717 188127364 88503243 + + Y - - N HCC1954 24 14.1666666666667 3 6 1 N - - N - Other 0 1 1 6 0.707033067832699 0.535631111994469 0.707033067832699 0.535631111994469 2 - - 33229 N N 3.50848272165904 3.25463311832853 3.25463311832853 1 0 0.997928677584065 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8754 11381 - + N 0.559268386776935 - N HCC1954 2 1.75 1 3 7 N 189 4.09957 N - - 0 0 0 4 0.671324327033068 0.93556900895034 0.93556900895034 0.671324327033068 2 0 - 16376 N N 3.25256697878875 3.44975210485255 3.25256697878875 1 0 0.0741704068596294 N 0 0 N N 49089 11330 ENSG00000117450 ENSG00000072135 - + 1 2 45760196 130849446 coding intron PRDX1 PTPN18 45749295 130830088 - + 0 45757275 130845808 + + Y - 0.684569644059298 N HCC1954 40 6.55 1 39 1 N - - N - SINE 0 1 1 40 1.07126222398894 0.385654400636018 1.07126222398894 0.385654400636018 2 - 0 34487 Y Y 3.17407904459906 3.50319358163022 3.17407904459906 240 0 0.0651870350904596 Y 0 0.989175724637681 N N 168 419 ENSG00000197646 ENSG00000120217 - + 9 9 5565421 5471569 intron intron PDCD1LG2 CD274 5500579 5440559 + + 0 5514535 5449186 - + N 0.779705576009402 1.05020223786365 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.521347615674617 0.535631111994469 0.535631111994469 0.521347615674617 1 0 0 9294 Y Y 3.36720643949681 3.09190410160392 3.09190410160392 223 0 0.0391061191959723 Y 0.832334198725513 0.989520887420344 N N 1775 97 ENSG00000176390 ENSG00000197522 + + 17 17 26175904 26109477 intron downstream CRLF3 SUZ12P 26133852 26082850 - + 0 26135923 26121105 - + N 0.573503931528385 - N HCC1954 8 2 1 3 1 N - - Y SINE - 1 0 1 9 0.678466075192994 0.707033067832699 0.707033067832699 0.678466075192994 2 0 - 44821 Y Y 3.20124507471334 3.42424163912411 3.20124507471334 278 0 0.127123641391435 Y 0.932063440156965 0.984902986701548 N N 2962 687 ENSG00000156521 ENSG00000042286 + - 10 10 71576502 71562696 coding utr5p TYSND1 AIFM2 71567739 71527985 - - 0 71576295 71553859 - + N 1.58865148473073 1.59980616953558 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.821301038391519 0.892718519990782 0.892718519990782 0.821301038391519 4 0 0 30239 Y Y 3.57233464462502 3.70719543103269 3.57233464462502 280 0 0.984294782401552 Y 0.946346153846154 0.992335164835165 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62646547 62569094 - + N - - N HCC1954 1 1 1 0 7 N - - Y LINE,LINE,LTR LTR 0.522292993630573 1 1 17 1.12125446110842 0.892718519990782 1.12125446110842 0.892718519990782 1 - - 19598 N Y 3.67849247003875 3.62398741826765 3.62398741826765 268 0.724110218140069 0.00170094488539774 N 0.724110218140069 0.724110218140069 N N 0 14314 ENSG00000176855 ENSG00000154845 + - 1 18 181196120 9604606 intron upstream KRT18P28 PPP4R1 181194832 9536789 - - 0.908036739380023 181195601 9669009 - + Y 1 - N HCC1954 13 8.36363636363636 7 11 1 N 16 26.5811 N - - 0 0 0 11 0.414221393275723 0.264244681917271 0.414221393275723 0.264244681917271 1 0 - 42331 Y Y 3.41679307359967 3.25472640428436 3.25472640428436 269 0 0.00289182093185869 Y 0.0197865451492987 0.983930926969661 N N 1913 501 ENSG00000038210 ENSG00000109618 - - 4 4 24889811 24771162 upstream upstream PI4K2B SEPSECS 24844751 24730734 + - 0 24844527 24807616 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE,LTR 0 0.697674418604651 0.697674418604651 7 0.464213630395207 0.614190341753658 0.614190341753658 0.464213630395207 1 - - 28819 N Y 3.51782959285392 3.50422665140011 3.50422665140011 0 0 0.107755774803753 N 0 0.794781783681214 N N 75177 224 ENSG00000125107 ENSG00000196684 + + 16 19 57221251 16130344 utr5p intron CNOT1 HSH2D 57111359 15938466 - + 0 57190783 16000737 - + Y - 0.177800770047835 N HCC1954 21 20.5 20 6 1 N - - N - SINE 0 1 1 6 0.421363141435649 0.299953422716903 0.421363141435649 0.299953422716903 2 - 0 48807 Y Y 3.31456730098965 3.46128890676658 3.31456730098965 0 0.160345873786407 0.860054902781692 Y 0.160345873786407 0.937803398058252 N N 55216 1458 ENSG00000028310 ENSG00000188818 + - 5 5 945915 904101 downstream coding BRD9 ZDHHC11 916856 848722 - - 0 912716 903717 - + N - 3.56801771905363 N HCC1954 2 1.6 1 3 2 N - - Y LTR,LTR - 0.875 0 0.875 5 0.51420586751469 0.735600060472404 0.735600060472404 0.51420586751469 4 - 0 8320 N Y 3.47233119514066 3.37126417066287 3.37126417066287 2 0 0.127891546009165 N 0 0.900632911392405 N N 20739 188 ENSG00000143951 ENSG00000152503 - + 2 5 63669355 114544142 utr3p downstream C2orf86 TRIM36 63202041 114488377 - - 0.884071729957806 63309485 114280985 + - Y - - N HCC1954 620 471.428571428571 420 7 1 N - - N LINE LINE 1 1 1 7 0.39993789695587 0.385654400636018 0.39993789695587 0.385654400636018 4 - - 31291 Y Y 3.61360747730289 3.60103760561896 3.60103760561896 196 0 0.745715967271413 Y 0.986909237379162 0.986909237379162 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 intron upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42867819 42826014 - + N 0.0692123342775211 - N HCC1954 1 1 1 0 6 N - - Y - LTR 0 1 1 12 0.942710757110266 0.51420586751469 0.942710757110266 0.51420586751469 2 0 - 38088 Y Y 3.43465208531242 3.62192127872787 3.43465208531242 261 0 0.703982118790774 Y 0 0.989514014922363 N N 2447 4331 ENSG00000157379 ENSG00000100949 + - 14 14 23838770 23810643 coding utr5p DHRS1 RABGGTA 23829646 23804661 - - 0 23831242 23810354 - + N 0.972831249105628 3.80639939049814 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 44 0.956994253430118 0.714174815992626 0.956994253430118 0.714174815992626 3 0 0 7306 Y Y 3.73912139251568 3.51360402781852 3.51360402781852 241 0 0.0890401937772481 Y 0 0.978351073425943 N N 120 38670 ENSG00000163009 ENSG00000171848 - + 2 2 10269307 10188996 intron coding C2orf48 RRM2 10198960 10179906 + + 0 10256110 10186813 - + N 0.30976571908614 - N HCC1954 12 5 2 6 2 N - - Y SINE,LTR - 0.573333333333333 0 0.573333333333333 6 0.535631111994469 0.678466075192994 0.678466075192994 0.535631111994469 1 0 - 36467 Y Y 3.34359427943881 3.31332620405544 3.31332620405544 0 0.483639623487225 0.0638728947548779 Y 0.483639623487225 0.956969968623936 N N 28 2985 ENSG00000135437 ENSG00000135441 - + 12 12 54404754 54399751 coding coding RDH5 BLOC1S1 54400488 54396088 + + 0 54401774 54399147 - + N 0.482625614886066 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.39993789695587 0.578481600954027 0.578481600954027 0.39993789695587 2 0 - 13016 N Y 2.96944535301082 3.35662815943916 2.96944535301082 3 0 0.345836416294967 N 0 0.111848967387525 N N 20747 119 ENSG00000073605 ENSG00000178187 + + 17 5 35328429 178326040 intron utr3p GSDMB ZNF454 35314374 178300830 - + 0 35326224 178325926 - + Y 1.3429789198597 - N HCC1954 40 31.8 25 5 1 N - - N SINE SINE 1 1 1 5 0.564198104634174 0.371370904316165 0.564198104634174 0.371370904316165 2 0 - 47591 N Y 3.56488607910057 3.55128313764676 3.55128313764676 232 0.928879310344827 0.0217305118449217 N 0.928879310344827 0.928879310344827 N Y 1289 756 ENSG00000198551 ENSG00000197647 - + 19 19 11590974 12007525 coding intron ZNF627 ZNF433 11569327 11986532 + - 0 11586342 12007352 - - N - 1.79030903358619 Y HCC1954 2 1.14285714285714 1 1 1 Y - - N - - 0 0 0 7 0.328520415356608 0.649899082553289 0.649899082553289 0.328520415356608 4 - 0 33925 N N 3.14160936921295 3.6550481438501 3.14160936921295 16 0.152786885245902 0.198784704111101 N 0.152786885245902 0.152786885245902 N N 544065 247001 ENSG00000198744 ENSG00000198786 + + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.152786885245902 8677 13302 + + N 0.567956504381133 0.87156031178364 Y HCC1954 2 1.25 1 1 2 N 316 3.86643 N - - 0 0 0 4 0.592765097273879 0.835584534711372 0.835584534711372 0.592765097273879 1 0 0 21793 N Y 3.43039601505348 3.5465630590714 3.43039601505348 0 0 0.0745421864272316 N 0.00549450549450559 0.831914564308931 N N 3863 3044 ENSG00000219481 ENSG00000139428 + + 1 12 146862781 108495741 utr5p utr3p NBPF15 MMAB 146827614 108475908 + - 0 146833477 108477571 + - Y - - N HCC1954 50 45.2222222222222 29 9 1 N 197 21.8592 N - SINE 0 1 1 9 0.499922371194838 0.321378667196682 0.499922371194838 0.321378667196682 1 - - 31511 Y Y 3.21063179870157 3.41885921313945 3.21063179870157 257 0 0.260426640877927 Y 0.0273289082169834 0.976562142366674 N N 1033 0 ENSG00000196639 ENSG00000213964 - - 3 3 11280243 11251366 intron downstream HRH1 AC083855.3 11269385 11250939 + - 0 11269735 11242735 - + N 0.100980360513097 - N HCC1954 1 1 1 0 3 N - - Y LTR LINE 1 1 1 4 0.5713398527941 0.664182578873142 0.664182578873142 0.5713398527941 3 0 - 30485 Y Y 3.47076375903745 3.38296880644625 3.38296880644625 0 0 0.980119895094648 Y 0 0.977108084613156 N N 111946 0 ENSG00000147065 ENSG00000219305 - - X X 64878517 64689026 coding upstream MSN RP3-475B7.3 64804283 64687503 + - 0 64853405 64725673 - + N 0.414665979762095 - N HCC1954 2 1.16666666666667 1 1 2 N - - Y - Simple_repeat 0 0.263565891472868 0.263565891472868 6 0.699891319672773 0.921285512630487 0.921285512630487 0.699891319672773 4 0 - 16490 N Y 3.69359248957888 3.25256697878875 3.25256697878875 0 0 0.075677605150474 N 0 0 N N 15776 49089 ENSG00000115963 ENSG00000117450 - - 2 1 151052427 45760196 upstream coding RND3 PRDX1 151032955 45749295 - - 0 151174334 45757275 + + Y - 3.11556065904221 N HCC1954 4 2.75 1 3 1 N 116 28.3329 N SINE - 1 0 1 4 0.357087407996313 0.492780623034912 0.492780623034912 0.357087407996313 2 - 0 47312 Y Y 3.55401162459584 3.10873004354678 3.10873004354678 0 0 0.990530960296113 Y 0 0.995875902908831 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 coding upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10599435 10574400 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.792734045751814 0.671324327033068 0.792734045751814 0.671324327033068 1 - - 46564 N Y 2.78130147148845 2.79628715205557 2.78130147148845 0 0.5078125 0.0310530070290008 N 0.5078125 0.5078125 N N 30762 36111 ENSG00000104853 ENSG00000099917 + + 19 22 50188438 19271918 intron utr5p CLPTM1 MED15 50150477 19191886 + + 0.5078125 50173095 19191950 + + Y 0.844905708498175 0.625962417472082 N HCC1954 22 20.3571428571429 20 14 1 N - - N SINE - 1 0 1 14 0.328520415356608 0.449930134075354 0.449930134075354 0.328520415356608 2 0 0 11744 N Y 3.2274272354209 3.54503547576155 3.2274272354209 1 0 0.738734369655563 N 0.914155317299333 0.8969863807592 N N 1649619 2 ENSG00000141736 ENSG00000156035 + - 17 9 35138441 78710823 coding intron ERBB2 PRUNE2 35104766 78593130 + - 0.8969863807592 35122227 78614423 + + Y - 0.8787023977433 N HCC1954 17 11.3333333333333 1 4 1 N - - N - SINE 0 1 1 6 0.757025304952183 0.314236919036755 0.757025304952183 0.314236919036755 3 - 0 41566 N N 3.46910819465161 3.4780843434859 3.46910819465161 0 0 0.786632666269907 N 0 0 Y N 11269 1602 ENSG00000164684 ENSG00000147650 + - 8 8 81949571 105670344 coding upstream ZNF704 LRP12 81713324 105570643 - - 0 81896166 105872353 - + N 1.49854789520879 - N HCC1954 1 1 1 0 1 N - - N - SINE 0 0.738805970149254 0.738805970149254 6 0.899860268150708 0.956994253430118 0.956994253430118 0.899860268150708 2 0 - 3689 N N 3.57696143724454 3.4797797606651 3.4797797606651 0 0 0.100042491876526 N 0 0.385219164118247 N N 21319 10428 ENSG00000184787 ENSG00000114346 + + 21 3 45046166 174021957 utr3p intron UBE2G2 ECT2 45013384 173951207 - + 0.385219164118247 45014856 173951474 - + Y - 0.443838089061747 N HCC1954 36 34.5 33 8 1 N - - N SINE - 1 0 1 8 0.349945659836387 0.542772860154395 0.542772860154395 0.349945659836387 2 - 0 47360 Y Y 3.12279699331701 3.64231043829683 3.12279699331701 193 0.00276243093922668 0.620574749780527 Y 0.0329817512137954 0 N N 560 584 ENSG00000063127 ENSG00000197813 - + 19 19 54520286 54535371 coding intron SLC6A16 AC011450.4 54484709 54523236 - - 0 54489621 54526144 + - N - 0.579920891682526 N HCC1954 1 1 1 0 4 N - - Y - LTR,SINE 0 0.703296703296703 0.703296703296703 4 0.999844742389676 0.649899082553289 0.999844742389676 0.649899082553289 1 - 0 12231 N Y 3.12328634918378 2.99930936485065 2.99930936485065 0 0 0.966434027580199 N 0.976398221509043 0.982298666131782 N N 4310 1021 ENSG00000183011 ENSG00000104714 - + 17 8 7701897 671226 coding upstream LSMD1 ERICH1 7700730 604201 - - 0 7701426 913663 + - Y - - N HCC1954 4 2.78963414634146 1 308 3 N - - N - Other 0 0.046875 0.046875 328 1.26408942430695 1.37121564670584 1.37121564670584 1.26408942430695 2 - - 13339 N N 3.36870351758313 3.30232144676095 3.30232144676095 0 0 0.0453323850465669 N 0 0 N N 417 3693 ENSG00000172986 ENSG00000198125 - + 3 22 73107077 34349347 intron coding GLT8D4 MB 73020075 34332757 + - 0 73043972 34343239 - - Y 0.597299285419338 - N HCC1954 16 2.94117647058824 1 15 1 N - - N SINE - 1 0 1 17 0.278528178237124 0.607048593593732 0.607048593593732 0.278528178237124 1 0 - 751 Y Y 3.61356762450953 2.88466990414258 2.88466990414258 0 0 0.986608050431847 Y 0.936961718570914 0.994269247142811 N N 103869 1594 ENSG00000117984 ENSG00000188082 + - 11 11 1741798 1728397 coding intron CTSD AC068580.3 1730561 1710216 - - 0 1731340 1725926 - + N - 7.83334716693519 N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 68 1.31408166142643 1.29265641694665 1.31408166142643 1.29265641694665 1 - 0 47384 N N 3.4210491438586 3.61530289448208 3.4210491438586 0 0 0.909296931722174 N 0 0.348557692307692 N N 1021 29248 ENSG00000028277 ENSG00000105738 - + 19 19 47328470 43390849 coding intron POU2F2 SIPA1L3 47284515 43089708 - + 0.348557692307692 47328377 43089875 + + N - 0.361292069306371 Y HCC1954 1 1 1 0 3 N 330 6.24336 N - - 0 0 0 12 0.764167053112109 0.985561246069823 0.985561246069823 0.764167053112109 1 - 0 7251 Y Y 3.51001030496889 3.54193626645188 3.51001030496889 230 0 0.0118184009955519 Y 0.822995169082126 0.988937198067633 N N 0 3669 ENSG00000221289 ENSG00000115365 + - 2 2 211078294 211049676 upstream upstream AC007970.3 LANCL1 211078202 211004223 - - 0 211092519 211050734 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 7 0.757025304952183 0.414221393275723 0.757025304952183 0.414221393275723 1 - - 39615 N Y 3.39128260787123 3.55334927718654 3.39128260787123 2 0 0.0435151496273961 N 0.886243386243386 0.886243386243386 N N 12271 13218 ENSG00000177479 ENSG00000173575 - + 3 15 48997971 91372237 intron intron ARIH2 CHD2 48931285 91244423 + + 0 48939897 91350501 - + Y 0.963247002497696 1.54216745468496 N HCC1954 29 21.25 11 4 1 N - - N - SINE,SINE 0 1 1 4 0.971277749749971 0.364229156156239 0.971277749749971 0.364229156156239 1 0 0 38468 Y Y 3.53039946453785 3.64553343878587 3.53039946453785 1 0 0.95569690836405 Y 0 0 N Y 31 6382 ENSG00000213145 ENSG00000182809 - + 14 14 105026173 105017543 coding coding CRIP1 CRIP2 105024249 105012176 + + 0 105025548 105016875 - + N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 8 0.942710757110266 1.15696320190805 1.15696320190805 0.942710757110266 4 - - 3356 N Y 3.29976079368121 3.78937037402784 3.29976079368121 0 0 0.926967558933044 Y 0 0 N Y 5621 4745 ENSG00000173638 ENSG00000186866 + - 21 21 45786813 45532239 coding intron SLC19A1 POFUT2 45740677 45508272 - - 0 45770159 45530271 - + N - 1.2631437454121 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 1.04983697950916 0.914143764470561 1.04983697950916 0.914143764470561 4 - 0 32443 N Y 3.59421153471047 3.79040344379773 3.59421153471047 0 0.0517523017523017 0.309174462603943 N 0.511508761508761 0.77012177012177 N N 1 4058 ENSG00000170961 ENSG00000134086 + - 8 3 122722811 10168744 upstream intron HAS2 VHL 122694719 10158319 - + 0.77012177012177 123070481 10166469 - - Y - 0.896492445358267 N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.442788385915428 0.442788385915428 0.328520415356608 1 - 0 29194 Y Y 3.79209886097693 3.28655907981151 3.28655907981151 259 0 0.518857566817728 Y 0.99126193863036 0.982523877260719 N N 154 27657 ENSG00000124743 ENSG00000001084 + - 6 6 53638465 53517790 downstream upstream KLHL31 GCLC 53620658 53470098 - - 0 53589643 53537646 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR SINE 1 1 1 5 0.664182578873142 0.699891319672773 0.699891319672773 0.664182578873142 4 - - 2167 N Y 3.5920919620082 3.4482245215427 3.4482245215427 242 0 0.0425138434450942 N 0.902365905039702 0.902365905039702 N N 14263 0 ENSG00000156976 ENSG00000212551 - + 3 11 187990377 32060094 intron downstream EIF4A2 U3 187984055 32059886 + + 0.902365905039702 187988792 32063539 - + Y 2.28567657066564 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.478497126715059 0.357087407996313 0.478497126715059 0.357087407996313 1 0 - 42354 Y Y 3.31270138772572 3.58424216889964 3.31270138772572 143 0 0.268230712200883 Y 0 0.984484265734266 N N 3530 1004 ENSG00000169762 ENSG00000007062 + - 4 4 15837259 15694766 downstream upstream TAPT1 PROM1 15771226 15574385 - - 0 15736533 15730557 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LINE 0 0.858407079646018 0.858407079646018 5 0.528489363834543 0.807017542071667 0.807017542071667 0.528489363834543 2 - - 24260 N N 3.8333716936548 3.40119854051958 3.40119854051958 0 0 0.449334290610156 N 0 0 N N 0 0 ENSG00000176183 ENSG00000217168 - - 5 1 97702893 78013137 downstream intron AC094106.3-1 RP4-706L14.2 97702584 78012138 + - 0 97703364 78012252 - + Y - 1 N HCC1954 3 2.4 2 5 1 N - - N - - 0 0 0 5 0.442788385915428 0.299953422716903 0.442788385915428 0.299953422716903 2 - 0 30384 N Y 3.55036438746605 3.55504469436574 3.55036438746605 0 0 0.95146613363858 Y 0 0.97242951907131 N N 8617 441 ENSG00000221867 ENSG00000147402 - + X X 151621480 151576655 upstream intron MAGEA6 GABRQ 151617901 151557293 + + 0 151617810 151558910 - + N - 0.628882399627712 N HCC1954 2 2 2 18 4 N - - N Low_complexity - 0.548387096774194 0 0.548387096774194 18 0.885576771830856 0.757025304952183 0.885576771830856 0.757025304952183 3 - 0 34416 Y Y 3.35616415112274 3.71976530271662 3.35616415112274 241 0 0.05504384308023 Y 0.696915027963197 0.935053220277828 N N 1727 0 ENSG00000147905 ENSG00000216536 - + 9 9 37348143 37037234 upstream downstream ZCCHC7 RP11-297B17.2 37110469 37036832 + + 0 37074237 37070559 - + N - - N HCC1954 2 1.6 1 3 3 N - - Y SINE - 1 0 1 5 0.485638874874985 1.01412823870953 1.01412823870953 0.485638874874985 1 - - 27160 N Y 3.353603498043 3.56807857436608 3.353603498043 315 0.220791415157612 0.0717843854183824 Y 0.992980102839258 0.985960205678516 N Y 1688 2234 ENSG00000124074 ENSG00000141098 - + 16 16 66258129 66310720 coding coding C16orf48 GFOD2 66254353 66265938 - - 0 66257669 66276861 + - N - 0.741417045188739 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.614190341753658 0.771308801272036 0.771308801272036 0.614190341753658 4 - 0 9482 Y Y 3.3755202409218 3.75016368088976 3.3755202409218 378 0 0.00145124600813229 Y 0 0 N N 335 8778 ENSG00000168517 ENSG00000186834 - + 17 17 40603189 40585251 intron coding HEXIM2 HEXIM1 40594054 40580467 + + 0 40594635 40583237 - + N 0.111013292762704 2.39125434522832 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.785592297591888 0.678466075192994 0.785592297591888 0.678466075192994 2 0 0 5024 N Y 3.57167229721571 3.37758638046158 3.37758638046158 11 0.0172912124131638 0.0942208000541795 N 0.0288524922671264 0 N N 887 0 ENSG00000123965 ENSG00000201959 + + 7 7 73960105 76509001 coding upstream PMS2L5 Y_RNA 73944358 76508900 + + 0 73954940 76507505 + + N - - Y HCC1954 10 8.5 6 4 1 N - - N - - 0 0 0 4 0.785592297591888 0.357087407996313 0.785592297591888 0.357087407996313 1 - - 46549 N N 3.41207299502431 3.42936294528359 3.41207299502431 2 0 0.0836534604999535 N 0 0.145931034482759 N N 112 3693 ENSG00000090659 ENSG00000198125 - + 19 22 7718420 34349347 utr3p utr5p CD209 MB 7710883 34332757 - - 0.145931034482759 7713307 34349263 + - Y - - N HCC1954 35 32.6 32 5 1 N - - N SINE SINE 1 0.409638554216867 1 5 0.364229156156239 0.592765097273879 0.592765097273879 0.364229156156239 2 - - 10062 Y Y 3.70144228268745 3.40129182647542 3.40129182647542 19 0.019876120920773 0.999732706193322 N 0.0370712766940927 0.994268281408893 Y N 1482 317991 ENSG00000171345 ENSG00000171346 - + 17 17 36938167 36932191 coding upstream KRT19 KRT15 36933396 36923523 - - 0 36937607 36946570 + - N - - N HCC1954 2 1.02857142857143 1 1 8 Y - - N - - 0 0 0 35 1.36407389854591 1.12839620926835 1.36407389854591 1.12839620926835 1 - - 30118 N N 3.47911741325579 3.4780843434859 3.4780843434859 0 0 0.0461995306334659 N 0 0 N N 975 18434 ENSG00000198487 ENSG00000136868 + + 6 9 42218335 115068495 coding utr3p AL512274.9 SLC31A1 42183124 115023638 - + 0 42183205 115063254 - + Y - - N HCC1954 24 20.6521739130435 6 46 1 N - - N - SINE 0 1 1 46 0.649899082553289 0.292811674556976 0.649899082553289 0.292811674556976 1 - - 38156 Y Y 3.45553575842133 3.29872772391132 3.29872772391132 240 0 0.270257421296499 Y 0 0 N N 4773 0 ENSG00000151320 ENSG00000202337 - - 14 14 32372018 31742226 upstream upstream AKAP6 U6 31868274 31742120 + - 0 31824922 31742680 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 6 0.499922371194838 0.442788385915428 0.499922371194838 0.442788385915428 4 - - 17547 N Y 3.71041843152174 3.5010341561346 3.5010341561346 0 0.188500321819352 0.746161276044532 Y 0.188500321819352 0 N N 14389 10984 ENSG00000163113 ENSG00000136631 - - 1 1 148249310 148384129 utr5p upstream OTUD7B VPS45 148178855 148305966 - + 0 148216132 148305636 + - N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 10 1.14982145374813 1.24980592798709 1.24980592798709 1.14982145374813 1 - - 39865 N Y 3.09549782445355 3.27079671286208 3.09549782445355 468 0 0.000556593245891412 Y 0 0.994456315289649 N N 33005 33005 ENSG00000166145 ENSG00000166145 - + 15 15 38937144 38937144 utr5p upstream SPINT1 SPINT1 38923538 38923538 + + 0 38923669 38920135 - + N 0.265487214464112 - N HCC1954 1 1 1 0 1 N - - N - LINE 0 0.428571428571429 0.428571428571429 7 1.07126222398894 0.999844742389676 1.07126222398894 0.999844742389676 3 0 - 18830 N N 3.65760879692984 3.71720464963688 3.65760879692984 1 0 0.0673645673575818 Y 0 0 N N 2101 0 ENSG00000203847 ENSG00000198137 + - 1 1 142559798 22522411 coding intron PPIAL4G AL591122.20 142555943 22521929 - - 0 142558880 22522167 - + N 0.0248403570690771 1 N HCC1954 38 24.8333333333333 18 12 1 N - - N - - 0 0 0 12 0.371370904316165 0.278528178237124 0.371370904316165 0.278528178237124 1 0 0 26643 Y Y 3.63655728995158 3.69359248957888 3.63655728995158 315 0 0.848195599490927 Y 0 0 N N 0 0 ENSG00000209496 ENSG00000209495 + - 16 16 3161032 3142681 downstream upstream AJ003147.1-1 AC108134.3-1 3160962 3142610 - - 0.986619793331203 3153302 3151306 - + N - - N HCC1954 35 4.625 1 6 4 N - - Y SINE - 0.691860465116279 0 0.691860465116279 32 1.22838068350732 1.1141127129485 1.22838068350732 1.1141127129485 4 - - 10228 Y Y 3.27767621693306 3.59321831773393 3.27767621693306 0 0 0.125032908581280 Y 0 0 N N 811 109725 ENSG00000136480 ENSG00000108654 - + 17 17 59923631 59932869 coding coding POLG2 DDX5 59904366 59926202 - - 0 59923029 59926843 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 5 0.899860268150708 1.07840397214886 1.07840397214886 0.899860268150708 2 - - 31327 N Y 3.69681549006792 3.34822107205833 3.34822107205833 253 0 0.180274899171149 Y 0.189656327460307 0.991558920077712 N N 763 95 ENSG00000205814 ENSG00000215837 - + 3 3 196924416 196900773 upstream downstream AC069513.28-3 AC069513.28-2 196912000 196900191 + + 0 196908414 196900851 - + N - - N HCC1954 8 3.13333333333333 2 15 4 N - - N LINE,LINE LINE 0.897058823529412 0.910569105691057 0.910569105691057 15 0.971277749749971 0.87843502367093 0.971277749749971 0.87843502367093 1 - - 1868 N N 3.31592438821476 3.08359030017893 3.08359030017893 0 0.208333333333333 0.178269161073597 N 0.530864197530864 0.579732510288066 N N 0 74591 ENSG00000213275 ENSG00000142089 - + 16 11 83511984 310848 intron coding AC025280.5 IFITM3 83511584 309678 + - 0.579732510288066 83511693 310672 - - Y 1 1.05074346928304 N HCC1954 2 1.33333333333333 1 2 1 N - - N - - 0 0 0 6 0.507064119354764 1.09982921662864 1.09982921662864 0.507064119354764 0 0 0 27949 N Y 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.0782394629043213 N 0 0 N N 86 45068 ENSG00000183690 ENSG00000205336 + + X 16 44087867 56256445 intron upstream EFHC2 GPR56 43892072 56220023 - + 0 43893807 56211646 - + Y 1.67235574147535 - N HCC1954 24 20.6 20 25 1 N - - N SINE - 1 0 1 25 0.385654400636018 0.657040830713216 0.657040830713216 0.385654400636018 1 0 - 41749 Y Y 3.24099032408136 3.29396779254261 3.24099032408136 0 0 0.996846575088618 Y 0.991487735390175 0.991487735390175 N N 9799 0 ENSG00000076554 ENSG00000222697 - - 8 8 81155565 81279688 coding upstream TPD52 SRP_euk_arch 81109662 81279396 - + 0 81139381 81246213 + - N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 5 0.742741808632331 0.649899082553289 0.742741808632331 0.649899082553289 2 - - 27146 Y Y 3.084614022379 3.50529022639353 3.084614022379 134 0 0.129749442003283 N 0.990136372127779 0.980272744255558 Y N 37 68 ENSG00000205084 ENSG00000135702 - + 16 16 74147671 74126569 coding downstream AC009163.6 CHST5 74131393 74119931 - - 0 74137353 74105168 + - N - - N HCC1954 2 1.4 1 2 1 N - - N - LINE 0 1 1 5 0.764167053112109 0.749883556792257 0.764167053112109 0.749883556792257 4 - - 34788 Y Y 3.33358506083463 3.21232721588077 3.21232721588077 107 0.00416666666666665 0.0999278916373482 Y 0.513148148148148 0.988935185185185 N N 901 0 ENSG00000137033 ENSG00000218509 - + 9 9 6247982 6187470 utr5p downstream IL33 RP11-575C20.1 6231678 6185934 + + 0 6231682 6205850 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.914143764470561 0.449930134075354 0.914143764470561 0.449930134075354 3 - - 33829 Y N 2.85067780311981 3.31489131844487 2.85067780311981 26 0.09870729455217 0.996226857059775 N 0.109187442289935 0.09870729455217 Y N 59837 247001 ENSG00000198695 ENSG00000198786 - - MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.09870729455217 14513 12429 + - N - 0.89008387699322 N HCC1954 3 1.23333333333333 1 6 7 N 189 4.09957 N - - 0 0 0 30 1.3069399132665 1.21409718718746 1.3069399132665 1.21409718718746 2 - 0 7793 N N 3.64656650855576 3.48656597878024 3.48656597878024 3 0 0.519197755460547 N 0.928809523809524 0 N N 0 0 ENSG00000183846 ENSG00000217928 + + 2 22 110575338 15435527 upstream upstream AC112229.4-1 KB-67B5.12 110574935 15432917 - + 0 110576432 15409438 - + Y - - N HCC1954 24 16.6153846153846 14 13 2 N 359 26.8809 N - - 0 0 0 13 0.871293275511003 0.564198104634174 0.871293275511003 0.564198104634174 1 - - 33045 N Y 3.34785034969775 3.28821464419736 3.28821464419736 326 0 0.938707844857235 Y 0 0.991960221650505 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0.991960221650505 10826 9134 - + N 0.288838264943628 0.537226037610456 N HCC1954 2 1.8 1 4 7 Y - - N - - 0 0 0 5 1.13553795742827 0.835584534711372 1.13553795742827 0.835584534711372 2 0 0 13691 Y Y 3.68168496530426 3.39487633072086 3.39487633072086 300 0 0.524279877280133 Y 0 0 N Y 12539 36 ENSG00000138869 ENSG00000128218 + - 22 22 22440141 22426655 coding intron CHCHD10 VPREB3 22438021 22424855 - - 0 22438315 22425385 - + N 3.05821247508013 5.68602801880394 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 8 0.899860268150708 1.09268746846872 1.09268746846872 0.899860268150708 4 0 0 24832 Y Y 3.51310951427856 2.76118227567621 2.76118227567621 298 0 0.115770283184032 Y 0.888435340078133 0.992562356005209 N N 962 0 ENSG00000184828 ENSG00000206944 - + 18 18 43821492 43950259 utr5p downstream ZBTB7C U6 43807746 43950153 - - 0 43821491 43917375 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 1.02126998686945 0.885576771830856 1.02126998686945 0.885576771830856 1 - - 47985 N N 3.3070415253363 3.48908677906663 3.3070415253363 0 0 0.352022645869636 N 0 0 N N 0 6627 ENSG00000213745 ENSG00000113269 + + 8 5 99987074 179431719 downstream coding AC016877.11-1 RNF130 99986636 179315111 - - 0 99964633 179372670 - - Y - - N HCC1954 1 1 1 0 1 N 420 19.7538 N DNA - 0.536912751677852 0 0.536912751677852 10 1.06412047582901 0.999844742389676 1.06412047582901 0.999844742389676 1 - - 30268 Y Y 3.55025006787687 3.10144931189168 3.10144931189168 241 0 0.0604996831387795 Y 0 0.990041493775934 N N 0 6773 ENSG00000220073 ENSG00000187325 + - X X 77314575 77281835 downstream upstream RP4-570L12.3 TAF9B 77307849 77271902 - - 0 77300087 77281841 - + N - - N HCC1954 7 4 1 4 1 N - - Y LINE - 1 0 1 6 0.521347615674617 0.542772860154395 0.542772860154395 0.521347615674617 2 - - 9746 Y Y 3.59102838701478 3.56335849579072 3.56335849579072 242 0 0.542597384023138 Y 0.924227452389508 0.989175350341358 N N 5891 10351 ENSG00000175832 ENSG00000067596 + + 17 17 38979288 38957206 intron coding ETV4 DHX8 38960738 38916860 - + 0 38969307 38956522 - + N 1.39424693966117 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 11 0.671324327033068 1.13553795742827 1.13553795742827 0.671324327033068 3 0 - 18486 Y Y 3.20869364023779 3.66951632120446 3.20869364023779 153 0 0.0210010931759961 Y 0 0.986753812636166 N N 0 7600 ENSG00000203342 ENSG00000157978 + + 1 1 25781673 25767964 downstream coding AL606491.19-1 LDLRAP1 25781498 25742663 - + 0 25780683 25762853 - + N - 1.08593761744726 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.764167053112109 0.485638874874985 0.764167053112109 0.485638874874985 1 - 0 33108 N Y 3.50848272165904 3.38486711211668 3.38486711211668 409 0.00244498777506108 0.164512651895087 Y 0.00244498777506108 0.994395758358287 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0 8754 6617 - + N 0.559268386776935 1.06532787164463 N HCC1954 2 2 2 4 5 N - - N - - 0 0 0 4 0.799875793911741 0.628473838073511 0.799875793911741 0.628473838073511 2 0 0 6920 Y Y 3.07676422927044 3.684245618384 3.07676422927044 280 0 0.0292240125598844 Y 0 0.989169254658385 N N 1152 409 ENSG00000115350 ENSG00000204792 - + 2 2 75050366 75013659 coding downstream POLE4 AC104135.5 75039283 75008874 + + 0 75039362 75014239 - + N 1.18716990661823 - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 23 1.05697872766909 0.728458312312478 1.05697872766909 0.728458312312478 1 0 - 38169 Y Y 3.51001030496889 3.44871903508266 3.44871903508266 276 0 0.113793120475367 Y 0 0.972702005161802 N N 4 4 ENSG00000181552 ENSG00000181562 - + 14 14 20308947 20286379 upstream downstream FAM12B FAM12A 20306426 20283939 + + 0 20301959 20293730 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR LTR 1 1 1 8 0.392796148795944 0.764167053112109 0.764167053112109 0.392796148795944 2 - - 29167 N N 3.45144752203174 2.77271907759025 2.77271907759025 0 0 0.563259476043473 Y 0.290090344438171 0.305194805194805 N N 7010 6367 ENSG00000146457 ENSG00000112096 - - 6 6 160097339 160034343 upstream intron WTAP SOD2 160068142 160020141 + - 0.305194805194805 160067914 160033998 - + N - 1.24105918703935 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 5 0.492780623034912 0.557056356474248 0.557056356474248 0.492780623034912 1 - 0 27657 N N 3.53143253430774 3.57336771439491 3.53143253430774 3 0 0.113053742143067 N 0.297800865800866 0.639411255411255 N N 45068 2048 ENSG00000205336 ENSG00000114107 - - 16 3 56256445 139795819 utr5p intron GPR56 CEP70 56220023 139695879 + - 0.00363636363636355 56241661 139729728 - + Y 0.00605519120852256 0.441139486407226 N HCC1954 3 2.5 2 4 1 N - - N - SINE 0 1 1 4 0.492780623034912 0.278528178237124 0.492780623034912 0.278528178237124 1 0 0 1420 N Y 3.61100697142979 3.23999710710482 3.23999710710482 1 0 0.16232417921904 N 0.472015209125475 0 N N 2030 1649619 ENSG00000137656 ENSG00000141736 - + 11 17 116148914 35138441 intron coding BUD13 ERBB2 116124096 35104766 - + 0 116144935 35122225 + + Y 1.43381380397648 0.989697288600257 N HCC1954 6 2.83333333333333 2 6 1 N 399 25.2516 N SINE - 1 0 1 6 0.278528178237124 0.499922371194838 0.499922371194838 0.278528178237124 2 0 0 35972 N Y 3.10088025043821 3.63296356710195 3.10088025043821 0 0.887448497638428 0.188783547257833 N 0.887448497638428 0.79097578132851 N N 0 712661 ENSG00000219930 ENSG00000111640 - + X 12 134988456 6517797 intron coding AL732579.5 GAPDH 134987668 6513918 + + 0.831172746457642 134988012 6516538 - + Y 1 - N HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.671324327033068 0.835584534711372 0.835584534711372 0.671324327033068 2 0 - 32445 N Y 3.55334927718654 3.39128260787123 3.39128260787123 0 0 0.106341846593844 N 0.895146426377227 0.895146426377227 N N 2 12271 ENSG00000169436 ENSG00000177479 + - 8 3 139995418 48997971 upstream intron COL22A1 ARIH2 139669661 48931285 - + 0 140025552 48939897 - - Y - 0.963247002497696 N HCC1954 56 31 20 4 1 N 381 24.7492 N SINE - 1 0 1 4 0.307095170876829 0.414221393275723 0.414221393275723 0.307095170876829 1 - 0 20818 N Y 3.31166831795583 3.24103017687471 3.24103017687471 0 0 0.455033138866820 N 0 0.984188988095238 N N 34471 0 ENSG00000116251 ENSG00000184531 - - 1 3 6182266 170910252 coding upstream RPL22 AC007849.24-1 6167668 170909777 - + 0 6180320 170863818 + - Y - - N HCC1954 8 3.86666666666667 2 15 1 N - - N - Low_complexity 0 0.0636363636363636 0.0636363636363636 15 0.914143764470561 0.764167053112109 0.914143764470561 0.764167053112109 3 - - 38327 Y Y 3.55760534744548 3.48167806633553 3.48167806633553 118 0.036789297658863 0.135629941160586 Y 0.989054423837033 0.989054423837033 N N 23 10932 ENSG00000139914 ENSG00000100897 - + 14 14 23671898 23664288 upstream coding AL136295.17 WDR23 23670515 23653861 + + 0 23670324 23662125 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.585623349113953 0.671324327033068 0.671324327033068 0.585623349113953 1 - - 3865 N Y 3.73808832274579 2.79422101251579 2.79422101251579 0 0 0.0673602016378068 N 0 0.925646492810672 N N 4702 0 ENSG00000120889 ENSG00000203446 + - 8 7 22982637 65814279 utr3p downstream TNFRSF10B AC027644.9 22933598 65814003 - - 0 22933887 65784753 - + Y - - N HCC1954 23 21.8333333333333 21 6 1 N - - N SINE - 1 0 1 6 0.299953422716903 0.585623349113953 0.585623349113953 0.299953422716903 1 - - 38076 Y N 3.60888739872753 3.49272035470961 3.49272035470961 0 0 0.582370274241477 Y 0 0.161623767798466 N N 51898 4802 ENSG00000100644 ENSG00000027075 - + 14 14 61284729 61087443 upstream coding HIF1A PRKCH 61231992 60858186 + + 0.161623767798466 61189900 61067013 - + N - 1.36464460265062 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.728458312312478 0.535631111994469 0.728458312312478 0.535631111994469 1 - 0 18829 Y Y 3.67526946954971 3.38080938095063 3.38080938095063 287 0 0.0541125537169218 Y 0.96415411225027 0.992830822450054 N N 1013 1125 ENSG00000164011 ENSG00000164010 - + 1 1 43090735 43083247 upstream coding ZNF691 ERMAP 43084867 43055363 + + 0 43084516 43073390 - + N - 0.515240397801023 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.557056356474248 0.557056356474248 0.557056356474248 0.557056356474248 1 - 0 33220 N Y 3.00500908003341 2.95058796664833 2.95058796664833 290 0 0.140861751227589 Y 0 0.96563614744352 N N 247001 336285 ENSG00000198786 ENSG00000198868 - + MT MT 14149 12138 coding coding MT-ND5 MT-ND4 12338 10471 + + 0.96563614744352 13972 12047 - + N 1.39700444604868 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.821301038391519 0.585623349113953 0.821301038391519 0.585623349113953 3 0 - 41605 N Y 3.32490053704905 3.62295434849776 3.32490053704905 266 0 0.0776916234660038 Y 0.0425739673859973 0.974123620740162 N N 45 45 ENSG00000214789 ENSG00000214789 - + 8 8 128893866 128893866 downstream intron AC084123.9 AC084123.9 128875961 128875961 + + 0 128898256 128877499 - + N - 3.73024630541872 N HCC1954 1 1 1 0 1 N - - N LINE - 1 0 1 4 0.485638874874985 0.956994253430118 0.956994253430118 0.485638874874985 4 - 0 47520 Y Y 3.72079837248651 3.21232721588077 3.21232721588077 111 0.442222222222222 0.0173743804736171 Y 0.800793650793651 0.760952380952381 N N 513 231 ENSG00000196081 ENSG00000213971 - + 19 19 23206938 23237276 coding downstream ZNF724P AC092329.3-1 23197360 23234603 - - 0.551785714285714 23206908 23224950 + - N - - N HCC1954 4 1.09677419354839 1 1 1 N - - Y - - 0 0 0 31 1.09268746846872 0.471355378555133 1.09268746846872 0.471355378555133 3 - - 256 N Y 3.24520654154694 3.33424740824393 3.24520654154694 257 0.00389105058365757 0.0794421037242107 Y 0.816807549532627 0.988550471845789 N N 1654 1882 ENSG00000168569 ENSG00000162227 + + 11 11 62316056 62311390 intron intron TMEM223 TAF6L 62314503 62295451 - + 0 62315726 62298712 - + N 1.75342661785026 0.639026362387382 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.578481600954027 0.385654400636018 0.578481600954027 0.385654400636018 1 0 0 27194 Y Y 3.4701412644215 3.18395512445406 3.18395512445406 0 0.0967116013071896 0.710701494649974 Y 0.0499897875816993 0.992213031045752 N N 172 4968 ENSG00000205047 ENSG00000104731 - + 16 16 86292831 86357056 coding coding AC010536.8 KLHDC4 86291389 86298920 - - 0 86292751 86299534 + - N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.260115606936416 0 0.260115606936416 13 1.23552243166724 1.31408166142643 1.31408166142643 1.23552243166724 1 - - 11058 N N 1.67870909903897 3.60000453584907 1.67870909903897 0 0 0.151176166209072 N 0 0 N N 37845 46217 ENSG00000204463 ENSG00000131746 - + 6 17 31728461 35911380 utr5p utr3p BAT3 TNS4 31714784 35885606 - - 0 31728105 35885937 + - Y - - N HCC1954 36 34.25 31 4 1 N - - N Simple_repeat Simple_repeat 0.972972972972973 0.147058823529412 0.972972972972973 4 0.264244681917271 0.87843502367093 0.87843502367093 0.264244681917271 2 - - 39984 Y Y 3.29553522864581 3.59681204058356 3.29553522864581 314 0 0.162305253121118 Y 0.00961577974111361 0.987137867269365 N N 194 3493 ENSG00000183208 ENSG00000185043 - - 15 15 88586316 88578160 utr5p upstream C15orf58 CIB1 88582726 88574487 + - 0 88582728 88578832 - + N 0.0788619438609891 - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.475 0.475 4 0.535631111994469 0.5713398527941 0.5713398527941 0.535631111994469 4 0 - 36254 Y Y 3.20869364023779 3.20657406753552 3.20657406753552 422 0 0.00290261183695628 Y 0 0.949165333413832 N N 1725 53 ENSG00000119242 ENSG00000197653 + + 12 12 123023317 122986218 intron intron CCDC92 DNAH10 122986936 122812995 - + 0 122993820 122976681 - + N 2.12718205370814 0.480247050624918 N HCC1954 1 1 1 0 2 N - - Y - DNA,SINE,SINE 0 0.798319327731092 0.798319327731092 7 0.914143764470561 0.742741808632331 0.914143764470561 0.742741808632331 2 0 0 47557 Y Y 3.30488209984069 3.40631984667906 3.30488209984069 145 0 0.0121407391700736 Y 0 0 N N 13250 4828 ENSG00000126461 ENSG00000126458 - - 19 19 54853710 54835212 coding upstream SCAF1 RRAS 54837194 54830364 + - 0 54840203 54835625 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.771308801272036 0.364229156156239 0.771308801272036 0.364229156156239 1 - - 26765 Y Y 2.94124109545346 2.86911522385584 2.86911522385584 211 0 0.00451312022090367 Y 0 0.956091441315863 N N 209 1817 ENSG00000205890 ENSG00000162069 - - 16 16 3029132 3025543 intron coding AC108134.3-2 CCDC64B 3022483 3017869 + - 0 3026895 3021110 - + N 4.94436967927541 1.94042501990992 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 28 0.414221393275723 1.19981369086761 1.19981369086761 0.414221393275723 0 0 0 45743 N N 3.24272559405391 3.57800808738356 3.24272559405391 0 0 0.393798527579204 N 0.0042372881355931 0 N N 0 17943 ENSG00000209727 ENSG00000105141 + + 3 19 5269908 15027900 intron downstream AC026202.7-1 CASP14 5269611 15024015 - + 0 5269617 15029502 - + Y 1 - N HCC1954 14 7.93333333333333 1 37 1 N - - N srpRNA SINE 1 0.201550387596899 1 45 0.28566992639705 0.914143764470561 0.914143764470561 0.28566992639705 3 0 - 29270 Y Y 3.72551845106187 3.23214731399625 3.23214731399625 237 0 0.78157228803853 Y 0 0.982682076683177 N N 11566 0 ENSG00000130338 ENSG00000188451 - - 6 6 158852842 158583817 upstream upstream TULP4 RP1-274L14.2 158653680 158578356 + - 0 158623283 158586353 - + N - - N HCC1954 1 1 1 0 3 N - - Y - SINE 0 0.826530612244898 0.826530612244898 5 0.799875793911741 0.699891319672773 0.799875793911741 0.699891319672773 4 - - 44978 Y Y 3.04483826778745 3.34256120966892 3.04483826778745 305 0 0.00945187773564593 Y 0.943276022924164 0.991896574703452 N N 9499 13 ENSG00000107485 ENSG00000197308 - - 10 10 8157170 8135453 utr5p upstream GATA3 AL390294.19 8136673 8132419 + - 0.991896574703452 8137258 8135749 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 72 0.921285512630487 0.999844742389676 0.999844742389676 0.921285512630487 1 - - 41550 Y Y 3.27039548527796 3.55504469436574 3.27039548527796 314 0 0.116464328497458 Y 0.993527173463479 0.987054346926958 N N 0 0 ENSG00000221261 ENSG00000221176 - + 8 8 129231616 129130666 upstream downstream hsa-mir-1208 hsa-mir-1207 129231544 129130580 + + 0.987054346926958 129182408 129181001 - + N - - N HCC1954 3 1.28571428571429 1 1 2 N - - Y LTR - 1 0 1 7 0.99270299422975 1.02841173502938 1.02841173502938 0.99270299422975 4 - - 34178 Y Y 3.58064844605001 3.18718747251292 3.18718747251292 320 0 0.181849062392791 Y 0.986883223684211 0.993441611842105 N N 630 1646 ENSG00000136895 ENSG00000136828 - + 9 9 129195647 129025264 upstream downstream GARNL3 RALGPS1 129045207 128716874 + + 0 129045180 129027504 - + N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.180232558139535 0.180232558139535 12 1.14982145374813 1.10697096478857 1.14982145374813 1.10697096478857 1 - - 33039 N Y 3.23420410596622 3.67952553980864 3.23420410596622 260 0 0.926804377754285 Y 0.00384615384615372 0.98868006993007 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0.0151660839160838 11238 9055 - + N 0.825751021874178 0.595061706283478 N HCC1954 2 1.57142857142857 1 4 7 N - - N - - 0 0 0 7 0.507064119354764 1.14982145374813 1.14982145374813 0.507064119354764 1 0 0 26468 N N 3.72721386824106 3.51529944499772 3.51529944499772 0 0.633937626774848 0.100942231269349 N 0.136092799188641 0.150735294117647 N N 18076 3776 ENSG00000168411 ENSG00000128271 + + 16 22 73258280 23168324 coding downstream RFWD3 ADORA2A 73212798 22996866 - + 0 73252778 23182660 - + Y - - N HCC1954 4 1.5 1 6 1 N - - N - SINE 0 1 1 20 0.642757334393363 0.349945659836387 0.642757334393363 0.349945659836387 1 - - 44412 N Y 3.54400240599166 3.65488030998075 3.54400240599166 18 0 0.221340217132962 N 0.631647375931505 0.00377358490566038 N N 906 27074 ENSG00000148814 ENSG00000137804 - - 10 15 134109058 39460535 utr3p intron LRRC27 NUSAP1 133995648 39412361 + + 0.0623751387347391 134041545 39451016 - - Y - 1.63324753593868 N HCC1954 37 32.5 31 8 1 N - - N SINE - 1 0 1 8 0.292811674556976 0.807017542071667 0.807017542071667 0.292811674556976 1 - 0 9959 Y Y 3.47336426491055 3.69784855983781 3.47336426491055 1 0 0.999999729184962 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 coding coding GSDMB ORMDL3 35314374 35330822 - - 0 35327049 35332406 + - N - - N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 23 1.14982145374813 1.1426797055882 1.14982145374813 1.1426797055882 0 - - 46245 N N 3.5246463161926 2.79102851725028 2.79102851725028 0 0 0.072764622943044 N 0 0.713774351208095 N N 18434 6115 ENSG00000136868 ENSG00000197256 - + 9 19 115068495 11167496 utr3p upstream SLC31A1 KANK2 115023638 11135947 + - 0.713774351208095 115066317 11169184 - - Y - - N HCC1954 24 22.75 20 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.421363141435649 0.421363141435649 0.28566992639705 1 - - 37088 N N 3.22423474015539 3.57800808738356 3.22423474015539 0 0 0.392249521766313 N 0.00398406374501981 0 N N 53 17943 ENSG00000197653 ENSG00000105141 - + 12 19 122986218 15027900 intron downstream DNAH10 CASP14 122812995 15024015 + + 0.0208656897832399 122858720 15029502 - + Y 0.775048481254282 - N HCC1954 25 14.2727272727273 1 43 1 N - - N SINE - 1 0 1 44 0.321378667196682 0.757025304952183 0.757025304952183 0.321378667196682 3 0 - 1491 N Y 3.10976311331667 3.30913817009962 3.10976311331667 0 0 0.326008937923967 N 0.077182979622004 0.951430683138 N N 1772 7321 ENSG00000187451 ENSG00000133812 - - 17 11 42483361 10272296 downstream intron AC068152.11-2 SBF2 42480430 9756790 + - 0 42499706 10110700 - + Y - 3.91424153436787 N HCC1954 20 20 20 8 1 N - - N - LTR 0 1 1 8 0.564198104634174 0.364229156156239 0.564198104634174 0.364229156156239 2 - 0 19463 N N 3.54872248456702 3.45872825368684 3.45872825368684 12 0 0.152888575708400 N 0.225560324272771 0 N N 49 3164 ENSG00000186973 ENSG00000143344 - - 1 1 43394654 182164289 upstream intron FAM183A RGL1 43382616 181871831 + + 0 43374043 181894086 - - N - 0.0580110911603265 Y HCC1954 25 23.75 23 4 1 N - - N LTR LINE 0.439024390243902 1 1 4 0.292811674556976 0.378512652476092 0.378512652476092 0.292811674556976 2 - 0 22471 N N 3.18192883770763 3.57336771439491 3.18192883770763 3 0 0.105691277348503 N 0 0 N N 2406 17904 ENSG00000104381 ENSG00000180198 - + 8 1 75441888 28738194 intron utr5p GDAP1 RCC1 75425173 28705083 + + 0 75434857 28707228 - + Y 0.215954723148888 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 1.19267194270768 0.371370904316165 1.19267194270768 0.371370904316165 2 0 - 48914 Y Y 3.23065023590994 3.60000453584907 3.23065023590994 351 0 0.284068234344134 Y 0 0.985652503638115 N N 106385 55216 ENSG00000071539 ENSG00000028310 - - 5 5 971156 945915 coding intron TRIP13 BRD9 946004 916856 + - 0 947902 945478 - + N 0.780509813242672 1.72203611175413 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 24 1.02841173502938 1.39264089118562 1.39264089118562 1.02841173502938 4 0 0 14078 Y Y 3.47336426491055 3.32163768376666 3.32163768376666 298 0 0.67927912005579 Y 0 0.971524448705657 N Y 4030 855 ENSG00000185214 ENSG00000099910 + - 22 22 19180122 19122146 coding coding KLHL22 SCARF2 19125806 19108874 - - 0 19130730 19116275 - + N - 17.213042250171 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.799875793911741 0.449930134075354 0.799875793911741 0.449930134075354 4 - 0 27481 N Y 3.04124454493782 2.86385658905055 2.86385658905055 223 0.141233980710794 0.0989509138537248 N 0.00383141762452122 0.673668912670102 N N 111030 0 ENSG00000167526 ENSG00000213916 - + 16 6 88157349 28937791 coding intron RPL13 AL662890.3-1 88154591 28937172 + + 0.673668912670102 88155181 28937311 - + Y 0.814792590312126 1 N HCC1954 2 1.31578947368421 1 6 2 N - - N - - 0 0 0 19 0.742741808632331 0.28566992639705 0.742741808632331 0.28566992639705 1 0 0 33042 N N 3.30335451653084 3.00455865208612 3.00455865208612 0 0.343220338983051 0.99785106280587 Y 0.343220338983051 0.343220338983051 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0.343220338983051 11099 9120 - + N 0.670997103293199 0.551657607152432 N HCC1954 4 2 1 6 7 N - - N - - 0 0 0 8 0.849868031031224 1.09268746846872 1.09268746846872 0.849868031031224 3 0 0 49169 N N 3.46910819465161 3.31489131844487 3.31489131844487 0 0 0.572508435952678 N 0 0 N N 5156 4938 ENSG00000164209 ENSG00000129595 - + 5 5 110126381 111782909 downstream coding SLC25A46 EPB41L4A 110102653 111507433 + - 0 110239906 111622825 - - N - - Y HCC1954 1 1 1 0 1 N - - N SINE,LINE - 0.446601941747573 0 0.446601941747573 5 0.735600060472404 0.93556900895034 0.93556900895034 0.735600060472404 4 - - 35348 N N 3.27192306858781 3.61360747730288 3.27192306858781 0 0 0.408800579905567 N 0 0 N N 921 1649619 ENSG00000111224 ENSG00000141736 + + 12 17 3852863 35138441 intron intron PARP11 ERBB2 3786511 35104766 - + 0 3806789 35123257 - + Y 1.1095393892738 0.991162890469566 N HCC1954 1 1 1 0 1 N 51 22.4015 N - SINE,LINE,SINE 0 0.447058823529412 0.447058823529412 10 1.08554572030879 0.607048593593732 1.08554572030879 0.607048593593732 2 0 0 7017 Y Y 3.20807114562183 3.37704782423165 3.20807114562183 332 0 0.0888079441918734 Y 0.0851169383416016 0.976541459957477 N N 4489 2 ENSG00000082258 ENSG00000153086 - + 2 2 135431056 135376074 upstream intron CCNT2 ACMSD 135392863 135312587 + + 0 135392429 135341781 - + N - 1.09857317847745 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.371370904316165 0.51420586751469 0.51420586751469 0.371370904316165 3 - 0 21866 N N 3.7061623612628 3.25256697878875 3.25256697878875 0 0 0.0738571731432477 N 0 0 N N 0 49089 ENSG00000173093 ENSG00000117450 - - 12 1 109829721 45760196 intron coding CCDC63 PRDX1 109769194 45749295 + - 0 109809382 45757275 - + Y 1 3.11556065904221 N HCC1954 21 14.25 6 4 1 N - - N SINE - 1 0 1 4 0.385654400636018 0.392796148795944 0.392796148795944 0.385654400636018 2 0 0 50 Y Y 2.84123764596909 3.47695798776018 2.84123764596909 337 0 0.966195767818212 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.993649473624525 1816335 1814664 - + N - 0.679260286911601 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 8 1.19981369086761 0.99270299422975 1.19981369086761 0.99270299422975 1 - 0 41727 N N 3.41000685548453 3.45720067037699 3.41000685548453 0 0 0.4803744014158 Y 0 0 N N 22 25232 ENSG00000164935 ENSG00000156471 - + 8 8 105438092 97415950 downstream coding TM7SF4 PTDSS1 105421228 97343340 + + 0 105449723 97391025 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 11 0.685607823352921 0.771308801272036 0.771308801272036 0.685607823352921 1 - - 8629 N N 3.50120199000394 2.80981554559588 2.80981554559588 5 0.00369003690036895 0.187150000602208 N 0.976830000858148 0.00369003690036895 N N 3866 6271 ENSG00000198740 ENSG00000170381 - + 17 7 44794834 83116262 utr3p downstream ZNF652 SEMA3E 44727485 82831158 - - 0.00369003690036895 44727766 82831141 + - Y - - N HCC1954 32 23.7272727272727 20 11 1 N - - N - SINE 0 1 1 11 0.871293275511003 0.956994253430118 0.956994253430118 0.871293275511003 2 - - 24149 N N 3.48908677906663 2.9699440564474 2.9699440564474 0 0 0.54408195975794 N 0 0 N N 6627 0 ENSG00000113269 ENSG00000208755 + - 5 1 179431719 147440605 coding downstream RNF130 AL356957.27-4 179315111 147440535 - + 0 179372670 147445655 - - Y 1.40921199260692 - N HCC1954 4 1.3125 1 4 1 N - - N - LTR 0 1 1 32 1.08554572030879 1.16410495006798 1.16410495006798 1.08554572030879 1 0 - 38195 Y Y 3.31638839653118 3.52208566311286 3.31638839653118 293 0 0.0378490174309765 Y 0 0.983390216154721 N N 7970 10628 ENSG00000029364 ENSG00000100632 - - 14 14 68997021 68934774 intron upstream SLC39A9 ERH 68935162 68916601 + - 0 68978155 68934900 - + N 1.18338756206812 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.528489363834543 0.314236919036755 0.528489363834543 0.314236919036755 1 0 - 25115 Y Y 3.41017468935388 3.50785087947327 3.41017468935388 292 0 0.0186324991498618 Y 0.992672240128928 0.992672240128928 N N 2333 987 ENSG00000005812 ENSG00000102805 + + 13 13 76499286 76474652 coding utr3p FBXL3 CLN5 76477391 76462796 - + 0 76487548 76474098 - + N - 1.59561664340474 N HCC1954 1 1 1 0 2 N - - Y - RNA 0 0.714285714285714 0.714285714285714 11 1.01412823870953 0.999844742389676 1.01412823870953 0.999844742389676 2 - 0 44441 N Y 3.50848272165904 3.09087103183403 3.09087103183403 5 0 0.224926348576255 N 0 0.951010293556996 N N 14565 3891 ENSG00000132824 ENSG00000166295 + + 20 10 42584140 73665622 intron intron SERINC3 C10orf104 42558279 73645812 - + 0 42580817 73645953 - + Y 0.985075254220401 0.744979490524871 N HCC1954 20 16.4444444444444 6 9 1 N - - N SINE - 1 0 1 9 0.39993789695587 0.757025304952183 0.757025304952183 0.39993789695587 1 0 0 34440 Y Y 3.73912139251568 3.43784458057793 3.43784458057793 0 0 0.156235719744824 Y 0.992831357689649 0.992831357689649 N N 3445 4170 ENSG00000147872 ENSG00000147874 + - 9 9 19117573 19092902 coding upstream ADFP FAM29A 19105760 19043142 - - 0 19106358 19098746 - + N 0.647268903430089 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.807017542071667 0.799875793911741 0.807017542071667 0.799875793911741 1 0 - 47075 Y Y 3.37808089400154 3.50744965188915 3.37808089400154 311 0 0.0257591952309030 Y 0 0 N N 0 62 ENSG00000198251 ENSG00000130612 + + 19 19 46108594 46098253 downstream intron AC008537.5-2 AC008537.5-1 46106322 46088571 - + 0 46102745 46091829 - + N - 2.09405122707361 N HCC1954 2 1.14285714285714 1 1 1 N - - Y LINE - 0.0347826086956522 0 0.0347826086956522 7 0.657040830713216 0.842726282871298 0.842726282871298 0.657040830713216 1 - 0 42299 Y Y 3.42680229220385 3.4561676006071 3.42680229220385 245 0 0.360654248304888 Y 0.63440971325239 0.974786876776027 N N 2010 0 ENSG00000138735 ENSG00000209291 + - 4 4 120769429 120574710 downstream upstream PDE5A AC093752.2-3 120635000 120574608 - - 0 120633934 120602489 - + N - - N HCC1954 5 3.41666666666667 1 11 4 N - - Y - - 0 0 0 12 0.5713398527941 0.885576771830856 0.885576771830856 0.5713398527941 3 - - 33091 N Y 3.50529022639353 3.1825606798934 3.1825606798934 357 0 0.433562321066605 Y 0 0.975276060837558 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0 10975 5449 - + N 0.53740631802697 1.53136739020212 N HCC1954 4 2.25 1 6 4 N - - N - - 0 0 0 8 0.892718519990782 1.34264865406614 1.34264865406614 0.892718519990782 3 0 0 41578 Y Y 3.04061270275205 3.32423818963975 3.04061270275205 227 0 0.0161094553412021 N 0 0 Y N 1144 0 ENSG00000154188 ENSG00000211995 + - 8 8 108579459 108335902 intron downstream ANGPT1 AP000428.3-2 108330899 108335811 - - 0 108335094 108305077 - + N 0.391564580975899 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 0.685607823352921 0.507064119354764 0.685607823352921 0.507064119354764 2 0 - 46501 N Y 3.67489874718912 3.528871881228 3.528871881228 4 0 0.251895187064257 N 0.0284090909090911 0.925262237762238 N N 5438 290 ENSG00000120992 ENSG00000142405 - - 8 19 55177130 59019460 coding utr5p LYPLA1 NALP12 55121492 58988669 - - 0 55140923 59002962 + + Y - - N HCC1954 54 43.25 25 4 1 N 211 24.8531 N - SINE 0 1 1 4 0.292811674556976 0.357087407996313 0.357087407996313 0.292811674556976 0 - - 11796 N Y 3.53721618787652 3.12804628055249 3.12804628055249 4 0 0.272293027631485 N 0 0.00390625 N N 2 1649619 ENSG00000156035 ENSG00000141736 + - 9 17 78710823 35138441 intron intron PRUNE2 ERBB2 78593130 35104766 - + 0.00390625 78614310 35125062 - - Y 0.8787023977433 0.991162890469566 N HCC1954 17 8.25 1 4 1 N 208 24.4947 N SINE - 1 0 1 8 0.314236919036755 0.414221393275723 0.414221393275723 0.314236919036755 1 0 0 36712 Y Y 3.42357929171481 2.69058398738845 2.69058398738845 0 0 0.230455897526695 Y 0 0 N N 3360 2279 ENSG00000090975 ENSG00000051825 - + 12 12 122160928 122272394 utr5p downstream PITPNM2 MPHOSPH9 122033980 122203033 - - 0 122160898 122201126 + - N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.110169491525424 0.110169491525424 20 0.828442786551446 0.842726282871298 0.842726282871298 0.828442786551446 1 - - 20797 N Y 3.41679307359967 3.6052936758779 3.41679307359967 1 0 0.0995566123850675 N 0.885740531373657 0.885740531373657 N N 49089 3142 ENSG00000117450 ENSG00000198689 - - 1 X 45760196 134957092 utr5p intron PRDX1 SLC9A6 45749295 134895252 - + 0 45760088 134932669 + - Y - 1.18952709329319 N HCC1954 6 3.25 1 7 1 N - - N - SINE 0 1 1 8 0.707033067832699 0.264244681917271 0.707033067832699 0.264244681917271 1 - 0 41984 N N 3.66592259835483 3.65960038855611 3.65960038855611 0 0 0.995672617218098 N 0 0 N N 86504 559 ENSG00000104408 ENSG00000102290 + + 8 X 109330135 91764885 coding upstream EIF3E PCDH11X 109283149 90920960 - + 0 109309672 90854612 - + Y - - N HCC1954 4 1.84 1 19 3 N - - N - - 0 0 0 25 1.07126222398894 1.19267194270768 1.19267194270768 1.07126222398894 4 - - 28641 N N 3.20227814448323 3.48593413659447 3.20227814448323 9 0 0.0909122924930852 N 0 0.0689368770764118 N N 7369 18076 ENSG00000042753 ENSG00000168411 + + 19 16 52046043 73258280 intron utr5p AP2S1 RFWD3 52033263 73212798 - - 0.0689368770764118 52042397 73258208 - - Y 1.39592708629833 2.4812755233539 N HCC1954 2 1.6 1 3 1 N - - N SINE - 1 0 1 5 0.264244681917271 0.592765097273879 0.592765097273879 0.264244681917271 2 0 0 16083 N N 3.60256518892881 3.43887765034782 3.43887765034782 0 0 0.0260135029647918 N 0.62523629489603 0.59640831758034 N N 3863 29 ENSG00000219481 ENSG00000138100 - + 1 2 146862781 27383811 upstream coding NBPF15 TRIM54 146827614 27358934 + + 0 146827472 27375944 - + Y - - N HCC1954 42 35.8571428571429 4 14 1 N - - N LINE SINE,SINE 0.0333333333333333 1 1 14 0.642757334393363 0.314236919036755 0.642757334393363 0.314236919036755 1 - - 38179 N Y 3.46720988898117 3.30025530722117 3.30025530722117 0 0 0.994166124033458 Y 0 0.985760818985575 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 upstream upstream SIPA1L1 SNORD56 71065795 70934807 + + 0 71065783 70857798 - + N - - N HCC1954 1 1 1 0 6 N - - N - Low_complexity 0 0.56043956043956 0.56043956043956 9 0.414221393275723 0.649899082553289 0.649899082553289 0.414221393275723 2 - - 37599 N Y 3.37287988225536 3.44785379918211 3.37287988225536 43 0.149357924674653 0.0289312163673536 N 0.149357924674653 0.90278376281996 N N 12320 936 ENSG00000108587 ENSG00000151338 - - 17 14 25877957 37090214 utr3p downstream GOSR1 MIPOL1 25828552 36736907 + + 0.149357924674653 25874049 37105946 - - Y - - N HCC1954 24 23.75 21 28 1 N - - N Other,Other SINE 1 1 1 28 0.599906845433805 0.985561246069823 0.985561246069823 0.599906845433805 1 - - 40912 Y Y 3.70889084821189 3.80297331548166 3.70889084821189 273 0 0.0440749019209733 Y 0 0.0474580364690256 N N 1 1149 ENSG00000124092 ENSG00000124097 + - 20 20 55534041 55497489 downstream upstream CTCFL HMGB1L1 55505630 55496854 - - 0 55503666 55498367 - + N - - N HCC1954 20 3.0377358490566 1 8 2 N - - Y - SINE 0 1 1 53 0.714174815992626 1.02126998686945 1.02126998686945 0.714174815992626 1 - - 36680 N Y 3.74913061111987 3.54552998930151 3.54552998930151 0 0 0.925325159129924 Y 0 0 N Y 600 1432 ENSG00000185046 ENSG00000111647 - + 12 12 98902563 99060773 coding coding ANKS1B UHRF1BP1L 97653469 98954996 - - 0 98743298 99020675 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 30 1.08554572030879 1.16410495006798 1.16410495006798 1.08554572030879 4 - - 28 Y Y 3.33784113109356 3.74337746277462 3.33784113109356 127 0 0.0538794465817842 Y 0.096456692913386 0.982283464566929 N N 1747 0 ENSG00000174804 ENSG00000197882 + - 11 11 86344081 86221791 downstream downstream FZD4 AP000654.4 86334370 86221278 - - 0 86309071 86212222 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE LINE 0.977272727272727 0.925531914893617 0.977272727272727 5 0.628473838073511 0.671324327033068 0.671324327033068 0.628473838073511 1 - - 16187 N N 3.33151892129485 3.43681151080804 3.33151892129485 3 0.181974741676234 0.165612011603574 N 0.181974741676234 0.419945725915875 N N 0 0 ENSG00000170226 ENSG00000198137 + - 2 1 174059336 22522411 intron intron AC073465.5-2 AL591122.20 174058839 22521929 - - 0.419945725915875 174058988 22522110 - + Y 1 1 N HCC1954 36 24.6666666666667 22 9 1 N - - N - - 0 0 0 9 0.314236919036755 0.278528178237124 0.314236919036755 0.278528178237124 3 0 0 48951 Y Y 3.57063922744582 3.52361324642271 3.52361324642271 258 0 0.116046728978053 Y 0 0 N N 46607 3556 ENSG00000146063 ENSG00000146054 - - 5 5 180595414 180564783 coding upstream TRIM41 TRIM7 180582912 180553531 + - 0 180584226 180567020 - + N 0.813291488326917 - N HCC1954 8 3.4 1 2 3 N - - Y - SINE 0 1 1 5 0.692749571512847 0.871293275511003 0.871293275511003 0.692749571512847 1 0 - 47915 N N 3.53205502892369 2.52044625793275 2.52044625793275 0 0 0.041636019079864 N 0 0 N N 551733 0 ENSG00000204628 ENSG00000209978 + - 5 8 180603512 6913604 coding upstream GNB2L1 AF238378.5-1 180596536 6913533 - - 0.237389770723104 180597264 6928736 - + Y 0.559193797750339 - N HCC1954 10 5.16666666666667 1 10 1 N - - N - LINE 0 1 1 12 0.51420586751469 0.264244681917271 0.51420586751469 0.264244681917271 1 0 - 17475 Y N 3.5816815158199 2.78417194111826 2.78417194111826 3 0.0116279069767441 0.749548446109142 Y 0 0 N N 2873 0 ENSG00000127124 ENSG00000216933 - - 1 1 42156965 42279987 utr5p upstream HIVEP3 RP1-21K4.1 41744623 42278855 - + 0 42156738 42274062 + - N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.0618556701030928 0.0618556701030928 20 0.892718519990782 0.692749571512847 0.892718519990782 0.692749571512847 2 - - 26797 Y N 2.78479443573421 3.01551281217755 2.78479443573421 0 0 0.511405437160364 Y 0 0 N N 23054 0 ENSG00000131149 ENSG00000220991 - + 16 16 84267311 83906889 intron downstream KIAA0182 AC092275.3 84202524 83906768 + + 0 84224907 83962323 - + N 0.126691903770604 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 15 1.01412823870953 0.956994253430118 1.01412823870953 0.956994253430118 1 0 - 29110 Y Y 3.19505084599062 3.33743990350944 3.19505084599062 312 0 0.848980578094337 Y 0.964715225777173 0.991178806444293 N N 1789 0 ENSG00000204599 ENSG00000203481 - - 6 6 30419485 30360468 upstream upstream TRIM39 AL662795.5 30402600 30360104 + - 0 30401768 30371996 - + N - - N HCC1954 1 1 1 0 5 N - - Y LINE LTR 0.323076923076923 1 1 11 1.38549914302569 0.799875793911741 1.38549914302569 0.799875793911741 2 - - 11426 N N 3.2274272354209 3.61823426992241 3.2274272354209 10 0 0.178304253005099 N 0.447762376237624 0.408316831683168 N N 1649619 4516 ENSG00000141736 ENSG00000144645 + - 17 3 35138441 31998242 coding intron ERBB2 OSBPL10 35104766 31674407 + - 0.0533069306930694 35122227 31804065 + + Y - 0.80268147607642 N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 9 0.757025304952183 0.299953422716903 0.757025304952183 0.299953422716903 2 - 0 47525 Y Y 3.68631175792378 3.22060116451241 3.22060116451241 0 0 0.205588914395725 Y 0 0.982827863176845 N N 155 39774 ENSG00000079435 ENSG00000189377 - + 19 19 47623418 47639040 coding coding LIPE CXCL17 47597499 47624280 - - 0 47606800 47628997 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.04269523134923 1.04269523134923 1.04269523134923 1.04269523134923 2 - - 48030 N N 3.40319013214585 2.96319769112561 2.96319769112561 0 0 0.970311732925797 N 0 0 N Y 10798 29840 ENSG00000113761 ENSG00000164830 - + 5 8 176426349 107834093 coding utr5p ZNF346 OXR1 176382303 107739270 + + 0 176421665 107739589 - + Y - - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 13 0.921285512630487 1.3069399132665 1.3069399132665 0.921285512630487 4 - - 47932 N N 3.46824295875107 3.7297745213208 3.46824295875107 0 0 0.999882147443345 N 0 0 N N 0 86504 ENSG00000182152 ENSG00000104408 + + 5 8 117142614 109330135 downstream coding AC114322.2 EIF3E 117142420 109283149 - - 0 116871207 109296012 - - Y - - N HCC1954 2 1.5390625 1 138 7 N 241 0.00319582 N DNA - 0.703030303030303 0 0.703030303030303 256 1.17838844638783 1.08554572030879 1.17838844638783 1.08554572030879 4 - - 33978 Y Y 3.06000864534446 3.41741556821562 3.06000864534446 417 0 0.9951196936197 Y 0 0.993072208899547 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.993072208899547 14318 13420 - + N - 0.900943343149558 N HCC1954 2 1.25 1 2 10 N - - Y - - 0 0 0 8 0.564198104634174 1.28551466878673 1.28551466878673 0.564198104634174 2 - 0 34775 Y Y 3.45041445226185 3.53205502892369 3.45041445226185 0 0 0.781681892401028 Y 0.97508445945946 0.99169481981982 N N 3476 3463 ENSG00000106992 ENSG00000160408 - + 9 9 129679843 129701753 utr5p downstream AK1 ST6GALNAC6 129668580 129687421 - - 0 129676749 129687286 + - N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.04 0 0.04 14 0.892718519990782 1.04983697950916 1.04983697950916 0.892718519990782 4 - - 23459 N N 3.30591516961058 3.56232542602083 3.30591516961058 4 0 0.118425651900539 N 0.00775193798449625 0.743935983995999 N N 47 5068 ENSG00000177553 ENSG00000129347 - + 1 19 11760935 10537696 intron utr3p C1orf167 KRI1 11749386 10525267 + - 0.599899974993748 11756909 10525427 - - Y 0.292527514964279 0.516295955972607 N HCC1954 3 1.54545454545455 1 5 1 N - - N SINE SINE 1 1 1 11 0.278528178237124 0.378512652476092 0.378512652476092 0.278528178237124 2 0 0 21563 N Y 3.4503745994685 3.55401162459584 3.4503745994685 270 0 0.0161495971763045 N 0.548553240740741 0.984432870370371 N N 3348 2833 ENSG00000165105 ENSG00000133019 + + 9 1 84867863 238139338 utr3p utr5p RASEF CHRM3 84787144 237858996 - + 0 84860280 237859424 - + Y - - N HCC1954 23 21.7272727272727 15 11 1 N - - N - LINE 0 1 1 11 0.528489363834543 0.499922371194838 0.528489363834543 0.499922371194838 3 - - 3338 N N 3.52936639476796 3.44615838200292 3.44615838200292 0 0 0.044617794861218 N 0.286576704545455 0.490411931818182 N N 49 18 ENSG00000186842 ENSG00000175894 - - 21 21 32870062 44955923 intron intron C21orf77 C21orf29 32866420 44742205 - - 0.490411931818182 32868401 44913715 + + N 3.7798074459128 1.05932632139529 Y HCC1954 20 3.8 1 23 1 N - - N - SINE 0 1 1 35 0.621332089913584 0.5713398527941 0.621332089913584 0.5713398527941 0 0 0 31414 Y Y 3.40375919359932 3.32104569437424 3.32104569437424 285 0 0.0147071540082750 Y 0.553809897879026 0.992563498297984 N N 24220 6 ENSG00000168137 ENSG00000206573 - - 3 3 9494838 9413668 upstream downstream SETD5 AC018506.5 9414403 9413147 + - 0 9414106 9408508 - + N - - N HCC1954 2 1.25 1 3 1 N - - Y - DNA 0 1 1 12 0.785592297591888 0.799875793911741 0.799875793911741 0.785592297591888 1 - - 6418 N N 1.44358374332174 2.1243796622549 1.44358374332174 0 0 0.113564088740076 N 0.123007215975835 0.375985903675113 N N 9095 0 ENSG00000211460 ENSG00000218597 - + 2 Y 122241899 10639907 downstream downstream TSN AC010970.1 122229591 10637986 + - 0.595234099681154 123074728 10631093 - - Y - - N HCC1954 6 2.25 1 1 1 N 7 4.87109 N Simple_repeat Low_complexity,Low_complexity 1 0.338983050847458 1 4 0.34280391167646 0.421363141435649 0.421363141435649 0.34280391167646 2 - - 43072 N Y 3.63080414160633 3.15372458015027 3.15372458015027 278 0 0.0169372090269858 N 0.900359712230216 0.880431654676259 N N 3011 0 ENSG00000018189 ENSG00000209177 - - 4 5 71891789 105917118 coding upstream RIPX AC114940.2-2 71806560 105917050 + + 0.681151079136691 71847102 105780854 - - Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 11 0.392796148795944 0.364229156156239 0.392796148795944 0.364229156156239 2 - - 40738 N Y 3.588962247475 3.65657572715995 3.588962247475 0 0.541703703703704 0.946170899379585 N 0.581555555555556 0.541703703703704 N N 29024 0 ENSG00000124208 ENSG00000219462 - + 20 X 48203678 120973146 coding upstream UBE2V1 RP11-417D4.1 48131068 120972510 - - 0.442074074074074 48163053 120973156 + - Y - - N HCC1954 5 3 1 6 3 N - - N - - 0 0 0 8 0.949852505270192 0.364229156156239 0.949852505270192 0.364229156156239 1 - - 36242 Y Y 3.20128492750669 3.58424216889964 3.20128492750669 311 0 0.0039456313051921 Y 0 0.989281886387996 N N 173 1985 ENSG00000127720 ENSG00000133773 - - 12 12 81397069 81276309 coding coding C12orf26 CCDC59 81276455 81271061 + - 0.989281886387996 81276484 81275127 - + N 1.02604571116754 1.55090321993368 N HCC1954 2 1.18181818181818 1 6 1 N - - Y - - 0 0 0 33 0.764167053112109 0.757025304952183 0.764167053112109 0.757025304952183 2 0 0 4437 Y Y 3.65488030998075 3.54396255319831 3.54396255319831 0 0 0.593439379573214 Y 0 0.9867131242741 N N 650 250 ENSG00000127957 ENSG00000170092 + + 7 7 74995330 74969197 utr3p upstream PMS2L3 SPDYE5 74975006 74962235 - + 0 74978190 74958837 - + N 0.555405740460687 - N HCC1954 108 54.5 10 4 1 N - - Y - SINE 0 0.91156462585034 0.91156462585034 4 0.428504889595575 0.778450549431962 0.778450549431962 0.428504889595575 1 0 - 18930 N Y 3.46704205511183 3.46551447180198 3.46551447180198 269 0 0.095123916363244 Y 0.923362882470689 0.980840720617672 N N 0 42 ENSG00000213353 ENSG00000134201 + + 1 1 110111760 110062411 upstream downstream AL158847.22 GSTM5 110111549 110056388 - + 0 110119217 110070213 - + N - - N HCC1954 4 1.6 1 1 1 N - - N - LTR,LTR 0 0.653543307086614 0.653543307086614 5 0.721316564152552 0.907002016310634 0.907002016310634 0.721316564152552 4 - - 2980 N Y 3.86785830821752 3.5016965035439 3.5016965035439 12 0 0.0397777159831885 N 0 0.0283434139784947 N N 290 14402 ENSG00000142405 ENSG00000156689 - - 19 11 59019460 58368833 utr3p utr5p NALP12 GLYATL2 58988669 58358118 - - 0.0283434139784947 58988945 58368485 + + Y - - N HCC1954 36 35.2857142857143 34 7 1 N - - N SINE - 1 0 1 7 0.314236919036755 0.578481600954027 0.578481600954027 0.314236919036755 1 - - 36930 N N 3.20861393465108 2.9878429209535 2.9878429209535 0 0 0.773456315295700 N 0 0 N N 1977 16017 ENSG00000196074 ENSG00000018236 + + 20 12 57942105 39750361 intron intron SYCP2 CNTN1 57872016 39588423 - + 0 57912476 39619645 - + Y 1.04240472424682 1.35136218450684 N HCC1954 1 1 1 0 3 N 470 0.598344 N LINE,LINE - 1 0 1 6 0.87843502367093 0.549914608314322 0.87843502367093 0.549914608314322 3 0 0 30101 N N 3.61104682422314 3.39610538909039 3.39610538909039 5 0.393831974477136 0.0264718866618585 N 0.393831974477136 0.649060616802552 N N 7540 3968 ENSG00000122692 ENSG00000124496 - - 9 6 33075989 42527767 utr3p utr3p SMU1 TRERF1 33031850 42300647 - - 0.425735554767813 33035746 42302800 + + Y - - N HCC1954 23 21.0833333333333 20 12 1 N - - N SINE DNA 1 1 1 12 0.34280391167646 0.499922371194838 0.499922371194838 0.34280391167646 1 - - 17805 N N 3.46025583699669 3.47439733468044 3.46025583699669 0 0 0.986102055288744 N 0 0.78273025001997 Y N 10857 14045 ENSG00000085832 ENSG00000117859 + + 1 1 51757583 52026729 coding intron EPS15 OSBPL9 51592523 51815439 - + 0 51683150 51914916 - + N - 0.59938350194942 N HCC1954 21 3.28888888888889 1 8 4 N - - N - SINE 0 0.961290322580645 0.961290322580645 45 1.18553019454776 1.10697096478857 1.18553019454776 1.10697096478857 1 - 0 46679 N Y 3.73912139251568 3.62295434849776 3.62295434849776 5 0 0.301584874209332 N 0.911764705882353 0.911764705882353 N N 10075 42670 ENSG00000105254 ENSG00000128050 - - 19 4 41308689 57022291 coding utr3p TBCB PAICS 41297728 56996672 + + 0.911764705882353 41304458 57021772 - - Y - - N HCC1954 22 21.4 21 5 1 N - - N - SINE 0 1 1 5 0.607048593593732 0.349945659836387 0.607048593593732 0.349945659836387 1 - - 28751 N N 3.33676820853032 3.35313948972658 3.33676820853032 5 0 0.127392215917304 N 0 0 N N 9809 0 ENSG00000072864 ENSG00000206758 - + 16 19 15727711 53988327 coding upstream NDE1 U6 15644625 53988221 + - 0 15666143 53988961 - - Y - - N HCC1954 4 3.2 3 5 1 N 146 23.7742 N - SINE 0 1 1 5 0.892718519990782 0.378512652476092 0.892718519990782 0.378512652476092 3 - - 19960 N Y 3.38912318237562 3.47233119514066 3.38912318237562 1 0 0.540761673710452 N 0.672574783337993 0 N N 25 4096 ENSG00000177800 ENSG00000103121 + - 1 16 227454180 79597997 intron coding TMEM78 C16orf61 227452006 79567206 + - 0 227452491 79567577 + + Y - 0.670518454535324 N HCC1954 28 25.5714285714286 25 7 1 N 238 25.662 N SINE - 1 0 1 7 0.34280391167646 0.414221393275723 0.414221393275723 0.34280391167646 3 - 0 9410 Y Y 3.27039548527796 3.41166241987037 3.27039548527796 283 0 0.832224410402844 Y 0.544717923723651 0.982819544291458 N N 830 7432 ENSG00000185158 ENSG00000178691 - + 17 17 27404630 27352162 upstream downstream LRRC37B SUZ12 27372156 27288185 + + 0 27369104 27359264 - + N - - N HCC1954 1 1 1 0 4 N - - Y SINE Low_complexity 0.0168067226890756 0.589041095890411 0.589041095890411 12 0.849868031031224 1.04269523134923 1.04269523134923 0.849868031031224 4 - - 15516 N N 3.19513055157732 3.61360747730288 3.19513055157732 0 0 0.0762318919081546 N 0 0 N N 0 179175 ENSG00000208307 ENSG00000163191 - + 7 1 145325416 150276135 upstream coding AC073308.4 S100A11 145325354 150271606 + - 0 145325211 150271845 - - Y - - N HCC1954 2 2 2 5 1 N - - N - - 0 0 0 5 0.292811674556976 0.664182578873142 0.664182578873142 0.292811674556976 1 - - 18674 Y Y 3.34831435801417 3.49640736351508 3.34831435801417 458 0 0.00535535327326986 Y 0 0.988725236227272 N N 0 1472 ENSG00000212577 ENSG00000117543 - - 1 1 101371483 101263950 upstream upstream SCARNA16 DPH5 101371297 101227773 + - 0 101321423 101264207 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.749883556792257 0.749883556792257 0.749883556792257 0.749883556792257 1 - - 33324 N Y 3.37444731835856 3.68783934123363 3.37444731835856 273 0 0.0737959990256737 Y 0 0.975699097650317 N N 59837 275222 ENSG00000198695 ENSG00000198763 + + MT MT 14674 5512 coding coding MT-ND6 MT-ND2 14150 4471 - + 0 14417 5060 - + N 1.31573020757828 - N HCC1954 6 2.2 1 2 3 N - - N - - 0 0 0 5 0.871293275511003 0.692749571512847 0.871293275511003 0.692749571512847 2 0 - 5477 N N 3.56439156556061 3.00431250855995 3.00431250855995 0 0.474342105263158 0.0181205123166160 N 0.628947368421053 0.598026315789474 N N 2708 49 ENSG00000173960 ENSG00000186842 - - 2 21 24077195 32870062 intron intron UBXN2A C21orf77 24003686 32866420 + - 0.598026315789474 24050928 32868363 - + Y 0.631703434907945 3.7798074459128 N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.364229156156239 0.364229156156239 0.321378667196682 1 0 0 5356 N Y 3.48167806633553 3.3257657729496 3.3257657729496 243 0.857730746619636 0.0309862225799901 N 0.654488956076258 0.776434030402284 N N 7234 0 ENSG00000115239 ENSG00000217019 + - 2 6 53940801 116207531 utr3p downstream ASB3 RP11-721G11.1 53613314 116205090 - - 0.857730746619636 53613841 115997923 - + Y - - N HCC1954 46 25.125 21 8 1 N - - N LINE LINE 1 1 1 8 0.464213630395207 0.314236919036755 0.464213630395207 0.314236919036755 2 - - 17888 Y Y 3.33528047801382 3.45041445226185 3.33528047801382 144 0 0.036437219795586 Y 0 0.991402237710932 N N 2306 348 ENSG00000158315 ENSG00000131233 + - 1 1 39180043 39119856 coding intron RHBDL2 GJA9 39124066 39102778 - - 0 39124801 39114393 - + N - 4.415024401642 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.857009779191151 0.842726282871298 0.857009779191151 0.842726282871298 2 - 0 32481 N Y 3.59425138750382 3.52567938596249 3.52567938596249 268 0 0.0312274649470694 N 0.935427031509121 0.944651741293532 N N 12 6846 ENSG00000214954 ENSG00000163755 + + 8 3 92300522 150373995 intron intron LRRC69 HPS3 92184049 150330061 + + 0.0221807628524046 92240140 150366527 + + Y 2.68614794675939 1.33045161304183 N HCC1954 2 1.99137931034483 1 115 1 N - - N - - 0 0 0 116 0.757025304952183 0.821301038391519 0.821301038391519 0.757025304952183 2 0 0 5088 N Y 3.09083117904067 3.49697642496854 3.09083117904067 2 0 0.316853417849286 N 0.940495542091523 0.977685828284321 N N 12743 0 ENSG00000122545 ENSG00000203462 + - 7 7 35911440 45731691 coding upstream SEPT7 AC091439.5-2 35807345 45731307 + - 0.977685828284321 35904516 45732987 + + N - - Y HCC1954 12 5.22222222222222 2 9 1 N - - N - LTR,LTR 0 0.583815028901734 0.583815028901734 9 0.914143764470561 1.23552243166724 1.23552243166724 0.914143764470561 2 - - 4194 Y Y 3.63978029044062 3.36145329115156 3.36145329115156 337 0 0.0132270639209592 Y 0 0.987690955050005 N N 0 0 ENSG00000206634 ENSG00000203448 - - 7 7 64858081 64832435 upstream upstream SNORA22 AC104057.4 64857948 64830585 + - 0 64853310 64843634 - + N - - N HCC1954 1 1 1 0 3 N - - Y - SINE 0 1 1 14 0.557056356474248 0.828442786551446 0.828442786551446 0.557056356474248 1 - - 41542 Y Y 3.46720988898117 3.59425138750382 3.46720988898117 303 0 0.00345772371600528 Y 0.983106785254797 0.991553392627398 N N 41561 5757 ENSG00000104517 ENSG00000048392 + - 8 8 103493671 103320522 downstream upstream UBR5 RRM2B 103334748 103285908 - - 0 103333200 103325522 - + N - - N HCC1954 11 2.85714285714286 1 5 1 N - - Y DNA SINE 0.87037037037037 1 1 14 1.15696320190805 0.87843502367093 1.15696320190805 0.87843502367093 1 - - 30320 Y Y 3.32799974635873 2.94170510376988 2.94170510376988 0 0 0.998137959110152 Y 0 0.986438875224357 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62697435 62569606 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 5 0.771308801272036 0.707033067832699 0.771308801272036 0.707033067832699 2 - - 13658 Y Y 3.72079837248651 3.66016945000958 3.66016945000958 263 0 0.0243882791753888 Y 0 0 N N 8708 2417 ENSG00000198792 ENSG00000185022 + + 22 22 36998962 36942458 intron downstream TMEM184B MAFF 36945244 36927944 - + 0 36950737 36942666 - + N 0.629440646317745 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.792734045751814 0.635615586233437 0.792734045751814 0.635615586233437 1 0 - 16761 N N 3.12804628055249 3.65128658713112 3.12804628055249 0 0 0.047407973575177 N 0 0.0025974025974026 N N 1649619 1472 ENSG00000141736 ENSG00000117543 - + 17 1 35138441 101263950 coding intron ERBB2 DPH5 35104766 101227773 + - 0.0025974025974026 35122227 101238030 - - Y - 0.522589979847924 N HCC1954 7 4.4 2 10 1 N - - N - SINE 0 1 1 10 0.757025304952183 0.314236919036755 0.757025304952183 0.314236919036755 1 - 0 31173 Y Y 3.47655676017605 3.60256518892881 3.47655676017605 262 0 0.680142148134759 Y 0.521832061068702 0.980076335877863 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 intron upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42855553 42825983 - + N 0.0692123342775211 - N HCC1954 1 1 1 0 6 N - - Y LTR LTR 1 1 1 185 1.32836515774628 0.757025304952183 1.32836515774628 0.757025304952183 2 0 - 3833 N N 3.56079784271098 3.33164690237084 3.33164690237084 0 0 0.577424518387523 N 0.546148721365244 0.533541741403167 N N 0 5014 ENSG00000185942 ENSG00000135250 - + 8 7 64008644 104816583 intron coding NKAIN3 SRPK2 63324187 104544060 + - 0.205760262389177 63940121 104553933 - - Y 1 0.394823549728163 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.335662163516534 0.535631111994469 0.535631111994469 0.335662163516534 1 0 0 19761 N N 3.48805370929674 3.68105312311849 3.48805370929674 1 0 0.140863354709818 N 0 0.155418559377028 N N 76996 49089 ENSG00000062038 ENSG00000117450 + - 16 1 67290440 45760196 intron coding CDH3 PRDX1 67236240 45749295 + - 0.155418559377028 67262423 45757265 + + Y 0.281495447811051 3.15080228592947 N HCC1954 42 4.94339622641509 2 53 1 N - - N SINE - 1 0 1 53 0.314236919036755 0.849868031031224 0.849868031031224 0.314236919036755 3 0 0 41330 N Y 2.84749465542412 3.48639814491089 2.84749465542412 180 0 0.00776306059024512 N 0.394776876267749 0 N N 0 0 ENSG00000101134 ENSG00000216027 - - 20 4 52701097 61212351 downstream downstream DOK5 AC095061.3 52525570 61212262 + - 0.590010141987829 52729755 60902269 - + Y - - N HCC1954 63 31.5 21 4 1 N 532 26.4592 N SINE SINE,SINE 1 0.875 1 4 0.278528178237124 0.28566992639705 0.28566992639705 0.278528178237124 1 - - 18907 Y Y 3.47592491799029 3.62464976567696 3.47592491799029 296 0 0.523087512453789 Y 0 0.992671899841017 N N 1166 27007 ENSG00000154198 ENSG00000142973 + + 1 1 47138734 47057605 intron intron CYP4Z2P CYP4B1 47096493 47037257 - + 0 47107090 47055441 - + N 0.197481874237702 1.5025329953805 N HCC1954 3 1.25 1 3 4 N - - Y LINE - 1 0 1 20 1.22838068350732 0.999844742389676 1.22838068350732 0.999844742389676 1 0 0 3631 N N 3.53768019619294 3.5246463161926 3.5246463161926 1 0.00383141762452099 0.969384259306575 Y 0.0327058692875787 0 N Y 5796 16900 ENSG00000159267 ENSG00000185658 - + 21 21 37284373 39607426 coding intron HLCS BRWD1 37045066 39479274 - - 0 37191301 39506462 + - N - 0.379415355952142 N HCC1954 1 1 1 0 2 Y 508 8.9854 N - - 0 0 0 4 0.421363141435649 0.328520415356608 0.421363141435649 0.328520415356608 4 - 0 10470 Y Y 3.39334874741101 3.24479173359369 3.24479173359369 0 0 0.283850836323506 Y 0.911977321048902 0.98532955350815 N N 6235 2674 ENSG00000213977 ENSG00000040531 + + 17 17 3518722 3513146 coding coding TAX1BP3 CTNS 3512939 3486511 - + 0 3514238 3510369 - + N - 1.40315827234453 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.12839620926835 0.99270299422975 1.12839620926835 0.99270299422975 4 - 0 41590 Y Y 3.43039601505348 3.27188321579446 3.27188321579446 298 0 0.294093912459730 Y 0.928241610738255 0.992026845637584 N N 0 0 ENSG00000222501 ENSG00000207110 + + 8 8 129092039 129080722 downstream upstream U4 U1 129091912 129080559 - + 0 129091019 129079788 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LINE 0 1 1 8 0.778450549431962 0.814159290231593 0.814159290231593 0.778450549431962 1 - - 28745 N Y 3.61038447681384 3.63399663687184 3.61038447681384 0 0 0.217683371781630 N 0.705722564288301 0.920771459616081 N N 3423 2307 ENSG00000169246 ENSG00000176920 - + 16 19 21365985 53901019 utr5p intron AC008740.7-1 FUT2 21321106 53891040 - + 0 21365941 53900320 + + Y - - N HCC1954 320 212.75 37 4 1 N - - N SINE SINE 0.130434782608696 1 1 4 0.492780623034912 0.328520415356608 0.492780623034912 0.328520415356608 1 - - 6399 N N 3.48656597878024 3.49744043328497 3.48656597878024 2 0 0.193639827515212 N 0.261634426689094 0 N N 153380 8194 ENSG00000185275 ENSG00000144036 + - Y 2 19614093 72906685 utr3p intron CD24L4 EXOC6B 19611898 72256621 - - 0 19612778 72434170 - + Y - 1.93045303734924 N HCC1954 13 10 6 5 1 N - - N SINE SINE 0.403846153846154 1 1 5 0.371370904316165 0.321378667196682 0.371370904316165 0.321378667196682 1 - 0 28131 N Y 3.58424216889964 3.23743645402508 3.23743645402508 0 0 0.210275579164960 N 0 0.848201566951567 N N 4898 45068 ENSG00000136816 ENSG00000205336 - + 9 16 131613381 56256445 utr3p upstream TOR1B GPR56 131605253 56220023 + + 0 131611902 56211245 - + Y - - N HCC1954 24 22.8 21 10 2 N - - N SINE - 1 0 1 10 0.299953422716903 0.735600060472404 0.735600060472404 0.299953422716903 1 - - 46480 N N 3.23034293992665 3.37790402551261 3.23034293992665 0 0 0.0448134183948939 N 0 0.0634920634920635 N N 0 4 ENSG00000182225 ENSG00000189233 + - 19 8 5527949 27997307 downstream intron AC011533.6 C8orf80 5527671 27935607 - - 0.0634920634920635 5518780 27989939 - + Y - 1.12757367783609 N HCC1954 21 20.25 20 4 1 N 439 26.742 N - SINE 0 1 1 4 0.464213630395207 0.321378667196682 0.464213630395207 0.321378667196682 1 - 0 49357 Y Y 3.65760879692984 3.43614916339873 3.43614916339873 277 0 0.860467325168253 Y 0.00361010830324915 0.989286130196809 N N 14691 26477 ENSG00000161013 ENSG00000161011 - - 5 5 179166547 179197681 utr5p coding MGAT4B SQSTM1 179156711 179180503 - + 0 179166195 179184831 + - N - - N HCC1954 1 1 1 0 5 N - - Y Low_complexity - 0.0490196078431373 0 0.0490196078431373 16 0.728458312312478 0.749883556792257 0.749883556792257 0.728458312312478 2 - - 45663 N N 3.5010341561346 3.65384724021086 3.5010341561346 0 0 0.120506011179458 N 0 0 N N 40617 559 ENSG00000130164 ENSG00000102290 + + 19 X 11105490 91764885 utr3p utr3p LDLR PCDH11X 11061132 90920960 + + 0 11104135 91025227 + + Y - - N HCC1954 39 37.6 35 5 1 N - - N SINE SINE 0.262295081967213 1 1 5 0.435646637755502 0.28566992639705 0.435646637755502 0.28566992639705 3 - - 32988 N N 3.51104337473878 3.30232144676095 3.30232144676095 18 0 0.128263025753328 N 0 0.0194923371647511 Y N 544065 0 ENSG00000198744 ENSG00000210194 - - MT MT 9988 14743 coding intron MT-CO3 AF347015.1-22 8367 14675 + - 0.0194923371647511 8752 14730 - + N 0.55820297354268 1 N HCC1954 4 2.4 1 4 1 N 189 4.09957 N - - 0 0 0 5 0.657040830713216 0.964136001590045 0.964136001590045 0.657040830713216 1 0 0 5613 N N 2.22766737700357 2.20644350762293 2.20644350762293 0 0 0.143477883667606 N 0 0.00277777777777766 N N 2859 4157 ENSG00000152056 ENSG00000124313 + - 2 X 224410563 53367247 upstream intron AP1S3 IQSEC2 224325785 53278784 - - 0.00277777777777766 224410610 53312973 - + Y - 7.80257179576739 N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.658536585365854 0 0.658536585365854 4 0.292811674556976 0.349945659836387 0.349945659836387 0.292811674556976 1 - 0 33057 N Y 2.77892265388278 3.00400651548706 2.77892265388278 281 0.00355871886120995 0.992817145106776 Y 0.0129591083059154 0.990599610555294 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8476 5116 - + N 0.675128136826734 0.968332928340944 N HCC1954 4 2 1 8 9 Y - - N - - 0 0 0 10 1.15696320190805 1.27123117246687 1.27123117246687 1.15696320190805 1 0 0 39663 N N 3.62464976567696 3.6491271616355 3.62464976567696 49 0.278063096111518 0.0599970168568971 N 0 0 N N 2 12271 ENSG00000206187 ENSG00000177479 - + 15 3 23849360 48997971 utr3p utr5p AC100836.2 ARIH2 23698600 48931285 + + 0 23812170 48939899 - + Y - - N HCC1954 38 24.25 2 4 1 N - - N SINE,SINE - 0.816666666666667 0 0.816666666666667 4 0.428504889595575 0.528489363834543 0.528489363834543 0.428504889595575 3 - - 7763 N Y 3.63296356710195 2.85910600525166 2.85910600525166 0 0 0.0983550514382923 N 0.97180866745283 0.97180866745283 N N 3 27 ENSG00000222017 ENSG00000164749 + + 2 8 198347792 76641600 coding upstream AC011997.1 HNF4G 198266075 76482732 + + 0 198266181 76299152 + + Y - - N HCC1954 24 22.5555555555556 21 9 1 N - - N LINE LINE 1 0.955696202531646 1 9 0.621332089913584 0.964136001590045 0.964136001590045 0.621332089913584 1 - - 35620 N N 3.5816815158199 3.3755202409218 3.3755202409218 0 0 0.766144908710355 N 0.409018228333866 0 N N 0 712661 ENSG00000216315 ENSG00000111640 + + 22 12 39400402 6517797 intron coding CTA-229A8.6 GAPDH 39399439 6513918 - + 0 39399475 6517405 - + Y 1 - N HCC1954 4 1.8 1 2 2 N - - N - - 0 0 0 5 0.264244681917271 0.471355378555133 0.471355378555133 0.264244681917271 1 0 - 35278 N Y 3.28292550416853 3.8333716936548 3.28292550416853 0 0 0.66164214688522 N 0 0.972594683603858 N N 194 0 ENSG00000139173 ENSG00000183846 - + 12 2 43069807 110575338 intron upstream TMEM117 AC112229.4-1 42516168 110574935 + - 0 42590127 110576429 - - Y 1.88582108707048 - N HCC1954 60 50 40 4 1 N - - N LINE - 1 0 1 4 0.549914608314322 0.592765097273879 0.592765097273879 0.549914608314322 3 0 - 6807 N Y 3.64656650855576 3.52361324642271 3.52361324642271 0 0 0.840528920210807 Y 0.912561853351327 0.781404633378317 N N 126 3186 ENSG00000186281 ENSG00000115042 + + 2 2 96064454 95442605 coding coding AC013272.5-2 FAHD2A 96051422 95432203 - + 0.781404633378317 96052147 95442237 - + N 1.75489942886997 - N HCC1954 4 2.66666666666667 2 6 2 N - - N - - 0 0 0 6 0.921285512630487 0.707033067832699 0.921285512630487 0.707033067832699 1 0 - 22207 N N 3.25256697878875 3.49913585046416 3.25256697878875 0 0 0.0748197052716779 N 0 0 N N 49089 2399 ENSG00000117450 ENSG00000137834 - - 1 15 45760196 64861377 coding downstream PRDX1 SMAD6 45749295 64781688 - + 0 45757275 64876589 + - Y - - N HCC1954 7 3.55555555555556 3 18 1 N - - N - SINE 0 1 1 18 1.02841173502938 0.257102933757345 1.02841173502938 0.257102933757345 2 - - 34307 Y Y 3.38958719069204 3.51889316784735 3.38958719069204 426 0 0.515004051709822 Y 0 0.989661631272957 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5594733 5567513 - + N - - N HCC1954 1 1 1 0 7 N - - Y LINE LTR 1 1 1 13 0.414221393275723 1.29265641694665 1.29265641694665 0.414221393275723 1 - - 13230 N Y 3.04426920633398 3.12946738033566 3.04426920633398 0 0.15464480874317 0.102066400244341 N 0.552459016393442 0.15464480874317 N N 551733 592 ENSG00000204628 ENSG00000170160 + + 5 17 180603512 16648492 utr3p intron GNB2L1 CCDC144A 180596536 16534271 - + 0.15464480874317 180596548 16597458 - + Y - 0.368918903289268 N HCC1954 1 1 1 0 1 N - - N - LINE 0 1 1 4 0.542772860154395 0.242819437437493 0.542772860154395 0.242819437437493 4 - 0 44080 N N 3.47911741325579 3.09087103183403 3.09087103183403 7 0 0.0760958687425206 N 0 0 N N 240 3891 ENSG00000147246 ENSG00000166295 - + X 10 114050880 73665622 upstream intron HTR2C C10orf104 113724807 73645812 + + 0 113713454 73645953 - + Y - 0.744979490524871 N HCC1954 28 25.6 23 5 1 N - - N SINE - 1 0 1 5 0.364229156156239 0.357087407996313 0.364229156156239 0.357087407996313 1 - 0 29355 N N 3.21488786896051 3.55976477294109 3.21488786896051 2 0.00446428571428559 0.77330321958496 N 0.00446428571428559 0.00446428571428559 N N 0 568998 ENSG00000219374 ENSG00000156508 + + 6 6 49436052 74288344 downstream utr3p RP1-142O9.1 EEF1A1 49433818 74282194 - - 0.00446428571428559 49433665 74284128 - - N - - Y HCC1954 14 10.0833333333333 5 12 2 N - - N - - 0 0 0 12 0.278528178237124 0.93556900895034 0.93556900895034 0.278528178237124 2 - - 374 Y Y 3.53871326596283 3.62977107183644 3.53871326596283 130 0.0024390243902439 0.369304858390253 Y 0.0024390243902439 0 N Y 1764 9180 ENSG00000149798 ENSG00000014138 - + 11 11 64846475 64821663 intron coding CDC42EP2 POLA2 64838907 64786006 + + 0 64844591 64820037 - + N 2.23534588080606 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 28 1.31408166142643 1.31408166142643 1.31408166142643 1.31408166142643 4 0 - 11528 N N 3.05368643554575 2.62266528142032 2.62266528142032 44 0.06360153256705 0.151025950251563 N 0.06360153256705 0.06360153256705 N N 7056 90030 ENSG00000154229 ENSG00000147140 - - 17 X 62237324 70437743 intron utr3p PRKCA NONO 61729216 70420165 + + 0.163218390804598 62220182 70436957 - - Y 1.75637523421336 1.66385898337574 N HCC1954 34 6.83333333333333 1 3 1 N - - N SINE SINE,SINE 0.784313725490196 0.454545454545455 0.784313725490196 6 0.364229156156239 1.07126222398894 1.07126222398894 0.364229156156239 1 0 0 40082 Y Y 3.3493779330076 3.40740634961144 3.3493779330076 61 0 0.119100676043151 Y 0.987565445026178 0.987565445026178 N N 194 3493 ENSG00000183208 ENSG00000185043 - - 15 15 88586316 88578160 utr5p upstream C15orf58 CIB1 88582726 88574487 + - 0 88582726 88578522 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.778450549431962 0.39993789695587 0.778450549431962 0.39993789695587 1 - - 36122 N N 3.30956232562269 3.43784458057793 3.30956232562269 1 0 0.183169390470511 N 0.657290322580645 0 N N 54 1917 ENSG00000166111 ENSG00000163832 - - 12 3 107856860 47530203 utr3p coding SVOP C3orf75 107828787 47512135 - - 0 107829609 47527719 + + Y - - N HCC1954 25 22.875 22 8 1 N - - N SINE - 1 0 1 8 0.321378667196682 0.499922371194838 0.499922371194838 0.321378667196682 1 - - 4576 Y Y 3.55504469436574 3.44781394638876 3.44781394638876 0 0 0.93450773295363 Y 0 0.986253337977476 N N 11641 25286 ENSG00000106244 ENSG00000130429 + + 7 7 98844228 98830338 intron coding PDAP1 ARPC1B 98830525 98810265 - + 0 98832776 98829678 - + N 0.245140742857324 - N HCC1954 1 1 1 0 2 N - - Y SINE - 0.44 0 0.44 9 1.07126222398894 0.821301038391519 1.07126222398894 0.821301038391519 4 0 - 47184 N N 3.16679831294397 3.09815176348912 3.09815176348912 0 0 0.99474930838886 N 0 0 Y N 8665 5583 ENSG00000079313 ENSG00000104885 + + 19 19 1799452 2181007 intron coding REXO1 DOT1L 1766245 2115148 - + 0 1767389 2161399 - + N 0.915714264252882 - N HCC1954 1 1 1 0 5 N 279 3.37031 N - - 0 0 0 5 0.778450549431962 0.592765097273879 0.778450549431962 0.592765097273879 1 0 - 33160 N Y 3.42360979693834 3.81145495077599 3.42360979693834 326 0 0.000931573080860337 Y 0 0.990853830134519 N N 247001 539404 ENSG00000198786 ENSG00000198712 - + MT MT 14149 8270 coding coding MT-ND5 MT-CO2 12338 7587 + + 0 13911 8016 - + N 1.13697291353428 1.93454761906259 N HCC1954 3 1.75 1 2 1 N - - N - - 0 0 0 4 0.742741808632331 0.778450549431962 0.778450549431962 0.742741808632331 0 0 0 40674 N Y 3.69255941980899 2.17788998109242 2.17788998109242 273 0 0.00297161892142539 N 0.528050896471949 0.563010089325879 N N 2099 483 ENSG00000101104 ENSG00000069122 + - 20 6 43021090 47030639 intron upstream PABPC1L GPR116 42972117 46928208 + - 0.563010089325879 42993061 47035292 + + Y 1.26256477589045 - N HCC1954 2 2 2 4 1 N - - N - Low_complexity 0 1 1 4 0.635615586233437 0.257102933757345 0.635615586233437 0.257102933757345 1 0 - 40489 N Y 3.64400585547602 3.46704205511183 3.46704205511183 8 0 0.180875167321689 N 0 0.946621274409044 N N 136 60677 ENSG00000188089 ENSG00000125740 + + 15 19 40130680 50670254 utr3p upstream PLA2G4E FOSB 40061072 50663093 - + 0 40062701 50644469 - + Y - - N HCC1954 29 24.1538461538462 21 13 1 N - - N SINE,SINE SINE 1 1 1 13 0.364229156156239 0.478497126715059 0.478497126715059 0.364229156156239 3 - - 4049 Y Y 3.28189243439864 3.55128313764676 3.28189243439864 0 0 0.989462672792906 Y 0 0.988924274593064 N N 0 0 ENSG00000219142 ENSG00000217741 + + 7 7 17039627 16944706 downstream upstream AC098592.8 AC098592.7 17039238 16944374 - + 0 17027497 16922535 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LTR 0 1 1 10 0.607048593593732 0.964136001590045 0.964136001590045 0.607048593593732 2 - - 19143 N N 3.46448140203209 3.51729103662399 3.46448140203209 0 0 0.736854695621244 N 0 0 Y N 49 2833 ENSG00000186973 ENSG00000133019 - + 1 1 43394654 238139338 intron utr5p FAM183A CHRM3 43382616 237858996 + + 0 43388912 237859191 - + N 0.472264910112202 - N HCC1954 25 24 23 4 3 N - - N - LINE 0 1 1 4 0.428504889595575 0.51420586751469 0.51420586751469 0.428504889595575 2 0 - 33017 N N 2.96319769112561 3.57373843675549 2.96319769112561 17 0 0.999997138343106 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.0428120490620492 8593 11024 - + N 0.65879648337433 0.556237025275747 N HCC1954 4 2 1 4 12 N 189 4.09957 N - - 0 0 0 8 0.978419497909897 1.22123893534739 1.22123893534739 0.978419497909897 2 0 0 5353 N Y 3.8333716936548 3.28292550416853 3.28292550416853 0 0 0.803028781131816 N 0 0.975504778783467 N N 3966 891 ENSG00000175772 ENSG00000183826 + - 2 6 110111006 38673848 upstream intron AC013268.5-1 BTBD9 110103138 38250713 + - 0 110102056 38350583 + + Y - 1.10404956566173 N HCC1954 40 40 40 4 1 N - - N - LINE 0 1 1 4 0.714174815992626 0.542772860154395 0.714174815992626 0.542772860154395 3 - 0 23715 N N 3.25679254382414 3.57952209032428 3.25679254382414 9 0 0.0380378393222668 N 0 0 N N 4159 0 ENSG00000012061 ENSG00000219735 - - 19 1 50619017 219374186 utr5p downstream ERCC1 RP11-453O22.1 50604712 219373830 - - 0 50618890 219282985 + + Y - - N HCC1954 26 24.75 21 4 1 N - - N - SINE 0 1 1 4 0.592765097273879 0.299953422716903 0.592765097273879 0.299953422716903 1 - - 7137 Y N 3.80400638525155 3.49896801659482 3.49896801659482 6 0 0.786342541261193 Y 0 0 N N 0 52 ENSG00000183846 ENSG00000214164 + - 2 2 110575338 110569923 upstream upstream AC112229.4-1 AC112229.4-2 110574935 110569013 - - 0 110576427 110571540 - + N - - N HCC1954 12 4.8 2 10 4 N - - Y - LTR,Simple_repeat,LTR 0 0.520231213872832 0.520231213872832 10 1.37835739486577 1.23552243166724 1.37835739486577 1.23552243166724 1 - - 48120 N N 3.49847350305486 3.38805025981237 3.38805025981237 0 0.0275239458328745 0.999998644507119 N 0.0355609380160741 0.0355609380160741 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117944557 2618805 - + Y - - N HCC1954 2 1.25 1 3 12 N 282 1.61558 N - - 0 0 0 12 1.27123117246687 1.10697096478857 1.27123117246687 1.10697096478857 2 - - 4594 N Y 3.20856565916179 3.62617734898681 3.20856565916179 0 0.293361623256268 0.565320464738533 Y 0.293361623256268 0 N N 2 1974 ENSG00000106258 ENSG00000197037 + + 7 7 99115555 99067966 intron coding CYP3A5 ZNF498 99083759 99052507 - + 0 99104654 99059739 - + N 1.13261372397841 - N HCC1954 1 1 1 0 1 N - - N DNA - 1 0 1 26 1.02841173502938 1.19981369086761 1.19981369086761 1.02841173502938 4 0 - 38989 N Y 3.61207989399303 3.58743466416515 3.58743466416515 23 0.179136181260325 0.0516292964576962 N 0.807882936039651 0.790417748406891 N N 16 0 ENSG00000215379 ENSG00000184565 - + 15 Y 20297366 19698690 utr5p intron AC116165.7-4 TTTY14 20294732 19553973 + - 0 20295932 19612795 - - Y - 1 N HCC1954 39 38.5 38 4 1 N 198 24.3644 N SINE SINE 1 0.494845360824742 1 4 0.28566992639705 0.692749571512847 0.692749571512847 0.28566992639705 1 - 0 17939 Y Y 3.37023110089298 3.71041843152174 3.37023110089298 103 0 0.507208475506744 Y 0 0.980276912153367 N N 10506 438 ENSG00000143437 ENSG00000143387 + - 1 1 149115815 149047436 utr3p utr5p ARNT CTSK 149048810 149035311 - - 0 149051111 149047425 - + N - 8.7988107984093 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 1.01412823870953 0.764167053112109 1.01412823870953 0.764167053112109 4 - 0 42167 Y Y 3.41782614336956 3.49528100778935 3.41782614336956 0 0 0.94393968278249 Y 0.989057950596412 0.989057950596412 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 coding downstream AFF1 AC093827.3 88147177 88089842 + - 0 88186350 88076657 - + N 0.155461753027553 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 21 0.807017542071667 1.04983697950916 1.04983697950916 0.807017542071667 2 0 - 21579 N N 2.89378609696779 3.04596733885829 2.89378609696779 0 0.177257525083612 0.257934275033330 N 0.415419820454145 0.177257525083612 N N 9281 11502 ENSG00000213240 ENSG00000159921 + + 1 9 144003011 36248450 utr3p utr3p NOTCH2NL GNE 143920462 36204430 + - 0.177257525083612 143995500 36206334 + - Y - - N HCC1954 851 803.25 756 4 1 N - - N Simple_repeat SINE 0.978723404255319 1 1 4 0.335662163516534 0.392796148795944 0.392796148795944 0.335662163516534 3 - - 29049 N N 2.86213066664782 2.92022944126855 2.86213066664782 0 0.100033014196104 0.192213429322384 N 0.674480026411357 0 N N 0 24621 ENSG00000219986 ENSG00000083307 + - 6 8 6740634 102750995 downstream utr3p RP11-320C15.1 GRHL2 6740080 102574162 - + 0 6703008 102750659 - - Y - 2.82555753683573 N HCC1954 2 1.75 1 3 1 N - - N SINE - 0.830188679245283 0 0.830188679245283 4 0.378512652476092 0.421363141435649 0.421363141435649 0.378512652476092 2 - 0 36365 Y Y 3.61889661733171 3.38656252929588 3.38656252929588 296 0 0.0264216264011508 Y 0.0467097532314924 0.982667450058754 N N 1240 896 ENSG00000139725 ENSG00000188735 + + 12 12 120715977 120698088 coding downstream RHOF TMEM120B 120700045 120635163 - + 0 120703215 120698735 - + N 1.48636125078888 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.985561246069823 0.742741808632331 0.985561246069823 0.742741808632331 2 0 - 732 Y Y 3.26720299001245 3.6533527266709 3.26720299001245 7 0 0.101822157516066 Y 0.00315457413249209 0.948080967402734 N N 775 4897 ENSG00000134627 ENSG00000196371 - + 11 11 93994234 93922712 coding intron PIWIL4 FUT4 93940162 93916775 + + 0 93940350 93919592 - + N - 2.2184197113865 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.792734045751814 0.678466075192994 0.792734045751814 0.678466075192994 1 - 0 38147 Y Y 3.69834307337777 3.49065421516983 3.49065421516983 216 0 0.00774203673377372 Y 0 0 N N 0 0 ENSG00000220653 ENSG00000219652 + + 14 14 53454221 53149873 downstream downstream AL138479.3 AL163953.1 53453738 53149192 - + 0 53305270 53286532 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 1.04269523134923 0.764167053112109 1.04269523134923 0.764167053112109 2 - - 35197 N N 3.29908909870209 3.81657625693547 3.29908909870209 0 0 0.0874446788121634 N 0 0.450204728569542 N N 411 0 ENSG00000183023 ENSG00000151952 - - 2 12 40691697 128953837 coding intron SLC8A1 TMEM132D 40192790 128122226 - - 0 40509134 128851248 + + Y - 1 N HCC1954 23 22.75 22 4 1 N - - N - LINE 0 1 1 4 0.449930134075354 0.307095170876829 0.449930134075354 0.307095170876829 1 - 0 41735 N N 3.38552945952599 3.48593413659447 3.38552945952599 0 0 0.478632624778343 N 0.00342465753424659 0 N N 0 8783 ENSG00000221261 ENSG00000147697 - + 8 8 129231616 130868316 upstream coding hsa-mir-1208 GSDMC 129231544 130829625 + - 0 129182406 130844056 - - N - 0.654578271661651 Y HCC1954 2 1.04901960784314 1 5 1 N 397 4.17426 N LTR - 1 0 1 102 1.26408942430695 0.828442786551446 1.26408942430695 0.828442786551446 2 - 0 35985 N Y 3.78887586048788 3.35144407254738 3.35144407254738 5 0 0.442662032947524 N 0.883460292443744 0.872865773574993 N N 0 6988 ENSG00000206662 ENSG00000126768 - + 12 X 17755247 48640370 upstream intron Y_RNA TIMM17B 17755135 48635676 + - 0.872865773574993 17444727 48637578 - - Y - 2.76607045111266 N HCC1954 1 1 1 0 1 N - - N - LINE 0 1 1 4 0.307095170876829 0.557056356474248 0.557056356474248 0.307095170876829 1 - 0 6961 Y Y 3.8333716936548 3.46551447180198 3.46551447180198 0 0.135807050092764 0.979956113309946 Y 0.318812615955473 0.969499072356215 N N 0 52 ENSG00000183846 ENSG00000214164 + - 2 2 110575338 110569923 upstream coding AC112229.4-1 AC112229.4-2 110574935 110569013 - - 0 110576428 110569890 - + N - 3.59001736518515 N HCC1954 21 12.1538461538462 4 26 4 N - - Y - LTR 0 0.323170731707317 0.323170731707317 26 1.05697872766909 1.17124669822791 1.17124669822791 1.05697872766909 1 - 0 33359 N N 3.39384326095097 3.17208745297279 3.17208745297279 2 0 0.999964033350512 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8863 14323 - + N - 0.886154936481912 N HCC1954 4 2.8 1 3 10 N 189 4.09957 N - - 0 0 0 5 0.899860268150708 0.757025304952183 0.899860268150708 0.757025304952183 2 - 0 41800 Y Y 3.47911741325579 3.09616017186285 3.09616017186285 91 0 0.243963730841676 Y 0.0144842105263159 0 N N 1097 1486 ENSG00000221850 ENSG00000181638 - + 8 8 144430474 144416250 coding intron GLI4 ZFP41 144420982 144400484 + + 0 144428258 144404819 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.971277749749971 1.18553019454776 1.18553019454776 0.971277749749971 1 - - 38083 Y Y 3.54296933622177 3.76951977068882 3.54296933622177 357 0 0.241815323246779 Y 0 0.990502867813792 N N 2793 27551 ENSG00000129472 ENSG00000100888 + - 14 14 21014972 20969237 downstream upstream RAB2B CHD8 20997019 20923198 - - 0 20994035 20969861 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 126 0.857009779191151 1.35693215038599 1.35693215038599 0.857009779191151 1 - - 14295 N N 3.30232144676095 3.50066343377401 3.30232144676095 6 0 0.147777821249115 N 0 0 N N 3693 28 ENSG00000198125 ENSG00000186479 + + 22 5 34349347 63943875 coding downstream MB RGS7BP 34332757 63838208 - + 0 34343239 63973773 - + Y - - N HCC1954 16 2.73913043478261 1 16 2 N 200 25.2949 N - SINE 0 1 1 23 0.642757334393363 0.278528178237124 0.642757334393363 0.278528178237124 1 - - 18168 Y Y 3.53871326596283 3.36295036923788 3.36295036923788 294 0 0.0169377902570467 Y 0 0.992617787855883 N N 0 56940 ENSG00000215899 ENSG00000168528 + + 1 1 31733954 31680111 downstream downstream AC114494.2-1 SERINC2 31733019 31654999 - + 0 31716498 31705935 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR LTR 1 1 1 11 0.942710757110266 1.18553019454776 1.18553019454776 0.942710757110266 1 - - 47425 Y N 3.26356941436947 3.21848159181014 3.21848159181014 0 0 0.137797608942535 Y 0.816372418387741 0.455675383077948 N N 1053 4590 ENSG00000171425 ENSG00000213015 - + 19 19 60848800 60846647 utr5p coding ZNF581 ZNF580 60846798 60844204 + + 0.455675383077948 60846940 60845688 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity,Low_complexity 0 0.255813953488372 0.255813953488372 6 0.914143764470561 0.742741808632331 0.914143764470561 0.742741808632331 3 - - 12184 N Y 3.12804628055249 3.4503745994685 3.12804628055249 0 0 0.190569435898555 N 0.851923076923077 0.851923076923077 N N 1649619 16 ENSG00000141736 ENSG00000197140 - - 17 8 35138441 39261592 coding intron ERBB2 ADAM32 35104766 39084207 + + 0 35122227 39139553 - - Y - 0.674597434238075 N HCC1954 20 18.8 14 5 1 N - - N - SINE 0 1 1 5 0.521347615674617 0.314236919036755 0.521347615674617 0.314236919036755 2 - 0 9594 Y Y 3.60273302279816 3.78208964237274 3.60273302279816 246 0 0.0845594111681687 Y 0.981208774351894 0.981208774351894 N N 7716 6537 ENSG00000055483 ENSG00000108669 + - 17 17 74348564 74289974 utr3p upstream USP36 CYTH1 74304560 74181725 - - 0 74306077 74295335 - + N 0.348941292305303 - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.640625 0.640625 5 0.657040830713216 0.785592297591888 0.785592297591888 0.657040830713216 4 0 - 36588 Y Y 3.52680574168822 3.45976132345673 3.45976132345673 76 0 0.980461792642022 Y 0.99330682812956 0.99330682812956 N Y 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6313671 6328154 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 19 1.17124669822791 1.35693215038599 1.35693215038599 1.17124669822791 4 - - 31149 Y Y 3.37911396377143 3.4765169073827 3.37911396377143 269 0 0.330423656847165 Y 0.992155255685976 0.984310511371952 N N 3381 7315 ENSG00000131368 ENSG00000177463 + + 3 3 15081820 15065784 utr3p utr3p MRPS25 NR2C2 15065024 14964095 - + 0 15066219 15059533 - + N 0.189314864450455 1.6039023304781 N HCC1954 2 1.07142857142857 1 1 2 N - - Y SINE - 0.547445255474453 0 0.547445255474453 14 0.978419497909897 0.93556900895034 0.978419497909897 0.93556900895034 4 0 0 13782 Y N 3.08101510467749 3.34888341946764 3.08101510467749 0 0 0.27146875942076 Y 0 0.247102803738318 N N 7566 10882 ENSG00000188064 ENSG00000130638 + + 22 22 44751395 44619493 downstream downstream WNT7B ATXN10 44696323 44446351 - + 0.247102803738318 44662280 44653690 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.549914608314322 0.892718519990782 0.892718519990782 0.549914608314322 3 - - 31448 Y Y 3.43209143223268 3.68527868815389 3.43209143223268 202 0 0.789328564677168 Y 0.751237623762376 0.989184244511408 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 utr5p upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42836124 42826025 - + N 0.00858884493427958 - N HCC1954 1 1 1 0 6 N - - Y - LTR 0 1 1 15 0.849868031031224 0.714174815992626 0.849868031031224 0.714174815992626 1 0 - 22396 N Y 3.78208964237274 3.60103760561896 3.60103760561896 0 0 0.742265562755846 N 0 0.974455732946299 N N 2833 27 ENSG00000133019 ENSG00000164749 + + 1 8 238139338 76641600 utr5p upstream CHRM3 HNF4G 237858996 76482732 + + 0 237859446 76388528 + + Y - - N HCC1954 23 22.2916666666667 20 24 1 N - - N LINE LTR 1 1 1 24 0.721316564152552 1.12125446110842 1.12125446110842 0.721316564152552 1 - - 20360 N N 3.61360747730288 3.36361271664718 3.36361271664718 4 0 0.0442623358087946 N 0 0 N N 49089 8572 ENSG00000117450 ENSG00000112335 - - 1 6 45760196 108689156 coding intron PRDX1 SNX3 45749295 108639411 - - 0.127231216272312 45757256 108661589 + + Y - 1.34929475878403 N HCC1954 20 12.4 5 5 1 N - - N - SINE 0 1 1 5 0.471355378555133 0.321378667196682 0.471355378555133 0.321378667196682 1 - 0 49337 Y Y 3.31279467368155 3.53974633573272 3.31279467368155 100 0 0.154331574019266 Y 0.60601180891036 0.993843934514224 N N 5254 3143 ENSG00000146007 ENSG00000112855 - + 5 5 140066423 140059073 coding utr3p ZMAT2 HARS2 140060216 140051202 + + 0 140060247 140058599 - + N - 1.3649925177703 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 1.08554572030879 1.26408942430695 1.26408942430695 1.08554572030879 2 - 0 29780 N Y 3.18714761971957 3.26889840719165 3.18714761971957 0 0.00467289719626152 0.0168161423547770 N 0.764992211838006 0 N Y 636 824 ENSG00000111981 ENSG00000131019 - + 6 6 150336537 150431924 coding coding ULBP1 ULBP3 150326836 150425979 + - 0 150332976 150426180 - - N - - Y HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 9 0.28566992639705 0.857009779191151 0.857009779191151 0.28566992639705 0 - - 36750 Y Y 3.45976132345673 3.52680574168821 3.45976132345673 76 0 0.991503432944175 Y 0.993566062748564 0.993566062748564 N Y 55227 23800 ENSG00000111319 ENSG00000067182 + - 12 12 6354976 6321522 coding intron SCNN1A TNFRSF1A 6326276 6308185 - - 0 6328154 6313671 - + N - 0.932309771787885 N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 208 1.57118459518378 1.14982145374813 1.57118459518378 1.14982145374813 4 - 0 31849 Y Y 3.67489874718912 3.52567938596249 3.52567938596249 171 0.0210676515024339 0.856406659669692 Y 0.946113815679033 0.982037938559678 N N 41283 6846 ENSG00000047457 ENSG00000163755 + + 3 3 150422519 150373995 coding intron CP HPS3 150373220 150330061 - + 0 150376727 150366527 - + N - 1.33045161304183 N HCC1954 2 1.69277108433735 1 115 3 N - - Y - - 0 0 0 166 1.49976711358451 0.842726282871298 1.49976711358451 0.842726282871298 4 - 0 48115 N N 3.58060859325666 3.64400585547602 3.58060859325666 0 0 0.999999867203172 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117944678 2608423 - + Y - - N HCC1954 2 1.22641509433962 1 12 12 N 282 1.61558 N - LINE 0 0.863354037267081 0.863354037267081 53 1.2783729206268 1.14982145374813 1.2783729206268 1.14982145374813 2 - - 37973 N Y 3.18974812559266 3.1175824012017 3.1175824012017 1 0 0.256731961382132 N 0.0441987829614604 0.84184584178499 N N 1054 18437 ENSG00000187621 ENSG00000163932 - + 14 3 95228718 53201771 utr5p utr5p TCL6 PRKCD 95186588 53170263 + + 0 95199966 53174271 - + Y - - N HCC1954 23 21.75 21 4 1 N - - N SINE Low_complexity 1 0.35 1 4 0.28566992639705 0.621332089913584 0.621332089913584 0.28566992639705 3 - - 6683 N N 3.33424740824393 2.93769362663605 2.93769362663605 25 0.168484848484848 0.0168784647012971 Y 0.564444444444444 0.604040404040404 N N 4147 0 ENSG00000173272 ENSG00000173284 + + 2 2 131966775 131935638 coding downstream FAM128A AC073869.5-19 131958003 131935060 - + 0.604040404040404 131965934 131944333 - + N - - N HCC1954 4 4 4 9 1 N - - N - - 0 0 0 9 0.592765097273879 0.485638874874985 0.592765097273879 0.485638874874985 0 - - 44208 N N 3.38400187621614 3.39909254818645 3.38400187621614 1 0 0.121602996405581 N 0 0 N N 13022 3891 ENSG00000164091 ENSG00000166295 - + 3 10 52287699 73665622 utr3p coding WDR82 C10orf104 52263478 73645812 - + 0 52264217 73653728 + + Y - - N HCC1954 35 33.5 32 12 1 N - - N SINE - 1 0 1 12 0.28566992639705 0.471355378555133 0.471355378555133 0.28566992639705 1 - - 36969 N N 3.54296933622177 3.58424216889964 3.54296933622177 18 0 0.998520005650745 N 0 0.20264417597447 N N 12084 3 ENSG00000177119 ENSG00000179242 + + 12 20 44112391 59945671 coding intron ANO6 CDH4 43896170 59260965 + + 0.20264417597447 44047752 59583872 + + Y - 0.929733246584255 N HCC1954 1 1 1 0 8 N 451 26.2081 N - - 0 0 0 5 0.721316564152552 0.542772860154395 0.721316564152552 0.542772860154395 0 - 0 46867 Y Y 3.1164696258451 3.6289058359359 3.1164696258451 235 0 0.121449253425975 N 0.324316109422492 0.97629179331307 Y N 4590 1053 ENSG00000213015 ENSG00000171425 - + 19 19 60846647 60848800 upstream upstream ZNF580 ZNF581 60844204 60846798 + + 0 60843304 60838890 - + N - - N HCC1954 1 1 1 0 2 N - - N - SINE 0 0.432624113475177 0.432624113475177 5 0.592765097273879 1.0069864905496 1.0069864905496 0.592765097273879 4 - - 42104 N Y 3.16889495770728 3.42633828388743 3.16889495770728 155 0 0.00302724420971678 N 0.858064516129032 0.971612903225806 N N 187 470 ENSG00000170927 ENSG00000186212 + - 6 4 52060382 78038026 intron upstream PKHD1 ANKRD56 51588104 78035645 - - 0 51954196 78038515 - + Y 0.519420972780984 - N HCC1954 20 7.57142857142857 1 16 1 N - - N Other - 1 0 1 21 0.721316564152552 0.764167053112109 0.764167053112109 0.721316564152552 1 0 - 28594 N Y 3.26356941436947 3.57800808738356 3.26356941436947 0 0 0.43819088752919 N 0.00389105058365735 0 N N 37 17943 ENSG00000154118 ENSG00000105141 - + 16 19 86289263 15027900 intron downstream JPH3 CASP14 86194000 15024015 + + 0.771384831281495 86224029 15029502 - + Y 0.550245499181669 - N HCC1954 25 20.7142857142857 20 7 1 N 73 23.192 N SINE - 1 0 1 7 0.264244681917271 0.592765097273879 0.592765097273879 0.264244681917271 3 0 - 41368 N N 3.59425138750382 3.06640893226016 3.06640893226016 0 0.00657894736842124 0.114482833871237 N 0.061769005847953 0.475694444444444 N N 12188 0 ENSG00000168724 ENSG00000219531 - + 5 20 34994825 21417263 utr3p downstream DNAJA5 RP5-984P4.1 34965455 21416882 + - 0.475694444444444 34991635 21416185 - - Y - - N HCC1954 78 57 46 4 1 N - - N SINE - 1 0 1 4 0.757025304952183 0.599906845433805 0.757025304952183 0.599906845433805 2 - - 5037 Y Y 2.96953348129346 3.47233119514066 2.96953348129346 565 0 0.000148458047437572 Y 0.543666245259166 0.996434892541087 N N 2975 4451 ENSG00000106603 ENSG00000164543 + + 7 7 43735620 43633502 utr3p intron C7orf44 STK17A 43645381 43589217 - + 0 43645443 43615740 - + N - 2.1079733636086 N HCC1954 1 1 1 0 2 N - - Y - LTR 0 0.72280701754386 0.72280701754386 19 1.12839620926835 1.78543703998156 1.78543703998156 1.12839620926835 2 - 0 34451 Y Y 3.45656882819122 3.29912895149544 3.29912895149544 387 0 0.0099665002705529 Y 0 0.990764666475261 N N 111 0 ENSG00000188152 ENSG00000218062 - + 9 9 98744393 98721421 downstream intron FAM22G RP11-330M2.3 98721960 98721031 + + 0 98744706 98721120 - + N - 1 N HCC1954 2 2 2 7 2 N - - Y - - 0 0 0 7 0.685607823352921 0.557056356474248 0.685607823352921 0.557056356474248 3 - 0 29936 N N 3.73080759109069 3.37076030955309 3.37076030955309 0 0 0.0409168265627957 N 0.637169471153846 0 N N 0 87 ENSG00000182707 ENSG00000180316 + + X 6 73013524 36384350 downstream intron FXYD8 PNPLA1 73011598 36318923 + + 0 73081224 36364625 + + Y - 0.261224489795918 N HCC1954 20 16 12 7 1 N - - N - SINE 0 1 1 7 0.592765097273879 0.292811674556976 0.592765097273879 0.292811674556976 2 - 0 25971 N N 3.66488952858494 3.16828604346046 3.16828604346046 0 0 0.0709594959407721 N 0 0.00284900284900302 N N 651 75177 ENSG00000115902 ENSG00000125107 - + 2 16 65104501 57221251 intron intron SLC1A4 CNOT1 65070098 57111359 + - 0.00284900284900302 65072353 57220949 - - Y 0.68623372868443 2.02597604330693 N HCC1954 22 21.2 20 5 1 N - - N SINE - 1 0 1 5 0.321378667196682 0.478497126715059 0.478497126715059 0.321378667196682 2 0 0 37329 N Y 3.47233119514066 3.66761801553402 3.47233119514066 0 0 0.51371601964279 N 0 0.942771230418546 N N 14326 6215 ENSG00000127947 ENSG00000129566 - + 7 14 77107324 19951420 coding utr3p PTPN12 TEP1 77004351 19905766 + - 0 77050902 19905811 - - Y - - N HCC1954 28 22.1666666666667 21 6 1 N - - N - SINE,SINE 0 1 1 6 0.578481600954027 0.34280391167646 0.578481600954027 0.34280391167646 1 - - 46941 Y Y 3.7061623612628 3.5816815158199 3.5816815158199 288 0 0.383225899941869 Y 0 0 N N 584 560 ENSG00000197813 ENSG00000063127 + - 19 19 54535371 54520286 intron intron AC011450.4 SLC6A16 54523236 54484709 - - 0 54526159 54506482 - + N 0.579920891682526 15.5522221839748 N HCC1954 1 1 1 0 4 N - - Y LTR,SINE - 0.662420382165605 0 0.662420382165605 4 0.778450549431962 0.785592297591888 0.785592297591888 0.778450549431962 1 0 0 6464 Y Y 3.49268050191626 3.61464054707278 3.49268050191626 167 0 0.96523982778997 Y 0 0.963125406107862 N Y 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 coding coding VAMP5 VAMP8 85665042 85658227 + + 0 85672359 85658283 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 9 0.99270299422975 0.664182578873142 0.99270299422975 0.664182578873142 4 - - 49286 Y Y 3.35719722089263 3.61720120015252 3.35719722089263 223 0 0.451802008033576 Y 0.607402261100234 0.971957304364302 N N 53 2006 ENSG00000006837 ENSG00000119048 - - 5 5 133730664 133755698 coding upstream CDKL3 UBE2B 133662010 133734769 - + 0 133714017 133734588 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.692749571512847 0.335662163516534 0.692749571512847 0.335662163516534 4 - - 19091 Y Y 3.5514509715161 3.4503745994685 3.4503745994685 261 0.812686249467859 0.171090629176036 Y 0.0549169859514687 0.991485738612175 N Y 6058 3826 ENSG00000197785 ENSG00000160072 - + 1 1 1459928 1421444 upstream downstream ATAD3A ATAD3B 1437394 1397006 + + 0 1459169 1402593 - + N - - N HCC1954 2 1.54545454545455 1 6 1 Y - - Y - - 0 0 0 11 0.692749571512847 0.749883556792257 0.749883556792257 0.692749571512847 4 - - 26663 N Y 3.53143253430774 3.67526946954971 3.53143253430774 274 0 0.00736170619357657 Y 0.992673894375268 0.992673894375268 N N 7466 563 ENSG00000167977 ENSG00000205918 - - 16 16 2699030 2633298 upstream upstream KCTD5 AC141586.2-3 2672499 2606123 + - 0.992673894375268 2653087 2651384 - + N - - N HCC1954 12 2.85714285714286 1 3 1 N - - N LTR,LTR LTR,LTR 1 0.688888888888889 1 7 0.857009779191151 0.956994253430118 0.956994253430118 0.857009779191151 1 - - 3434 Y Y 3.54040868314203 3.2452463943403 3.2452463943403 225 0 0.442080343222263 Y 0.894089834515366 0.978817966903073 N N 3641 6040 ENSG00000142188 ENSG00000159128 + + 21 21 33774151 33731698 downstream downstream TMEM50B IFNGR2 33743321 33697072 - + 0 33742959 33733474 - + N - - N HCC1954 4 1.27272727272727 1 1 2 N - - Y SINE - 1 0 1 11 0.678466075192994 0.635615586233437 0.678466075192994 0.635615586233437 4 - - 16849 N Y 3.41679307359967 3.5246463161926 3.41679307359967 0 0 0.099182107205443 N 0.860238832375055 0.860238832375055 N N 49089 9 ENSG00000117450 ENSG00000213373 - - 1 17 45760196 38304247 utr5p intron PRDX1 AC016889.28-2 45749295 38280217 - - 0 45760088 38290391 + + Y - 1.07814909006182 N HCC1954 3 1.5 1 1 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.264244681917271 0.39993789695587 0.264244681917271 1 - 0 38857 N Y 3.55141111872275 3.42424163912411 3.42424163912411 164 0.891291920731707 0.00224861084892847 N 0.906821646341463 0.891291920731707 N N 16956 0 ENSG00000100911 ENSG00000176183 + - 14 5 23685695 97702893 coding upstream PSME2 AC094106.3-1 23682414 97702584 - + 0.891291920731707 23685619 97574874 - - Y 0.907951348368956 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.407079645115797 0.507064119354764 0.507064119354764 0.407079645115797 1 0 - 41413 Y Y 3.3755202409218 2.89251969725115 2.89251969725115 0 0 0.405170998317639 Y 0 0.989040137581251 N N 6286 910 ENSG00000012232 ENSG00000104290 - + 8 8 28667116 28477878 utr5p downstream EXTL3 FZD3 28615050 28407692 + + 0 28629026 28536445 - + N 0.246809117384196 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.0625 0.0625 24 0.714174815992626 0.5713398527941 0.714174815992626 0.5713398527941 2 0 - 29960 N N 3.49744043328497 3.54400240599166 3.49744043328497 3 0 0.0738195604487986 N 0 0 N N 8096 975 ENSG00000010404 ENSG00000198487 + + X 6 148394714 42218335 utr3p coding IDS AL512274.9 148368206 42183124 - - 0 148368571 42183238 - - Y - - N HCC1954 36 28.6190476190476 21 42 1 N 204 27.5823 N SINE - 1 0 1 42 0.385654400636018 0.814159290231593 0.814159290231593 0.385654400636018 2 - - 45600 N N 3.57989088800989 3.46704205511183 3.46704205511183 0 0 0.398684453202804 N 0 0 N N 128 60677 ENSG00000204385 ENSG00000125740 - + 6 19 31954802 50670254 utr3p upstream SLC44A4 FOSB 31938948 50663093 - + 0 31939052 50644469 + + Y - - N HCC1954 26 23 20 6 1 N - - N SINE SINE 1 0.9625 1 6 0.414221393275723 0.5713398527941 0.5713398527941 0.414221393275723 3 - - 32741 N Y 3.26191384998362 3.45656882819122 3.26191384998362 0 0 0.0230564536273209 N 0.908024691358025 0.88962962962963 N N 81 5 ENSG00000152380 ENSG00000174004 - - 5 3 79873962 197873269 upstream intron FAM151B LRRC33 79819556 197851046 + + 0 79817047 197868244 - - Y - 1.01722153574581 N HCC1954 20 16 4 4 1 N - - N LINE SINE 1 1 1 4 0.599906845433805 0.39993789695587 0.599906845433805 0.39993789695587 1 - 0 48927 N N 3.44210065083686 3.39168383545536 3.39168383545536 0 0 0.196194719323370 N 0.38003089682088 0.369867468899911 Y N 15242 1641 ENSG00000198961 ENSG00000131188 + + 5 5 108773594 176815889 downstream intron PJA2 PRR7 108698309 176806400 - + 0.369867468899911 108691534 176806570 - + N - 0.224786877039992 N HCC1954 1 1 1 0 1 N 41 5.35277 N - Low_complexity 0 0.256578947368421 0.256578947368421 9 0.757025304952183 0.907002016310634 0.907002016310634 0.757025304952183 1 - 0 38105 Y Y 3.22948402739086 3.62192127872787 3.22948402739086 199 0 0.132225709034447 Y 0.835993152576067 0.989066210171738 N N 2447 4331 ENSG00000157379 ENSG00000100949 + - 14 14 23838770 23810643 intron utr5p DHRS1 RABGGTA 23829646 23804661 - - 0 23837658 23810354 - + N 1.7936746240795 3.80639939049814 N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 10 0.685607823352921 0.507064119354764 0.685607823352921 0.507064119354764 3 0 0 6212 N Y 3.24359082995445 3.4895278594441 3.24359082995445 0 0 0.301914877606304 N 0 0.926742919389978 N N 3221 0 ENSG00000115163 ENSG00000219985 + - 2 9 26870961 106459818 intron downstream CENPA RP11-413C10.4 26862386 106458870 + - 0 26869803 106446712 + + Y 2.68134887026394 - N HCC1954 20 9.8 1 3 1 N - - N - SINE 0 1 1 5 0.449930134075354 0.378512652476092 0.449930134075354 0.378512652476092 3 0 - 19967 N Y 3.57696143724454 3.36716658670346 3.36716658670346 7 0 0.413852437273471 N 0.460008709536943 0.916001354816858 N N 12911 5170 ENSG00000103479 ENSG00000116918 + + 16 1 52083060 229768890 coding upstream RBL2 TSNAX 52025862 229731022 + + 0.916001354816858 52045754 229725012 + + Y - - N HCC1954 26 23.3846153846154 21 26 1 N - - N SINE LTR 1 1 1 26 0.421363141435649 0.564198104634174 0.564198104634174 0.421363141435649 3 - - 47124 Y Y 3.39384326095097 3.57063922744582 3.39384326095097 299 0 0.0326070612168207 Y 0.989283273995756 0.978566547991513 N N 3272 17901 ENSG00000141971 ENSG00000130303 - - 19 19 17397140 17377401 coding upstream FAM125A BST2 17391856 17374750 + - 0 17392122 17378105 - + N 0.516899860347996 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.678466075192994 1.02841173502938 1.02841173502938 0.678466075192994 4 0 - 18268 Y Y 3.21279122419719 3.25832012713399 3.21279122419719 234 0 0.0485020099547964 Y 0.85290404040404 0.977369852369852 N N 0 0 ENSG00000213037 ENSG00000220338 - + 1 1 209682923 209657899 upstream downstream AL590101.9 RP11-318L16.4 209682219 209656990 + + 0 209672284 209666248 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 56 0.971277749749971 0.592765097273879 0.971277749749971 0.592765097273879 4 - - 12658 N Y 3.37192651807217 3.57800808738356 3.37192651807217 0 0 0.437294924887702 N 0 0 N N 4143 17943 ENSG00000154217 ENSG00000105141 - + 17 19 63120107 15027900 intron downstream PITPNC1 CASP14 62804386 15024015 + + 0 62823422 15029502 - + Y 0.701391692996099 - N HCC1954 9 8.125 2 8 1 N - - N SINE - 1 0 1 8 0.257102933757345 0.428504889595575 0.428504889595575 0.257102933757345 3 0 - 3826 N Y 3.56129235625094 3.54719490125717 3.54719490125717 1 0 0.0634506260641591 N 0 0.89850485648805 N N 0 2004 ENSG00000156687 ENSG00000105793 - + 8 7 35771722 89854586 intron utr3p UNC5D GTPBP10 35212845 89813926 + + 0 35502325 89854507 - + Y 1 - N HCC1954 68 63 60 4 1 N - - N - SINE 0 1 1 4 0.414221393275723 0.442788385915428 0.442788385915428 0.414221393275723 1 0 - 40541 N Y 3.60103760561896 3.48912663185998 3.48912663185998 10 0 0.0245919718085249 N 0 0.601465201465201 N N 232 219 ENSG00000205464 ENSG00000034053 - - 5 15 81649981 27234776 utr5p utr3p ATP6AP1L APBA2 81611037 27001141 + + 0 81636616 27234665 - - Y - - N HCC1954 814 782.5 748 4 1 N - - N SINE SINE 1 1 1 4 0.28566992639705 0.307095170876829 0.307095170876829 0.28566992639705 2 - - 12465 N Y 3.32470219795617 3.48639814491089 3.32470219795617 0 0 0.0881121687271192 N 0.531422825540473 0.0433216021451315 N N 0 0 ENSG00000220462 ENSG00000216027 - - 17 4 20430363 61212351 upstream downstream AC087499.2 AC095061.3 20427663 61212262 - - 0.746187363834423 20430524 60902269 + + Y - - N HCC1954 22 20.4 20 5 1 N 455 19.014 N SINE SINE 1 0.837837837837838 1 5 0.28566992639705 0.264244681917271 0.28566992639705 0.264244681917271 1 - - 38871 N N 3.07936473514353 3.41319935075004 3.07936473514353 0 0.00288184438040362 0.0688729372126858 N 0 0.00288184438040362 N N 182 38037 ENSG00000183484 ENSG00000131446 - - 14 5 104602799 180175147 utr3p upstream GPR132 MGAT1 104586773 180150147 - - 0.00288184438040362 104587324 180191315 + + Y - - N HCC1954 22 21.4 20 10 1 N 244 24.7956 N SINE - 1 0 1 10 0.28566992639705 0.821301038391519 0.821301038391519 0.28566992639705 2 - - 36322 Y Y 3.39384326095097 3.51100352194543 3.39384326095097 89 0 0.0507930401970202 Y 0.0337078651685393 0.97752808988764 N N 34 3127 ENSG00000111405 ENSG00000005175 + - 12 12 46405617 46386041 intron upstream AC004241.2 RPAP3 46389795 46343344 - - 0 46399302 46386178 - + N 1.78504348083294 - N HCC1954 1 1 1 0 1 N - - Y DNA - 0.175572519083969 0 0.175572519083969 14 0.93556900895034 0.592765097273879 0.93556900895034 0.592765097273879 2 0 - 3774 N N 3.57489529770476 3.35719722089263 3.35719722089263 11 0 0.216561538195192 N 0 0 N N 241 7736 ENSG00000128383 ENSG00000154639 - + 22 21 37690573 17887768 utr3p intron APOBEC3A CXADR 37678702 17807201 + + 0 37688706 17862821 - + Y - 7.36190083851724 N HCC1954 38 34 29 5 1 N 543 25.8351 N SINE - 1 0 1 5 0.371370904316165 0.649899082553289 0.649899082553289 0.371370904316165 3 - 0 37333 N Y 3.35612429832939 3.12855014166226 3.12855014166226 225 0.900444444444444 0.00322097448367920 N 0.900444444444444 0.900444444444444 N N 1 26519 ENSG00000218823 ENSG00000090060 - + 7 14 4868151 96103178 coding coding PAPOLB PAPOLA 4863890 96038515 - + 0.900444444444444 4867808 96056292 + + Y - 1.22105516163923 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 6 0.292811674556976 0.871293275511003 0.871293275511003 0.292811674556976 1 - 0 31393 Y Y 3.55401162459584 3.76848670091893 3.55401162459584 0 0 0.996563917164422 Y 0.228112449799197 0.962650602409638 N N 2481 3 ENSG00000158092 ENSG00000168917 - + 3 3 138150657 138057422 upstream intron NCK1 TMEM22 138063763 138020551 + + 0 138063105 138048118 - + N - 0.87027027027027 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 5 0.892718519990782 0.428504889595575 0.892718519990782 0.428504889595575 4 - 0 33014 N N 2.77892265388278 3.22270715684554 2.77892265388278 3 0 0.999996675042178 N 0 0.346551028640581 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.346551028640581 8476 10858 - + N 0.675128136826734 0.351991594151195 N HCC1954 4 1.84615384615385 1 6 12 Y 189 4.09957 N - - 0 0 0 13 1.1426797055882 1.40692438750547 1.40692438750547 1.1426797055882 1 0 0 30809 N Y 3.32423818963975 3.81079260336669 3.32423818963975 0 0 0.464207995562409 N 0.859917953667954 0.844353281853282 N N 9759 0 ENSG00000101846 ENSG00000218564 - - X Y 7282682 16077348 coding upstream STS AC006998.1 7147472 15969936 + - 0 7181237 16099201 - + Y - - N HCC1954 2 1.25 1 5 1 N 489 27.7105 N - - 0 0 0 20 0.635615586233437 0.335662163516534 0.635615586233437 0.335662163516534 3 - - 29217 Y Y 3.36464578641707 3.70463477795295 3.36464578641707 274 0 0.601467250807474 Y 0.991765699463111 0.983531398926223 N N 30978 0 ENSG00000112245 ENSG00000213312 - - 6 6 64351447 64317378 utr5p downstream PTP4A1 RPL7AP34 64339879 64316572 + - 0 64344300 64300394 - + N 0.363404336258786 - N HCC1954 1 1 1 0 3 N - - Y - DNA 0 1 1 5 0.649899082553289 0.742741808632331 0.742741808632331 0.649899082553289 4 0 - 47429 Y Y 3.29590595100639 3.45139668416007 3.29590595100639 109 0.634958957025592 0.0831144937460057 Y 0.869628198937711 0.869628198937711 N N 3678 521 ENSG00000198466 ENSG00000204517 - + 19 19 63068299 63045300 coding upstream ZNF587 AC010522.3 63053081 63042237 + + 0.869628198937711 63059319 63042234 - + N - - N HCC1954 4 2.5 2 6 2 N - - Y - - 0 0 0 6 0.621332089913584 0.657040830713216 0.657040830713216 0.621332089913584 3 - - 37554 N Y 3.12804628055249 3.46973068926756 3.12804628055249 0 0 0.254997315008463 N 0.785463355542096 0.785463355542096 N N 1649619 407 ENSG00000141736 ENSG00000140025 - - 17 14 35138441 89490827 coding intron ERBB2 C14orf143 35104766 89331669 + - 0 35122227 89434910 - + Y - 0.163665416808901 N HCC1954 9 8.16666666666667 8 6 1 N 413 17.6745 N - SINE 0 1 1 6 0.478497126715059 0.257102933757345 0.478497126715059 0.257102933757345 2 - 0 16828 N Y 3.25256697878875 3.41848849077886 3.25256697878875 0 0 0.0636665026596481 N 0 0.788200769075086 N N 49089 9 ENSG00000117450 ENSG00000153930 - - 1 17 45760196 51915006 coding intron PRDX1 ANKFN1 45749295 51585835 - + 0 45757275 51640437 + - Y - 0.771056910569106 N HCC1954 4 3.4 1 9 1 N - - N - SINE 0 1 1 10 0.757025304952183 0.357087407996313 0.757025304952183 0.357087407996313 1 - 0 17894 Y Y 3.448886868952 3.34355442664546 3.34355442664546 256 0 0.0151737882850642 Y 0.810267857142857 0.988141741071429 N N 323 1498 ENSG00000187642 ENSG00000187583 + + 1 1 907336 900339 utr3p utr3p C1orf170 PLEKHN1 900447 891740 - + 0.988141741071429 900953 899829 - + N - 1.27909584210799 N HCC1954 1 1 1 0 1 N - - Y DNA - 1 0 1 6 0.471355378555133 0.549914608314322 0.549914608314322 0.471355378555133 2 - 0 26835 Y Y 3.69784855983781 3.39590940049075 3.39590940049075 312 0.0378160612535612 0.0318867976158375 Y 0.0378160612535612 0.986155626780627 N N 1733 223 ENSG00000174943 ENSG00000174939 + + 16 16 29845046 29824876 intron utr3p KCTD13 ASPHD1 29825166 29819648 - + 0 29838353 29824781 - + N 1.32589300141614 2.2180987038778 N HCC1954 1 1 1 0 1 N - - Y LINE - 0.177631578947368 0 0.177631578947368 5 0.971277749749971 0.99270299422975 0.99270299422975 0.971277749749971 4 0 0 25949 N Y 3.34256120966892 3.40695168886483 3.34256120966892 196 0.785714285714286 0.0182810769490365 N 0.785714285714286 0.785714285714286 N N 10704 0 ENSG00000180398 ENSG00000180598 + + 2 16 47022498 32176496 utr3p upstream MCFD2 TP53TG3 46982517 32172145 - + 0.785714285714286 46984341 32146874 - + Y - - N HCC1954 6 3 1 3 1 N - - N LTR LTR 1 1 1 4 0.664182578873142 0.34280391167646 0.664182578873142 0.34280391167646 2 - - 10079 Y Y 3.34000055658918 3.34152813989903 3.34000055658918 156 0.114409141583055 0.39570687406239 Y 0.524804905239688 0 N N 9613 185 ENSG00000132510 ENSG00000183914 - + 17 17 7698831 7677783 utr5p downstream JMJD3 DNAH2 7683947 7562746 + + 0 7683947 7680121 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.5713398527941 0.45707188223528 0.5713398527941 0.45707188223528 2 - - 16515 N N 3.61360747730288 3.22332965146149 3.22332965146149 0 0 0.0379105805594385 N 0.124467005076142 0 N N 4227 5170 ENSG00000154803 ENSG00000116918 + + 17 1 17081227 229768890 utr3p upstream FLCN TSNAX 17056254 229731022 - + 0 17056778 229725008 - + Y - - N HCC1954 27 23.5714285714286 22 7 1 N - - N SINE LTR 1 1 1 7 0.34280391167646 0.51420586751469 0.51420586751469 0.34280391167646 1 - - 31769 Y Y 3.70889084821189 3.44768596531277 3.44768596531277 0 0.152703677000721 0.718787118979877 Y 0.160201874549387 0.992501802451334 N N 298 397 ENSG00000182983 ENSG00000180432 - - 3 3 42933958 42892661 utr5p upstream ZNF662 CYP8B1 42922406 42888688 + - 0 42922664 42904196 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 11 1.52119235806429 0.956994253430118 1.52119235806429 0.956994253430118 2 - - 30648 Y Y 3.47076375903745 3.38296880644625 3.38296880644625 0 0 0.98389854736856 Y 0 0.986709956709957 N N 111946 0 ENSG00000147065 ENSG00000219305 - - X X 64878517 64689026 coding upstream MSN RP3-475B7.3 64804283 64687503 + - 0 64853405 64725673 - + N - - N HCC1954 2 1.28571428571429 1 4 2 N - - Y - Simple_repeat 0 0.236111111111111 0.236111111111111 14 1.08554572030879 1.02841173502938 1.08554572030879 1.02841173502938 4 - - 45388 N N 3.24359082995445 3.15046688454107 3.15046688454107 3 0 0.041160598024201 N 0 0 N N 0 551733 ENSG00000209771 ENSG00000204628 + + 10 5 36763548 180603512 downstream utr3p AL590730.6-2 GNB2L1 36763490 180596536 - - 0.0065295903019823 36648311 180596549 - - Y - - N HCC1954 20 15.3333333333333 1 8 1 N - - N LINE - 1 0 1 9 0.264244681917271 0.471355378555133 0.471355378555133 0.264244681917271 1 - - 38565 Y Y 3.61360747730288 3.54872248456702 3.54872248456702 240 0 0.0493187791326722 Y 0.36849593495935 0.975711382113821 N N 13440 435 ENSG00000165929 ENSG00000133962 + - 14 14 91372436 91268166 utr3p coding TC2N CATSPERB 91316281 91116871 - - 0 91316673 91265576 - + N - 10.7363715027401 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.999844742389676 0.578481600954027 0.999844742389676 0.578481600954027 4 - 0 45640 N Y 3.22167408707565 3.40897378571464 3.22167408707565 224 0 0.0615504140353177 N 0 0.964445153061225 N N 1287 267 ENSG00000212635 ENSG00000213967 - + X 19 42218751 23910101 coding coding Z93403.1 AC011503.4 42029377 23889552 + + 0 42029550 23907199 - + Y - - N HCC1954 25 19.4 6 5 1 N - - N Other - 1 0 1 5 0.549914608314322 0.5713398527941 0.5713398527941 0.549914608314322 2 - - 1915 N Y 3.5758885146813 3.33168675516419 3.33168675516419 1 0 0.140169671689105 N 0.892726728524394 0.923376234660281 N N 1114 0 ENSG00000198331 ENSG00000221151 - + 11 16 125275750 88689322 utr5p upstream HYLS1 AC133919.3-4 125258719 88689218 + - 0 125258856 88710195 - - Y - - N HCC1954 88 85.6 84 5 1 N - - N SINE - 1 0 1 5 0.264244681917271 0.357087407996313 0.357087407996313 0.264244681917271 2 - - 7755 N N 3.39231567764112 2.68847799505532 2.68847799505532 0 0 0.128530179913175 N 0 0.318808777429467 N N 0 71032 ENSG00000189277 ENSG00000160932 + + 2 8 186406259 144175199 downstream intron AC008174.2-2 LY6E 186378006 144171300 + + 0.318808777429467 186496780 144171537 + + Y - 1.33866756416173 N HCC1954 20 20 20 7 1 N - - N SINE Low_complexity 1 0.0842105263157895 1 7 0.28566992639705 0.678466075192994 0.678466075192994 0.28566992639705 3 - 0 16807 N N 3.1416492220063 2.97423997949969 2.97423997949969 2 0 0.288413965160408 N 0 0 N N 317991 0 ENSG00000171346 ENSG00000212679 - - 17 1 36932191 559619 coding intron KRT15 RP5-857K21.10 36923523 558939 - + 0 36928473 559001 + - Y - 1 N HCC1954 3 2.36363636363636 2 11 2 N - - N Simple_repeat - 0.328282828282828 0 0.328282828282828 11 1.17124669822791 1.22123893534739 1.22123893534739 1.17124669822791 2 - 0 26575 Y Y 3.08139102188996 3.21910408642609 3.08139102188996 308 0 0.02160026781921 Y 0 0 N N 11912 7967 ENSG00000102974 ENSG00000039523 - + 16 16 66230587 66138189 intron downstream CTCF FAM65A 66153811 66120255 + + 0 66154700 66140752 - + N 0.154413710681491 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 1.01412823870953 0.814159290231593 1.01412823870953 0.814159290231593 1 0 - 36865 N Y 2.32192809488736 3.40422320191574 2.32192809488736 215 0 0.00296632930437912 N 0.834108527131783 0.668217054263567 N N 3002 0 ENSG00000179104 ENSG00000222619 + - 12 14 82052194 49399317 intron intron TMTC2 SRP_euk_arch 81605065 49399021 + - 0.834108527131783 81824444 49399301 + + Y 1.27978790699491 1 N HCC1954 8 5.75 4 4 1 N 472 28.3737 N SINE srpRNA 1 1 1 4 0.292811674556976 0.45707188223528 0.45707188223528 0.292811674556976 2 0 0 41003 Y Y 3.61936062564813 3.66951632120446 3.61936062564813 318 0 0.0242077481096807 Y 0 0 N N 0 0 ENSG00000210843 ENSG00000222689 - + 20 20 54697157 54697156 downstream upstream AL121920.21-2 SRP_euk_arch 54696864 54696864 + + 0 54697244 54694781 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.720779220779221 0 0.720779220779221 4 0.714174815992626 0.785592297591888 0.785592297591888 0.714174815992626 1 - - 8353 N N 3.17407904459906 3.45293525254824 3.17407904459906 309 0 0.000970410506084374 N 0 0 N N 12188 4816 ENSG00000168724 ENSG00000152284 - + 5 2 34994825 85391012 utr3p downstream DNAJA5 TCF7L1 34965455 85214245 + + 0.451779935275081 34991719 85393973 - + Y - - N HCC1954 23 22.75 22 4 1 N - - N SINE SINE,DNA 1 0.772727272727273 1 4 0.621332089913584 0.314236919036755 0.621332089913584 0.314236919036755 1 - - 20490 N N 3.52424508860847 3.54400240599166 3.52424508860847 0 0 0.0774194435992611 N 0 0 N N 9374 975 ENSG00000160049 ENSG00000198487 + + 1 6 10455200 42218335 utr3p coding DFFA AL512274.9 10443192 42183124 - - 0 10443669 42183238 - - Y - - N HCC1954 40 32.5357142857143 24 28 1 N - - N SINE - 1 0 1 28 0.378512652476092 0.87843502367093 0.87843502367093 0.378512652476092 2 - - 47805 N Y 3.25719377140827 3.41741556821562 3.25719377140827 1 0 0.527426342390783 N 0 0.783429040196883 N N 1303 1187 ENSG00000197573 ENSG00000055147 - - 19 5 46148403 153398690 downstream intron CYP2B7P1 FAM114A2 46122010 153351464 + - 0.731452009844135 46162057 153382799 - + Y - 0.537202627596723 N HCC1954 20 20 20 5 1 N - - N LINE LINE 1 1 1 5 0.614190341753658 0.335662163516534 0.614190341753658 0.335662163516534 1 - 0 47974 N N 2.13627541934831 3.12747721909902 2.13627541934831 0 0.388344893240854 0.0529417222125388 N 0.475724194206446 0 N N 2 551733 ENSG00000169436 ENSG00000204628 + + 8 5 139995418 180603512 upstream utr3p COL22A1 GNB2L1 139669661 180596536 - - 0 140277509 180596544 - - Y - - N HCC1954 19 15 1 17 1 N - - N SINE - 0.9 0 0.9 18 0.357087407996313 0.907002016310634 0.907002016310634 0.357087407996313 3 - - 7435 Y Y 3.65488030998075 3.36873402280666 3.36873402280666 302 0 0.049195725592688 N 0.558513711720521 0.993310813813947 Y N 5801 13069 ENSG00000115825 ENSG00000055332 - + 2 2 37398541 37405184 utr5p upstream PRKD3 EIF2AK2 37331149 37179857 - - 0 37397825 37405327 + - N - - N HCC1954 1 1 1 0 2 N - - N rRNA Low_complexity 0.122994652406417 0.051948051948052 0.122994652406417 114 1.33550690590621 1.09982921662864 1.33550690590621 1.09982921662864 1 - - 33425 N Y 2.9144762929233 3.48167806633553 2.9144762929233 345 0 0.810002534189963 Y 0.0232475598935225 0.993216996943705 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding coding MT-CO3 MT-ND1 8367 3308 + + 0 8594 4133 - + N - - N HCC1954 6 5 4 4 6 Y - - N - - 0 0 0 4 0.699891319672773 0.728458312312478 0.728458312312478 0.699891319672773 1 - - 3778 N N 3.78208964237274 3.71873223294673 3.71873223294673 0 0 0.681101818525386 N 0 0 N N 6245 3931 ENSG00000159256 ENSG00000183579 + + 21 22 36670814 27783475 coding intron MORC3 ZNRF3 36614357 27609890 + + 0 36627886 27634463 + + Y - 0.797113443186575 N HCC1954 1 1 1 0 1 N 527 9.38037 N - - 0 0 0 6 0.628473838073511 0.621332089913584 0.628473838073511 0.621332089913584 4 - 0 46747 Y Y 3.46448140203209 3.46973068926756 3.46448140203209 304 0.662404499151103 0.0115431697780913 Y 0.99196201188455 0.99196201188455 N N 521 2375 ENSG00000204517 ENSG00000178935 - - 19 19 63045300 63018093 upstream upstream AC010522.3 ZNF552 63042237 63010262 + - 0 63042204 63023126 - + N - - N HCC1954 3 1.81818181818182 1 16 3 N - - Y - - 0 0 0 22 0.949852505270192 1.31408166142643 1.31408166142643 0.949852505270192 1 - - 26746 Y Y 3.61464054707278 3.28292550416853 3.28292550416853 345 0 0.00403308762033594 Y 0.940293326390697 0.99402933263907 N N 3400 24220 ENSG00000156873 ENSG00000080603 - + 16 16 30676183 30658951 upstream downstream PHKG2 SRCAP 30667238 30617963 + + 0 30667026 30660728 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.914143764470561 0.999844742389676 0.999844742389676 0.914143764470561 2 - - 36700 Y Y 3.17824182890216 3.29699245393877 3.17824182890216 0 0 0.349438322562158 Y 0 0.985173470396362 N N 119 1870 ENSG00000111275 ENSG00000111271 - + 12 12 110732165 110679284 coding downstream ALDH2 ACAD10 110688729 110608285 + + 0 110704195 110680940 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.949852505270192 0.528489363834543 0.949852505270192 0.528489363834543 1 - - 7800 N N 3.45976132345673 3.68527868815389 3.45976132345673 2 0 0.0371534673707878 N 0 0 N N 30801 185 ENSG00000144063 ENSG00000198904 + + 2 22 110231432 37759190 utr3p coding MALL APOBEC3D 110198738 37747276 - + 0 110199487 37747483 - + Y 0.822731146975801 - N HCC1954 40 36.75 35 4 1 N - - N Low_complexity SINE 0.404761904761905 1 1 4 0.299953422716903 0.321378667196682 0.321378667196682 0.299953422716903 0 0 - 22238 N N 3.33461813060452 2.9129088568201 2.9129088568201 0 0 0.0896204303809422 N 0.165316550348953 0 N N 0 7001 ENSG00000207985 ENSG00000160783 - + 20 1 26136914 154479736 upstream intron hsa-mir-663 PMF1 26136822 154449408 - + 0 26138488 154453273 + + Y - 1.64378688920725 N HCC1954 1 1 1 0 1 N 503 6.82238 N DNA Low_complexity 1 0.2 1 31 0.39993789695587 0.785592297591888 0.785592297591888 0.39993789695587 2 - 0 13415 N N 3.3241983368464 3.47552369040616 3.3241983368464 1 0 0.209079922390858 N 0 0 N N 0 850768 ENSG00000213857 ENSG00000075624 + + 22 7 39801189 5536758 downstream utr3p AL080243.21-3 ACTB 39800114 5533313 - - 0 39799719 5533741 - - Y - - N HCC1954 5 3.4 3 5 2 N - - N - Simple_repeat 0 0.247191011235955 0.247191011235955 5 0.51420586751469 0.5713398527941 0.5713398527941 0.51420586751469 1 - - 41401 Y Y 3.33680806132367 3.54040868314203 3.33680806132367 151 0 0.083089006729939 Y 0 0.986754966887417 N N 434 4746 ENSG00000213865 ENSG00000175073 - - 8 8 67935244 67742036 utr5p upstream C8orf44 VCPIP1 67751008 67703300 + - 0 67751597 67742450 - + N 0.288258191074925 - N HCC1954 1 1 1 0 2 N - - Y DNA - 0.320610687022901 0 0.320610687022901 64 0.93556900895034 0.735600060472404 0.93556900895034 0.735600060472404 2 0 - 41615 Y Y 3.63296356710195 3.53784803006229 3.53784803006229 317 0 0.0760910020687937 Y 0.49804237420856 0.978790522853883 N N 0 0 ENSG00000208449 ENSG00000221399 - + 8 8 144695711 144695713 downstream intron AC067930.7-1 7SK 144695423 144695423 + + 0 144702969 144695709 - + N - 1 N HCC1954 6 1.625 1 1 1 N - - Y - RNA 0 1 1 8 0.885576771830856 1.05697872766909 1.05697872766909 0.885576771830856 4 - 0 7703 N Y 3.47233119514066 3.37126417066287 3.37126417066287 1 0 0.119423263885156 N 0 0.860248447204969 N N 20739 269 ENSG00000143951 ENSG00000076641 - - 2 8 63669355 82186858 utr3p upstream C2orf86 PAG1 63202041 82042605 - - 0.813664596273292 63309485 82243135 + + Y - - N HCC1954 620 496 400 5 1 N - - N LINE LINE 1 1 1 5 0.699891319672773 0.45707188223528 0.699891319672773 0.45707188223528 4 - - 31539 Y Y 3.47336426491055 3.51525959220437 3.47336426491055 0 0 0.51612150784343 Y 0.993609651218347 0.993609651218347 N Y 168 139 ENSG00000144649 ENSG00000206552 - + 3 3 43076707 42959283 utr5p coding C3orf41 C3orf41 42995833 42952856 + + 0 43048763 42958567 - + N 0.162378751569097 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 1.17838844638783 1.17124669822791 1.17838844638783 1.17124669822791 4 0 - 38196 Y Y 3.25992225835735 3.41273534243362 3.25992225835735 0 0 0.289822134613164 Y 0.988933691756272 0.988933691756272 N N 8350 4025 ENSG00000179364 ENSG00000185024 - - 14 14 104935529 104838374 intron coding PACS2 BRF1 104852126 104746670 + - 0 104852703 104810275 - + N 0.328314398751677 1.9594976264902 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.635615586233437 0.728458312312478 0.728458312312478 0.635615586233437 1 0 0 48899 Y Y 2.82140062299921 3.35975787397237 2.82140062299921 327 0 0.0058096763561184 Y 0.521467889908257 0.990030581039755 N N 390 17875 ENSG00000131459 ENSG00000050748 + - 5 5 179712931 179640218 downstream upstream GFPT2 MAPK9 179660296 179595388 - - 0 179651453 179646672 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity,Simple_repeat,Low_complexity LINE 0.141078838174274 1 1 42 1.56404284702385 0.742741808632331 1.56404284702385 0.742741808632331 1 - - 2102 N N 3.47911741325579 3.4780843434859 3.4780843434859 0 0 0.0464217923494218 N 0 0 N N 975 4 ENSG00000198487 ENSG00000188682 + - 6 11 42218335 31347933 coding intron AL512274.9 AL135932.7 42183124 30921325 - - 0 42183205 31131797 - + Y - 0.887918998836977 N HCC1954 22 20.8 20 10 1 N - - N - SINE 0 1 1 10 0.449930134075354 0.271386430077198 0.449930134075354 0.271386430077198 1 - 0 13376 N Y 3.64231043829683 3.20600500608205 3.20600500608205 0 0 0.177661950464851 N 0 0.144076305220884 N N 3116 18603 ENSG00000185219 ENSG00000099940 - + 3 22 44472885 19574109 utr3p downstream ZNF445 SNAP29 44456266 19543292 - + 0 44460085 19575218 + + Y - - N HCC1954 33 30.2857142857143 21 7 1 N - - N SINE SINE,SINE 1 0.5625 1 7 0.371370904316165 0.34280391167646 0.371370904316165 0.34280391167646 1 - - 29722 Y Y 3.6491271616355 3.14846594534498 3.14846594534498 317 0.136590576020269 0.00968239106052882 Y 0.152288929183537 0 N N 3755 30335 ENSG00000204387 ENSG00000204388 - + 6 6 31915520 31906010 coding coding C6orf48 HSPA1B 31910383 31903667 + + 0 31911168 31905510 - + N - - N HCC1954 2 1.5 1 2 1 N - - Y - - 0 0 0 4 0.757025304952183 0.835584534711372 0.835584534711372 0.757025304952183 1 - - 44870 N Y 3.53039946453785 3.353603498043 3.353603498043 211 0 0.00687183814750436 N 0 0.819671420521046 Y N 12 282831 ENSG00000134460 ENSG00000099194 + + 10 10 6144278 102114577 intron downstream IL2RA SCD 6081835 102096762 - + 0 6090003 102131319 - + N 0.973524258022123 - N HCC1954 22 22 22 5 1 N 487 26.3306 N LTR LTR 1 1 1 5 0.28566992639705 0.671324327033068 0.671324327033068 0.28566992639705 2 0 - 30412 Y Y 3.32267075353655 3.66951632120446 3.32267075353655 248 0 0.272331692436483 Y 0 0.673590403903497 N N 0 0 ENSG00000219493 ENSG00000216396 - - X X 117957125 117897176 upstream upstream RP13-347D8.1 RP4-562J12.1 117956144 117895877 + - 0 117933348 117903214 - + N - - N HCC1954 23 6.45454545454545 1 8 2 N - - Y SINE,SINE LTR,LTR 1 1 1 11 0.785592297591888 0.93556900895034 0.93556900895034 0.785592297591888 4 - - 1735 N N 3.41423242051993 3.61257440753299 3.41423242051993 13 0 0.174417160787004 N 0.869193869193869 0.0139230139230139 N N 6632 14314 ENSG00000158636 ENSG00000154845 - + 11 18 75940234 9604606 upstream intron C11orf30 PPP4R1 75833717 9536789 + - 0.0139230139230139 75832968 9601736 - - Y - 2.41970611859676 N HCC1954 21 20.25 20 4 1 N - - N - SINE 0 1 1 4 0.542772860154395 0.314236919036755 0.542772860154395 0.314236919036755 2 - 0 45533 N N 3.51576345331414 3.43937216388778 3.43937216388778 0 0.149748743718593 0.104957954104207 N 0.149748743718593 0.149748743718593 N N 13582 78560 ENSG00000105723 ENSG00000112493 - + 19 6 47438591 33390114 utr5p utr3p GSK3A TAPBP 47426182 33375449 - - 0.149748743718593 47437267 33375989 + - Y - 0.622657104455216 N HCC1954 39 38.125 37 8 1 N - - N SINE DNA 1 0.708333333333333 1 8 0.314236919036755 0.871293275511003 0.871293275511003 0.314236919036755 3 - 0 30638 N Y 3.47655676017605 3.57167229721571 3.47655676017605 4 0.00303030303030305 0.193689997041474 Y 0.992979086641058 0.950853606487409 N N 884 2220 ENSG00000158301 ENSG00000125962 - + X X 101859316 101745743 utr5p downstream GPRASP2 ARMCX5 101853760 101740752 + + 0 101854801 101747236 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 1.19981369086761 0.921285512630487 1.19981369086761 0.921285512630487 1 - - 26876 Y Y 3.38552945952599 3.38080938095063 3.38080938095063 396 0.0303876756390721 0.109901600074594 Y 0.994427515377236 0.988855030754472 N N 8642 3792 ENSG00000099381 ENSG00000175938 - + 16 16 30903482 30873757 upstream coding SETD1A ORAI3 30876116 30867916 + + 0 30875022 30868339 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE - 0.451086956521739 0 0.451086956521739 79 1.31408166142643 1.57118459518378 1.57118459518378 1.31408166142643 4 - - 38168 N Y 3.42464286670823 3.31233066536513 3.31233066536513 218 0 0.00621860480498426 Y 0 0.981218625584213 N N 0 0 ENSG00000211932 ENSG00000211913 + - 14 14 105456422 105428110 upstream downstream AB019441.1-14 AL122127.6-14 105456406 105428094 - - 0 105457911 105427023 - + N - - N HCC1954 6 2.14285714285714 1 3 1 N - - N LTR - 1 0 1 7 0.664182578873142 0.485638874874985 0.664182578873142 0.485638874874985 0 - - 47028 Y Y 3.60103760561896 3.68680627146374 3.60103760561896 365 0 0.0195986500338762 Y 0 0.992269300201763 N N 22 0 ENSG00000185792 ENSG00000203305 + + 19 19 60941580 60900406 downstream downstream NLRP9 AC010525.6-1 60911610 60899900 - + 0 60907604 60901139 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR LTR 0.777227722772277 0.37593984962406 0.777227722772277 4 1.02841173502938 0.685607823352921 1.02841173502938 0.685607823352921 2 - - 30444 Y Y 3.26464233693271 3.12845685570642 3.12845685570642 162 0 0.00455327559292296 Y 0.982253086419753 0.982253086419753 N N 0 23619 ENSG00000219763 ENSG00000147274 + - X X 135857958 135790605 downstream upstream RP11-308D16.1 RBMX 135857573 135783288 - - 0 135835073 135819535 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE,LTR - 0.847826086956522 0 0.847826086956522 6 0.657040830713216 0.799875793911741 0.799875793911741 0.657040830713216 2 - - 30489 N Y 3.60256518892881 3.34252135687557 3.34252135687557 223 0 0.100446835680613 Y 0 0.976576101292535 N N 0 3991 ENSG00000208602 ENSG00000165704 + + X X 133488116 133462354 downstream coding AC004383.1 HPRT1 133487977 133421923 - + 0 133475631 133460380 - + N - 2.29951692924023 N HCC1954 2 1.33333333333333 1 2 1 N - - N SINE - 0.901639344262295 0 0.901639344262295 6 0.435646637755502 0.542772860154395 0.542772860154395 0.435646637755502 4 - 0 42400 Y Y 3.38593068711011 3.20487865035632 3.20487865035632 225 0 0.0386699744808325 Y 0.972724505327245 0.972724505327245 N N 107 1287 ENSG00000174792 ENSG00000174796 - + 4 4 76710105 76674260 upstream downstream C4orf26 THAP6 76700297 76658678 + + 0.972724505327245 76688562 76686720 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,SINE SINE 0.826086956521739 0.6875 0.826086956521739 4 0.542772860154395 0.678466075192994 0.678466075192994 0.542772860154395 4 - - 20389 N N 3.33317448568069 3.46807512488172 3.33317448568069 0 0.274948024948025 0.067634475080168 N 0.288374913374913 0.422643797643798 N N 6539 517 ENSG00000120253 ENSG00000162676 - + 6 1 150109507 92725021 utr3p downstream NUP43 GFI1 150087147 92712907 - - 0.301801801801802 150087439 92707089 + - Y - - N HCC1954 1 1 1 0 1 N - - N LINE,SINE SINE 0.645161290322581 1 1 4 0.442788385915428 0.292811674556976 0.442788385915428 0.292811674556976 2 - - 39745 N N 3.30484224704734 3.56232542602083 3.30484224704734 1 0.110919540229885 0.112944231171988 N 0.145114942528736 0.743534482758621 N N 3290 4 ENSG00000148343 ENSG00000103569 - + 9 15 130874182 56265402 intron downstream FAM73B AQP9 130838745 56217700 + + 0.179310344827586 130859834 56339667 - + Y 0.748493412034769 - N HCC1954 360 80.5 20 6 1 N 213 19.9252 N SINE LTR 1 1 1 6 0.299953422716903 0.321378667196682 0.321378667196682 0.299953422716903 3 0 - 42154 Y Y 3.63296356710195 3.33680806132368 3.33680806132368 214 0.0389945214308732 0.735937027811998 Y 0.805510796003867 0.988559458588463 N N 12865 0 ENSG00000172493 ENSG00000152575 - - 4 4 88281215 88090258 coding downstream AFF1 AC093827.3 88147177 88089842 + - 0 88186337 88088742 - + N 0.14862175406537 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 29 0.907002016310634 0.599906845433805 0.907002016310634 0.599906845433805 1 0 - 48326 N N 3.62192127872787 3.04015804200544 3.04015804200544 8 0 0.222416143000867 N 0 0.00381679389312972 N N 427 1830 ENSG00000164308 ENSG00000147124 - - 5 X 96279365 47227289 utr3p upstream LRAP ZNF41 96237960 47191352 + - 0.00381679389312972 96279168 47241491 - + Y - - N HCC1954 21 21 21 4 1 N 571 24.5963 N SINE LTR 1 1 1 4 0.278528178237124 0.392796148795944 0.392796148795944 0.278528178237124 3 - - 40904 Y Y 3.41679307359967 3.41848849077886 3.41679307359967 175 0 0.125263673216401 Y 0 0 N N 6319 0 ENSG00000197818 ENSG00000217373 - - 20 20 47942179 47779786 upstream upstream SLC9A8 SNRPFP1 47862657 47779535 + - 0 47822237 47819346 - + N - - N HCC1954 2 1.14285714285714 1 2 3 N - - Y - LTR 0 1 1 14 0.564198104634174 0.578481600954027 0.578481600954027 0.564198104634174 2 - - 3910 N Y 3.60256518892881 3.62039369541802 3.60256518892881 0 0.725178919973975 0.861568293378308 N 0 0.759531554977228 N N 355 2360 ENSG00000106066 ENSG00000069509 - - 7 X 29201417 44287160 coding upstream CPVL FUNDC1 29001772 44267847 - - 0 29098843 44317598 + + Y - - N HCC1954 20 14.8 1 4 1 N - - N - SINE 0 1 1 5 0.649899082553289 0.299953422716903 0.649899082553289 0.299953422716903 4 - - 21936 N N 3.50016892023405 3.46807512488172 3.46807512488172 8 0 0.158003336363438 N 0 0 N N 8122 2963 ENSG00000134717 ENSG00000133983 - + 1 14 52328976 69896147 utr3p intron BTF3L4 COX16 52294385 69680762 + - 0 52327109 69895937 - - Y - 0.805004874878128 N HCC1954 25 20 12 6 1 N - - N SINE - 1 0 1 6 0.299953422716903 0.585623349113953 0.585623349113953 0.299953422716903 2 - 0 26080 N Y 3.66745018166468 3.48809356209009 3.48809356209009 9 0 0.067263341229787 N 0 0 N N 234 45068 ENSG00000154240 ENSG00000205336 + + 17 16 61618435 56256445 intron upstream CCDC46 GPR56 61062121 56220023 - + 0 61399447 56211646 - + Y 0.611008930206743 - N HCC1954 27 21.4210526315789 20 19 1 N - - N SINE - 1 0 1 19 0.357087407996313 0.478497126715059 0.478497126715059 0.357087407996313 1 0 - 41521 Y N 3.40340222945757 3.5319270478477 3.40340222945757 0 0 0.481862142694789 Y 0 0 N N 0 0 ENSG00000222231 ENSG00000211422 + - 8 8 77340522 77211212 upstream upstream U2 AC021311.8 77340333 77211077 - - 0 77381200 77216600 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 1 0 1 4 0.621332089913584 0.671324327033068 0.671324327033068 0.621332089913584 3 - - 9262 N N 3.11444333909867 3.74913061111987 3.11444333909867 0 0 0.229268856753071 N 0 0 N N 149 5791 ENSG00000161381 ENSG00000133195 + + 17 17 34561298 68600427 intron downstream PLXDC1 SLC39A11 34473083 68153684 - - 0 34508407 68100003 - - N 1.4072855500226 - Y HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 0.714174815992626 0.864151527351077 0.864151527351077 0.714174815992626 1 0 - 41503 Y N 3.63552422018169 3.55231620741665 3.55231620741665 0 0 0.939758911362428 Y 0 0.35476902625457 N N 0 0 ENSG00000222501 ENSG00000207110 + + 8 8 129092039 129080722 downstream downstream U4 U1 129091912 129080559 - + 0.35476902625457 129091049 129084997 - + N - - N HCC1954 1 1 1 0 4 N - - Y - Low_complexity,SINE 0 0.654320987654321 0.654320987654321 14 0.999844742389676 1.15696320190805 1.15696320190805 0.999844742389676 3 - - 28155 N N 1.67720760714817 3.19396434305824 1.67720760714817 27 0 0.536744005067585 N 0.481301229508197 0.356813524590164 N N 1892 6894 ENSG00000176058 ENSG00000159792 - - 9 16 139215578 66521078 coding utr5p C9orf75 PSKH1 139205890 66484705 - + 0 139214511 66484708 + - Y - - N HCC1954 17 11.5 2 4 1 N - - N Simple_repeat,Low_complexity - 0.5 0 0.5 4 0.28566992639705 0.39993789695587 0.39993789695587 0.28566992639705 2 - - 17683 Y Y 3.45612774781375 3.65909652744634 3.45612774781375 246 0 0.183428872415936 Y 0.98951647411211 0.968549422336329 N N 5252 11611 ENSG00000054116 ENSG00000116871 - - 1 1 36387685 36419037 coding upstream TRAPPC3 MAP7D1 36374762 36394153 - + 0 36378354 36394071 + - N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.252873563218391 0.252873563218391 4 0.521347615674617 0.621332089913584 0.621332089913584 0.521347615674617 4 - - 42225 Y Y 3.56335849579072 3.65231965690101 3.56335849579072 257 0 0.0280867379031066 Y 0.949350392402559 0.99155839873376 N N 0 0 ENSG00000213632 ENSG00000214988 + - 4 4 83636070 83631821 upstream downstream AC067942.6-2 RPL7AP26 83635017 83631000 - - 0 83636247 83630417 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 0.785592297591888 0.849868031031224 0.849868031031224 0.785592297591888 1 - - 39950 Y Y 3.57229479183167 3.43039601505348 3.43039601505348 0 0 0.726834615409232 Y 0 0.989827806122449 N N 0 0 ENSG00000180987 ENSG00000215302 + - 15 15 30678304 30608228 downstream upstream AC123768.8-1 AC135983.4-1 30677791 30606298 - - 0 30659066 30616500 - + N - - N HCC1954 24 10.5 5 4 3 N - - Y SINE - 1 0 1 4 0.528489363834543 0.614190341753658 0.614190341753658 0.528489363834543 1 - - 4279 Y Y 3.329991337985 3.33631354778371 3.329991337985 260 0 0.0449804697137387 Y 0.954304869442484 0.981721947776994 N N 0 8260 ENSG00000222897 ENSG00000011275 + - 7 7 5878207 5787818 downstream upstream SRP_euk_arch RNF216 5877912 5626204 - - 0 5837338 5829683 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 5 0.771308801272036 0.99270299422975 0.99270299422975 0.771308801272036 4 - - 33247 N Y 3.37192651807217 2.95228338382753 2.95228338382753 233 0.00429184549356232 0.0178765618978995 Y 0.00429184549356232 0.970714466043928 N N 59837 171855 ENSG00000198695 ENSG00000198886 + + MT MT 14674 12138 coding coding MT-ND6 MT-ND4 14150 10761 - + 0 14574 12107 - + N 2.07752728071294 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.792734045751814 0.971277749749971 0.971277749749971 0.792734045751814 1 0 - 7925 N Y 3.68680627146374 3.47076375903745 3.47076375903745 250 0.317808219178082 0.0172688031325352 N 0.522465753424658 0.808986301369863 N N 31210 2763 ENSG00000084754 ENSG00000109472 + + 2 4 26321098 166638926 utr3p intron HADHA CPE 26267009 166519540 - + 0.808986301369863 26267384 166544423 - + Y - 0.615702127448076 N HCC1954 2 1.125 1 1 1 N - - N - - 0 0 0 8 0.521347615674617 0.314236919036755 0.521347615674617 0.314236919036755 2 - 0 36433 Y Y 3.41741556821562 3.47233119514066 3.41741556821562 140 0.0262181548355181 0.953806004387208 Y 0 0.946326984912194 N N 37 351 ENSG00000139194 ENSG00000205885 + + 12 12 7172754 7165701 intron coding RBP5 AC018653.29-1 7167557 7152443 - + 0 7171451 7164497 - + N 1.00814598354028 - N HCC1954 1 1 1 0 3 N - - Y DNA,LINE - 0.571428571428571 0 0.571428571428571 9 0.93556900895034 1.16410495006798 1.16410495006798 0.93556900895034 4 0 - 29144 N Y 3.47080361183081 3.16782203514404 3.16782203514404 361 0 0.0110729240074655 Y 0.146814404432133 0.988919667590028 N N 7010 6367 ENSG00000146457 ENSG00000112096 - - 6 6 160097339 160034343 utr5p intron WTAP SOD2 160068142 160020141 + - 0 160068317 160033972 - + N 0.858908032370761 1.24105918703935 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 23 0.799875793911741 1.17838844638783 1.17838844638783 0.799875793911741 1 0 0 3739 N Y 3.51529944499772 3.30761058678977 3.30761058678977 1 0 0.0707683945844637 N 0.910889646530874 0.910889646530874 N N 1582 108 ENSG00000185917 ENSG00000204054 - + 21 9 36373557 131325878 utr5p intron SETD4 AL391056.25-1 36328709 131291741 - + 0 36353538 131295693 + + Y - 4.50715835140998 N HCC1954 39 36.5714285714286 35 7 1 N 467 23.3214 N SINE SINE,LINE 1 0.50561797752809 1 7 0.392796148795944 0.635615586233437 0.635615586233437 0.392796148795944 1 - 0 35144 N Y 3.39653189510671 3.60632674564779 3.39653189510671 0 0 0.0904641654616888 N 0 0.946115927248003 N N 0 559 ENSG00000209951 ENSG00000178401 + + 7 12 86960 48031950 upstream utr3p AC097646.2-1 DNAJC22 86858 48026967 - + 0 126062 48031926 - + Y - - N HCC1954 148 115.515151515152 69 33 1 N - - N - SINE 0 1 1 33 0.664182578873142 0.357087407996313 0.664182578873142 0.357087407996313 2 - - 11421 N Y 3.31063524818594 3.43142908482337 3.31063524818594 4 0 0.298127765549621 N 0.249802828750197 0.016983016983017 N N 1649619 1500 ENSG00000141736 ENSG00000114739 + + 17 3 35138441 38509637 coding intron ERBB2 ACVR2B 35104766 38470794 + + 0.016983016983017 35122222 38478686 + + Y - 0.560014371489977 N HCC1954 11 4.7 2 10 1 N - - N - SINE 0 1 1 10 0.499922371194838 0.257102933757345 0.499922371194838 0.257102933757345 1 - 0 37841 N N 3.30484224704734 3.10823553000682 3.10823553000682 0 0 0.448503519787515 N 0 0.469854070660522 N N 8888 0 ENSG00000112159 ENSG00000221236 + - 6 14 90586163 72985644 intron downstream MDN1 AC005280.3 90409952 72985548 - + 0 90436146 72994846 - - Y 1.91573150519183 - N HCC1954 3 1.5 1 1 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.471355378555133 0.471355378555133 0.28566992639705 3 0 - 24770 Y Y 3.55231620741665 3.5016965035439 3.5016965035439 315 0 0.0284629612506099 Y 0.993029193029193 0.986058386058386 N N 13271 14651 ENSG00000081923 ENSG00000134440 + - 18 18 53550037 53440175 downstream upstream ATP8B1 NARS 53464656 53418894 - - 0 53459789 53448748 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 7 0.778450549431962 0.921285512630487 0.921285512630487 0.778450549431962 4 - - 29225 Y Y 3.5246463161926 3.38400187621614 3.38400187621614 0 0 0.421641036547982 Y 0 0 N N 267 3 ENSG00000164484 ENSG00000164483 - - 6 6 130805901 130728238 intron intron KIAA1913 SAMD3 130728572 130507153 + - 0 130803244 130623712 - + N 0.208308443941346 1.09238924649754 N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 9 0.899860268150708 0.871293275511003 0.899860268150708 0.871293275511003 1 0 0 35751 N Y 3.38809011260573 3.47336426491055 3.38809011260573 259 0 0.00967815285996954 N 0.664565440075644 0.745882909148215 N N 267 16390 ENSG00000166153 ENSG00000140950 + - 12 16 99184988 83095794 intron intron DEPDC4 KIAA1609 99121578 83068608 - - 0 99178943 83089222 - + Y 1.30213170439491 1.98970794067006 N HCC1954 1 1 1 0 1 N - - N SINE,SINE - 1 0 1 14 0.22853594111764 0.585623349113953 0.585623349113953 0.22853594111764 1 0 0 33352 N N 3.40744620240479 2.96895083947086 2.96895083947086 0 0 0.999963613632604 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8548 14548 - + N - 1.94091719403344 N HCC1954 3 2 1 4 10 N 189 4.09957 N - - 0 0 0 6 0.87843502367093 0.899860268150708 0.899860268150708 0.87843502367093 2 - 0 47328 Y N 2.85538854220753 3.06675501066625 2.85538854220753 0 0 0.351371349533522 Y 0.162753036437247 0.238866396761134 N N 288 38635 ENSG00000152475 ENSG00000083845 - - 19 19 63573051 63597982 intron upstream ZNF837 RPS5 63570805 63590448 - + 0.238866396761134 63572516 63584150 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.5713398527941 0.557056356474248 0.5713398527941 0.557056356474248 2 - - 43464 N Y 3.49015970162987 3.48809356209009 3.48809356209009 0 0 0.269472148523882 N 0.637911025145068 0.637911025145068 N N 0 2643 ENSG00000108231 ENSG00000003402 - + 10 2 95547904 201737246 intron downstream LGI1 CFLAR 95507632 201689135 + + 0.637911025145068 95545219 201737955 - + Y 1 - N HCC1954 3 1.5 1 1 1 N - - N LTR LTR 1 1 1 4 0.271386430077198 0.321378667196682 0.321378667196682 0.271386430077198 2 0 - 7072 Y Y 3.54144175291192 3.04586198998753 3.04586198998753 274 0 0.585106611862746 Y 0.991697080291971 0.983394160583942 N N 126 0 ENSG00000186281 ENSG00000222119 + - 2 2 96064454 96034328 downstream upstream AC013272.5-2 SRP_euk_arch 96051422 96034040 - - 0 96048676 96040207 - + N - - N HCC1954 2 2 2 6 3 N - - Y - - 0 0 0 6 0.592765097273879 0.564198104634174 0.592765097273879 0.564198104634174 4 - - 46046 N N 3.43209143223268 3.41526549028982 3.41526549028982 0 0 0.213805211499566 N 0 0.359532660647902 N N 1354 850768 ENSG00000130544 ENSG00000075624 - - 19 7 7038979 5536758 upstream utr3p ZNF557 ACTB 7020471 5533313 + - 0 7015660 5533763 - + Y - 0.980591607573384 N HCC1954 4 2.8 1 3 1 N - - N - - 0 0 0 5 0.22853594111764 0.435646637755502 0.435646637755502 0.22853594111764 2 - 0 4816 N N 3.53974633573272 2.77741622822666 2.77741622822666 0 0 0.49123660871468 N 0 0 Y N 1830 4358 ENSG00000146776 ENSG00000091127 - + 7 7 105310263 104949921 coding utr5p ATXN7L1 PUS7 105032750 104884194 - - 0 105092893 104949735 + - N - 1.92459637775741 N HCC1954 1 1 1 0 2 N 12 15.1376 N - - 0 0 0 21 1.29979816510658 1.17124669822791 1.29979816510658 1.17124669822791 3 - 0 9259 N Y 3.07101108092519 3.56591914887046 3.07101108092519 0 0 0.255709230160328 N 0 0.866457389872376 N N 1649619 9881 ENSG00000141736 ENSG00000008294 - + 17 17 35138441 46553204 coding intron ERBB2 SPAG9 35104766 46397083 + - 0 35125066 46508329 - - N 0.990793461175642 1.25161174319894 Y HCC1954 25 21 20 8 1 N - - N - SINE 0 1 1 8 0.799875793911741 0.28566992639705 0.799875793911741 0.28566992639705 1 0 0 29824 N Y 3.55504469436574 2.8046314587041 2.8046314587041 1 0 0.933014216960846 Y 0 0.995271841187517 N Y 17595 13029 ENSG00000196821 ENSG00000124664 + - 6 6 34772603 34632069 coding utr5p C6orf106 SPDEF 34663050 34613558 - - 0 34722356 34620239 - + N - 1.59374403518881 N HCC1954 2 1.08037825059102 1 34 1 Y - - N - - 0 0 0 423 1.55690109886392 1.59975158782348 1.59975158782348 1.55690109886392 4 - 0 41954 N N 3.66592259835483 3.17101453040955 3.17101453040955 0 0 0.296693497623284 N 0 0 N N 86504 0 ENSG00000104408 ENSG00000217212 + - 8 X 109330135 90703253 coding upstream EIF3E RP13-222H17.1 109283149 90702093 - - 0.0140817901234568 109309672 90742760 - + Y 0.593852950305209 - N HCC1954 1 1 1 0 1 N - - N - SINE 0 0.635294117647059 0.635294117647059 6 0.635615586233437 0.607048593593732 0.635615586233437 0.607048593593732 3 0 - 13123 N N 2.9903730688097 3.60525382308454 2.9903730688097 0 0 0.409226101046452 N 0 0 N N 317991 1139 ENSG00000171346 ENSG00000132570 - + 17 5 36932191 134326223 coding intron KRT15 PCBD2 36923523 134268709 - + 0 36928443 134291403 + + Y - 1.57189749691755 N HCC1954 3 2.25 2 4 1 N 538 20.0071 N Simple_repeat - 0.81981981981982 0 0.81981981981982 4 0.714174815992626 0.692749571512847 0.714174815992626 0.692749571512847 1 - 0 18118 Y Y 3.18768198605288 3.53937561337214 3.18768198605288 284 0 0.00782795088086197 Y 0 0 N N 6613 0 ENSG00000142875 ENSG00000220124 - - 1 1 84476765 84256642 upstream upstream PRKACB RP4-552O12.1 84316329 84254125 + - 0 84302905 84276267 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR LINE 1 1 1 20 1.03555348318931 0.585623349113953 1.03555348318931 0.585623349113953 2 - - 44957 Y Y 3.50376264308368 3.31125774280189 3.31125774280189 83 0 0.743232105547768 Y 0 0 N Y 73 1854 ENSG00000148805 ENSG00000148824 - + 10 10 135131941 135084164 coding coding AL161645.14-1 MTG1 135117422 135057611 + + 0 135119731 135066267 - + N 0.470298006710085 - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 6 1.02126998686945 0.942710757110266 1.02126998686945 0.942710757110266 4 0 - 42201 Y Y 3.62824348852659 3.57848902055439 3.57848902055439 280 0 0.730743287107149 Y 0 0.97833850931677 N N 1615 108 ENSG00000156219 ENSG00000169248 - - 4 4 77252964 77176376 upstream upstream ART3 CXCL11 77214887 77173975 + - 0 77198167 77194451 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 96 0.799875793911741 1.20695543902754 1.20695543902754 0.799875793911741 4 - - 18718 Y Y 3.28292550416853 3.62039369541802 3.28292550416853 257 0 0.394220909052052 Y 0.990137535154294 0.990137535154294 N N 0 33 ENSG00000209354 ENSG00000177757 + + 1 1 798820 745077 downstream downstream AL669831.13-2 FAM87B 798710 742614 - + 0 772895 754345 - + N - - N HCC1954 40 8.14285714285714 2 7 3 N - - Y - SINE,SINE 0 1 1 7 0.864151527351077 0.649899082553289 0.864151527351077 0.649899082553289 2 - - 41382 Y Y 3.29396779254261 3.24099032408136 3.24099032408136 0 0 0.998461627531264 Y 0.991486509133568 0.991486509133568 N N 0 9799 ENSG00000222697 ENSG00000076554 - - 8 8 81279688 81155565 upstream coding SRP_euk_arch TPD52 81279396 81109662 + - 0 81246213 81139381 - + N - 31.6570974291493 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 40 1.06412047582901 0.792734045751814 1.06412047582901 0.792734045751814 2 - 0 31105 N N 3.40215706237596 3.76273355257368 3.40215706237596 0 0 0.187811516580169 N 0 0 N N 2311 12271 ENSG00000046647 ENSG00000177479 + + X 3 13967880 48997971 utr3p intron GEMIN8 ARIH2 13934766 48931285 - + 0 13935701 48940354 - + Y - 1.30476084270739 N HCC1954 32 28.1666666666667 24 6 1 N - - N SINE - 1 0 1 6 0.385654400636018 0.499922371194838 0.499922371194838 0.385654400636018 1 - 0 11872 N Y 3.12804628055249 3.60785432895764 3.12804628055249 0 0 0.218995843209616 N 0.946180963572268 0.946180963572268 N N 1649619 0 ENSG00000141736 ENSG00000199133 - - 17 9 35138441 95981023 coding downstream ERBB2 hsa-let-7d 35104766 95980937 + + 0 35122227 96001761 - - Y - - N HCC1954 22 19 1 7 1 N - - N - SINE 0 1 1 8 0.721316564152552 0.357087407996313 0.721316564152552 0.357087407996313 2 - - 33074 N Y 3.12486313285679 2.99146714902667 2.99146714902667 427 0 0.615027050604293 Y 0 0.980814267699514 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0 14054 9428 - + N 1.74877270001884 1.26946268370106 N HCC1954 2 1.83333333333333 1 5 7 Y - - N - - 0 0 0 6 1.18553019454776 0.835584534711372 1.18553019454776 0.835584534711372 1 0 0 3317 N N 3.12747721909902 3.52208566311286 3.12747721909902 0 0 0.301653823685566 N 0.0215493726132023 0 N N 551733 22054 ENSG00000204628 ENSG00000166889 + - 5 11 180603512 59182996 utr3p intron GNB2L1 PATL1 180596536 59160770 - - 0 180596544 59177318 - + Y - 0.839682778820193 N HCC1954 22 7.64705882352941 1 20 2 N 395 21.2836 N - - 0 0 0 34 0.714174815992626 0.28566992639705 0.714174815992626 0.28566992639705 2 - 0 29203 Y Y 3.47449062063627 3.34256120966892 3.34256120966892 271 0 0.0218877796673378 Y 0.961081642066421 0.992216328413284 N N 0 6539 ENSG00000220506 ENSG00000009413 + - 6 6 111923609 111911125 upstream upstream RP3-415N12.1 REV3L 111922887 111726927 - - 0 111931194 111912759 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.978419497909897 0.964136001590045 0.978419497909897 0.964136001590045 1 - - 3482 N N 3.02652882812741 3.51576345331414 3.02652882812741 0 0 0.979691517733355 N 0 0 N N 24125 166846 ENSG00000157557 ENSG00000142192 - + 21 21 39118749 26465003 upstream coding ETS2 APP 39099101 26174733 + - 0 39032610 26384130 - - N - - Y HCC1954 1 1 1 0 3 N - - N SINE - 1 0 1 12 0.485638874874985 0.749883556792257 0.749883556792257 0.485638874874985 4 - - 6755 Y Y 3.52105259334297 3.38590018188657 3.38590018188657 378 0 0.00222346226308201 Y 0 0.988793769692646 N N 5507 4897 ENSG00000119760 ENSG00000115254 + + 2 2 27740011 27727215 coding intron SUPT7L GPN1 27727183 27705029 - + 0 27731790 27723560 - + N - 1.29394331736441 N HCC1954 1 1 1 0 2 N - - Y - DNA 0 0.840909090909091 0.840909090909091 4 0.585623349113953 0.628473838073511 0.628473838073511 0.585623349113953 1 - 0 34985 Y Y 3.39065076568547 3.79143651356762 3.39065076568547 252 0 0.235109485613271 Y 0.0271843390303451 0 N N 96280 22394 ENSG00000099219 ENSG00000107036 + + 9 9 5823081 5766555 utr3p intron ERMP1 KIAA1432 5774571 5619120 - + 0 5777061 5754697 - + N - 2.03581766691327 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.971277749749971 0.757025304952183 0.971277749749971 0.757025304952183 4 - 0 35237 N N 3.59425138750382 3.50785087947327 3.50785087947327 25 0 0.130414440619761 N 0.142559523809524 0 N N 21810 2591 ENSG00000213699 ENSG00000111696 + + 2 12 26857603 102759064 utr3p utr3p C2orf18 NT5DC3 26840646 102690219 + - 0.142559523809524 26855452 102692492 + - Y - - N HCC1954 714 205.5 35 4 1 N - - N SINE SINE 1 1 1 4 0.664182578873142 0.278528178237124 0.664182578873142 0.278528178237124 2 - - 31223 Y Y 3.28296535696188 2.86377688346385 2.86377688346385 270 0 0.981173263490193 Y 0 0.983113622096673 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 upstream upstream LPP AC022498.18 189413415 189379637 + + 0 189408737 189354577 - + N - - N HCC1954 1 1 1 0 7 N - - Y - - 0 0 0 9 0.807017542071667 0.749883556792257 0.807017542071667 0.749883556792257 2 - - 39387 N Y 3.18296190747752 3.48167806633553 3.18296190747752 350 0 0.00720414427263516 N 0.96978354978355 0.96374025974026 N N 238 0 ENSG00000211643 ENSG00000203613 - + 22 15 21003581 18610046 coding downstream IGLV5-52 AC087386.7-2 21003021 18609410 + + 0 21003256 18626095 - + Y 0.0508770010575065 - N HCC1954 24 8.16 2 50 1 N - - N - - 0 0 0 50 1.38549914302569 1.13553795742827 1.38549914302569 1.13553795742827 1 0 - 33166 N Y 3.01191908932792 3.53209488171704 3.01191908932792 426 0 0.639981007833073 Y 0 0.995157026300196 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0.995157026300196 10857 8983 - + N 0.350439220498621 - N HCC1954 6 2.875 1 7 7 Y - - N - - 0 0 0 8 0.907002016310634 1.34979040222606 1.34979040222606 0.907002016310634 1 0 - 6668 Y Y 3.59165088163073 3.30232144676095 3.30232144676095 0 0 0.91213814289515 Y 0 0 N N 307 4039 ENSG00000214184 ENSG00000135968 + + 2 2 108517107 108492286 intron coding AC012487.12-1 GCC2 108492643 108432063 - + 0 108494818 108451933 - + N - 0.904109452682716 N HCC1954 3 1.28571428571429 1 1 1 N - - Y SINE LINE 0.45679012345679 0.25 0.45679012345679 7 1.03555348318931 0.857009779191151 1.03555348318931 0.857009779191151 4 - 0 16387 N Y 3.41679307359967 3.49272035470961 3.41679307359967 0 0 0.135253266634562 N 0.787807820594706 0.771485345255837 N N 49089 1125 ENSG00000117450 ENSG00000115750 - + 1 2 45760196 9991994 utr5p intron PRDX1 TAF1B 45749295 9890887 - + 0 45759868 9953064 + + Y - 1.64233852599773 N HCC1954 6 4.6 3 5 1 N - - N - SINE 0 1 1 5 0.742741808632331 0.257102933757345 0.742741808632331 0.257102933757345 2 - 0 41912 N N 3.16828604346046 3.51145545787351 3.16828604346046 9 0.0555555555555555 0.0521071033408679 N 0.219806763285024 0.0555555555555555 N N 29840 0 ENSG00000164830 ENSG00000208693 + - 8 8 107834093 112016351 utr5p upstream OXR1 AC104946.4-4 107739270 112016284 + - 0.0555555555555555 107739488 112527779 + + N - - Y HCC1954 1 1 1 0 1 N 424 14.2913 N - LTR 0 1 1 5 0.414221393275723 0.357087407996313 0.414221393275723 0.357087407996313 2 - - 4630 Y Y 3.24887996998328 3.2305569499541 3.2305569499541 0 0 0.612915272500654 Y 0.993352219074599 0.986704438149197 N N 202 1558 ENSG00000106526 ENSG00000127399 - - 7 7 149631002 149666171 utr5p utr5p AC006008.2 LRRC61 149575235 149651346 - + 0 149623369 149651491 + - N - 0.246808956762565 N HCC1954 2 1.63636363636364 1 28 1 N - - Y - - 0 0 0 44 1.39978263934555 1.09982921662864 1.39978263934555 1.09982921662864 4 - 0 38162 Y Y 3.31844518850115 3.30488209984069 3.30488209984069 304 0 0.00240763721518222 Y 0 0.98653093883357 N N 251 5482 ENSG00000198513 ENSG00000012983 - - 14 14 50169508 50069126 utr5p upstream SPG3A MAP4K5 50096580 49954999 + - 0 50096662 50069460 - + N 0.349049077386314 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.792734045751814 0.549914608314322 0.792734045751814 0.549914608314322 1 0 - 8799 N N 3.1416492220063 2.97423997949969 2.97423997949969 0 0.200482121333869 0.057762600069535 N 0.208096577321165 0.0253496336260499 N N 317991 892 ENSG00000171346 ENSG00000185304 - + 17 2 36932191 87906586 coding intron KRT15 RGPD2 36923523 87836589 - - 0.0253496336260499 36928473 87905799 + - Y - 2.62981467744803 N HCC1954 3 2.75 2 4 1 N - - N Simple_repeat - 0.442622950819672 0 0.442622950819672 4 1.0069864905496 0.578481600954027 1.0069864905496 0.578481600954027 2 - 0 8412 N N 3.44615838200292 3.52258017665282 3.44615838200292 0 0 0.794050654052295 N 0 0 N N 4347 0 ENSG00000170265 ENSG00000213180 - + 7 17 148554260 62651616 upstream intron ZNF282 AC007448.14-1 148523487 62651306 + + 0 148519107 62651459 - + Y - 1 N HCC1954 4 4 4 5 1 N - - N - - 0 0 0 5 0.299953422716903 0.235677689277566 0.299953422716903 0.235677689277566 2 - 0 4673 N Y 3.20443756997885 3.5774559507845 3.20443756997885 284 0 0.090786575956074 Y 0.992882293762575 0.978646881287726 N Y 124 12405 ENSG00000176402 ENSG00000160862 - + 7 7 99365260 99411623 coding coding GJC3 AZGP1 99358828 99402290 - - 0 99359162 99407305 + - N - 0.739016906416787 N HCC1954 3 1.19047619047619 1 2 2 N - - N LTR - 0.897435897435897 0 0.897435897435897 21 1.1141127129485 1.01412823870953 1.1141127129485 1.01412823870953 4 - 0 20467 N N 3.26510634524913 3.36191729946799 3.26510634524913 7 0 0.110931242676120 N 0 0 N N 50714 0 ENSG00000154380 ENSG00000217482 - - 1 6 223907468 135999544 upstream upstream ENAH RP1-38C16.3 223741157 135999043 - - 0.152002681414446 223946521 136090122 + + Y - - N HCC1954 20 19.2 18 5 1 N 25 25.1811 N - LTR 0 1 1 5 0.39993789695587 0.28566992639705 0.39993789695587 0.28566992639705 2 - - 27215 N Y 3.30910766487608 3.53465553479678 3.30910766487608 258 0.525655223329642 0.00800488368320817 N 0.988141380583241 0.976282761166482 Y Y 173 3083 ENSG00000185710 ENSG00000185984 - + 16 16 21837978 21439266 utr5p utr5p AC092375.4-5 SLC7A5P1 21822947 21382027 - - 0 21837887 21403357 + - N - 0.243940900791136 N HCC1954 6 4.53333333333333 2 15 1 N 429 23.577 N - - 0 0 0 15 0.421363141435649 1.1141127129485 1.1141127129485 0.421363141435649 1 - 0 47270 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 0 0 0.657638694211254 Y 0 0.993526849326222 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 21 1.32836515774628 0.899860268150708 1.32836515774628 0.899860268150708 4 - - 47566 N Y 2.5707604397886 3.3070415253363 2.5707604397886 26 0 0.0791525943697806 Y 0.0104854037200759 0.992269417216563 N N 13582 12189 ENSG00000105723 ENSG00000105722 - + 19 19 47438591 47451093 coding coding GSK3A ERF 47426182 47443564 - - 0 47438253 47450984 + - N - 3.64479858633101 N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.709219858156028 0.709219858156028 5 0.785592297591888 0.649899082553289 0.785592297591888 0.649899082553289 1 - 0 37419 N Y 3.47233119514066 3.37126417066287 3.37126417066287 3 0 0.117012186846256 N 0 0.924707194645845 N N 20739 1 ENSG00000143951 ENSG00000092009 - - 2 14 63669355 24047311 utr3p downstream C2orf86 CMA1 63202041 24044552 - - 0.924707194645845 63309485 24033895 + + Y - - N HCC1954 620 515 420 4 1 N - - N LINE LINE 1 1 1 4 0.364229156156239 0.364229156156239 0.364229156156239 0.364229156156239 4 - - 24094 N N 3.55600321622212 3.53039946453785 3.53039946453785 0 0 0.184799458825722 N 0 0 N N 0 2470 ENSG00000207418 ENSG00000151883 + + 1 5 144680790 50173926 upstream coding U1 PARP8 144680627 49998570 - + 0 144690478 49999684 - + Y - - N HCC1954 5 4.4 2 5 1 N - - N - - 0 0 0 5 0.314236919036755 0.385654400636018 0.385654400636018 0.314236919036755 2 - - 16098 N Y 3.39743698380061 3.78208964237274 3.39743698380061 0 0 0.375776787427547 N 0.317216117216117 0.895685795685796 N N 2836 3966 ENSG00000067533 ENSG00000175772 - + 1 2 216577948 110111006 upstream upstream RRP15 AC013268.5-1 216525252 110103138 + + 0 216476006 110102054 - + Y - - N HCC1954 60 44.2105263157895 40 19 1 N 353 24.6684 N LINE - 1 0 1 19 0.442788385915428 0.671324327033068 0.671324327033068 0.442788385915428 2 - - 37565 N Y 3.07101108092519 3.51001030496889 3.07101108092519 1 0 0.088068291475671 N 0.790804597701149 0.870498084291188 N N 1649619 131 ENSG00000141736 ENSG00000183032 - + 17 14 35138441 36711306 coding intron ERBB2 SLC25A21 35104766 36218830 + - 0 35125066 36350481 - - Y - 2.66268764695243 N HCC1954 25 24.5 23 6 1 N - - N - SINE 0 1 1 6 0.599906845433805 0.307095170876829 0.599906845433805 0.307095170876829 1 - 0 643 Y Y 3.46824295875106 3.50529022639353 3.46824295875106 6 0 0.78769935570538 Y 0 0 N Y 5767 4805 ENSG00000110237 ENSG00000171631 - + 11 11 72757783 72687292 coding intron ARHGEF17 P2RY6 72697317 72653218 + + 0 72735576 72661159 - + N - 0.693440573389612 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.358407079646018 0.358407079646018 22 1.19981369086761 1.57118459518378 1.57118459518378 1.19981369086761 4 - 0 29294 Y Y 3.5278388114581 3.43568515508231 3.43568515508231 246 0 0.179229387080139 Y 0.00406504065040658 0.990423702313946 N N 0 1209 ENSG00000219891 ENSG00000197279 - + 6 6 28168598 28165320 upstream coding ZSCAN12L1 ZNF165 28168305 28154551 + + 0 28167012 28164431 - + N - 0.762766546162667 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.585623349113953 0.549914608314322 0.585623349113953 0.549914608314322 1 - 0 47189 Y Y 3.29400764533596 3.0521588522359 3.0521588522359 291 0 0.0689635990505867 Y 0.992334126354745 0.98466825270949 N N 2053 36141 ENSG00000099203 ENSG00000079805 + + 19 19 10807983 10803579 downstream coding TMED1 DNM2 10804115 10685143 - + 0.98466825270949 10803980 10802054 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 29 0.949852505270192 0.985561246069823 0.985561246069823 0.949852505270192 4 - - 26693 N Y 3.4503745994685 3.67423639977982 3.4503745994685 255 0 0.0593122018057181 Y 0 0.98905408317173 N N 6566 27302 ENSG00000167513 ENSG00000103335 - - 16 16 87403166 87330317 upstream upstream CDT1 FAM38A 87397687 87302916 + - 0 87364368 87343432 - + N - - N HCC1954 1 1 1 0 2 N - - N SINE - 0.342657342657343 0 0.342657342657343 6 0.899860268150708 0.471355378555133 0.899860268150708 0.471355378555133 2 - - 38174 Y Y 3.43105836246279 3.14205979716024 3.14205979716024 289 0 0.0324418232579941 Y 0.646617094898034 0.992932341897961 N N 21399 24 ENSG00000100852 ENSG00000176127 - - 14 14 31698685 31615105 utr5p upstream ARHGAP5 C14orf128 31616246 31614935 + - 0 31629460 31615175 - + N 0.281668926562708 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.871293275511003 0.849868031031224 0.871293275511003 0.849868031031224 1 0 - 48307 N N 3.53205502892369 3.4780843434859 3.4780843434859 0 0 0.119813756956934 N 0.00512820512820522 0.0377469525010508 N N 551733 3987 ENSG00000204628 ENSG00000198947 + - 5 X 180603512 33267479 coding intron GNB2L1 DMD 180596536 31042729 - - 0.0377469525010508 180597264 31530457 - + Y 0.559193797750339 41.8145045358826 N HCC1954 21 15.0769230769231 1 12 1 N - - N - - 0 0 0 13 0.599906845433805 0.28566992639705 0.599906845433805 0.28566992639705 2 0 0 41612 Y Y 3.42001607408871 3.50529022639353 3.42001607408871 248 0 0.0511075848596437 Y 0.863709677419355 0.989516129032258 N N 293 3661 ENSG00000180938 ENSG00000170873 - - 8 8 126060809 125809911 upstream upstream ZNF572 MTSS1 126054733 125632212 + - 0 126022888 125931378 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE SINE 1 0.596330275229358 1 6 0.678466075192994 0.778450549431962 0.778450549431962 0.678466075192994 1 - - 6288 N Y 3.55553920790569 3.25000632570901 3.25000632570901 289 0 0.0988087600129226 N 0 0.971928456552464 N N 2643 210 ENSG00000136682 ENSG00000214990 - + 2 9 113970218 69717464 downstream utr3p CBWD2 BX284632.11-2 113911807 69672192 + - 0.978946342414348 113971445 69672194 - - Y - 0.356291964479099 N HCC1954 42 28.5 12 4 1 N - - N - - 0 0 0 4 0.492780623034912 0.899860268150708 0.899860268150708 0.492780623034912 4 - 0 34392 N Y 3.17151839151932 3.49528100778935 3.17151839151932 261 0 0.0283205507070807 Y 0 0 N N 0 545 ENSG00000218062 ENSG00000196597 - - 9 9 98721421 98655175 upstream upstream RP11-330M2.3 ZNF782 98721031 98619094 + - 0 98720745 98663705 - + N - - N HCC1954 3 1.8 1 3 2 N - - N - SINE 0 1 1 5 0.435646637755502 0.485638874874985 0.485638874874985 0.435646637755502 1 - - 30546 Y Y 3.69784855983781 3.42320856935422 3.42320856935422 399 0 0.00378178735307355 Y 0 0 N N 0 10286 ENSG00000215197 ENSG00000130119 - + X X 54715796 54608698 upstream utr3p AL109854.10 GNL3L 54715144 54570464 + + 0 54679413 54603837 - + N - - N HCC1954 13 3 1 1 2 N - - Y LINE,LINE - 0.5 0 0.5 6 1.03555348318931 0.799875793911741 1.03555348318931 0.799875793911741 2 - - 21780 N N 3.58593758607883 3.21911343399591 3.21911343399591 25 0.23515406162465 0.24256552920238 N 0.252941176470588 0.270728291316527 N N 8082 2883 ENSG00000135090 ENSG00000168389 - + 12 1 117295133 40208214 intron intron TAOK3 MFSD2 117071992 40193407 - + 0.270728291316527 117168950 40201503 + + Y 1.81465990966334 0.719150508550464 N HCC1954 3 3 3 4 1 N - - N - - 0 0 0 4 0.328520415356608 0.299953422716903 0.328520415356608 0.299953422716903 1 0 0 46425 N Y 3.23640338425519 3.33098455496154 3.23640338425519 5 0 0.211072108912612 N 0 0.834074074074074 N N 4691 1303 ENSG00000152253 ENSG00000197573 - - 2 19 169455190 46148403 utr3p downstream SPC25 CYP2B7P1 169435648 46122010 - + 0.778765432098765 169435879 46162184 + - Y - - N HCC1954 62 32.7857142857143 23 14 1 N 237 25.654 N LINE LINE 1 1 1 14 0.521347615674617 0.899860268150708 0.899860268150708 0.521347615674617 1 - - 24777 Y Y 3.26294691975352 3.32320511986986 3.26294691975352 112 0 0.123756699757747 Y 0.993077671620665 0.993077671620665 N N 13001 7460 ENSG00000141385 ENSG00000176014 + + 18 18 12367194 12316567 utr3p coding AFG3L2 TUBB6 12319108 12298257 - + 0 12319144 12301051 - + N 0.263117053027993 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 63 1.2783729206268 1.08554572030879 1.2783729206268 1.08554572030879 1 0 - 42813 N Y 3.32064446679012 3.71976530271662 3.32064446679012 138 0 0.0327268248196598 N 0 0.801449275362319 N N 2010 12743 ENSG00000138735 ENSG00000122545 + + 4 7 120769429 35911440 downstream coding PDE5A SEPT7 120635000 35807345 - + 0 120633971 35885980 - + Y - - N HCC1954 5 4.66666666666667 4 6 1 N - - N - - 0 0 0 6 0.492780623034912 0.378512652476092 0.492780623034912 0.378512652476092 2 - - 34375 Y Y 3.43937216388778 3.48912663185998 3.43937216388778 261 0 0.104756634436628 Y 0.989402461889622 0.989402461889622 N N 630 1646 ENSG00000136895 ENSG00000136828 - + 9 9 129195647 129025264 upstream downstream GARNL3 RALGPS1 129045207 128716874 + + 0 129045178 129026790 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 1.05697872766909 0.728458312312478 1.05697872766909 0.728458312312478 1 - - 49261 Y Y 3.49528100778935 3.67320333000993 3.49528100778935 207 0 0.0181306225347129 Y 0 0.970730321113953 N N 109 322 ENSG00000177738 ENSG00000215068 - - 5 5 43054583 43081249 utr3p downstream AC008875.9 AC025171.8 43050282 43077952 - + 0 43051002 43103164 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.785592297591888 0.707033067832699 0.785592297591888 0.707033067832699 2 - - 13759 Y Y 3.5016965035439 3.35297165585723 3.35297165585723 272 0 0.327910788630415 Y 0 0 N N 28 140 ENSG00000128298 ENSG00000100156 + - 22 22 36836622 36809116 utr3p upstream BAIAP2L2 SLC16A8 36810843 36804093 - - 0.984432444852941 36811069 36809141 - + N 1.25364260099618 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 0.892718519990782 0.99270299422975 0.99270299422975 0.892718519990782 4 0 - 24314 N N 3.59425138750382 3.33680806132368 3.33680806132368 28 0 0.327965166179903 N 0.974005223536642 0.0901828237824551 N N 12188 2806 ENSG00000168724 ENSG00000143674 - + 5 1 34994825 231587517 utr3p utr3p DNAJA5 MAP3K19 34965455 231530137 + + 0.159502227684744 34991634 231585767 - + Y - 2.37004660865496 N HCC1954 38 26.5882352941176 22 17 1 N - - N SINE - 1 0 1 17 1.09268746846872 0.799875793911741 1.09268746846872 0.799875793911741 2 - 0 39192 N Y 3.73080759109069 3.2274272354209 3.2274272354209 1 0 0.389821536072354 N 0 0.84121995227286 N N 2509 1649619 ENSG00000103942 ENSG00000141736 + + 15 17 81412481 35138441 intron coding HOMER2 ERBB2 81314792 35104766 - + 0.84121995227286 81334398 35122227 - + Y 1.06516466127256 - N HCC1954 22 22 22 6 1 N 100 21.19 N SINE - 1 0 1 6 0.28566992639705 0.499922371194838 0.499922371194838 0.28566992639705 2 0 - 19242 N Y 3.11857142828161 3.38958719069204 3.11857142828161 171 0 0.00946287244780142 Y 0.151656920077973 0 N N 7 53732 ENSG00000142959 ENSG00000142937 + + 1 1 45026013 45017038 downstream utr3p BEST4 RPS8 45021844 45013828 - + 0 45020498 45016961 - + N - - N HCC1954 3 1.75 1 2 1 N - - N SINE - 0.2 0 0.2 4 0.892718519990782 0.635615586233437 0.892718519990782 0.635615586233437 2 - - 36196 Y Y 3.18718747251292 3.32886498225927 3.18718747251292 0 0 0.97848161494223 Y 0 0.98406106870229 N N 0 4523 ENSG00000210846 ENSG00000070961 - - 12 12 88644930 88573975 upstream upstream AC009522.11 ATP2B1 88644842 88505959 + - 0 88627127 88574015 - + N - - N HCC1954 1 1 1 0 2 N - - Y Simple_repeat - 0.353333333333333 0 0.353333333333333 39 1.07126222398894 0.899860268150708 1.07126222398894 0.899860268150708 4 - - 23722 N N 3.65384724021086 3.5010341561346 3.5010341561346 0 0 0.121258875030808 N 0 0 N N 2836 40617 ENSG00000067533 ENSG00000130164 - + 1 19 216577948 11105490 utr3p utr3p RRP15 LDLR 216525252 11061132 + + 0 216571894 11104135 - + Y - 2.27267372255859 N HCC1954 39 37 35 6 1 N - - N SINE SINE 1 0.0408163265306122 1 6 0.371370904316165 0.349945659836387 0.371370904316165 0.349945659836387 3 - 0 17803 N N 3.46551447180198 3.19343513439813 3.19343513439813 0 0 0.0665782019072321 N 0 0 N N 13137 1725 ENSG00000163486 ENSG00000196369 + + 1 1 204704406 142805834 coding intron SRGAP2 SRGAP2P2 204582820 142627547 + + 0 204632784 142627771 + + N - 0.890704633541674 Y HCC1954 6 5.5 3 6 1 N - - N - - 0 0 0 6 0.814159290231593 0.749883556792257 0.814159290231593 0.749883556792257 1 - 0 42341 Y Y 3.24272559405391 3.73233517440054 3.24272559405391 269 0 0.0152702606896568 Y 0 0 N N 9627 0 ENSG00000154447 ENSG00000201818 + + 4 4 170428824 170163070 downstream downstream SH3RF1 Y_RNA 170251982 170162975 - + 0 170228372 170204227 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.542772860154395 0.449930134075354 0.542772860154395 0.449930134075354 1 - - 45157 N Y 3.448886868952 3.29590595100639 3.29590595100639 1 0.00406504065040647 0.898767583374899 N 0.00406504065040647 0.906043871759472 N N 963 0 ENSG00000215033 ENSG00000215065 + + 10 10 47240877 46676017 intron intron AL603965.10-2 AL391137.11-1 47216968 46511545 + + 0.00406504065040647 47240533 46560001 + + N - 1 Y HCC1954 2 2 2 5 2 N - - N LINE,LINE LINE 1 0.972222222222222 1 5 0.857009779191151 0.771308801272036 0.857009779191151 0.771308801272036 1 - 0 39831 Y Y 3.55401162459584 3.29231222815676 3.29231222815676 167 0 0.00572561436196062 Y 0.542754491017964 0.980119760479042 N N 6235 0 ENSG00000174197 ENSG00000210507 - + 15 15 39849433 39694789 coding downstream MGA AC016134.7 39739902 39694722 + + 0 39748390 39701041 - + N 0.319435321560829 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 32 1.16410495006798 0.449930134075354 1.16410495006798 0.449930134075354 1 0 - 31561 Y Y 3.54449691953162 3.77104735399867 3.54449691953162 0 0 0.107441212099877 Y 0.3795701084773 0 N N 0 4350 ENSG00000213165 ENSG00000136521 - + 3 3 180826851 180824981 downstream coding AC090425.15-2 NDUFB5 180826317 180805269 + + 0 180833143 180819002 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 24 0.792734045751814 1.07126222398894 1.07126222398894 0.792734045751814 1 - - 18614 Y Y 3.31063524818594 3.70463477795295 3.31063524818594 254 0 0.0176419554740345 Y 0 0 N N 3347 86 ENSG00000135847 ENSG00000121454 + + 1 1 178738639 178510811 downstream downstream ACBD6 LHX4 178524002 178466065 - + 0 178522992 178511152 - + N - - N HCC1954 11 4.5 1 2 1 N - - Y SINE - 1 0 1 4 0.535631111994469 0.949852505270192 0.949852505270192 0.535631111994469 2 - - 46958 Y N 2.36039077559651 3.33105491297843 2.36039077559651 0 0 0.22608423886546 Y 0 0.259375 N N 692 912 ENSG00000175885 ENSG00000167766 + - 19 19 57930109 57833456 downstream upstream AC022150.6-2 ZNF83 57898675 57807432 - - 0.259375 57885605 57855867 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 0.771308801272036 0.549914608314322 0.771308801272036 0.549914608314322 1 - - 31181 Y Y 3.20191676969246 3.46551447180198 3.20191676969246 324 0 0.0148365513665966 Y 0.0165582248915581 0.993264097430764 N N 15053 3393 ENSG00000132155 ENSG00000075975 + + 3 3 12680678 12600205 utr3p utr3p RAF1 MKRN2 12600108 12573594 - + 0.993264097430764 12600285 12598839 - + N 0.511552833946193 1.53431292637829 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.20695543902754 1.04269523134923 1.20695543902754 1.04269523134923 1 0 0 11779 N N 3.45872825368684 3.47449062063627 3.45872825368684 0 0 0.177291084422125 N 0.465532518164097 0 N N 48166 6949 ENSG00000168610 ENSG00000137073 + - 17 9 37794039 34038947 utr3p intron STAT3 UBAP2 37718869 33911691 - - 0 37720696 34004201 - + Y 0.478540083131077 1.4077221301942 N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 4 0.442788385915428 0.271386430077198 0.442788385915428 0.271386430077198 2 0 0 47157 N N 3.55231620741665 3.30931977610606 3.30931977610606 0 0 0.0617634926852318 N 0 0 Y N 302 32 ENSG00000167637 ENSG00000204869 - - 19 19 42062306 51238037 intron upstream ZNF345 IGFL4 42033103 51234846 + - 0 42033403 51255307 - + N 0.191267882868105 - N HCC1954 5 2 1 1 1 N 138 5.8892 N - LTR 0 1 1 4 0.542772860154395 0.649899082553289 0.649899082553289 0.542772860154395 1 0 - 4616 N Y 3.65488030998075 3.34359427943881 3.34359427943881 286 0 0.559343658055237 Y 0.991022491022491 0.991022491022491 N N 3729 0 ENSG00000178234 ENSG00000208257 - - 7 7 151450178 151353493 utr5p upstream GALNT11 AC006017.2-1 151407293 151353212 + - 0.290776790776791 151407426 151353901 - + N - - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 54 0.93556900895034 0.871293275511003 0.93556900895034 0.871293275511003 1 - - 47717 Y Y 3.63655728995158 3.4718366816007 3.4718366816007 145 0 0.0790333488979782 Y 0.99148319289662 0.982966385793241 N N 243 105 ENSG00000119559 ENSG00000115266 + + 19 19 1430198 1424243 coding intron C19orf25 APC2 1425814 1401148 - + 0 1429773 1412823 - + N - 1.0483436809282 N HCC1954 23 3.64285714285714 1 4 1 N - - Y - SINE 0 1 1 14 0.821301038391519 0.87843502367093 0.87843502367093 0.821301038391519 4 - 0 56 Y Y 3.56761456604966 3.09759446921686 3.09759446921686 274 0 0.448276228952003 Y 0 0 N N 4525 1952 ENSG00000179119 ENSG00000151116 + - 11 11 18612596 18566857 downstream upstream SPTY2D1 UEVLD 18584527 18509821 - - 0 18579215 18567118 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.499922371194838 0.821301038391519 0.821301038391519 0.499922371194838 4 - - 31409 Y Y 3.27717235582328 3.62295434849776 3.27717235582328 251 0 0.893483656829138 Y 0 0.989939232967121 N N 168 73312 ENSG00000113946 ENSG00000163347 - - 3 3 191611027 191522909 upstream upstream CLDN16 CLDN1 191588535 191506197 + - 0 191558112 191548562 - + N - - N HCC1954 11 4.25 1 2 4 N - - Y - LINE,SINE 0 0.693181818181818 0.693181818181818 4 0.564198104634174 0.628473838073511 0.628473838073511 0.564198104634174 2 - - 29206 N N 3.34785034969775 2.78130147148845 2.78130147148845 0 0 0.0949426218497947 Y 0.0119047619047615 0 N N 95833 99 ENSG00000204525 ENSG00000204623 + - 6 6 31432935 30136900 utr3p utr5p HLA-C C6orf12 31344505 30076768 - - 0 31429657 30085501 - + N 0.997062761845253 0.338165971674006 N HCC1954 4 2.25 1 3 1 N - - N - - 0 0 0 4 0.685607823352921 0.521347615674617 0.685607823352921 0.521347615674617 2 0 0 306 Y Y 3.66273010308932 3.25256697878875 3.25256697878875 314 0 0.00837087101808276 Y 0 0.981876085697742 N N 724 2039 ENSG00000149292 ENSG00000149294 - + 11 11 112759476 112654343 upstream downstream TTC12 NCAM1 112690461 112337302 + + 0 112690323 112656703 - + N - - N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 10 0.785592297591888 0.835584534711372 0.835584534711372 0.785592297591888 2 - - 29065 N N 3.60966847741989 3.11700399217841 3.11700399217841 0 0 0.116778225562650 N 0 0 N N 6539 29840 ENSG00000009413 ENSG00000164830 - + 6 8 111911125 107834093 coding utr5p REV3L OXR1 111726927 107739270 - + 0 111735932 107739489 + + Y - 1.01618091025984 N HCC1954 21 21 21 4 1 N - - N LINE - 1 0 1 4 0.392796148795944 0.692749571512847 0.692749571512847 0.392796148795944 3 - 0 24635 Y Y 3.46079439322662 3.3248606842557 3.3248606842557 410 0 0.163573929900779 Y 0.587428485395965 0.98768443239988 N N 10593 4475 ENSG00000134779 ENSG00000134775 + + 18 18 32663156 32614016 coding downstream C18orf10 FHOD3 32630033 32131700 - + 0 32632410 32620943 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LTR 0 0.326923076923077 0.326923076923077 10 0.857009779191151 1.49976711358451 1.49976711358451 0.857009779191151 4 - - 41060 Y Y 3.40272612382943 3.32423818963975 3.32423818963975 97 0 0.336365477222723 Y 0.201045534492867 0.988420949775259 N N 16 16276 ENSG00000124103 ENSG00000022277 - + 20 20 54534605 54527350 downstream coding C20orf106 C20orf43 54532955 54477077 + + 0 54535586 54525663 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 4 0.51420586751469 0.585623349113953 0.585623349113953 0.51420586751469 1 - - 34644 N Y 3.45297510534159 3.30910766487608 3.30910766487608 39 0 0.31411763071409 Y 0.388040712468193 0.950381679389313 N N 2515 13277 ENSG00000137074 ENSG00000086061 - - 9 9 32991626 33029277 utr5p upstream APTX DNAJA1 32962609 33015242 - + 0 32987274 33015060 + - N - - N HCC1954 1 1 1 0 3 N - - N SINE - 0.783132530120482 0 0.783132530120482 5 0.592765097273879 0.464213630395207 0.592765097273879 0.464213630395207 1 - - 48843 Y Y 3.07208400348843 3.63974043764727 3.07208400348843 255 0 0.201444692674059 Y 0 0.991699346405229 N N 39039 25 ENSG00000145623 ENSG00000205785 - + 5 5 38970159 38859954 upstream intron OSMR AC091435.3-1 38881893 38848753 + + 0 38881529 38858571 - + N - 0.625341194453543 N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 21 0.685607823352921 0.657040830713216 0.685607823352921 0.657040830713216 2 - 0 34434 Y Y 3.61207989399303 3.38383404234679 3.38383404234679 290 0 0.0278005756128262 Y 0 0.983390804597701 N N 0 271 ENSG00000218219 ENSG00000165181 - - 9 9 113605531 113597044 downstream upstream RP11-430K21.2 C9orf84 113605081 113488274 + - 0 113610894 113597151 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.664182578873142 0.364229156156239 0.664182578873142 0.364229156156239 1 - - 31642 Y Y 2.88274380859372 3.63552422018169 2.88274380859372 269 0 0.312350164714761 Y 0.78541607091793 0.992336288247069 N N 1131 2216 ENSG00000214116 ENSG00000185485 - + 3 3 197173943 197201530 coding coding AC024937.21-2 AC024937.21-3 197171055 197174603 - - 0 197171356 197176699 + - N - 0.190317829380596 N HCC1954 12 5.5 1 13 3 N - - Y LINE - 0.53125 0 0.53125 14 0.914143764470561 0.914143764470561 0.914143764470561 0.914143764470561 2 - 0 9483 Y Y 3.7297745213208 3.49744043328497 3.49744043328497 214 0 0.468493230869542 Y 0.159120206252014 0.982839187882694 N N 13858 5085 ENSG00000108439 ENSG00000167182 - + 17 17 43381673 43361320 upstream intron PNPO SP2 43373916 43328515 + + 0 43373714 43350938 - + N - 1.10606245746149 N HCC1954 1 1 1 0 3 N - - Y - SINE 0 0.205128205128205 0.205128205128205 6 0.378512652476092 0.814159290231593 0.814159290231593 0.378512652476092 1 - 0 29790 Y Y 3.28651922701816 3.29976079368121 3.28651922701816 86 0 0.270283395501125 Y 0.99069042961675 0.9813808592335 N N 161 6845 ENSG00000112293 ENSG00000112294 - - 6 6 24597829 24645414 coding utr5p GPLD1 ALDH5A1 24536384 24603176 - + 0 24597706 24603176 + - N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.141414141414141 0.141414141414141 6 0.642757334393363 0.707033067832699 0.707033067832699 0.642757334393363 2 - - 35076 Y Y 3.45872825368684 3.68527868815389 3.45872825368684 0 0 0.545406427200168 Y 0.993729925182236 0.987459850364472 N N 5174 42 ENSG00000107281 ENSG00000180539 + + 9 9 139060476 139051055 coding downstream NPDC1 C9orf139 139053746 139041737 - + 0 139054244 139052183 - + N - - N HCC1954 2 1.2 1 1 1 N - - Y - LTR 0 1 1 5 1.1141127129485 0.899860268150708 1.1141127129485 0.899860268150708 4 - - 29277 Y Y 3.31638839653118 3.38383404234679 3.31638839653118 317 0 0.00108277941597479 Y 0.992879675529518 0.992879675529518 N N 0 2751 ENSG00000220105 ENSG00000187189 + - 6 6 116686971 116682014 downstream upstream AL050331.11-1 TSPYL4 116686349 116677817 - - 0 116686300 116682237 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.564198104634174 0.714174815992626 0.714174815992626 0.564198104634174 1 - - 34353 Y Y 3.5816815158199 3.51889316784735 3.51889316784735 290 0 0.990401337210338 Y 0.252586206896552 0.989619252873563 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5618792 5567513 - + N - - N HCC1954 1 1 1 0 7 N - - Y Low_complexity LTR 0.127659574468085 1 1 19 1.28551466878673 0.678466075192994 1.28551466878673 0.678466075192994 1 - - 4352 Y Y 3.56129235625094 3.48337348351473 3.48337348351473 152 0 0.0192568342031154 Y 0 0.986202485380117 N N 2675 0 ENSG00000177706 ENSG00000209951 - - 7 7 304072 86960 upstream upstream FAM20C AC097646.2-1 288052 86858 + - 0 190368 170704 - + N - - N HCC1954 3 2.13333333333333 1 13 1 N - - Y LINE,DNA LINE 0.507042253521127 1 1 15 0.507064119354764 0.821301038391519 0.821301038391519 0.507064119354764 2 - - 6728 Y Y 3.25562633530506 3.30744275292043 3.25562633530506 234 0 0.365874205986984 Y 0 0.978586526973624 N N 93 0 ENSG00000181798 ENSG00000223198 + - 2 2 232087294 232075156 coding upstream C2orf52 U2 232081383 232074987 - - 0 232082133 232076159 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.649899082553289 0.528489363834543 0.649899082553289 0.528489363834543 4 - - 17757 N N 3.37448717115191 3.44719145177281 3.37448717115191 0 0 0.116100977650506 N 0 0 N N 3473 3835 ENSG00000077157 ENSG00000143740 + + 1 1 200824320 226035550 intron downstream PPP1R12B SNAP47 200584459 225982981 + + 0 200609341 226037695 + + N 0.810360790370028 - Y HCC1954 2 1.25 1 1 1 N - - N LINE LINE 1 1 1 4 0.314236919036755 0.642757334393363 0.642757334393363 0.314236919036755 2 0 - 11713 N Y 3.49065421516983 3.66592259835483 3.49065421516983 201 0 0.769263736846586 N 0.746542580846418 0.983102838723095 N N 0 275 ENSG00000217435 ENSG00000204303 + + 9 17 104867701 72068110 downstream utr5p RP11-341A22.1 SNORD1C 104867519 72065446 + + 0.594468129354268 105006953 72065531 + + Y - 3.60650928260371 N HCC1954 2 1.875 1 28 3 N - - N - - 0 0 0 32 1.32122340958636 0.956994253430118 1.32122340958636 0.956994253430118 3 - 0 41836 Y Y 3.69255941980899 2.92232608603187 2.92232608603187 0 0 0.998866035822818 Y 0.354444444444444 0.880111111111111 N N 2237 3297 ENSG00000147408 ENSG00000104613 - - 8 8 19584374 19753864 utr5p upstream CSGALNACT1 INTS10 19305952 19719198 - + 0 19503656 19658977 + - N - - N HCC1954 1 1 1 0 5 N - - Y - Low_complexity 0 0.101123595505618 0.101123595505618 4 0.542772860154395 0.635615586233437 0.635615586233437 0.542772860154395 4 - - 618 N Y 3.23487580094534 3.13896058785057 3.13896058785057 313 0 0.0793986845926558 Y 0.985860920399701 0.985860920399701 N N 12075 3798 ENSG00000149187 ENSG00000110536 - - 11 11 47531264 47549942 utr5p upstream CUGBP1 PTPMT1 47446522 47543751 - + 0 47467152 47543402 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.842726282871298 1.1141127129485 1.1141127129485 0.842726282871298 4 - - 30803 N Y 3.58743466416515 3.61207989399303 3.58743466416515 137 0.188727858293076 0.010249430904957 N 0.815619967793881 0.834057971014493 N N 153380 0 ENSG00000185275 ENSG00000219462 + - Y X 19614093 120973146 utr3p upstream CD24L4 RP11-417D4.1 19611898 120972510 - - 0 19612795 121201453 - + Y - - N HCC1954 23 14.25 6 4 1 N - - N SINE SINE 0.338709677419355 1 1 4 0.442788385915428 0.271386430077198 0.442788385915428 0.271386430077198 1 - - 4732 Y Y 3.93849644929864 3.48333363072138 3.48333363072138 16 0 0.999003853183042 Y 0.988684514637905 0.988684514637905 N Y 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding intron CRCP ASL 65216341 65178207 + + 0 65230126 65195085 - + N - 2.40587305234717 N HCC1954 2 1.75 1 6 6 N - - Y - - 0 0 0 8 0.885576771830856 0.628473838073511 0.885576771830856 0.628473838073511 4 - 0 49084 Y Y 3.67320333000993 3.660633458326 3.660633458326 259 0.0790413054563998 0.0372620069583532 Y 0.990602462300576 0.981204924601151 N N 397 0 ENSG00000145779 ENSG00000222450 - - 5 5 118756975 118670225 coding upstream TNFAIP8 SRP_euk_arch 118752897 118669938 + - 0 118756410 118697225 - + N 0.0250352751461399 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.1426797055882 0.771308801272036 1.1426797055882 0.771308801272036 4 0 - 36192 Y Y 3.71720464963688 3.425274708894 3.425274708894 276 0 0.0903070188915888 Y 0.140380789997158 0 N N 1284 0 ENSG00000123415 ENSG00000202146 + - 12 12 52869024 52779353 downstream upstream SMUG1 Y_RNA 52861519 52779242 - - 0 52845425 52801498 - + N - - N HCC1954 7 3.44444444444444 1 5 1 N - - Y SINE LTR 0.858585858585859 1 1 9 0.707033067832699 0.928427260790413 0.928427260790413 0.707033067832699 4 - - 35683 N Y 3.64503892524591 3.13180783727146 3.13180783727146 7 0 0.07295956689154 N 0 0.851485148514851 N N 302 0 ENSG00000090382 ENSG00000141650 - - 12 18 68034280 53657194 utr3p upstream LYZ AC022724.8-1 68028401 53656706 + + 0 68033583 53621260 - - Y - - N HCC1954 38 32 25 5 1 N - - N SINE Low_complexity 1 0.46875 1 5 0.349945659836387 0.45707188223528 0.45707188223528 0.349945659836387 1 - - 6472 Y Y 3.52936639476796 3.36873402280666 3.36873402280666 140 0 0.507854041705283 N 0.894701542588866 0.978940308517773 Y N 5801 13069 ENSG00000115825 ENSG00000055332 - + 2 2 37398541 37405184 coding upstream PRKD3 EIF2AK2 37331149 37179857 - - 0 37373918 37405328 + - N - - N HCC1954 1 1 1 0 2 N - - N - Low_complexity 0 0.0152671755725191 0.0152671755725191 36 1.17838844638783 0.93556900895034 1.17838844638783 0.93556900895034 4 - - 33050 N Y 3.13999365762046 2.93868044237372 2.93868044237372 402 0 0.962952220189274 Y 0.136606881558594 0.916175425394038 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0.0946945942556127 8502 5412 - + N 0.58925071454747 1.1781446307412 N HCC1954 3 1.77777777777778 1 4 9 Y - - N - - 0 0 0 9 0.914143764470561 1.24980592798709 1.24980592798709 0.914143764470561 1 0 0 8192 N N 3.12747721909902 2.21353522688964 2.21353522688964 0 0.322755352458323 0.0764499096946937 N 0.386646356943387 0 N N 551733 0 ENSG00000204628 ENSG00000219858 + - 5 2 180603512 58542671 utr3p upstream GNB2L1 IK 180596536 58540931 - - 0 180596544 58908080 - + Y - - N HCC1954 21 14.8 2 10 1 N - - N - SINE,LINE 0 0.916666666666667 0.916666666666667 10 0.585623349113953 0.257102933757345 0.585623349113953 0.257102933757345 4 - - 41402 Y Y 3.22952388018421 3.59577897081367 3.22952388018421 246 0 0.986325756399012 Y 0 0.982055225957665 N N 0 9799 ENSG00000222697 ENSG00000076554 - - 8 8 81279688 81155565 upstream upstream SRP_euk_arch TPD52 81279396 81109662 + - 0 81246215 81202419 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 7 0.757025304952183 0.99270299422975 0.99270299422975 0.757025304952183 4 - - 44185 N N 3.37295958784206 3.78208964237274 3.37295958784206 16 0.130813143971039 0.0983155041178833 N 0.304650515176831 0.209830130882762 N N 10044 95 ENSG00000151150 ENSG00000215837 + + 10 3 61819494 196900773 intron downstream ANK3 AC069513.28-2 61458165 196900191 - + 0.209830130882762 61759874 196900870 - + Y 29.8795150976198 - N HCC1954 12 11.5 10 4 1 N - - N LINE,LINE LINE 1 1 1 4 0.271386430077198 0.34280391167646 0.34280391167646 0.271386430077198 2 0 - 42473 Y Y 3.44975210485255 2.94268474037728 2.94268474037728 0 0 0.97339524649104 Y 0.988794330536964 0.988794330536964 N N 5644 1 ENSG00000109686 ENSG00000189099 - - 4 4 152367022 152432055 utr5p downstream SH3D19 AC104819.4 152260886 152417775 - + 0 152366688 152465843 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 127 1.34264865406614 1.32836515774628 1.34264865406614 1.32836515774628 4 - - 16855 N N 2.32517209153747 2.56398356924328 2.32517209153747 43 0.084054928715123 0.25991861102794 N 0.084054928715123 0.131199160325374 N N 46217 20219 ENSG00000131746 ENSG00000162545 - + 17 1 35911380 20685315 utr3p utr3p TNS4 CAMK2N1 35885606 20681472 - - 0.131199160325374 35886174 20681954 + - Y - 1.29610796322965 N HCC1954 34 20.5 1 3 1 N - - N Simple_repeat,Simple_repeat Simple_repeat 0.301507537688442 0.0979020979020979 0.301507537688442 4 0.735600060472404 0.971277749749971 0.971277749749971 0.735600060472404 1 - 0 24073 N N 3.40695168886483 3.50848272165904 3.40695168886483 1 0 0.0655696483504518 N 0 0.569315199236459 N N 53009 551733 ENSG00000131236 ENSG00000204628 - + 1 5 40310908 180603512 upstream coding CAP1 GNB2L1 40278492 180596536 + - 0.569315199236459 40260637 180599139 - - Y - - N HCC1954 20 20 20 5 1 N 96 23.8153 N SINE - 1 0 1 5 0.278528178237124 0.685607823352921 0.685607823352921 0.278528178237124 1 - - 47627 Y Y 3.25512763186849 3.27088999881792 3.25512763186849 0 0 0.883233790224648 Y 0 0 N Y 2565 1811 ENSG00000090971 ENSG00000197483 - + 19 19 60690747 60687666 utr5p utr5p NAT14 ZNF628 60688406 60679511 + + 0 60688840 60679986 - + N - 0.201771333115363 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.87843502367093 0.778450549431962 0.87843502367093 0.778450549431962 4 - 0 10191 N Y 3.56695221864035 3.25360004855864 3.25360004855864 17 0.0660919540229886 0.369308188433356 Y 0.137246852764094 0 N N 5791 4290 ENSG00000133195 ENSG00000166685 - - 17 17 68600427 68716241 utr5p intron SLC39A11 COG1 68153684 68700768 - + 0 68596509 68701225 + - N - 0.527532451435525 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.849868031031224 0.678466075192994 0.849868031031224 0.678466075192994 2 - 0 11342 N N 3.60103760561896 3.46448140203209 3.46448140203209 0 0 0.20790058298833 N 0 0 N N 567 252027 ENSG00000114790 ENSG00000141738 - + 3 17 155457031 35157070 utr3p intron AC018452.11 GRB7 155321884 35147713 + + 0 155456977 35153504 - + Y - 0.802196664093379 N HCC1954 21 16.25 7 4 1 N - - N SINE SINE 1 0.647619047619048 1 4 0.292811674556976 0.678466075192994 0.678466075192994 0.292811674556976 1 - 0 38414 Y Y 3.30128837699106 3.52105259334297 3.30128837699106 0 0.00354609929077998 0.151418813164398 Y 0 0 N N 6188 459 ENSG00000196136 ENSG00000188488 - + 14 14 94160150 94129200 utr5p downstream SERPINA3 SERPINA5 94148387 94117564 + + 0 94148411 94135546 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.628473838073511 0.28566992639705 0.628473838073511 0.28566992639705 1 - - 29243 Y Y 3.57167229721571 3.61360747730288 3.57167229721571 0 0 0.92521343618141 Y 0 0 N N 0 5317 ENSG00000210937 ENSG00000124813 - + 6 6 45721898 45626796 downstream coding AL161907.17 RUNX2 45721819 45404032 + + 0 45738830 45588122 - + N - 0.966032186518949 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.814159290231593 0.621332089913584 0.814159290231593 0.621332089913584 4 - 0 45476 N Y 3.25832012713399 2.39788152983156 2.39788152983156 0 0 0.0393381568109185 N 0 0 N N 128 0 ENSG00000182404 ENSG00000182225 - + 6 19 5054467 5527949 coding downstream AL035653.12 AC011533.6 5048887 5527671 - - 0 5049077 5518621 + - Y - - N HCC1954 38 32.6666666666667 22 6 1 N - - N SINE Low_complexity 1 0.116504854368932 1 6 0.357087407996313 0.735600060472404 0.735600060472404 0.357087407996313 1 - - 29028 N N 3.49744043328497 3.54400240599166 3.49744043328497 0 0 0.253234846831993 N 0 0 N N 7904 975 ENSG00000104763 ENSG00000198487 + + 8 6 17986787 42218335 upstream coding ASAH1 AL512274.9 17958214 42183124 - - 0 17991792 42183238 - - Y - - N HCC1954 20 20 20 6 2 N - - N SINE,SINE - 1 0 1 6 0.271386430077198 0.599906845433805 0.599906845433805 0.271386430077198 2 - - 31730 Y Y 3.35872480420248 2.92824706824646 2.92824706824646 2 0 0.995618216960152 Y 0.985973216347264 0.985973216347264 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 utr5p upstream LPP AC022498.18 189413415 189379637 + + 0 189426009 189354733 - + N - - N HCC1954 1 1 1 0 7 N - - Y - Simple_repeat 0 0.53125 0.53125 42 1.64260207678304 0.45707188223528 1.64260207678304 0.45707188223528 2 - - 5547 N N 3.53039946453785 3.58081627991935 3.53039946453785 14 0.0548738588396978 0.075449601741898 N 0.413369981348778 0.266712476685972 N N 3 0 ENSG00000222017 ENSG00000218530 + + 2 X 198347792 17862864 coding downstream AC011997.1 RP1-272E8.1 198266075 17861390 + + 0.0711691371355648 198271779 17953517 + + Y - - N HCC1954 25 23.75 22 4 1 N - - N LINE - 1 0 1 4 0.449930134075354 0.378512652476092 0.449930134075354 0.378512652476092 3 - - 41177 Y Y 3.55553920790569 3.4439989565073 3.4439989565073 275 0 0.166158177560097 Y 0 0.985017088174983 N N 3174 4127 ENSG00000125967 ENSG00000101412 - + 20 20 31725925 31737854 coding coding NECAB3 E2F1 31708555 31727150 - - 0 31723889 31728572 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.885576771830856 0.907002016310634 0.907002016310634 0.885576771830856 4 - - 47207 Y Y 3.47552369040616 3.07717480442437 3.07717480442437 0 0 0.901668172935382 Y 0.96330072403692 0.993883454006153 N N 1423 1848 ENSG00000083842 ENSG00000198131 - + 19 19 63499066 63466822 upstream coding ZNF8 ZNF544 63482130 63431882 + + 0 63477545 63464029 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR - 1 0 1 6 0.864151527351077 1.09982921662864 1.09982921662864 0.864151527351077 2 - - 1719 N N 3.4722913423473 3.49528100778935 3.4722913423473 2 0 0.595831009531922 N 0 0 N N 12635 4030 ENSG00000109919 ENSG00000185214 + - 11 22 47620640 19180122 coding upstream MTCH2 KLHL22 47595444 19125806 - - 0 47612851 19183638 - + Y - - N HCC1954 20 7 1 2 3 N 341 20.4969 N - SINE 0 1 1 4 0.45707188223528 0.45707188223528 0.45707188223528 0.45707188223528 2 - - 4 Y Y 3.18929769764537 3.46182746299651 3.18929769764537 425 0 0.0128679295210629 Y 0.99493580173186 0.99493580173186 N N 8 13917 ENSG00000150676 ENSG00000137501 - - 11 11 85308699 85146692 upstream upstream CCDC83 SYTL2 85243792 85082915 + - 0 85199643 85146803 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 133 1.4140661356654 1.6854525657426 1.6854525657426 1.4140661356654 2 - - 38677 N N 3.61360747730288 3.39640391403072 3.39640391403072 0 0 0.462343170126138 N 0 0 N N 1602 0 ENSG00000147650 ENSG00000219778 + + 8 14 105670344 53528463 intron upstream LRP12 AL138479.2 105570643 53527568 - - 0 105579700 53657982 - - Y 0.714027886019711 - N HCC1954 3 1.09090909090909 1 1 1 N - - N LINE - 1 0 1 22 1.01412823870953 1.22838068350732 1.22838068350732 1.01412823870953 2 0 - 36458 Y Y 3.56335849579072 3.35513108135285 3.35513108135285 0 0 0.321821406620006 Y 0.993355119825708 0.96677559912854 N N 6663 10492 ENSG00000061273 ENSG00000211584 + + 12 12 46499924 46461719 downstream coding HDAC7 SLC48A1 46462776 46453258 - + 0.96677559912854 46462269 46460340 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.864516129032258 0 0.864516129032258 26 1.10697096478857 1.07126222398894 1.10697096478857 1.07126222398894 1 - - 47507 Y Y 3.48276456926791 3.14740237035155 3.14740237035155 256 0 0.682509965959106 Y 0 0.973787006578947 N N 3492 8067 ENSG00000123815 ENSG00000086544 - - 19 19 45914440 45938603 utr5p coding ADCK4 ITPKC 45889274 45914848 - + 0 45912380 45915823 + - N - 0.972909187055288 N HCC1954 1 1 1 0 2 N - - Y SINE - 0.0606060606060606 0 0.0606060606060606 7 0.471355378555133 0.314236919036755 0.471355378555133 0.314236919036755 4 - 0 42084 N Y 3.52783881145811 3.48487056160104 3.48487056160104 15 0 0.0535522177265744 N 0.0024330900243309 0.862404564141287 N N 86504 148 ENSG00000104408 ENSG00000205682 + + 8 4 109330135 61976534 coding utr3p EIF3E AC020741.4 109283149 61968559 - - 0 109321449 61968856 - - Y - - N HCC1954 38 31 25 5 1 N - - N - SINE 0 1 1 5 0.335662163516534 0.528489363834543 0.528489363834543 0.335662163516534 1 - - 41170 N Y 3.22266730405219 3.19872427442695 3.19872427442695 76 0 0.0831063839262196 Y 0 0 N N 6247 7153 ENSG00000125971 ENSG00000078747 - + 20 20 32592422 32562858 coding utr3p DYNLRB1 ITCH 32567865 32414745 + + 0 32577745 32559421 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE - 0.0151515151515152 0 0.0151515151515152 4 0.807017542071667 0.785592297591888 0.807017542071667 0.785592297591888 1 - - 16538 N N 3.60256518892881 3.40016547074969 3.40016547074969 0 0.145763373682156 0.179530908977203 N 0.386177274502148 0.386177274502148 N N 0 453 ENSG00000207623 ENSG00000065320 - + 1 17 207672210 9088042 upstream intron hsa-mir-205 NTN1 207672101 8865584 + + 0 207669147 8900032 - + Y - 0.472194484056773 N HCC1954 20 8.4 2 5 1 N - - N - SINE 0 1 1 5 0.299953422716903 0.5713398527941 0.5713398527941 0.299953422716903 1 - 0 127 Y Y 3.2948728812365 3.16572539038072 3.16572539038072 313 0 0.0944282987265265 Y 0.993264830325533 0.993264830325533 N N 107 0 ENSG00000196763 ENSG00000177848 + + 11 11 71317136 71282913 downstream upstream AP002490.4-1 AP002495.3-1 71306229 71282263 - + 0 71304770 71254550 - + N - - N HCC1954 4 3.25 1 3 2 N - - Y - DNA 0 0.842857142857143 0.842857142857143 4 0.649899082553289 0.707033067832699 0.707033067832699 0.649899082553289 3 - - 48696 N N 2.72029709021333 2.15802245289899 2.15802245289899 0 0.199294117647059 0.380164153967585 N 0.375058823529412 0 N N 5996 4233 ENSG00000187678 ENSG00000119522 + - 5 9 141684750 125732252 utr3p upstream SPRY4 DENND1A 141670189 125181754 - - 0 141671688 125733956 - + Y 1.14614386371356 - N HCC1954 34 31.5 30 4 1 N - - N - Simple_repeat 0 0.918918918918919 0.918918918918919 4 0.407079645115797 0.264244681917271 0.407079645115797 0.264244681917271 1 0 - 71 N N 3.3755202409218 3.61823426992241 3.3755202409218 0 0.112515592515593 0.466180198035523 Y 0.311434511434512 0.342037422037422 N N 0 951 ENSG00000223269 ENSG00000172818 - + 11 11 98496430 65321259 upstream coding 7SK OVOL1 98496116 65311105 + + 0.342037422037422 98342241 65311473 - + N - 1.12715446062792 N HCC1954 1 1 1 0 2 N 108 7.42619 N - - 0 0 0 10 0.771308801272036 1.03555348318931 1.03555348318931 0.771308801272036 3 - 0 31810 Y Y 3.4676111165653 2.92706909254617 2.92706909254617 0 0 0.299459600573778 Y 0.00940540540540535 0 N N 708 14912 ENSG00000012171 ENSG00000114353 - + 3 3 50289574 50271775 utr5p downstream SEMA3B GNAI2 50280044 50248640 + + 0 50280134 50273890 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.464213630395207 0.449930134075354 0.464213630395207 0.449930134075354 1 - - 29784 Y Y 2.88636532132177 3.41529599551336 2.88636532132177 0 0 0.517256138065084 Y 0 0.987982003200773 N N 417 17344 ENSG00000204273 ENSG00000204267 - + 6 6 32892803 32914525 utr5p coding HLA-DOB TAP2 32888530 32897588 - - 0 32892707 32905155 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 8 1.4140661356654 1.04269523134923 1.4140661356654 1.04269523134923 4 - - 35235 N Y 3.44975210485255 3.40744620240479 3.40744620240479 2 0 0.0201479605183468 N 0 0.884007707129094 N N 4691 6543 ENSG00000152253 ENSG00000136021 + + 2 12 169455190 99258043 utr3p intron SPC25 SCYL2 169435648 99185680 - + 0.867437379576108 169435705 99223858 - + Y - 1.05114913408702 N HCC1954 640 600 500 4 1 N - - N LINE LINE 1 1 1 4 0.371370904316165 0.349945659836387 0.371370904316165 0.349945659836387 1 - 0 33043 N Y 3.33105491297843 3.64400585547602 3.33105491297843 474 0.0066871830604267 0.000246868154178070 Y 0 0.990845043161847 N N 336285 544065 ENSG00000198868 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10471 8367 + + 0.990845043161847 10754 9637 - + N 0.851125003249936 1.40694217977442 N HCC1954 2 1.8 1 4 1 Y - - N - - 0 0 0 5 0.807017542071667 0.728458312312478 0.807017542071667 0.728458312312478 1 0 0 517 Y Y 3.5587317031712 3.32696667658884 3.32696667658884 272 0.00367647058823528 0.661800731750967 Y 0.0670788770053475 0.990942513368984 N Y 4055 28586 ENSG00000168000 ENSG00000214753 - + 11 11 62233562 62251397 utr5p intron BSCL2 HNRNPUL2 62214323 62238798 - - 0 62231372 62239548 + - N - 0.476843034244621 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 17 1.18553019454776 0.792734045751814 1.18553019454776 0.792734045751814 4 - 0 34919 Y Y 3.86529765513778 3.64759957832565 3.64759957832565 243 0.00411522633744865 0.0503010224119856 Y 0 0 N N 24 0 ENSG00000165140 ENSG00000204343 - + 9 9 96441624 96519926 coding downstream FBP1 C9orf118 96405244 96458174 - - 0 96422594 96451189 + - N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 5 0.764167053112109 0.649899082553289 0.764167053112109 0.649899082553289 4 - - 25276 N N 3.40740634961144 3.55657227767559 3.40740634961144 0 0 0.293249219763011 N 0 0 N N 0 291864 ENSG00000218901 ENSG00000196230 + + 13 6 40857319 30801182 downstream coding RP11-396A22.4 TUBB 40856909 30796136 - + 0 40856833 30800130 - + Y - 1.49430125041368 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.378512652476092 0.685607823352921 0.685607823352921 0.378512652476092 1 - 0 33052 N Y 2.82917163539494 3.49424793801946 2.82917163539494 15 0 0.468626105061007 Y 0 0.962410413924236 N N 544065 0 ENSG00000198744 ENSG00000210144 - - MT MT 9988 5892 coding upstream MT-CO3 AF347015.1-13 8367 5827 + - 0 8481 5895 - + N 0.655982901569647 - N HCC1954 9 5.28571428571429 2 7 1 N - - N - - 0 0 0 7 0.87843502367093 0.907002016310634 0.907002016310634 0.87843502367093 1 0 - 36542 Y Y 3.40062947906611 3.26460248413936 3.26460248413936 0 0 0.816308132547384 Y 0.912766768292683 0.993769054878049 N N 16017 12 ENSG00000018236 ENSG00000205592 - + 12 12 39750361 39250827 utr5p downstream CNTN1 MUC19 39588423 39222629 + + 0 39588427 39372662 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 361 1.1426797055882 1.24266417982717 1.24266417982717 1.1426797055882 1 - - 44794 Y Y 3.61464054707278 3.45447218342791 3.45447218342791 373 0 0.000828611055050277 Y 0.190146949142293 0.992501360640206 N N 104 1442 ENSG00000065621 ENSG00000148834 - + 10 10 106049166 106017201 upstream upstream GSTO2 GSTO1 106018621 106004651 + + 0 106018302 105998341 - + N - - N HCC1954 1 1 1 0 1 N - - Y DNA DNA 0.708542713567839 1 1 5 0.835584534711372 0.528489363834543 0.835584534711372 0.528489363834543 1 - - 27228 Y Y 3.38440310380026 3.1897786308162 3.1897786308162 24 0.0619957537154988 0.201277095656911 Y 0.0719745222929936 0.940127388535032 N N 17449 23840 ENSG00000038358 ENSG00000102898 - + 16 16 66475899 66462727 coding coding EDC4 NUTF2 66464456 66438331 + + 0 66464671 66459959 - + N - 0.958750983916778 N HCC1954 2 1.42857142857143 1 3 1 N - - Y - - 0 0 0 7 1.26408942430695 0.928427260790413 1.26408942430695 0.928427260790413 3 - 0 7704 N Y 3.47233119514066 3.37126417066287 3.37126417066287 2 0 0.111192161144199 N 0 0.913549039433772 N N 20739 82 ENSG00000143951 ENSG00000137561 - - 2 8 63669355 64161152 utr3p intron C2orf86 TTPA 63202041 64134926 - - 0.899140546006067 63309485 64156048 + + Y - 1.17075653177344 N HCC1954 620 540 420 4 1 N - - N LINE LINE 1 1 1 4 0.407079645115797 0.378512652476092 0.407079645115797 0.378512652476092 4 - 0 23233 N N 3.12023634023727 3.52105259334297 3.12023634023727 200 0.143932748538011 0.008684775165416 N 0.213815789473684 0.126461988304093 N N 34 0 ENSG00000107611 ENSG00000217333 + - 10 1 17211822 169680726 intron upstream CUBN RP1-81F6.1 16905971 169680447 - - 0.563230994152047 16966125 169691434 - + Y 1.51241768025223 - N HCC1954 154 85.25 20 4 1 N 426 23.9048 N SINE SINE 1 0.923076923076923 1 4 0.278528178237124 0.278528178237124 0.278528178237124 0.278528178237124 1 0 - 47164 Y Y 3.25360004855864 3.34252135687557 3.25360004855864 339 0 0.0497953064852681 Y 0.842889067667829 0.993957271833378 N N 6 14186 ENSG00000213052 ENSG00000171570 + + 19 19 46048180 46006176 downstream coding CYP2A6 EGLN2 46041284 45996959 - + 0 46024307 45999158 - + N - - N HCC1954 2 1.74166666666667 1 89 3 N - - Y - - 0 0 0 120 1.28551466878673 1.24980592798709 1.28551466878673 1.24980592798709 1 - - 26512 N N 3.65488030998075 3.48809356209009 3.48809356209009 9 0 0.0524841214989307 N 0 0.00358422939068093 N N 2576 45068 ENSG00000197563 ENSG00000205336 - + 18 16 58005269 56256445 intron upstream PIGN GPR56 57862440 56220023 - + 0.00358422939068093 57903237 56211646 + + Y 0.475137202130105 - N HCC1954 25 23.3333333333333 21 6 1 N - - N SINE - 1 0 1 6 0.299953422716903 0.335662163516534 0.335662163516534 0.299953422716903 1 0 - 43428 N Y 3.44975210485255 3.40744620240479 3.40744620240479 1 0 0.016538017828304 N 0 0.90530612244898 N N 4691 0 ENSG00000152253 ENSG00000217698 + + 2 10 169455190 19269888 utr3p downstream SPC25 RP11-288D15.1 169435648 19269436 - + 0 169435705 19301620 - + Y - - N HCC1954 640 595 500 4 1 N - - N LINE LINE 1 1 1 4 0.385654400636018 0.278528178237124 0.385654400636018 0.278528178237124 1 - - 29976 N Y 3.47911741325579 3.67849247003875 3.47911741325579 251 0 0.0390124312011886 N 0.927120785152075 0.914974249344087 N N 165508 0 ENSG00000196262 ENSG00000214975 - + 7 6 44807754 25085188 intron intron PPIA AL160400.20-1 44802805 25084626 + + 0.914974249344087 44804939 25084761 - + Y 1.06624172269141 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.742741808632331 0.685607823352921 0.742741808632331 0.685607823352921 3 0 0 14340 N Y 3.54296933622177 3.52105259334297 3.52105259334297 0 0 0.0825101197529308 N 0.777526595744681 0 N N 2923 14402 ENSG00000169403 ENSG00000156689 - - 1 11 28392971 58368833 utr3p utr5p PTAFR GLYATL2 28348451 58358118 - - 0 28348592 58368484 + + Y - - N HCC1954 36 35.4285714285714 34 7 1 N - - N SINE - 1 0 1 7 0.314236919036755 0.721316564152552 0.721316564152552 0.314236919036755 1 - - 33076 N Y 2.87060295437234 3.50785087947327 2.87060295437234 318 0 0.253444853056019 Y 0 0.941361450240474 N N 339915 544065 ENSG00000198727 ENSG00000198744 - + MT MT 15882 9988 coding coding MT-CYB MT-CO3 14748 8367 + + 0.0837726600073991 14764 9195 - + N 0.343791605542793 0.52510626929365 N HCC1954 2 1.5 1 2 5 N - - N - - 0 0 0 4 0.621332089913584 0.5713398527941 0.621332089913584 0.5713398527941 1 0 0 9377 Y Y 3.39231567764112 3.15575602456989 3.15575602456989 307 0 0.0110680523197201 Y 0.648208469055375 0.991624011167985 N N 808 547 ENSG00000141337 ENSG00000108932 - - 17 17 63930467 63799002 upstream upstream ARSG SLC16A6 63814772 63775933 + - 0 63814680 63799305 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 1.14982145374813 0.907002016310634 1.14982145374813 0.907002016310634 1 - - 18838 N N 3.46551447180198 3.49594335519865 3.46551447180198 0 0 0.974564783165946 N 0 0 Y N 11287 0 ENSG00000178104 ENSG00000213223 + + 1 1 143787552 147820286 intron downstream PDE4DIP AL451058.16-1 143562784 147819627 - + 0 143687072 147843324 - + N 60.8384791381689 - N HCC1954 10 10 10 8 2 N - - N - - 0 0 0 8 1.07126222398894 0.985561246069823 1.07126222398894 0.985561246069823 4 0 - 14846 N N 3.61360747730288 3.32912610208445 3.32912610208445 0 0 0.0456997829958169 N 0 0 N N 49089 3346 ENSG00000117450 ENSG00000149311 - - 1 11 45760196 107745036 coding intron PRDX1 ATM 45749295 107598769 - + 0 45757256 107608874 + - Y - 0.57612554538352 N HCC1954 14 4.67857142857143 2 28 1 N - - N - SINE,SINE 0 1 1 28 0.821301038391519 0.357087407996313 0.821301038391519 0.357087407996313 1 - 0 340 N Y 3.14996302343129 3.09715338883939 3.09715338883939 282 0 0.489629675754841 Y 0.876408818516686 0.992275551157293 N N 0 9074 ENSG00000202276 ENSG00000166444 + - 11 11 8855641 8817478 downstream intron Y_RNA ST5 8855540 8671478 - - 0 8849076 8809810 - + N - 5.36028008162191 N HCC1954 4 1.21428571428571 1 1 5 N - - N - SINE 0 0.752 0.752 14 1.08554572030879 0.892718519990782 1.08554572030879 0.892718519990782 1 - 0 27881 N N 3.54552998930151 3.448886868952 3.448886868952 11 0 0.0325916330030661 N 0.811465444683438 0 N N 1294 0 ENSG00000144681 ENSG00000221481 + + 3 16 36564500 26565771 coding downstream STAC AC002331.1 36397101 26565700 + + 0 36460135 26754411 + + Y 1.36990340242264 - N HCC1954 22 20.2 17 5 1 N 273 27.7624 N - LTR 0 1 1 5 0.471355378555133 0.45707188223528 0.471355378555133 0.45707188223528 1 0 - 26533 N Y 3.448886868952 3.44768596531277 3.44768596531277 0 0 0.482050939208486 N 0.974132863021752 0.948265726043504 N N 21380 6304 ENSG00000185164 ENSG00000196696 + + 16 16 18480999 68657352 downstream coding NOMO2 PDXDC2 18418684 68567713 - - 0 18409455 68602158 - - N - 0.448921633734258 Y HCC1954 8 5.94444444444444 3 18 1 N 56 14.0678 N LINE - 1 0 1 18 1.07126222398894 0.5713398527941 1.07126222398894 0.5713398527941 2 - 0 19249 Y Y 3.58999531724489 3.14424972787939 3.14424972787939 0 0.00352112676056349 0.193296250132568 Y 0.302464788732395 0 N N 8380 14630 ENSG00000186141 ENSG00000131788 + + 1 1 144322294 144297903 coding coding POLR3C PIAS3 144303963 144287345 - + 0 144304115 144296864 - + N 0.427753440709132 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.885576771830856 0.592765097273879 0.885576771830856 0.592765097273879 1 0 - 9633 Y Y 3.56807857436608 3.66016945000958 3.56807857436608 269 0 0.0302038406029503 Y 0.989512815495989 0.989512815495989 N N 31 45264 ENSG00000204815 ENSG00000131473 - - 17 17 37371174 37328798 upstream intron TTC25 ACLY 37340424 37276696 + - 0 37340138 37323680 - + N - 1.24512750537255 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.849868031031224 0.678466075192994 0.849868031031224 0.678466075192994 1 - 0 47014 Y Y 3.41103992525442 3.61889661733171 3.41103992525442 181 0 0.0151055709301939 Y 0 0 N N 7167 13250 ENSG00000126456 ENSG00000126461 + + 19 19 54860926 54853710 intron coding IRF3 SCAF1 54854642 54837194 - + 0 54855754 54852956 - + N 0.962304419391095 0.99302297650957 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.5713398527941 0.642757334393363 0.642757334393363 0.5713398527941 2 0 0 18163 N Y 3.49168728493972 3.33461813060452 3.33461813060452 0 0 0.969306689697693 N 0 0 Y N 10857 14045 ENSG00000085832 ENSG00000117859 + + 1 1 51757583 52026729 intron intron EPS15 OSBPL9 51592523 51815439 - + 0 51684828 51907878 - + N 1.60195515387961 0.59938350194942 N HCC1954 21 6.58333333333333 1 10 4 N - - N SINE - 1 0 1 12 0.499922371194838 0.578481600954027 0.578481600954027 0.499922371194838 3 0 0 16349 N N 3.25256697878875 3.50848272165904 3.25256697878875 0 0 0.074893101167779 N 0 0 N N 49089 6863 ENSG00000117450 ENSG00000068724 - - 1 2 45760196 47156780 coding intron PRDX1 TTC7A 45749295 46996800 - + 0 45757275 47050700 + - Y - 0.526115286317017 N HCC1954 16 3.44 1 22 1 N - - N - SINE 0 1 1 25 0.735600060472404 0.264244681917271 0.735600060472404 0.264244681917271 2 - 0 42346 Y Y 2.81999259806941 3.66169703331943 2.81999259806941 222 0 0.199770929507661 Y 0 0.98557252905079 N N 1615 108 ENSG00000156219 ENSG00000169248 - - 4 4 77252964 77176376 upstream upstream ART3 CXCL11 77214887 77173975 + - 0 77198770 77194452 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.364229156156239 0.885576771830856 0.885576771830856 0.364229156156239 1 - - 39882 Y Y 3.5920919620082 3.5465630590714 3.5465630590714 243 0 0.00150902406671394 Y 0.976839888984592 0.988419944492296 N N 100 7152 ENSG00000169330 ENSG00000166557 - + 15 15 77551687 77402237 upstream coding KIAA1024 TMED3 77511913 77390540 + + 0 77490800 77393328 - + N - 1.11202214546203 N HCC1954 1 1 1 0 1 N - - Y LINE - 0.824242424242424 0 0.824242424242424 7 1.08554572030879 0.971277749749971 1.08554572030879 0.971277749749971 1 - 0 26282 N N 3.49528100778935 3.72824693801095 3.49528100778935 0 0 0.173787404357273 N 0.76760374832664 0.759303882195448 N N 261 59171 ENSG00000161664 ENSG00000189091 - + 17 16 39611977 69163701 utr3p utr5p ASB16 SF3B3 39603600 69115202 + + 0 39611550 69115331 - + Y - 0.931108794735079 N HCC1954 27 22.5 21 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.335662163516534 0.335662163516534 0.28566992639705 1 - 0 46921 Y Y 3.04540039749943 3.30803474231284 3.04540039749943 0 0 0.251997449336927 Y 0 0.363809523809524 N N 18 2053 ENSG00000214212 ENSG00000099203 - - 19 19 10841043 10807983 coding upstream C19orf38 TMED1 10820160 10804115 + - 0.363809523809524 10820199 10808376 - + N 0.583291139240506 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.592765097273879 0.707033067832699 0.707033067832699 0.592765097273879 3 0 - 43459 N N 3.30438758630073 3.63296356710195 3.30438758630073 0 0 0.0765684197403934 N 0 0 N N 3320 1992 ENSG00000136770 ENSG00000003436 + - 10 2 22332704 188127464 intron intron DNAJC1 TFPI 22085484 188037202 - - 0 22165915 188120722 - + Y 1.02493253913973 11.2383441972674 N HCC1954 4 3.5 3 4 1 N - - N Other - 1 0 1 4 0.278528178237124 0.714174815992626 0.714174815992626 0.278528178237124 2 0 0 31215 Y Y 3.61360747730289 3.36464578641707 3.36464578641707 247 0 0.170495875912559 Y 0.045983379501385 0.989516300873642 N N 409 7741 ENSG00000154917 ENSG00000144867 + + 3 3 135097381 135022213 utr3p utr3p RAB6B SRPRB 135025769 135007355 - + 0 135026924 135021352 - + N 0.575397362658862 3.12512809092173 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.914143764470561 0.678466075192994 0.914143764470561 0.678466075192994 2 0 0 43117 N N 3.12747721909902 3.51104337473878 3.12747721909902 0 0 0.0829710700843108 N 0.0392571058080438 0 N N 551733 273 ENSG00000204628 ENSG00000173320 + + 5 4 180603512 185175835 utr3p intron GNB2L1 STOX2 180596536 185063503 - + 0 180596544 185066846 - + Y - 0.128088815477243 N HCC1954 22 16.8 1 4 1 N - - N - Simple_repeat 0 0.4 0.4 5 0.521347615674617 0.357087407996313 0.521347615674617 0.357087407996313 2 - 0 41672 Y Y 3.6052936758779 3.69255941980899 3.6052936758779 0 0 0.99956631953803 Y 0.132671755725191 0.984783715012723 N N 3297 2237 ENSG00000104613 ENSG00000147408 - - 8 8 19753864 19584374 upstream utr5p INTS10 CSGALNACT1 19719198 19305952 + - 0 19659641 19503656 - + N - 32.3462799146343 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 7 0.907002016310634 0.792734045751814 0.907002016310634 0.792734045751814 4 - 0 18111 Y Y 3.28399842673177 3.66951632120446 3.28399842673177 297 0 0.41816781589289 Y 0 0 N N 24302 2003 ENSG00000198952 ENSG00000160781 + - 1 1 154519240 154484471 utr3p intron SMG5 PAQR6 154485641 154479831 - - 0 154485986 154483173 - + N 0.500134081063535 17.3407765253176 N HCC1954 2 1.02777777777778 1 1 4 N - - Y - - 0 0 0 36 1.18553019454776 0.621332089913584 1.18553019454776 0.621332089913584 1 0 0 9760 Y Y 3.48912663185998 3.27551679143744 3.27551679143744 0 0 0.289855485818438 Y 0.992563225538972 0.992563225538972 N N 26 28437 ENSG00000108950 ENSG00000108946 + + 17 17 64109125 64040503 intron coding FAM20A PRKAR1A 64044607 64019705 - + 0 64058822 64038014 - + N 1.98998587273438 - N HCC1954 2 1.23076923076923 1 3 1 N - - Y DNA - 0.590604026845638 0 0.590604026845638 13 1.06412047582901 0.849868031031224 1.06412047582901 0.849868031031224 2 0 - 17077 N Y 3.44313372060675 3.6035982586987 3.44313372060675 1 0 0.0722400442196471 N 0.796999117387467 0.777665699995797 N N 3735 2251 ENSG00000087995 ENSG00000186275 + + 17 1 57881186 143541658 intron upstream METTL2A NBPF8 57854996 143326471 + + 0 57867333 143310135 + + Y 1.45267245502177 - N HCC1954 40 36 20 5 1 N - - N SINE - 1 0 1 5 0.34280391167646 0.435646637755502 0.435646637755502 0.34280391167646 1 0 - 41481 Y Y 3.09868097214924 3.35400472562712 3.09868097214924 116 0 0.0377405836190776 Y 0.617362371445856 0.982607380520266 N N 0 23415 ENSG00000212451 ENSG00000168672 - - 8 8 127753081 127639648 upstream intron U11 FAM84B 127752949 127633871 + - 0 127698858 127639349 - + N - 2.857429555871 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.678466075192994 0.357087407996313 0.678466075192994 0.357087407996313 1 - 0 7760 N N 3.42208221362849 3.75016368088976 3.42208221362849 0 0 0.757473995766104 N 0.00271002710027102 0 N N 19339 0 ENSG00000177570 ENSG00000208291 + + 8 2 119703365 140456957 coding upstream SAMD12 AC078851.4-1 119270880 140456723 - + 0 119460977 140432327 - + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 29 1.61403508414333 1.0069864905496 1.61403508414333 1.0069864905496 1 - - 17469 Y Y 3.38127338926705 3.5963175270436 3.38127338926705 295 0 0.0288881251871952 Y 0.992617702448211 0.992617702448211 N N 118 118 ENSG00000174827 ENSG00000117281 - - 1 1 144475431 144426971 utr5p upstream PDZK1 CD160 144454620 144407155 + - 0 144454689 144439104 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.0598802395209581 0 0.0598802395209581 6 0.956994253430118 0.928427260790413 0.956994253430118 0.928427260790413 2 - - 41849 Y Y 3.57592836747465 3.18508148017979 3.18508148017979 0 0 0.733550266880564 Y 0.930110991765127 0.982527747941282 N N 7576 0 ENSG00000147526 ENSG00000207258 - + 8 8 38829702 38720806 coding upstream TACC1 Y_RNA 38734008 38720695 + + 0 38765379 38719126 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.5713398527941 0.442788385915428 0.5713398527941 0.442788385915428 4 - - 38780 N Y 3.45889608755619 3.377215658101 3.377215658101 7 0 0.161960019929629 N 0.218054143952694 0.886491730573778 N N 0 11666 ENSG00000222639 ENSG00000117877 - + 14 19 49123344 50605864 intron utr3p SRP_euk_arch CD3EAP 49123048 50601307 + + 0 49123078 50605105 - + Y 1 - N HCC1954 266 201 135 4 1 N - - N srpRNA SINE 1 1 1 4 0.499922371194838 0.478497126715059 0.499922371194838 0.478497126715059 2 0 - 2414 N Y 3.55653242488223 3.37192651807217 3.37192651807217 273 0 0.00412666272655371 N 0.983799398433545 0.991899699216772 N N 0 3567 ENSG00000219468 ENSG00000177951 - + 9 11 140250262 197428 upstream coding RP11-885N19.5 BET1L 140249980 157784 + - 0.975699097650317 140244729 170210 - - Y - 2.65430538639016 N HCC1954 15 12.75 12 4 1 N - - N LTR - 1 0 1 4 0.314236919036755 0.821301038391519 0.821301038391519 0.314236919036755 1 - 0 4657 Y Y 3.45823374014688 3.34256120966892 3.34256120966892 0 0 0.464705811462323 Y 0 0.993607649333906 N N 12632 996 ENSG00000146963 ENSG00000164898 - + 7 7 138758738 138681605 coding coding LUC7L2 C7orf55 138695174 138676614 + + 0 138711348 138680977 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.928427260790413 0.842726282871298 0.928427260790413 0.842726282871298 3 - - 31049 N N 3.57233464462502 2.5 2.5 0 0 0.0538252693657353 N 0 0 N N 123944 0 ENSG00000174748 ENSG00000207041 - + 3 X 23937334 140039987 coding intron RPL15 U6 23933643 140039881 + - 0 23935866 140039978 - - Y - 1 N HCC1954 120 75 20 4 1 N - - N - snRNA 0 1 1 4 0.714174815992626 0.392796148795944 0.714174815992626 0.392796148795944 2 - 0 47976 N N 3.15212244892691 3.12747721909902 3.12747721909902 0 0 0.0684272838214912 N 0.0251643618227159 0 N N 3661 551733 ENSG00000170873 ENSG00000204628 + + 8 5 125809911 180603512 intron utr3p MTSS1 GNB2L1 125632212 180596536 - - 0 125798303 180596544 - - Y 1.28497319928059 - N HCC1954 19 15.8333333333333 8 6 1 N - - N LINE - 1 0 1 6 0.271386430077198 0.471355378555133 0.471355378555133 0.271386430077198 2 0 - 7458 N Y 3.51104337473878 3.5001290674407 3.5001290674407 0 0 0.327816651597054 Y 0 0.901426265974615 N N 1992 757 ENSG00000003436 ENSG00000144426 - - 2 2 188127464 203790962 utr5p intron TFPI NBEAL1 188037202 203708718 - + 0.901426265974615 188127365 203779438 + - N - 1.6561431847391 N HCC1954 21 20.1176470588235 20 17 1 N 223 27.7742 N - Other 0 1 1 17 0.871293275511003 0.614190341753658 0.871293275511003 0.614190341753658 2 - 0 31064 N Y 3.25993583872649 3.52936639476796 3.25993583872649 0 0 0.434919226908521 N 0.506301957629391 0.806047197640118 N N 18437 0 ENSG00000163932 ENSG00000204594 - + 3 X 53201771 135717702 utr5p downstream PRKCD RP11-1114A5.3 53170263 135717090 + - 0.806047197640118 53174271 135711191 - - Y - - N HCC1954 20 20 20 8 1 N - - N - SINE 0 1 1 8 0.699891319672773 0.307095170876829 0.699891319672773 0.307095170876829 1 - - 30299 Y Y 3.46448140203209 3.38552945952599 3.38552945952599 299 0 0.989247926520326 Y 0 0.98523473306082 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 upstream upstream STS HDHD1A 7147472 6976961 + - 0 7118921 7088094 - + N - - N HCC1954 2 1.0625 1 1 5 N - - Y - - 0 0 0 16 0.921285512630487 1.22123893534739 1.22123893534739 0.921285512630487 4 - - 2114 N Y 3.54040868314203 3.22536109588112 3.22536109588112 0 0 0.818963330334811 N 0.878532713898567 0.854239256678281 N N 0 99790 ENSG00000216280 ENSG00000186676 - + X 11 114844696 62106622 intron intron RP1-241P17.3 EEF1G 114843387 62083651 + - 0.854239256678281 114843399 62097879 - - Y 1 28.5706997546715 N HCC1954 2 1.875 1 7 1 N - - N - - 0 0 0 8 0.299953422716903 0.39993789695587 0.39993789695587 0.299953422716903 3 0 0 10131 Y Y 3.77001428422878 3.63080414160633 3.63080414160633 0 0 0.859852104116961 Y 0 0 N Y 38 6057 ENSG00000108878 ENSG00000075461 - + 17 17 62483375 62459980 coding coding CACNG1 CACNG4 62471168 62391475 + + 0 62480574 62451578 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.964136001590045 0.928427260790413 0.964136001590045 0.928427260790413 4 - - 46362 N N 2.8591365104752 1.47517170608791 1.47517170608791 0 0 0.0945587593017512 N 0.0176120002678632 0.0176120002678632 N N 122595 0 ENSG00000130402 ENSG00000206951 - - 19 2 43913010 33024022 utr5p downstream ACTN4 Y_RNA 43830167 33023910 + - 0.0176120002678632 43830167 32994931 - + Y 0.000429062257660811 - N HCC1954 2 1.8 1 4 1 N 59 13.796 N - Simple_repeat 0 1 1 5 0.814159290231593 0.614190341753658 0.814159290231593 0.614190341753658 1 0 - 42655 N Y 3.48639814491089 3.24471718568018 3.24471718568018 236 0.0042372881355931 0.0042452579175184 N 0.601694915254237 0.203389830508475 N N 0 13 ENSG00000216027 ENSG00000010671 - - 4 X 61212351 100527838 downstream intron AC095061.3 BTK 61212262 100491091 - - 0.818952234206471 60902269 100493684 + + Y - 0.808423737019031 N HCC1954 147 47.6 20 15 1 N - - N SINE,SINE SINE 0.853658536585366 1 1 15 0.292811674556976 0.307095170876829 0.307095170876829 0.292811674556976 1 - 0 32475 N N 3.5016965035439 3.3755202409218 3.3755202409218 8 0 0.351125908392357 N 0.610594405594406 0.0310139860139861 N N 3297 2525 ENSG00000174840 ENSG00000156170 - + 3 8 57522721 96140114 utr3p coding PDE12 C8orf38 57517044 95977217 + + 0.0310139860139861 57521117 96123030 - + Y - - N HCC1954 23 22.25 21 4 1 N - - N SINE - 1 0 1 4 0.292811674556976 0.621332089913584 0.621332089913584 0.292811674556976 3 - - 30391 Y Y 3.30694823938047 3.55401162459584 3.30694823938047 238 0 0.0589804823407698 Y 0.991264927023441 0.991264927023441 N N 51 1011 ENSG00000205662 ENSG00000205663 + - X X 3848751 3810322 downstream upstream BX890604.9-2 BX890604.9-1 3834245 3792439 - - 0 3826955 3821394 - + N - - N HCC1954 9 7.8 3 5 2 N - - Y LTR - 1 0 1 5 0.557056356474248 0.478497126715059 0.557056356474248 0.478497126715059 2 - - 37918 N Y 3.45976132345673 3.6769648867289 3.45976132345673 1 0 0.22247493210395 N 0 0 N N 4657 190 ENSG00000198252 ENSG00000158352 - + 14 X 52311409 50573784 coding utr3p STYX SHROOM4 52266675 50351387 + - 0 52266999 50351659 - - Y - - N HCC1954 37 28.2 2 5 1 N 587 22.9636 N - SINE 0 1 1 5 0.407079645115797 0.371370904316165 0.407079645115797 0.371370904316165 1 - - 6727 Y Y 3.60888739872753 3.50678730447985 3.50678730447985 298 0 0.0522530281289366 Y 0.991897200851203 0.983794401702406 N N 719 7532 ENSG00000189362 ENSG00000151690 + + 2 2 191107693 191075286 coding intron TMEM194B MFSD6 191077313 190981326 - + 0 191083332 191028542 - + N - 1.49873317046851 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.74251497005988 0.74251497005988 12 0.757025304952183 1.19267194270768 1.19267194270768 0.757025304952183 4 - 0 45889 N N 3.57800808738356 3.2499266201223 3.2499266201223 12 0 0.373704588460697 N 0 0 N N 17943 3 ENSG00000105141 ENSG00000146555 + + 19 7 15027900 4275158 downstream intron CASP14 SDK1 15024015 3307606 + + 0.0217068093963722 15029502 3838203 + + Y - 0.978694022489643 N HCC1954 14 8.71428571428571 1 39 1 N - - N SINE SINE,Low_complexity 0.201550387596899 0.82051282051282 0.82051282051282 42 0.914143764470561 0.278528178237124 0.914143764470561 0.278528178237124 3 - 0 34121 N Y 3.4561676006071 3.63080414160633 3.4561676006071 0 0 0.876985849981025 N 0.922504025764895 0.922504025764895 N N 0 111 ENSG00000216662 ENSG00000188152 + - 9 9 96140843 98744393 upstream intron RP11-307E17.9 FAM22G 96140453 98721960 - + 0 96140939 98735898 - - N - 1.24438055773419 Y HCC1954 8 3.66666666666667 2 6 1 N - - N - SINE 0 0.0233918128654971 0.0233918128654971 6 0.464213630395207 0.964136001590045 0.964136001590045 0.464213630395207 4 - 0 5251 N N 3.5246463161926 3.63552422018169 3.5246463161926 0 0.0285254198297676 0.0357948106593666 N 0.289164941338855 0.0285254198297676 N N 0 0 ENSG00000216897 ENSG00000196205 + + 7 9 20589354 134886082 intron intron AC007095.2 AL593851.6-1 20588220 134884659 + + 0.0285254198297676 20588883 134885580 + + Y 1 1 N HCC1954 10 8 6 5 1 N - - N - - 0 0 0 5 0.22853594111764 0.364229156156239 0.364229156156239 0.22853594111764 0 0 0 13612 Y Y 3.18296190747752 3.48167806633553 3.18296190747752 375 0 0.0218883328634200 Y 0.994268199233716 0.994268199233716 N N 238 110 ENSG00000211643 ENSG00000198312 - + 22 22 21003581 20993088 coding downstream IGLV5-52 D87018.1-3 21003021 20991471 + + 0 21003256 20994768 - + N 0.0508770010575065 - N HCC1954 14 3.82666666666667 1 71 2 N - - Y - - 0 0 0 150 1.49976711358451 1.2783729206268 1.49976711358451 1.2783729206268 1 0 - 17462 N Y 3.53871326596283 3.65488030998075 3.53871326596283 1 0 0.239509019209109 N 0.585040983606557 0.986168032786885 N N 1186 1403 ENSG00000137968 ENSG00000171735 - + 1 1 75849389 7752350 coding intron SLC44A5 CAMTA1 75440404 6767971 - + 0 75634856 7400223 + + N - 8.99300975463692 Y HCC1954 24 19.4444444444444 6 9 1 N - - N - LINE 0 1 1 9 0.921285512630487 0.51420586751469 0.921285512630487 0.51420586751469 2 - 0 26772 Y Y 3.64809409186561 3.69359248957888 3.64809409186561 300 0 0.78893552187329 Y 0 0 N N 0 0 ENSG00000209496 ENSG00000209495 + - 16 16 3161032 3142681 upstream upstream AJ003147.1-1 AC108134.3-1 3160962 3142610 - - 0 3164066 3151306 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.735600060472404 0.749883556792257 0.749883556792257 0.735600060472404 4 - - 6444 Y Y 3.10806769613747 3.59528445727371 3.10806769613747 0 0 0.623453149503376 Y 0.14691850525116 0.988471871692583 N N 6252 0 ENSG00000179833 ENSG00000223130 - - 2 2 64734550 64898312 utr5p upstream SERTAD2 SRP_euk_arch 64712260 64898016 - + 0 64734258 64830920 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 28 1.22838068350732 1.36407389854591 1.36407389854591 1.22838068350732 2 - - 33109 N Y 3.51935717616377 3.44871903508266 3.44871903508266 441 0 0.152435819585585 Y 0 0.995036157083065 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0.995036157083065 8552 6619 - + N 0.673386205156865 1.06334427338524 N HCC1954 2 1.5 1 3 5 N - - N - - 0 0 0 6 0.985561246069823 1.21409718718746 1.21409718718746 0.985561246069823 2 0 0 47022 Y Y 3.36870351758313 3.30128837699106 3.30128837699106 322 0 0.839832344850651 Y 0 0 N N 675 793 ENSG00000179922 ENSG00000171443 + + 19 19 60827753 60806316 downstream downstream ZNF784 ZNF524 60823919 60803542 - + 0 60816771 60806894 - + N - - N HCC1954 1 1 1 0 4 N - - Y Simple_repeat - 0.285714285714286 0 0.285714285714286 7 0.978419497909897 0.921285512630487 0.978419497909897 0.921285512630487 4 - - 45247 N Y 3.14376879470857 3.71617157986699 3.14376879470857 49 0.0380802277695867 0.177390151485872 N 0.0716355686613452 0.899333977324724 N N 0 1060 ENSG00000177051 ENSG00000196233 + + 19 10 50906933 98708680 upstream intron FBXO46 LCOR 50906323 98582029 - + 0.161116477706035 50925948 98584874 - + Y - 0.825604177214828 N HCC1954 21 20.25 20 4 1 N - - N - SINE 0 1 1 4 0.735600060472404 0.371370904316165 0.735600060472404 0.371370904316165 1 - 0 41630 N Y 3.56232542602083 3.40591861909494 3.40591861909494 0 0 0.38083087788865 Y 0 0.0557593543653705 N N 0 7529 ENSG00000176571 ENSG00000185900 - + 8 8 88435220 43097480 intron downstream CNBD1 AC113191.13-2 87947840 43067818 + + 0 88032784 43098565 - + N 1 - N HCC1954 22 8.6 3 5 1 N - - N SINE LINE,SINE 1 0.734939759036145 1 5 0.264244681917271 0.592765097273879 0.592765097273879 0.264244681917271 2 0 - 47489 Y Y 3.45872825368684 3.27551679143744 3.27551679143744 0 0 0.291167849209160 Y 0 0.989740285487708 N N 18477 0 ENSG00000099797 ENSG00000207707 - + 19 19 14537791 14501452 coding upstream GPSN2 hsa-mir-639 14501382 14501355 + + 0 14534339 14499636 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.592765097273879 0.649899082553289 0.649899082553289 0.592765097273879 1 - - 5610 N N 3.2843996543159 3.62039369541802 3.2843996543159 16 0 0.121603267668378 N 0 0.0609304784562515 N N 2978 0 ENSG00000021574 ENSG00000182707 - + 2 X 32236209 73013524 intron downstream SPAST FXYD8 32142184 73011598 + + 0.0609304784562515 32225860 73081025 - + Y 1.68623075076857 - N HCC1954 24 18.8333333333333 9 6 1 N 178 18.2146 N SINE - 1 0 1 6 0.299953422716903 0.557056356474248 0.557056356474248 0.299953422716903 3 0 - 35764 N N 3.56232542602083 3.49065421516983 3.49065421516983 100 0.641381390438848 0.0219983359053560 N 0.650128185793998 0.632634595083698 N N 234233 15670 ENSG00000150991 ENSG00000102910 + + 12 16 123965530 46944908 coding intron UBC LONP2 123962147 46835712 - + 0.632634595083698 123962429 46926135 - + Y 0.357720857771575 1.63580644390784 N HCC1954 5 2.875 2 8 1 N - - N - - 0 0 0 8 1.1426797055882 0.378512652476092 1.1426797055882 0.378512652476092 2 0 0 38760 N Y 3.50848272165904 3.49272035470961 3.49272035470961 0 0 0.113530399662102 N 0.00358422939068104 0.870032725572698 N N 2963 0 ENSG00000133983 ENSG00000213464 + - 14 4 69896147 126824034 coding upstream COX16 AC093589.3 69680762 126821786 - - 0 69879130 126856316 - + Y - - N HCC1954 20 16.5 14 4 1 N - - N - SINE 0 1 1 4 0.378512652476092 0.28566992639705 0.378512652476092 0.28566992639705 2 - - 4102 Y Y 3.41319935075004 3.36716658670346 3.36716658670346 303 0 0.0321704965472922 Y 0 0.987541254125412 N N 0 524 ENSG00000203446 ENSG00000218609 + + 7 7 65814279 65743252 upstream downstream AC027644.9 KCTD7 65814003 65731380 - + 0 65814448 65757034 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE - 1 0 1 4 0.407079645115797 0.528489363834543 0.528489363834543 0.407079645115797 1 - - 41822 Y Y 3.21484801616716 3.60256518892881 3.21484801616716 9 0.021881496881497 0.836764334780111 Y 0.987214137214137 0.974428274428274 N N 2650 3685 ENSG00000104231 ENSG00000164695 - - 8 8 82796090 82834305 coding upstream ZFAND1 CHMP4C 82776513 82807243 - + 0 82793014 82806989 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 44 1.57118459518378 1.1426797055882 1.57118459518378 1.1426797055882 4 - - 9628 Y Y 3.63721963736088 3.26356941436947 3.26356941436947 389 0 0.951391960907413 N 0 0.990409333596994 Y N 317991 1482 ENSG00000171346 ENSG00000171345 + - 17 17 36932191 36938167 upstream utr5p KRT15 KRT19 36923523 36933396 - - 0 36942288 36938108 - + N - 31.2361134255402 N HCC1954 1 1 1 0 8 N - - N LINE - 0.879032258064516 0 0.879032258064516 5 0.828442786551446 0.592765097273879 0.828442786551446 0.592765097273879 3 - 0 47313 Y Y 3.60000453584907 3.15848451151898 3.15848451151898 0 0 0.997662403162663 Y 0.986375018412137 0.986375018412137 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 coding upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10597344 10574234 - + N - - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.0208333333333333 0.0208333333333333 8 0.421363141435649 0.685607823352921 0.685607823352921 0.421363141435649 3 - - 29593 Y Y 3.04955834636281 3.60169995302827 3.04955834636281 104 0.0595744680851065 0.289759123522475 Y 0.0595744680851065 0.990780141843972 N N 4273 21550 ENSG00000180992 ENSG00000137216 - - 6 6 44203169 44231234 utr5p intron MRPL14 TMEM63B 44189353 44203354 - + 0 44192343 44204379 + - N - 0.157725121879989 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.771308801272036 0.707033067832699 0.771308801272036 0.707033067832699 1 - 0 4661 Y Y 3.52361324642271 3.44040523365767 3.44040523365767 362 0.00276243093922657 0.00605311680117393 Y 0.482913853079599 0.993844212536662 N N 327 0 ENSG00000187221 ENSG00000201862 - + 7 7 72081568 72091927 utr5p downstream AC005488.2-4 Y_RNA 72076586 72091826 - - 0 72081318 72088412 + - N - - N HCC1954 9 8.11111111111111 4 18 1 N - - Y - SINE 0 0.0248447204968944 0.0248447204968944 18 1.32122340958636 1.14982145374813 1.32122340958636 1.14982145374813 1 - - 7497 Y Y 3.30062602958175 3.64400585547602 3.30062602958175 0 0 0.150892552062906 Y 0 0 N N 6032 12618 ENSG00000115204 ENSG00000115207 - + 2 2 27402051 27433372 coding coding MPV17 GTF3C2 27385864 27402220 - - 0 27398837 27403253 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.685607823352921 0.585623349113953 0.685607823352921 0.585623349113953 2 - - 13608 Y Y 3.21704729445613 2.65604393966323 2.65604393966323 230 0 0.115480316420392 Y 0 0.988812896922325 N N 26397 1 ENSG00000197077 ENSG00000206069 - - 22 22 23923415 23672662 upstream upstream CTA-221G9.5 TMEM211 23753158 23661077 + - 0 23751619 23678721 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 39 1.13553795742827 0.764167053112109 1.13553795742827 0.764167053112109 2 - - 37267 N N 3.12747721909902 3.04790278197696 3.04790278197696 0 0.0567175138566488 0.0631417127534708 N 0.101165379695864 0 N N 551733 1574 ENSG00000204628 ENSG00000178449 + + 5 12 180603512 48800501 utr3p intron GNB2L1 C12orf62 180596536 48792167 - + 0 180596544 48795283 - + Y - 1.13412487608059 N HCC1954 19 12.4782608695652 2 23 1 N - - N - SINE,SINE 0 0.783783783783784 0.783783783783784 23 0.607048593593732 0.264244681917271 0.607048593593732 0.264244681917271 2 - 0 26560 Y Y 3.38552945952599 3.38080938095063 3.38080938095063 396 0.0303876756390721 0.109853881107038 Y 0.994427515377236 0.988855030754472 N N 8642 3792 ENSG00000099381 ENSG00000175938 - + 16 16 30903482 30873757 upstream coding SETD1A ORAI3 30876116 30867916 + + 0 30875022 30868339 - + N - 1.03477024627917 N HCC1954 1 1 1 0 3 N - - Y SINE - 0.454054054054054 0 0.454054054054054 80 1.32122340958636 1.59975158782348 1.59975158782348 1.32122340958636 4 - 0 9525 Y Y 3.58424216889964 3.33424740824393 3.33424740824393 275 0 0.0355952358953421 Y 0.327241647241647 0.982968142968143 N N 11059 0 ENSG00000160551 ENSG00000222363 - + 17 17 24895628 24739827 upstream upstream TAOK1 U4 24742069 24739704 + + 0 24741053 24721449 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.885576771830856 0.699891319672773 0.885576771830856 0.699891319672773 4 - - 36255 Y N 3.22895481873075 3.50000108636471 3.22895481873075 0 0 0.109772016437615 Y 0.657900154400411 0 N N 2120 37 ENSG00000214826 ENSG00000186611 + - 12 12 9492091 9446360 downstream upstream DDX12 AC137766.2 9461576 9440930 - - 0 9455898 9452780 - + N - - N HCC1954 9 5 1 6 1 N - - Y - - 0 0 0 7 0.956994253430118 0.721316564152552 0.956994253430118 0.721316564152552 1 - - 41977 N Y 3.53718568265298 3.67489874718912 3.53718568265298 2 0 0.442249890106883 N 0.00380228136882133 0.905124026797031 N N 241 5438 ENSG00000101842 ENSG00000120992 - - X 8 107209069 55177130 utr3p coding VSIG1 LYPLA1 107174856 55121492 + - 0 107208348 55140923 - + Y - - N HCC1954 70 59.5 34 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.292811674556976 0.321378667196682 0.292811674556976 0 - - 38766 N Y 3.85425536676371 3.60632674564779 3.60632674564779 0 0 0.409855403666298 N 0.924193807155463 0.891705438793518 N N 2963 3492 ENSG00000133983 ENSG00000123815 + - 14 19 69896147 45914440 coding intron COX16 ADCK4 69680762 45889274 - - 0 69895989 45907579 - + Y 0.803532643437988 1.83039323569056 N HCC1954 16 3.66666666666667 1 14 1 N - - N - SINE 0 1 1 21 0.771308801272036 0.357087407996313 0.771308801272036 0.357087407996313 3 0 0 11714 N N 3.62568283544685 3.68527868815389 3.62568283544685 1 0 0.548523504939303 N 0 0 N N 0 275 ENSG00000217435 ENSG00000204303 + + 9 17 104867701 72068110 downstream utr5p RP11-341A22.1 SNORD1C 104867519 72065446 + + 0.00272479564032679 105007162 72065535 + + Y - 3.53544189664622 N HCC1954 2 1.16666666666667 1 1 3 N - - N - - 0 0 0 6 0.799875793911741 0.407079645115797 0.799875793911741 0.407079645115797 1 - 0 25297 N N 3.37080016234644 3.6727393216935 3.37080016234644 2 0 0.089413493273043 N 0 0 N N 1733 0 ENSG00000101928 ENSG00000151778 + + X 13 133876963 43869849 utr5p upstream MOSPD1 SERP2 133849323 43845978 - + 0 133876911 43791155 - + Y 0.581216333838105 - N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 4 0.34280391167646 0.307095170876829 0.34280391167646 0.307095170876829 2 0 - 41012 Y Y 3.55334927718654 3.67489874718912 3.55334927718654 273 0 0.00764621913937047 Y 0 0 N N 0 268 ENSG00000209577 ENSG00000196209 + - 20 20 1457805 1420042 downstream upstream AL049634.8 SIRPB2 1457702 1403236 - - 0 1439494 1430197 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 4 0.807017542071667 0.949852505270192 0.949852505270192 0.807017542071667 1 - - 19603 N Y 3.73808832274579 3.24893340314576 3.24893340314576 0 0 0.949966095903832 N 0.975379594153541 0.975379594153541 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0.975379594153541 109336418 45272639 - - Y - - N HCC1954 8 4.84955752212389 4 113 2 N - - N - - 0 0 0 113 1.1141127129485 1.34979040222606 1.34979040222606 1.1141127129485 3 - - 44592 N Y 3.40319013214585 3.2907752972771 3.2907752972771 0 0 0.137824293467985 N 0 0.831920903954802 N N 265 0 ENSG00000170509 ENSG00000222451 - - 4 10 88463062 91913697 utr3p upstream HSD17B13 7SK 88443965 91913388 - - 0.731073446327684 88444365 92168837 + + Y - - N HCC1954 24 23.5714285714286 23 7 1 N - - N SINE DNA 1 1 1 7 0.321378667196682 0.378512652476092 0.378512652476092 0.321378667196682 2 - - 24924 N Y 3.43649194885083 3.23420410596622 3.23420410596622 17 0.161609033168666 0.0644987487040877 N 0.161609033168666 0.92378263937897 N N 0 3221 ENSG00000179399 ENSG00000115163 - + 13 2 92316693 26870961 intron utr3p GPC5 CENPA 90848919 26862386 + + 0 91719735 26869655 - + Y 1 2.45041991079049 N HCC1954 20 15 4 4 1 N - - N SINE - 1 0 1 4 0.414221393275723 0.349945659836387 0.414221393275723 0.349945659836387 2 0 0 39869 Y Y 3.53039946453785 3.36079094374226 3.36079094374226 253 0 0.0149308131445942 Y 0.432252964426877 0.9900395256917 N N 0 9 ENSG00000210485 ENSG00000166143 + - 15 15 38925032 38908227 downstream upstream AC012476.8 PPP1R14D 38924962 38894943 - - 0.9900395256917 38917661 38915774 - + N - - N HCC1954 2 1.5 1 3 1 N - - Y SINE LTR 0.774509803921569 1 1 6 0.728458312312478 0.599906845433805 0.728458312312478 0.599906845433805 1 - - 29734 Y Y 3.08983369255491 3.42936294528359 3.08983369255491 0 0 0.547850398281172 Y 0.0430934078732823 0.963195900302819 N N 1384 0 ENSG00000124787 ENSG00000209924 - + 6 6 4949270 4991334 coding downstream RPP40 AL359643.27 4940280 4991186 - - 0 4949124 4987737 + - N - - N HCC1954 1 1 1 0 2 N - - Y - LTR,LTR,LTR 0 0.712121212121212 0.712121212121212 5 0.45707188223528 0.735600060472404 0.735600060472404 0.45707188223528 3 - - 39726 N N 3.3958695476974 3.60103760561896 3.3958695476974 1 0 0.073177717994774 N 0 0 N N 4162 4 ENSG00000129680 ENSG00000103569 - + X 15 135161404 56265402 utr3p downstream MAP7D3 AQP9 135123047 56217700 - + 0 135123859 56339844 + + Y - - N HCC1954 34 28.5 22 4 1 N 49 27.4336 N SINE LTR 1 1 1 4 0.278528178237124 0.357087407996313 0.357087407996313 0.278528178237124 2 - - 36434 Y Y 3.53035961174449 3.39128260787123 3.39128260787123 4 0 0.662742192337798 Y 0 0.94681861348528 N N 37 351 ENSG00000139194 ENSG00000205885 + + 12 12 7172754 7165701 intron coding RBP5 AC018653.29-1 7167557 7152443 - + 0 7172049 7164392 - + N 1.00814598354028 - N HCC1954 1 1 1 0 3 N - - Y - Simple_repeat 0 0.15018315018315 0.15018315018315 6 0.785592297591888 0.857009779191151 0.857009779191151 0.785592297591888 1 0 - 2168 N N 3.36720643949681 3.18660906348964 3.18660906348964 0 0 0.0235911974826393 N 0.651848654869803 0.0821464537476623 N N 30872 343 ENSG00000058262 ENSG00000198168 - - 3 11 129273215 22807958 intron upstream SEC61A1 SVIP 129253902 22800176 + - 0.0821464537476623 129268312 23106592 - + Y 1.65832413471081 - N HCC1954 19 15.6 11 5 1 N - - N - SINE 0 1 1 5 0.449930134075354 0.335662163516534 0.449930134075354 0.335662163516534 1 0 - 44258 N N 3.51104337473878 3.17983219294431 3.17983219294431 4 0 0.266143046330579 N 0.00403225806451601 0.00403225806451601 N N 3 18434 ENSG00000075891 ENSG00000136868 - + 10 9 102579688 115068495 upstream utr3p PAX2 SLC31A1 102495458 115023638 + + 0.00403225806451601 102398233 115066274 - + Y - 3.98702590511987 N HCC1954 2 1.4 1 2 1 N - - N SINE SINE 1 0.339285714285714 1 5 0.257102933757345 0.39993789695587 0.39993789695587 0.257102933757345 1 - 0 40051 Y Y 3.57912086274016 3.48064499656564 3.48064499656564 304 0 0.00275366079944872 Y 0.993310667608619 0.993310667608619 N N 269689 3297 ENSG00000067225 ENSG00000137817 - + 15 15 70310738 70350682 utr5p downstream PKM2 PARP6 70278424 70320577 - - 0 70298504 70316785 + - N - - N HCC1954 2 1.29268292682927 1 12 1 N - - Y - - 0 0 0 41 1.12839620926835 1.0069864905496 1.12839620926835 1.0069864905496 1 - - 19637 N N 3.68577320169385 3.56232542602083 3.56232542602083 0 0 0.319683914873475 N 0 0 N N 168 18703 ENSG00000186543 ENSG00000046604 + + 1 18 16843765 27380754 utr3p downstream AL137798.8-2 DSG2 16828752 27332170 - + 0 16828997 27381379 - + Y - - N HCC1954 31 23 21 6 1 N - - N SINE - 1 0 1 6 0.307095170876829 0.621332089913584 0.621332089913584 0.307095170876829 3 - - 36624 Y Y 3.80297331548166 3.45343911365801 3.45343911365801 123 0 0.270748999399627 Y 0.988679084073821 0.988679084073821 N N 10291 48182 ENSG00000111639 ENSG00000010292 - - 12 12 6472718 6511381 coding upstream MRPL51 NCAPD2 6471579 6473529 - + 0.988679084073821 6472485 6473145 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 60 0.721316564152552 0.621332089913584 0.721316564152552 0.621332089913584 2 - - 43671 N Y 3.50120199000394 2.80981554559588 2.80981554559588 5 0 0.276811437770239 N 0.990044052863436 0 N N 3866 282831 ENSG00000198740 ENSG00000099194 - + 17 10 44794834 102114577 utr3p intron ZNF652 SCD 44727485 102096762 - + 0.303083700440529 44727766 102108362 + + Y - 1.620921740032 N HCC1954 16 10.8 8 5 1 N - - N Low_complexity SINE 0.0761904761904762 1 1 5 0.749883556792257 0.485638874874985 0.749883556792257 0.485638874874985 2 - 0 6457 Y Y 3.47076375903745 3.51423587000429 3.47076375903745 157 0 0.862928726790972 Y 0.985861806084968 0.992930903042484 N N 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 coding utr3p VAMP5 VAMP8 85665042 85658227 + + 0 85665127 85662509 - + N - 2.75334480348128 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 26 1.18553019454776 1.02126998686945 1.18553019454776 1.02126998686945 3 - 0 13270 N N 2.63991085035322 3.10400996497142 2.63991085035322 0 0 0.476341127339887 N 0.267282215977519 0.135768767563228 N N 194 478 ENSG00000185760 ENSG00000172250 - - 6 22 73965295 41238510 utr3p intron KCNQ5 SERHL 73388241 41226540 + + 0.135768767563228 73964067 41235801 - - Y - 0.0510899100692592 N HCC1954 682 286.5 34 4 1 N - - N Simple_repeat LINE,SINE 0.925 0.723684210526316 0.925 4 0.28566992639705 0.542772860154395 0.542772860154395 0.28566992639705 3 - 0 26586 Y Y 3.63193049733206 3.55401162459584 3.55401162459584 285 0 0.00480641887318034 Y 0.418713450292398 0.990773229369721 N N 1 1140 ENSG00000167194 ENSG00000149927 - - 16 16 29943524 29930243 upstream upstream AC093512.2 DOC2A 29942156 29924338 + - 0 29939945 29932417 - + N - - N HCC1954 6 1.5 1 2 2 N - - Y - SINE,SINE 0 0.822429906542056 0.822429906542056 18 0.87843502367093 0.764167053112109 0.87843502367093 0.764167053112109 1 - - 3343 N N 3.5465630590714 3.51832410639388 3.51832410639388 0 0.00272479564032702 0.971305477292737 Y 0.00845626233204932 0 N Y 16900 5796 ENSG00000185658 ENSG00000159267 + - 21 21 39607426 37284373 coding coding BRWD1 HLCS 39479274 37045066 - - 0 39506462 37191301 - + N - 1.10595650954906 N HCC1954 1 1 1 0 2 Y 508 8.9854 N - - 0 0 0 40 1.3069399132665 1.42834963198525 1.42834963198525 1.3069399132665 4 - 0 25826 N N 3.61360747730288 3.28867865251378 3.28867865251378 0 0 0.103965480975385 N 0 0 N N 56725 45068 ENSG00000077809 ENSG00000205336 + + 7 16 73812956 56256445 intron upstream GTF2I GPR56 73709966 56220023 + + 0 73719551 56211629 + + Y 0.464616402978617 - N HCC1954 20 16.2666666666667 6 15 1 N - - N SINE - 1 0 1 15 0.314236919036755 0.649899082553289 0.649899082553289 0.314236919036755 1 0 - 36378 N Y 3.7297745213208 3.51104337473878 3.51104337473878 267 0 0.0108846568172536 Y 0.991697877652934 0.983395755305868 N N 278 5028 ENSG00000198353 ENSG00000180818 - + 12 12 52736081 52670327 intron coding HOXC4 HOXC10 52696909 52665213 + + 0 52714340 52666052 - + N 0.314022379653777 0.590489620999359 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.771308801272036 0.964136001590045 0.964136001590045 0.771308801272036 2 0 0 25199 Y Y 3.22532124308776 3.38701719004248 3.22532124308776 0 0 0.8145990663377 Y 0.991700133868809 0.983400267737617 N N 47278 1817 ENSG00000189403 ENSG00000132952 - - 13 13 30089734 30131686 utr5p intron HMGB1 USPL1 29930877 30089920 - + 0 29935831 30090355 + - N - 0.409572336846869 N HCC1954 5 4.5 4 4 1 N - - Y - - 0 0 0 4 0.307095170876829 0.557056356474248 0.557056356474248 0.307095170876829 4 - 0 36203 Y Y 3.40062947906611 3.26460248413936 3.26460248413936 0 0 0.531662334921025 Y 0.963088939279415 0.992617787855883 N N 16017 12 ENSG00000018236 ENSG00000205592 - + 12 12 39750361 39250827 utr5p downstream CNTN1 MUC19 39588423 39222629 + + 0 39588427 39372662 - + N 0.0257959138592769 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 1.06412047582901 1.13553795742827 1.13553795742827 1.06412047582901 1 0 - 33400 N N 3.73912139251568 2.95228338382753 2.95228338382753 1 0 0.99788679208056 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8563 12106 - + N - - N HCC1954 3 1.92 1 17 7 N 189 4.09957 N - - 0 0 0 25 0.956994253430118 1.4140661356654 1.4140661356654 0.956994253430118 2 - - 14355 N N 3.6623288755052 3.57336771439491 3.57336771439491 1 0 0.251840889847983 N 0 0.662163956189844 N N 50281 2 ENSG00000135862 ENSG00000118113 - + 1 11 181381350 102100868 coding intron LAMC1 MMP8 181259218 102088599 + - 0.662163956189844 181364501 102093913 - - Y - 0.856143856143856 N HCC1954 20 19.2 18 5 1 N - - N - SINE 0 1 1 5 0.585623349113953 0.392796148795944 0.585623349113953 0.392796148795944 1 - 0 11087 N N 3.3755202409218 3.48167806633553 3.3755202409218 0 0 0.0771046966961224 N 0 0 N N 0 34343 ENSG00000182447 ENSG00000011052 - + 3 17 162704424 46604104 downstream intron AC104471.6 NME1-NME2 162697290 46585919 + + 0 163169726 46602603 - + Y - 0.422855616204492 N HCC1954 8 5.71428571428571 4 7 1 N - - N SINE - 1 0 1 7 0.28566992639705 0.628473838073511 0.628473838073511 0.28566992639705 2 - 0 39793 Y Y 3.38908332958227 3.68953475841283 3.38908332958227 249 0 0.0490295350310118 Y 0.94466755912539 0.977867023650156 N N 3186 10214 ENSG00000092531 ENSG00000103994 - - 15 15 40612548 40537022 upstream upstream SNAP23 ZFP106 40575127 40492314 + - 0.170013386880857 40570467 40551808 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 83 0.864151527351077 0.699891319672773 0.864151527351077 0.699891319672773 1 - - 16853 N Y 3.48167806633553 3.52936639476796 3.48167806633553 33 0 0.191752749843587 N 0 0.0400699300699301 N N 46217 2162 ENSG00000131746 ENSG00000162458 - + 17 1 35911380 15985676 utr3p utr3p TNS4 FBLIM1 35885606 15955741 - + 0.0310139860139861 35886742 15984331 + + Y - - N HCC1954 38 37 36 5 1 N 616 29.8497 N SINE SINE 0.180555555555556 1 1 5 0.51420586751469 0.39993789695587 0.51420586751469 0.39993789695587 1 - - 39167 N N 3.67167574670007 3.39483647792751 3.39483647792751 4 0 0.0709596121061119 N 0 0 N N 24923 252027 ENSG00000137845 ENSG00000141738 + - 15 17 56829469 35157070 intron utr5p ADAM10 GRB7 56675802 35147713 - + 0 56695297 35147875 - - Y 0.946029159803257 0.410465831783318 N HCC1954 20 20 20 8 1 N 105 23.4795 N SINE - 1 0 1 8 0.28566992639705 0.778450549431962 0.778450549431962 0.28566992639705 2 0 0 44900 Y Y 3.3446273492087 3.33151892129485 3.33151892129485 349 0 0.00260226282831999 Y 0 0 N N 0 0 ENSG00000150201 ENSG00000221468 - + 10 10 43191787 43157364 upstream downstream FXYD4 U6atac 43187096 43157240 + + 0 43177628 43166656 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.742741808632331 0.87843502367093 0.87843502367093 0.742741808632331 3 - - 13024 N Y 3.07101108092519 3.5816815158199 3.07101108092519 0 0.00363636363636366 0.193277496563156 N 0.641931818181818 0.875454545454545 N N 1649619 0 ENSG00000141736 ENSG00000197823 - + 17 5 35138441 171969041 coding downstream ERBB2 AC027309.3 35104766 171968850 + - 0 35125066 171897831 - - Y - - N HCC1954 22 19.3125 3 16 1 N 169 15.7803 N - SINE 0 1 1 16 1.10697096478857 0.378512652476092 1.10697096478857 0.378512652476092 1 - - 16822 N N 3.1416492220063 2.97423997949969 2.97423997949969 47 0.109928295642581 0.149961846943601 N 0.118918918918919 0.0514892443463874 N N 317991 0 ENSG00000171346 ENSG00000212679 - - 17 1 36932191 559619 coding intron KRT15 RP5-857K21.10 36923523 558939 - + 0.0514892443463874 36928473 559001 + - Y - 1 N HCC1954 3 2.6 2 5 2 N - - N Simple_repeat - 0.215384615384615 0 0.215384615384615 5 0.749883556792257 0.757025304952183 0.757025304952183 0.749883556792257 2 - 0 22108 N N 3.38230645903694 3.30062602958175 3.30062602958175 3 0 0.425620460032911 N 0 0.596742842132913 N N 4347 0 ENSG00000140299 ENSG00000219001 - + 15 1 57769025 224693668 upstream downstream BNIP2 RP11-118H4.1 57738637 224692888 - + 0 57848656 224693707 + + Y - - N HCC1954 7 7 7 8 1 N - - N - - 0 0 0 8 0.357087407996313 0.278528178237124 0.357087407996313 0.278528178237124 3 - - 47273 Y Y 3.36295036923788 3.40422320191574 3.36295036923788 0 0 0.84029919448952 Y 0.993482057653181 0.986964115306361 N N 617 302 ENSG00000197863 ENSG00000167637 - - 19 19 42021124 42062306 utr5p upstream ZNF790 ZNF345 42000176 42033103 - + 0 42008434 42032744 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 31 1.05697872766909 1.36407389854591 1.36407389854591 1.05697872766909 4 - - 46995 N N 3.40422320191574 3.4210491438586 3.40422320191574 0 0 0.958207059533418 N 0 0 Y N 302 7 ENSG00000167637 ENSG00000204866 - + 19 19 42062306 51356385 upstream upstream ZNF345 IGFL2 42033103 51274062 + + 0 42032744 51261295 - + N - - N HCC1954 1 1 1 0 2 N 138 5.8892 N - DNA 0 0.0555555555555556 0.0555555555555556 8 0.978419497909897 1.07840397214886 1.07840397214886 0.978419497909897 4 - - 45924 N N 3.58593758607883 1.47231942795945 1.47231942795945 0 0.0192903995229575 0.0945174469731458 N 0.0579010137149673 0.127400119260584 N N 1 850768 ENSG00000204851 ENSG00000075624 - - 19 7 51690562 5536758 upstream utr3p AC011484.7 ACTB 51686293 5533313 - - 0.127400119260584 51739523 5533821 + + Y - 0.969230197368115 N HCC1954 36 22.75 6 4 1 N - - N Low_complexity,SINE Simple_repeat 0.672727272727273 0.0561797752808989 0.672727272727273 4 0.392796148795944 0.635615586233437 0.635615586233437 0.392796148795944 2 - 0 8148 N Y 3.1986844216336 3.8333716936548 3.1986844216336 0 0 0.730757159145829 N 0.20543883429346 0.952134869535751 N N 0 3966 ENSG00000214684 ENSG00000175772 + + 5 2 136221933 110111006 upstream upstream AC109439.3 AC013268.5-1 136221216 110103138 + + 0 136189052 110102056 + + Y - - N HCC1954 60 44.0869565217391 34 23 1 N 50 25.8656 N LINE - 1 0 1 23 0.478497126715059 0.657040830713216 0.657040830713216 0.478497126715059 3 - - 4686 N N 3.42680229220385 3.35356364524965 3.35356364524965 1 0 0.915285467211697 N 0 0 Y N 7862 0 ENSG00000091073 ENSG00000196898 - - 7 7 75973241 76436410 utr5p upstream DTX2 AC114737.3-1 75928954 76435514 + - 0 75947674 76448513 - + N - - N HCC1954 2 2 2 5 2 N 249 9.15227 N - - 0 0 0 5 0.607048593593732 0.478497126715059 0.607048593593732 0.478497126715059 4 - - 47188 N N 3.358283723825 3.09815176348912 3.09815176348912 0 0 0.955242746707725 N 0 0.0489528377298162 Y N 8665 5583 ENSG00000079313 ENSG00000104885 + + 19 19 1799452 2181007 intron coding REXO1 DOT1L 1766245 2115148 - + 0.0489528377298162 1770501 2161400 - + N 1.34255386677917 - N HCC1954 1 1 1 0 5 N 279 3.37031 N - - 0 0 0 6 0.907002016310634 0.93556900895034 0.93556900895034 0.907002016310634 1 0 - 26529 N Y 3.39657174790006 3.36654409208751 3.36654409208751 0 0 0.365539684611871 N 0 0.957637629997138 N N 3423 11887 ENSG00000169246 ENSG00000198064 + - 16 16 21365985 22455333 upstream upstream AC008740.7-1 AC106788.3-3 21321106 22432584 - + 0 21366744 22432261 - - N - - Y HCC1954 42 17.25 9 4 1 N 191 23.837 N - SINE 0 0.388489208633094 0.388489208633094 4 0.335662163516534 0.649899082553289 0.649899082553289 0.335662163516534 3 - - 42202 Y Y 3.62824348852659 3.57848902055439 3.57848902055439 164 0 0.7347673626036 Y 0 0.97515243902439 N N 1615 108 ENSG00000156219 ENSG00000169248 - - 4 4 77252964 77176376 upstream upstream ART3 CXCL11 77214887 77173975 + - 0 77198167 77194451 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.749883556792257 0.45707188223528 0.749883556792257 0.45707188223528 4 - - 1758 N Y 3.41423242051993 3.65384724021086 3.41423242051993 0 0 0.27953285882625 N 0.871955503512881 0.857728337236534 N N 6632 406 ENSG00000158636 ENSG00000120693 - - 11 13 75940234 36392375 upstream intron C11orf30 SMAD9 75833717 36316968 + - 0 75832968 36374884 - + Y - 3.94253576400764 N HCC1954 37 31.4 23 5 1 N - - N - SINE 0 1 1 5 0.371370904316165 0.321378667196682 0.371370904316165 0.321378667196682 1 - 0 18770 Y Y 3.48805370929674 3.13487235146098 3.13487235146098 325 0 0.0155939646736606 Y 0.519214402618658 0.992929623567921 N N 305 3763 ENSG00000162572 ENSG00000160087 - - 1 1 1217267 1199097 utr5p upstream SCNN1D UBE2J2 1204310 1179157 + - 0 1204312 1200543 - + N 0.160329341317365 - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR - 0.173611111111111 0 0.173611111111111 7 0.93556900895034 1.13553795742827 1.13553795742827 0.93556900895034 1 0 - 22102 N Y 3.30803474231284 3.64656650855576 3.30803474231284 0 0 0.190258018609664 N 0.836435798535413 0.821566325674996 N N 1 0 ENSG00000166206 ENSG00000200729 - - 15 1 24767329 172101193 intron downstream GABRB3 SNORD79 24339786 172101109 - - 0.821566325674996 24441910 172101041 + + Y 1.01325966850829 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 0.392796148795944 0.385654400636018 0.392796148795944 0.385654400636018 2 0 - 24913 N Y 3.55401162459584 3.25463311832853 3.25463311832853 0 0 0.387826229017006 N 0 0.944690265486726 N N 52 4312 ENSG00000214164 ENSG00000102531 + + 2 13 110569923 48681915 downstream intron AC112229.4-2 FNDC3A 110569013 48448049 - + 0 110566591 48627105 - + Y - 0.880516123924578 N HCC1954 200 121.6 28 5 1 N - - N - LINE 0 1 1 5 0.828442786551446 0.407079645115797 0.828442786551446 0.407079645115797 4 - 0 16988 N N 3.60000453584907 3.71823771940677 3.60000453584907 0 0 0.377421954689551 N 0.102047930283224 0.141089324618736 N N 699 317991 ENSG00000188295 ENSG00000171346 - + 1 17 245334251 36932191 utr3p intron ZNF669 KRT15 245328029 36923523 - - 0.141089324618736 245330183 36924920 + - Y - 1.61822492111163 N HCC1954 13 4 1 1 1 N - - N SINE,SINE SINE 0.675 1 1 4 0.28566992639705 0.5713398527941 0.5713398527941 0.28566992639705 1 - 0 36337 Y Y 3.52617389950245 3.58337693299909 3.52617389950245 280 0 0.0550125422154281 Y 0.977524167561762 0.992508055853921 N N 0 584 ENSG00000179821 ENSG00000136052 + - 12 12 103895935 103846563 downstream upstream AC090051.8 SLC41A2 103894657 103722495 - - 0 103876510 103846603 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 13 0.871293275511003 1.03555348318931 1.03555348318931 0.871293275511003 1 - - 33347 N N 2.9144762929233 3.63655728995158 2.9144762929233 0 0 0.998392104595577 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8594 10684 - + N - - N HCC1954 3 1.5 1 1 7 Y 189 4.09957 N - - 0 0 0 4 1.01412823870953 1.02841173502938 1.02841173502938 1.01412823870953 1 - - 38372 Y Y 3.3244060235091 3.62088820895798 3.3244060235091 32 0.109856708640903 0.902411666360261 Y 0.991098567086409 0.982197134172818 N N 3765 2 ENSG00000165804 ENSG00000178107 - - 14 14 20636639 20654701 utr5p upstream ZNF219 AL161668.6-2 20628076 20646042 - + 0 20631673 20642510 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.871293275511003 0.792734045751814 0.871293275511003 0.792734045751814 4 - - 9337 Y Y 3.16150917291514 3.69103183649914 3.16150917291514 155 0.482235347569287 0.114149898456228 Y 0.482235347569287 0.986006360745116 N N 16 0 ENSG00000108370 ENSG00000211170 - + 17 17 60654281 60502890 upstream downstream RGS9 AC015821.9 60564011 60502725 + + 0 60537298 60527624 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.585623349113953 0.392796148795944 0.585623349113953 0.392796148795944 1 - - 10836 N Y 3.18188898491428 3.54193626645188 3.18188898491428 1 0 0.139177198804694 N 0.935728250244379 0.914304333659172 N N 20793 802 ENSG00000141027 ENSG00000164379 + + 17 6 16059570 1259981 utr5p downstream NCOR1 FOXQ1 15875443 1257675 - + 0 16059401 1266445 - + Y - - N HCC1954 21 20.75 20 4 1 N - - N Simple_repeat SINE 0.9 1 1 4 0.28566992639705 0.34280391167646 0.34280391167646 0.28566992639705 3 - - 366 Y Y 3.51207644450867 3.15745144174909 3.15745144174909 406 0 0.282357934359055 Y 0 0.993990741290284 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 upstream intron C11orf66 C11orf79 61005168 60954173 + + 0 60996791 60954376 - + N - 2.04447011682617 N HCC1954 1 1 1 0 6 N - - Y LTR - 1 0 1 4 0.871293275511003 0.528489363834543 0.871293275511003 0.528489363834543 1 - 0 40920 N Y 3.27085014602457 3.49843365026151 3.27085014602457 237 0 0.00593373051829993 Y 0.990693639339091 0.990693639339091 N N 828 0 ENSG00000130684 ENSG00000210036 + - 20 20 25625469 25583517 downstream downstream ZNF337 AL031673.19-2 25602851 25583232 - - 0 25602486 25574282 - + N - - N HCC1954 20 6.33333333333333 1 4 1 N - - N LTR SINE 0.2 1 1 6 0.535631111994469 0.707033067832699 0.707033067832699 0.535631111994469 1 - - 31811 N N 3.59528445727371 3.66592259835483 3.59528445727371 0 0 0.578169707719537 N 0.502145922746781 0 N Y 5 12271 ENSG00000198685 ENSG00000177479 - + 3 3 129777619 48997971 utr5p utr5p C3orf27 ARIH2 129773533 48931285 - + 0 129776919 48935248 + + N - - Y HCC1954 32 20 2 4 1 N - - N SINE - 0.924528301886792 0 0.924528301886792 4 0.378512652476092 0.542772860154395 0.542772860154395 0.378512652476092 4 - - 41366 N Y 3.40319013214585 3.63296356710195 3.40319013214585 0 0 0.264851295022683 N 0.895966973642426 0.955414417275325 N N 2078 6463 ENSG00000182621 ENSG00000085365 - + 20 5 8813547 77812318 utr5p coding PLCB1 SCAMP1 8061296 77692163 + + 0 8556937 77789441 - + Y - - N HCC1954 25 22.1666666666667 11 6 1 N - - N - LINE 0 1 1 6 0.749883556792257 0.378512652476092 0.749883556792257 0.378512652476092 3 - - 49335 N Y 3.51360402781852 3.55401162459584 3.51360402781852 0 0.00218818380743979 0.125177675950043 Y 0.00792273447521319 0 N N 2543 17911 ENSG00000037241 ENSG00000113719 - + 5 5 172329378 172312287 utr5p utr3p RPL26L1 ERGIC1 172319045 172193928 + + 0 172319049 172310428 - + N - - N HCC1954 3 2.25 2 4 1 N - - N - - 0 0 0 4 0.828442786551446 0.921285512630487 0.921285512630487 0.828442786551446 2 - - 49477 Y Y 3.32679884271949 3.43681151080804 3.32679884271949 0 0 0.959819194598507 Y 0.0275839207202176 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883894 140816150 - + N - 0.194212665568841 N HCC1954 4 1.39130434782609 1 7 2 N - - Y - LTR 0 1 1 23 1.1141127129485 1.26408942430695 1.26408942430695 1.1141127129485 4 - 0 22011 N Y 3.24462389972434 3.72655152083176 3.24462389972434 8 0 0.426663528560708 N 0.904620756862108 0.851632288452168 N N 8 3163 ENSG00000143199 ENSG00000151327 + - 1 14 166149964 34622340 intron intron ADCY10 C14orf24 166045507 34583864 - + 0.0356098749390938 166056015 34588990 - - Y 0.886992348440259 0.578766413872441 N HCC1954 21 9 1 3 1 N - - N - SINE 0 1 1 5 0.34280391167646 0.428504889595575 0.428504889595575 0.34280391167646 3 0 0 31396 Y Y 3.10546719026438 3.72551845106187 3.10546719026438 296 0 0.00830968193341242 Y 0.762344074844075 0.99233367983368 N N 243 4516 ENSG00000197385 ENSG00000144645 - - 3 3 32007186 31998242 upstream upstream ZNF860 OSBPL10 32005624 31674407 + - 0 32002753 31998418 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE,SINE - 0.284974093264249 0 0.284974093264249 8 1.22123893534739 0.685607823352921 1.22123893534739 0.685607823352921 1 - - 21503 N N 3.48912663185998 3.13636008197748 3.13636008197748 0 0 0.0726961544214206 N 0 0 N N 2080 0 ENSG00000067208 ENSG00000214121 - - 1 9 93030549 12963437 intron intron EVI5 AL161449.7 92746841 12962842 - - 0 92875473 12963410 + + Y 0.589774829039507 1 N HCC1954 12 5 4 10 1 N - - N SINE - 1 0 1 10 0.264244681917271 0.599906845433805 0.599906845433805 0.264244681917271 2 0 0 41444 Y Y 3.06422486281005 3.46717003618782 3.06422486281005 298 0 0.00648363696911514 Y 0.99317366921026 0.99317366921026 N N 0 2391 ENSG00000204756 ENSG00000147799 - - 8 8 145904474 145804869 upstream intron AF186192.4 AC084125.9-2 145903923 145725371 + - 0 145881880 145801889 - + N - 29.5747935148363 N HCC1954 1 1 1 0 1 N - - Y Low_complexity,Simple_repeat - 0.597014925373134 0 0.597014925373134 21 0.956994253430118 1.02841173502938 1.02841173502938 0.956994253430118 1 - 0 31698 Y Y 3.41319935075004 3.45078517462244 3.41319935075004 267 0.0227215980024968 0.0340572781629234 Y 0.535081148564295 0.990511860174782 N N 763 0 ENSG00000205814 ENSG00000207650 - + 3 3 196924416 196911548 coding upstream AC069513.28-3 hsa-mir-570 196912000 196911452 + + 0 196913718 196911259 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 1.0069864905496 0.714174815992626 1.0069864905496 0.714174815992626 0 - - 31883 Y Y 3.3305739798076 3.54296933622177 3.3305739798076 4 0 0.566298801043536 Y 0 0.989403257978723 N N 2372 18789 ENSG00000163923 ENSG00000073849 + + 3 3 188339957 188279035 coding intron RPL39L ST6GAL1 188321435 188131210 - + 0 188321775 188229570 - + N - 0.510306086578901 N HCC1954 5 1.8 1 1 2 N - - Y - SINE 0 1 1 5 0.792734045751814 0.528489363834543 0.792734045751814 0.528489363834543 1 - 0 6754 Y Y 3.63296356710195 3.35869429897894 3.35869429897894 0 0 0.386798503778142 Y 0 0.945881489634929 N N 5507 4897 ENSG00000119760 ENSG00000115254 + + 2 2 27740011 27727215 utr5p intron SUPT7L GPN1 27727183 27705029 - + 0 27738635 27723401 - + N - 1.29394331736441 N HCC1954 1 1 1 0 2 N - - Y LINE DNA 0.467625899280576 0.848214285714286 0.848214285714286 5 0.914143764470561 0.771308801272036 0.914143764470561 0.771308801272036 1 - 0 3743 N N 3.67167574670007 3.39640391403071 3.39640391403071 0 0 0.0640334396801977 N 0.00581395348837199 0 N N 983 26452 ENSG00000205670 ENSG00000119139 - - 21 9 34696945 71059938 utr3p coding C21orf51 TJP2 34669619 70956382 + + 0 34683111 71021104 - - Y - 0.358934479972443 N HCC1954 37 29.5 22 6 1 N - - N SINE - 1 0 1 6 0.34280391167646 0.585623349113953 0.585623349113953 0.34280391167646 1 - 0 35892 N N 3.38809011260573 3.26616992024256 3.26616992024256 0 0 0.645984400661525 N 0 0 N N 0 712661 ENSG00000218582 ENSG00000111640 + + 6 12 80720444 6517797 downstream utr3p RP3-357D13.1 GAPDH 80719441 6513918 - + 0 80719344 6517673 - + Y - - N HCC1954 3 1.375 1 2 2 N - - N - - 0 0 0 8 0.278528178237124 0.742741808632331 0.742741808632331 0.278528178237124 2 - - 6770 Y Y 3.7297745213208 3.41895249909529 3.41895249909529 159 0.0991829140037214 0.741529178171723 Y 0.109780762074266 0 N N 19744 7234 ENSG00000068878 ENSG00000115239 + - 2 2 54051481 53940801 coding upstream PSME4 ASB3 53944708 53613314 - - 0 53946726 53940840 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.764167053112109 0.649899082553289 0.764167053112109 0.649899082553289 4 - - 10460 Y Y 3.56129235625094 3.5319270478477 3.5319270478477 0 0.408619467886362 0.139792927893120 Y 0.408619467886362 0.98840430329189 N N 4316 4890 ENSG00000141569 ENSG00000132481 + - 17 17 71404649 71386251 coding upstream TRIM65 TRIM47 71396640 71381842 - - 0 71398850 71388307 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.657040830713216 0.549914608314322 0.657040830713216 0.549914608314322 2 - - 49100 Y Y 3.779528989293 3.40791021072121 3.40791021072121 227 0 0.00254995464862662 Y 0 0 N N 401 4691 ENSG00000113140 ENSG00000086570 + - 5 5 151046710 150928698 downstream upstream SPARC FAT2 151021212 150863847 - - 0 150978749 150928710 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 5 0.535631111994469 0.821301038391519 0.821301038391519 0.535631111994469 1 - - 27303 N Y 3.58849823915857 3.29912895149544 3.29912895149544 3 0.0028490028490028 0.96926735255552 Y 0.0028490028490028 0.99076712039675 N N 69736 15881 ENSG00000181019 ENSG00000102908 + + 16 16 68318034 68296054 coding coding NQO1 NFAT5 68300808 68156498 - + 0 68302612 68284261 - + N - 1.389705042436 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 8 0.914143764470561 0.699891319672773 0.914143764470561 0.699891319672773 1 - 0 41486 N Y 3.61513506061274 3.44615838200292 3.44615838200292 302 0 0.927142258892319 Y 0.970899598781844 0.985449799390922 N N 0 4 ENSG00000207110 ENSG00000184090 - - 8 8 129080722 129029462 upstream downstream U1 TMEM75 129080559 129029046 + - 0 129070590 129021104 - + N - - N HCC1954 1 1 1 0 5 N - - N - SINE 0 0.255952380952381 0.255952380952381 67 1.02841173502938 1.19981369086761 1.19981369086761 1.02841173502938 4 - - 2093 N Y 3.36617336972692 3.64656650855576 3.36617336972692 255 0.317501815541031 0.0769787965285265 N 0.889324618736383 0.963108206245461 N N 0 0 ENSG00000213592 ENSG00000214975 - + 11 6 57242578 25085188 intron intron AP000662.4-2 AL160400.20-1 57242094 25084626 - + 0.963108206245461 57242362 25084912 + + Y 1 1 N HCC1954 13 6.58823529411765 5 17 1 N - - N - - 0 0 0 17 0.328520415356608 0.34280391167646 0.34280391167646 0.328520415356608 3 0 0 29748 Y Y 3.45976132345673 3.49164743214637 3.45976132345673 0 0 0.99864501441337 Y 0.975506268081003 0.983670845387335 N Y 399 1730 ENSG00000221988 ENSG00000168452 - + 6 6 32244040 32239433 coding coding EGFL8 PPT2 32240360 32229279 + + 0 32242253 32238377 - + N - - N HCC1954 1 1 1 0 5 Y - - Y - - 0 0 0 6 1.08554572030879 0.799875793911741 1.08554572030879 0.799875793911741 4 - - 6160 N Y 3.43937216388778 3.53983683101182 3.43937216388778 0 0.0998217468805705 0.0315722858431281 N 0.144830659536542 0.549910873440285 N N 1194 12076 ENSG00000212691 ENSG00000148219 - + 2 9 201257138 119217138 coding utr3p AC007163.3-1 ASTN2 201255742 118227328 + - 0.549910873440285 201255952 118415234 - - Y - - N HCC1954 588 447.375 18 16 1 N - - N Other LINE 1 1 1 16 0.507064119354764 0.592765097273879 0.592765097273879 0.507064119354764 2 - - 6628 N Y 3.8333716936548 3.25463311832853 3.25463311832853 0 0.0183657833062917 0.733726648505434 N 0.28889489814314 0.969082386875789 N N 3966 39 ENSG00000175772 ENSG00000183091 + - 2 2 110111006 152299247 upstream intron AC013268.5-1 NEB 110103138 152050096 + - 0 110102056 152266075 + + N - 1.09702773143224 Y HCC1954 40 39.8666666666667 38 15 1 N - - N - LINE 0 1 1 15 1.22838068350732 0.657040830713216 1.22838068350732 0.657040830713216 3 - 0 29460 N N 3.36191729946799 3.42572936964061 3.36191729946799 0 0 0.907609260953967 N 0 0 Y Y 28710 1905 ENSG00000111912 ENSG00000066651 - + 6 6 126293949 126402115 coding coding ESNA1 TRMT11 126144000 126349269 + + 0 126241102 126361523 - + N - - N HCC1954 1 1 1 0 1 Y 117 3.97072 N - - 0 0 0 14 0.928427260790413 0.842726282871298 0.928427260790413 0.842726282871298 4 - - 45933 N Y 3.44871903508266 3.44143830342756 3.44143830342756 128 0 0.00802047166140873 N 0.764565677966102 0.831832627118644 N N 33105 1630 ENSG00000105372 ENSG00000160991 + + 19 7 47067322 101876168 coding utr3p RPS19P3 ORAI2 47055828 101861022 + + 0.0246292372881356 47065645 101876149 + + Y - - N HCC1954 23 21.1111111111111 20 9 1 N - - N - SINE 0 1 1 9 0.499922371194838 0.34280391167646 0.499922371194838 0.34280391167646 2 - - 349 Y Y 3.2493439782997 3.75065819442972 3.2493439782997 133 0 0.260102587866359 Y 0.15533514637658 0.978883378659414 N N 0 0 ENSG00000129586 ENSG00000222048 + - 11 11 10836165 10836196 upstream upstream AC069360.7 ZBED5 10830921 10830827 - - 0 10884574 10836435 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR DNA 1 0.786407766990291 1 5 0.607048593593732 0.664182578873142 0.664182578873142 0.607048593593732 2 - - 47990 N N 3.72717401544771 3.56338900101426 3.56338900101426 1 0 0.748355579534056 N 0 0.00305810397553519 N Y 79632 11413 ENSG00000182197 ENSG00000112877 + - 8 5 119193119 706664 coding coding EXT1 CEP72 118875910 665405 - + 0.00305810397553519 119191505 693523 - - Y 0.296748039644633 1.93127124714549 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 18 0.978419497909897 1.28551466878673 1.28551466878673 0.978419497909897 4 0 0 13478 N Y 3.18296190747752 3.3984700535705 3.18296190747752 295 0 0.0119677130817341 N 0.936723163841808 0.928813559322034 N N 238 0 ENSG00000211643 ENSG00000218532 - + 22 9 21003581 66704009 coding downstream IGLV5-52 RP11-381O7.1 21003021 66700433 + + 0 21003256 66704011 - + Y 0.0508770010575065 - N HCC1954 24 9.8974358974359 7 78 1 N - - N - - 0 0 0 78 0.971277749749971 0.642757334393363 0.971277749749971 0.642757334393363 1 0 - 4401 Y Y 3.33680806132368 3.66336194527509 3.33680806132368 245 0.917006802721088 0.0265536000783038 Y 0.988143828960155 0.964431486880466 N N 293 432 ENSG00000214605 ENSG00000188463 + - 7 7 71936739 71936739 upstream upstream AC092536.3-1 AC092536.3-2 71677439 71677439 - - 0.964431486880466 71940118 71938298 - + N - - N HCC1954 2 1.28571428571429 1 2 1 N - - Y - - 0 0 0 7 0.807017542071667 0.649899082553289 0.807017542071667 0.649899082553289 4 - - 21418 N N 2.9642307608955 2.07976942838113 2.07976942838113 0 0.110499462943072 0.370335727775466 N 0.359559613319012 0.395139634801289 N N 12308 1122 ENSG00000163382 ENSG00000151967 - + 1 3 154830715 161097816 utr5p intron APOA1BP SCHIP1 154828178 160474304 + + 0.395139634801289 154828187 160964454 - + Y - 0.0376697253372245 N HCC1954 2 1.2 1 1 1 N - - N - Simple_repeat 0 0.976190476190476 0.976190476190476 5 0.478497126715059 0.299953422716903 0.478497126715059 0.299953422716903 1 - 0 47629 Y Y 3.58527523866953 3.55041790174621 3.55041790174621 108 0 0.0942799275562114 Y 0 0 N N 12 3079 ENSG00000204666 ENSG00000142528 - + 19 19 55261862 55243841 utr3p coding AC010624.8-1 ZNF473 55245658 55221024 + + 0 55256970 55234341 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.535631111994469 0.578481600954027 0.578481600954027 0.535631111994469 2 - - 47146 N Y 3.67849247003875 3.30335451653084 3.30335451653084 283 0 0.0206209991253666 Y 0 0.980837184017396 N N 0 155 ENSG00000213904 ENSG00000079435 + - 19 19 47681706 47623418 upstream downstream AC011497.6 LIPE 47681065 47597499 - - 0 47684823 47593191 - + N - - N HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 5 0.549914608314322 0.414221393275723 0.549914608314322 0.414221393275723 2 - - 13299 N N 3.44040523365767 3.5351195431132 3.44040523365767 2 0 0.241788190840909 N 0 0 N N 0 39477 ENSG00000215347 ENSG00000005022 + + 22 X 40727988 118489310 intron coding Z99716.4-1 SLC25A5 40727019 118486436 - + 0 40727524 118487912 - + Y 1 1.13937624842436 N HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.28566992639705 0.735600060472404 0.735600060472404 0.28566992639705 2 0 0 47430 N Y 3.39380340815762 3.64231043829683 3.39380340815762 0 0.0526388888888887 0.532477698896232 Y 0.788090277777778 0.987534722222222 N N 3678 2375 ENSG00000198466 ENSG00000178935 - - 19 19 63068299 63018093 coding upstream ZNF587 ZNF552 63053081 63010262 + - 0 63059288 63023730 - + N - - N HCC1954 2 2 2 7 2 N - - N - LTR 0 1 1 7 0.999844742389676 0.51420586751469 0.999844742389676 0.51420586751469 1 - - 42175 Y Y 3.3755202409218 3.09868097214924 3.09868097214924 200 0 0.111683953140807 Y 0.0879166666666668 0.917083333333333 N N 0 0 ENSG00000214796 ENSG00000213466 + + 4 4 125577725 125203592 downstream downstream AC097474.3 AC108075.3 125576352 125203103 - + 0 125448821 125350594 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.678466075192994 0.792734045751814 0.792734045751814 0.678466075192994 2 - - 48760 N N 3.26407327547924 2.69526421317045 2.69526421317045 8 0 0.0833714316185356 N 0.016463526541364 0 N N 551733 0 ENSG00000204628 ENSG00000219293 + + 5 9 180603512 102534442 utr3p upstream GNB2L1 RP11-394D2.1 180596536 102533343 - + 0 180596551 102482918 - + Y - - N HCC1954 18 14 3 4 1 N 369 23.5452 N - - 0 0 0 4 0.371370904316165 0.257102933757345 0.371370904316165 0.257102933757345 2 - - 1074 N Y 3.59321831773393 3.29908909870209 3.29908909870209 0 0 0.365070193701188 N 0 0 N N 1873 0 ENSG00000109911 ENSG00000221152 + + 11 7 31761903 124570287 intron downstream ELP4 AC019155.4 31487873 124570222 + + 0 31522231 124580901 + + Y 1.03229596693357 - N HCC1954 23 21.4 20 5 1 N - - N LINE SINE 0.983050847457627 0.946808510638298 0.983050847457627 5 0.421363141435649 0.671324327033068 0.671324327033068 0.421363141435649 1 0 - 47401 Y Y 3.39760481766995 2.81143125718837 2.81143125718837 114 0 0.688710680276872 Y 0.972331154684096 0.986165577342048 N N 746 2845 ENSG00000126460 ENSG00000142546 - - 19 19 54785999 54775625 coding upstream PRRG2 NOSIP 54778280 54750782 + - 0 54783588 54776485 - + N - - N HCC1954 1 1 1 0 4 N - - Y Simple_repeat - 0.108333333333333 0 0.108333333333333 5 0.828442786551446 0.849868031031224 0.849868031031224 0.828442786551446 1 - - 38718 N Y 3.32523140661629 3.70889084821189 3.32523140661629 0 0 0.0214864476147557 N 0.880166299828809 0.880166299828809 N N 73 5185 ENSG00000109743 ENSG00000006432 - + 4 14 15343508 70345641 upstream utr3p BST1 MAP3K9 15313739 70264605 + - 0 15292111 70264639 - - Y - - N HCC1954 23 21.8 21 5 1 N - - N - SINE 0 1 1 5 0.521347615674617 0.299953422716903 0.521347615674617 0.299953422716903 1 - - 19141 N N 3.52833332499807 3.51729103662399 3.51729103662399 21 0.0619712768050363 0.680668855994743 N 0.875418060200669 0.670224277001771 Y N 49 2833 ENSG00000186973 ENSG00000133019 - + 1 1 43394654 238139338 upstream utr5p FAM183A CHRM3 43382616 237858996 + + 0.0546429274050756 43375581 237859192 - + N - - N HCC1954 24 23 20 6 3 N - - N SINE LINE 0.737226277372263 1 1 6 0.821301038391519 0.478497126715059 0.821301038391519 0.478497126715059 1 - - 32602 N N 3.06886100299938 3.45343911365801 3.06886100299938 0 0.28327988429856 0.0421321789312048 N 0.21335597057159 0.28327988429856 N N 18920 2079 ENSG00000082781 ENSG00000170365 - + 3 4 126088834 146699773 utr5p intron ITGB5 SMAD1 125964488 146622401 - + 0 126088579 146634611 + + Y - 0.388877531462293 N HCC1954 21 20.25 20 8 1 N 529 24.8175 N - SINE,SINE 0 1 1 8 0.621332089913584 0.328520415356608 0.621332089913584 0.328520415356608 1 - 0 1776 N Y 3.26824964015148 3.50000108636471 3.26824964015148 36 0 0.325269226091948 N 0.982373422312491 0.938306978093718 N N 8014 0 ENSG00000149084 ENSG00000207858 - + 11 13 43834736 89681532 utr3p downstream HSD17B12 hsa-mir-622 43658719 89681437 + + 0.330190047874655 43834016 89713597 - + Y - - N HCC1954 64 45 10 4 1 N - - N - SINE 0 1 1 4 0.649899082553289 0.678466075192994 0.678466075192994 0.649899082553289 1 - - 34196 N Y 3.55504469436573 3.45720067037699 3.45720067037699 386 0 0.00596776108044594 Y 0.706284370132553 0.993880924377762 N N 0 640 ENSG00000219396 ENSG00000178445 + - 9 9 6660008 6635692 intron upstream RNF2P GLDC 6659004 6522469 - - 0 6659542 6636083 - + N 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 23 1.19267194270768 1.63546032862311 1.63546032862311 1.19267194270768 2 0 - 33013 N N 2.91783662205815 3.39483647792751 2.91783662205815 21 0.157141601476663 0.999997568741544 N 0.202179836512262 0.022026896369869 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.022026896369869 8407 12084 - + N 0.984947018030751 6.97806364728775 N HCC1954 4 1.69230769230769 1 7 12 Y 189 4.09957 N - - 0 0 0 13 0.99270299422975 1.42834963198525 1.42834963198525 0.99270299422975 1 0 0 16522 N N 3.26680176242833 3.09549782445355 3.09549782445355 13 0.0382437242845917 0.234107166200478 N 0.0588160510378625 0.0639591327261801 N N 0 317991 ENSG00000212678 ENSG00000171346 - - 1 17 560165 36932191 intron coding RP5-857K21.11 KRT15 559619 36923523 + - 0.0639591327261801 559631 36928517 - + Y 1 23.7148257093497 N HCC1954 2 1.5 1 5 2 N - - N - Simple_repeat 0 0.473958333333333 0.473958333333333 10 0.642757334393363 0.99270299422975 0.99270299422975 0.642757334393363 2 0 0 32005 N Y 2.24460443743887 2.95696360960954 2.24460443743887 0 0 0.248156778154141 N 0 0.849507178195671 N N 6858 5448 ENSG00000164715 ENSG00000131374 - + 7 3 97673537 17757403 intron upstream LMTK2 TBC1D5 97574133 17174903 + - 0 97648178 17759063 - - Y 0.728085935442038 - N HCC1954 2 1.42105263157895 1 8 1 N - - N - Low_complexity,Low_complexity 0 0.124113475177305 0.124113475177305 19 0.671324327033068 0.99270299422975 0.99270299422975 0.671324327033068 2 0 - 33761 N N 2.77892265388278 3.22270715684554 2.77892265388278 0 0 0.999995893951447 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8476 10858 - + N - 0.351991594151195 N HCC1954 4 2 1 5 12 Y 189 4.09957 N - - 0 0 0 10 0.849868031031224 1.3069399132665 1.3069399132665 0.849868031031224 1 - 0 48005 N N 3.36447795254773 3.25459326553517 3.25459326553517 0 0.00434782608695639 0.991231662531754 N 0.00434782608695639 0 N N 0 10798 ENSG00000212451 ENSG00000113761 - - 8 5 127753081 176426349 downstream intron U11 ZNF346 127752949 176382303 + + 0 128092286 176410356 - - Y - 1.34575632127257 N HCC1954 1 1 1 0 5 N - - N LINE - 0.179775280898876 0 0.179775280898876 10 0.635615586233437 1.05697872766909 1.05697872766909 0.635615586233437 1 - 0 29118 N N 3.69632097652796 3.72551845106187 3.69632097652796 0 0 0.917043436350528 Y 0 0 N N 343 52571 ENSG00000178729 ENSG00000096433 + + 6 6 48144384 33772324 intron coding C6orf138 ITPR3 47953998 33697139 - + 0 48120072 33697445 - + N 5.08738813241339 0.34248403896945 N HCC1954 1 1 1 0 4 N 104 11.3593 N - - 0 0 0 30 1.15696320190805 0.799875793911741 1.15696320190805 0.799875793911741 1 0 0 48378 N N 1.6758568209105 2.42680847320244 1.6758568209105 0 0 0.314519819803446 N 0.385604345857854 0 N N 2 5996 ENSG00000187754 ENSG00000187678 + - X 5 52752974 141684750 utr3p utr3p SSX2 SPRY4 52742671 141670189 - - 0.152557718424627 52742846 141671703 - + Y - 1.17999248232857 N HCC1954 36 34.25 33 4 1 N - - N Simple_repeat - 0.976190476190476 0 0.976190476190476 4 0.299953422716903 0.307095170876829 0.307095170876829 0.299953422716903 1 - 0 42309 N Y 3.28292550416853 3.56591914887046 3.28292550416853 0 0 0.237397452602197 Y 0.991832140383283 0.991832140383283 N N 2970 2700 ENSG00000163293 ENSG00000170448 - - 4 4 47736947 47611390 coding upstream NPAL1 NFXL1 47713548 47544017 + - 0 47721843 47611479 - + N 1.05096662957123 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.93556900895034 0.785592297591888 0.93556900895034 0.785592297591888 1 0 - 17278 N N 3.62192127872787 2.85165743972721 2.85165743972721 0 0 0.0885613853673084 N 0 0.293070953436807 N N 1908 4363 ENSG00000079974 ENSG00000173436 - + 22 1 49568957 19839759 utr3p intron RABL2B C1orf151 49552786 19796054 - + 0.293070953436807 49553318 19796335 + + Y - 4.29483891648856 N HCC1954 35 32.5 30 4 1 N - - N SINE - 1 0 1 4 0.357087407996313 0.528489363834543 0.528489363834543 0.357087407996313 2 - 0 545 N Y 3.42424163912411 3.23632367866849 3.23632367866849 0 0 0.282539354755044 Y 0.936642743221691 0.873285486443381 N N 3207 8014 ENSG00000177225 ENSG00000149084 - - 11 11 767487 43834736 utr3p utr3p PDDC1 HSD17B12 757225 43658719 - + 0 759916 43834017 + - N - 1.56696486080893 N HCC1954 99 64.1428571428571 33 28 1 N - - N SINE,SINE - 1 0 1 28 0.414221393275723 0.635615586233437 0.635615586233437 0.414221393275723 2 - 0 29448 N Y 2.8046314587041 3.55504469436574 2.8046314587041 0 0 0.811501404428278 Y 0 0.993730284684261 N Y 13029 17595 ENSG00000124664 ENSG00000196821 - + 6 6 34632069 34772603 utr5p coding SPDEF C6orf106 34613558 34663050 - - 0 34620239 34722356 + - N - - N HCC1954 2 1.25 1 1 1 Y - - N - - 0 0 0 4 0.642757334393363 0.799875793911741 0.799875793911741 0.642757334393363 4 - - 2733 N Y 3.26824964015148 3.4780843434859 3.26824964015148 24 0 0.352132011603636 N 0.983259970654929 0.94140989729225 N N 8014 92 ENSG00000149084 ENSG00000169439 - + 11 8 43834736 97693213 utr3p intron HSD17B12 SDC2 43658719 97575058 + + 0.26343870881686 43834016 97658122 - + Y 1.56799368003871 1.73118973460818 N HCC1954 69 46 23 4 1 N - - N - SINE,SINE 0 1 1 4 0.621332089913584 0.392796148795944 0.621332089913584 0.392796148795944 1 0 0 30484 Y Y 3.32799974635873 3.38974567699157 3.32799974635873 0 0 0.997346523640771 Y 0 0.970250442701746 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62697436 62563762 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 5 0.307095170876829 0.321378667196682 0.321378667196682 0.307095170876829 1 - - 36898 N N 3.31353688881791 3.73552766966605 3.31353688881791 0 0 0.077602771008979 N 0.181409295352324 0.283733133433283 N N 16017 10 ENSG00000018236 ENSG00000157890 - + 12 15 39750361 64333139 utr5p intron CNTN1 MEGF11 39588423 63974688 + - 0.283733133433283 39588491 64290706 - - Y - 1.13828589805435 N HCC1954 22 15.125 9 8 1 N - - N - SINE 0 1 1 8 0.528489363834543 0.449930134075354 0.528489363834543 0.449930134075354 2 - 0 7310 N Y 3.23640338425519 3.67320333000993 3.23640338425519 0 0 0.86367844452383 Y 0.986620203063156 0.939790913784202 N N 0 5406 ENSG00000208752 ENSG00000153561 - + 2 2 87193155 86855943 downstream coding AC092651.3 RMND5A 87193084 86800948 + + 0 87221461 86821703 - + N - - N HCC1954 8 6.25806451612903 4 31 1 N - - N - - 0 0 0 31 1.20695543902754 1.12125446110842 1.20695543902754 1.12125446110842 4 - - 30461 N Y 3.56079784271098 3.57167229721571 3.56079784271098 291 0 0.0102244187986351 Y 0.977350827866292 0.992450275955431 N N 123 2220 ENSG00000198932 ENSG00000125962 - + X X 101800664 101745743 upstream downstream GPRASP1 ARMCX5 101792950 101740752 + + 0 101791537 101747236 - + N - - N HCC1954 2 1.25 1 2 2 N - - N LTR - 1 0 1 8 0.907002016310634 0.87843502367093 0.907002016310634 0.87843502367093 1 - - 40354 N Y 3.61360747730288 3.54296933622177 3.54296933622177 0 0 0.157938495915049 N 0.736358885017422 0.907369337979094 N N 27074 216 ENSG00000137804 ENSG00000179284 - + 15 19 39460535 12946567 coding utr3p NUSAP1 DAND5 39412361 12936973 + + 0 39445077 12945816 - + Y - - N HCC1954 37 29 22 24 1 N 389 22.6782 N - SINE 0 1 1 24 1.34979040222606 0.34280391167646 1.34979040222606 0.34280391167646 1 - - 14617 N Y 3.70889084821189 3.23577154206942 3.23577154206942 1 0 0.292875191209889 N 0.980470588235294 0.980470588235294 N N 6 1110 ENSG00000137672 ENSG00000198358 + + 11 1 100959869 153865810 upstream upstream TRPC6 ERVK5 100827577 153863173 - - 0 101072004 153873808 - - Y - - N HCC1954 20 18.0833333333333 12 12 1 N 494 14.5898 N LTR,LTR LTR 0.761467889908257 1 1 12 0.649899082553289 0.642757334393363 0.649899082553289 0.642757334393363 1 - - 28416 N N 3.48639814491089 3.6289058359359 3.48639814491089 0 0 0.105285108188472 N 0 0.525925925925926 N N 2377 1 ENSG00000103510 ENSG00000163116 - - 16 4 31050206 99283414 upstream intron MYST1 C4orf37 31036488 98699050 + - 0.525925925925926 31034869 99124453 - + Y - 0.907096774193548 N HCC1954 154 68.8 1 4 1 N - - N SINE LINE,SINE 1 0.894736842105263 1 5 0.328520415356608 0.271386430077198 0.328520415356608 0.271386430077198 1 - 0 40089 Y Y 3.49065421516983 3.52833332499807 3.49065421516983 120 0 0.97317132254501 Y 0 0.98120354488279 N Y 856 4995 ENSG00000129007 ENSG00000128973 - + 15 15 66285502 66309079 coding coding CALML4 CLN6 66270098 66286386 - - 0 66277020 66297928 + - N - - N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 7 1.02126998686945 0.907002016310634 1.02126998686945 0.907002016310634 4 - - 36688 N Y 3.46653819400206 3.43677165801469 3.43677165801469 0 0 0.992704929792145 Y 0 0.99373016336624 N Y 9765 351 ENSG00000139182 ENSG00000205885 - + 12 12 7202793 7165701 coding coding CLSTN3 AC018653.29-1 7174234 7152443 + + 0 7176887 7164497 - + N - - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 4 0.707033067832699 0.721316564152552 0.721316564152552 0.707033067832699 4 - - 212 Y Y 3.52833332499807 3.73808832274579 3.52833332499807 181 0 0.0201029197932133 Y 0.298976541979893 0.983697128883253 N N 0 1856 ENSG00000197188 ENSG00000149231 + - 11 11 95762591 95757574 downstream upstream AP003781.3-1 CCDC82 95762258 95725589 - - 0 95762159 95759096 - + N - - N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 8 0.757025304952183 0.407079645115797 0.757025304952183 0.407079645115797 1 - - 28694 N N 3.56591914887046 3.36397409143795 3.36397409143795 0 0.00537634408602172 0.228006135497901 N 0.00537634408602172 0.00537634408602172 N N 18725 45068 ENSG00000130202 ENSG00000205336 - + 19 16 50084325 56256445 intron coding PVRL2 GPR56 50041233 56220023 + + 0.00537634408602172 50047558 56242685 - + Y 0.513925569528207 - N HCC1954 7 2.6 1 2 1 N - - N SINE - 0.976744186046512 0 0.976744186046512 5 0.307095170876829 0.321378667196682 0.321378667196682 0.307095170876829 1 0 - 31573 N Y 3.67526946954971 3.42001607408871 3.42001607408871 114 0 0.045449394738846 Y 0 0.980570079271378 N N 144 873 ENSG00000007402 ENSG00000114395 + + 3 3 50516032 50366477 intron coding CACNA2D2 CYB561D2 50375237 50363301 - + 0 50380239 50365774 - + N 1.44388671192805 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.757025304952183 0.735600060472404 0.757025304952183 0.735600060472404 2 0 - 24389 N Y 3.24893340314576 3.65384724021086 3.24893340314576 0 0 0.908336922868278 N 0.817605786618445 0.965801084990959 N N 0 2527 ENSG00000206696 ENSG00000186001 + + 18 3 45272097 199082851 upstream intron SNORD58 LRCH3 45272032 199002542 - + 0.965801084990959 45272639 199062232 - + Y - 1.31517858497148 N HCC1954 8 2.2797619047619 1 160 2 N - - N - - 0 0 0 168 1.5783263433437 1.02126998686945 1.5783263433437 1.02126998686945 3 - 0 9571 Y N 3.31439680490491 3.41679307359967 3.31439680490491 12 0 0.99999983729539 Y 0.137117903930131 0.15924308588064 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p coding ORMDL3 GSDMB 35330822 35314374 - - 0.15924308588064 35332237 35322190 - + N 3.36083655937109 1.21091641250926 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 5 0.771308801272036 0.857009779191151 0.857009779191151 0.771308801272036 1 0 0 4019 N Y 3.04376534522421 3.64652665576241 3.04376534522421 303 0.762325463315562 0.763774522272902 Y 0.992333079461792 0.992333079461792 N N 524 0 ENSG00000218609 ENSG00000201515 - - 7 7 65743252 65653116 upstream upstream KCTD7 5S_rRNA 65731380 65652992 + - 0 65694681 65679353 - + N - - N HCC1954 4 1.09803921568627 1 2 5 N - - N - - 0 0 0 51 1.0069864905496 1.17124669822791 1.17124669822791 1.0069864905496 2 - - 35107 N Y 3.28296535696188 3.73808832274579 3.28296535696188 12 0.0417527904092601 0.00780980606803838 N 0.899131872674659 0.899131872674659 N N 18 871 ENSG00000175894 ENSG00000084453 + + 21 12 44955923 21439638 intron utr5p C21orf29 SLCO1A2 44742205 21311651 - - 0.815075099903541 44831199 21439305 - - Y 1.05932632139529 - N HCC1954 440 436 420 5 1 N - - N LINE LINE,LINE 1 1 1 5 0.335662163516534 0.39993789695587 0.39993789695587 0.335662163516534 1 0 - 38318 N Y 3.79040344379773 3.07680408206379 3.07680408206379 0 0 0.91166389513406 Y 0 0 N N 4773 21399 ENSG00000151320 ENSG00000100852 - + 14 14 32372018 31698685 upstream coding AKAP6 ARHGAP5 31868274 31616246 + + 0 31868156 31685221 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.5713398527941 0.642757334393363 0.642757334393363 0.5713398527941 2 - - 43816 N Y 3.27085014602457 3.67320333000993 3.27085014602457 0 0 0.374271409457311 N 0.942837044286763 0.96733545387815 N N 0 0 ENSG00000206696 ENSG00000216961 + - 18 10 45272097 74436359 upstream upstream SNORD58 RP11-344N10.3 45272032 74435597 - - 0.96733545387815 45272634 74436364 - + Y - - N HCC1954 6 4.55769230769231 1 51 1 N - - N - - 0 0 0 52 1.06412047582901 0.714174815992626 1.06412047582901 0.714174815992626 2 - - 32448 N N 3.00935843624818 3.39384326095097 3.00935843624818 0 0 0.169798127360886 N 0 0 N N 0 8185 ENSG00000217620 ENSG00000074416 - - 8 3 103888783 129040709 upstream intron AP003356.2 MGLL 103888246 128890601 + - 0.00414937759336109 103838036 128927359 - + Y - 2.13485567447408 N HCC1954 20 18.4736842105263 18 19 1 N - - N - SINE 0 1 1 19 0.707033067832699 0.278528178237124 0.707033067832699 0.278528178237124 2 - 0 33110 N Y 3.46551447180198 3.45504124488137 3.45504124488137 470 0 0.000463909158936904 Y 0.023915265260615 0.995642478862771 N N 0 1291380 ENSG00000210156 ENSG00000198804 - + MT MT 8365 7446 intron coding AF347015.1-16 MT-CO1 8296 5905 + + 0.995642478862771 8333 6375 - + N 1 1.03930211878925 N HCC1954 4 2.28571428571429 1 5 1 N - - N - - 0 0 0 7 1.09268746846872 0.942710757110266 1.09268746846872 0.942710757110266 2 0 0 5416 N N 3.49744043328497 3.54400240599166 3.49744043328497 3 0 0.0737694975024278 N 0 0 N N 42 975 ENSG00000118997 ENSG00000198487 + + 2 6 196643975 42218335 intron coding DNAH7 AL512274.9 196310672 42183124 - - 0 196590100 42183238 - - Y 0.430160349120909 - N HCC1954 33 24.5 21 4 1 N - - N SINE - 1 0 1 4 0.314236919036755 0.521347615674617 0.521347615674617 0.314236919036755 2 0 - 7354 Y Y 3.48639814491089 3.44190231174398 3.44190231174398 14 0.0135060129509713 0.222229130050703 Y 0.0135060129509713 0.989392537773667 N N 6582 41212 ENSG00000204634 ENSG00000071082 + + 2 2 101134278 101002510 intron utr3p TBC1D8 RPL31 100990123 100985123 - + 0 101006545 101000857 - + N 0.830912216885319 - N HCC1954 15 4.16666666666667 1 8 1 N - - Y - - 0 0 0 12 0.714174815992626 1.1141127129485 1.1141127129485 0.714174815992626 3 0 - 24659 Y Y 3.26294691975352 3.32320511986986 3.26294691975352 112 0 0.11594687624424 Y 0.993077671620665 0.993077671620665 N N 13001 7460 ENSG00000141385 ENSG00000176014 + + 18 18 12367194 12316567 utr3p coding AFG3L2 TUBB6 12319108 12298257 - + 0 12319144 12301051 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 63 1.2783729206268 1.08554572030879 1.2783729206268 1.08554572030879 1 - - 11066 N N 3.53399318738748 3.44871903508266 3.44871903508266 11 0 0.0426659354641235 N 0 0.0923728813559322 N N 8421 1041 ENSG00000012048 ENSG00000204315 - - 17 6 38530994 32206045 utr5p coding BRCA1 FKBPL 38449840 32204465 - - 0.0923728813559322 38530376 32205485 + + Y - 0.85551933152443 N HCC1954 25 23.6 21 5 1 N - - N SINE - 1 0 1 5 0.307095170876829 0.678466075192994 0.678466075192994 0.307095170876829 1 - 0 6378 N N 3.30761058678977 3.65657572715995 3.30761058678977 0 0.323955669224211 0.257966078955528 N 0.479113384484228 0.0302642796248934 N N 131026 29655 ENSG00000115053 ENSG00000136938 - + 2 9 232037449 99818046 coding intron NCL ANP32B 232027706 99785310 - + 0.0302642796248934 232034576 99807299 + + Y - 1.06943068044159 N HCC1954 1 1 1 0 2 Y - - N Simple_repeat,Simple_repeat,Simple_repeat - 0.242677824267782 0 0.242677824267782 5 1.12125446110842 0.949852505270192 1.12125446110842 0.949852505270192 1 - 0 6465 Y Y 3.49268050191626 3.52567938596249 3.49268050191626 142 0 0.90409354771894 Y 0.690546441638145 0.973090994925056 N Y 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 coding coding VAMP5 VAMP8 85665042 85658227 + + 0 85672359 85659801 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 8 0.857009779191151 0.942710757110266 0.942710757110266 0.857009779191151 4 - - 9297 Y Y 3.33424740824393 3.6272104187567 3.33424740824393 320 0 0.929868229451943 Y 0 0 N N 252027 170868 ENSG00000141738 ENSG00000141741 - - 17 17 35157070 35140314 utr5p intron GRB7 C17orf37 35147713 35138937 + - 0 35147806 35140073 - + N 0.563461297271341 1.69054296358442 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 24 1.29979816510658 1.17124669822791 1.29979816510658 1.17124669822791 2 0 0 5365 N N 3.63193049733206 3.31588453542141 3.31588453542141 0 0 0.0708912375137631 N 0 0 N N 4028 78560 ENSG00000064012 ENSG00000112493 + + 2 6 201860679 33390114 utr3p utr3p CASP8 TAPBP 201806411 33375449 + - 0 201859878 33375891 + - Y - - N HCC1954 40 37.25 34 4 1 N - - N SINE DNA 1 0.123655913978495 1 4 0.307095170876829 0.592765097273879 0.592765097273879 0.307095170876829 1 - - 3397 Y Y 3.57063922744582 3.5555392079057 3.5555392079057 178 0 0.0115434423406324 Y 0 0 N N 24125 6 ENSG00000157557 ENSG00000157554 - - 21 21 39118749 38955488 upstream upstream ETS2 ERG 39099101 38673819 + - 0 39034090 39019436 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.442788385915428 0.5713398527941 0.5713398527941 0.442788385915428 2 - - 8802 N N 3.54296933622177 3.51207644450867 3.51207644450867 0 0.0332681017612523 0.360810684722637 N 0.0332681017612523 0.0332681017612523 N N 12320 1992 ENSG00000108587 ENSG00000003436 - - 17 2 25877957 188127464 utr3p intron GOSR1 TFPI 25828552 188037202 + - 0.0332681017612523 25873847 188120686 - + Y - 11.2383441972674 N HCC1954 24 22.1333333333333 17 15 2 N - - N Other - 1 0 1 15 0.607048593593732 0.649899082553289 0.649899082553289 0.607048593593732 3 - 0 34170 Y Y 3.21232721588077 3.2875921495814 3.21232721588077 306 0 0.0733555807652773 Y 0 0.984303432659153 N Y 382 1792 ENSG00000171448 ENSG00000186130 + - 9 9 124733600 124715430 utr5p intron ZBTB26 ZBTB6 124720200 124710157 - - 0 124733537 124714181 - + N 1.03670082967301 0.259512207046749 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 14 0.928427260790413 0.928427260790413 0.928427260790413 0.928427260790413 4 0 0 6985 Y Y 3.8333716936548 3.25463311832853 3.25463311832853 20 0 0.992913235311753 Y 0.0823292498741399 0.990132572579292 N N 0 52 ENSG00000183846 ENSG00000214164 + - 2 2 110575338 110569923 upstream downstream AC112229.4-1 AC112229.4-2 110574935 110569013 - - 0 110576429 110545945 - + N - - N HCC1954 60 41.6144578313253 18 83 4 N - - Y - LINE 0 1 1 83 1.35693215038599 0.757025304952183 1.35693215038599 0.757025304952183 3 - - 49184 Y Y 3.34256120966892 3.63040291402221 3.34256120966892 111 0 0.243426847098078 Y 0.00434782608695661 0 N N 5515 6069 ENSG00000152620 ENSG00000145604 + + 5 5 36278015 36219902 utr3p coding C5orf33 SKP2 36228451 36187946 - + 0 36228480 36213151 - + N 0.00822613642258928 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.542772860154395 0.792734045751814 0.792734045751814 0.542772860154395 4 0 - 28130 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.139784506733212 N 0 0 N N 4898 45068 ENSG00000136816 ENSG00000205336 - + 9 16 131613381 56256445 utr3p upstream TOR1B GPR56 131605253 56220023 + + 0 131611903 56211646 - + Y - - N HCC1954 28 23 20 51 2 N - - N SINE - 1 0 1 51 0.321378667196682 0.699891319672773 0.699891319672773 0.321378667196682 0 - - 18434 N Y 3.47233119514066 3.70040921291755 3.47233119514066 323 0 0.0849563027065877 Y 0 0 N N 10984 14389 ENSG00000136631 ENSG00000163113 - - 1 1 148384129 148249310 upstream intron VPS45 OTUD7B 148305966 148178855 + - 0 148305640 148216136 - + N - 1.51699937936104 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 10 1.1426797055882 0.942710757110266 1.1426797055882 0.942710757110266 1 - 0 49288 Y Y 3.29127915838687 3.66273010308932 3.29127915838687 0 0 0.70000340636898 Y 0.979110476492676 0.994777619123169 N N 1313 0 ENSG00000133835 ENSG00000202092 - + 5 5 118905923 118809427 coding upstream HSD17B4 5S_rRNA 118816122 118809310 + + 0 118816227 118784406 - + N - - N HCC1954 6 1.46551724137931 1 12 2 N - - Y - LTR,LTR 0 1 1 58 1.42120788382533 1.549759350704 1.549759350704 1.42120788382533 1 - - 39896 Y Y 3.56079784271098 3.34355442664546 3.34355442664546 248 0 0.137457137883020 Y 0.381451612903226 0.989516129032258 N N 803 2124 ENSG00000169609 ENSG00000169612 + + 15 15 81471362 81450795 intron intron C15orf40 FAM103A1 81464398 81445975 - + 0 81468303 81448583 - + N 0.457511688582964 3.86431756115535 N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 5 0.685607823352921 0.549914608314322 0.685607823352921 0.549914608314322 1 0 0 9769 Y Y 3.66641711189479 3.38080938095063 3.38080938095063 7 0 0.99097895384468 Y 0 0.966080876795163 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron utr3p C17orf76 C17orf45 16286053 16283081 - + 0 16304917 16285119 - + N 2.8965503530481 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 8 0.985561246069823 1.09268746846872 1.09268746846872 0.985561246069823 1 0 - 17783 N Y 3.03226839610352 3.49272035470961 3.03226839610352 0 0 0.542693012573901 N 0.645653846153846 0.837192307692308 N N 3863 0 ENSG00000219481 ENSG00000219033 + - 1 1 146862781 147396926 upstream upstream NBPF15 RP11-744H18.2 146827614 147356499 + - 0.837192307692308 146822895 147404065 + + N - - Y HCC1954 2 2 2 6 1 N 352 16.0273 N - - 0 0 0 6 0.421363141435649 0.349945659836387 0.421363141435649 0.349945659836387 1 - - 25220 Y Y 3.6988816296077 3.21228736308742 3.21228736308742 8 0 0.150716454994045 Y 0.0638221665062345 0.992388798101677 N N 1675 2405 ENSG00000120697 ENSG00000120699 - - 13 13 36471477 36481538 utr5p utr5p ALG5 EXOSC8 36421967 36472678 - + 0 36471452 36472852 + - N - 0.0242754231712216 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.799875793911741 0.749883556792257 0.799875793911741 0.749883556792257 2 - 0 40102 Y Y 3.45872825368684 3.42420178633076 3.42420178633076 0 0 0.843268351249828 N 0.940587774792121 0.986797283287138 Y N 40 0 ENSG00000178115 ENSG00000180987 - - 15 15 30680425 30678304 coding downstream AC123768.8-3 AC123768.8-1 30672949 30677791 + - 0 30674761 30666918 - + N - - N HCC1954 40 15.5555555555556 4 9 1 N - - N - - 0 0 0 9 1.1426797055882 1.12839620926835 1.1426797055882 1.12839620926835 4 - - 31136 Y Y 2.42313901988871 3.45447218342791 2.42313901988871 347 0 0.0619140923098038 Y 0 0.99117594552549 N N 0 20663 ENSG00000198579 ENSG00000133657 + - 3 3 195703392 195670257 downstream intron AC108676.8 ATP13A3 195700704 195604698 - - 0 195688602 195664387 - + N - 168.228683185932 N HCC1954 1 1 1 0 4 N - - Y Simple_repeat - 0.845588235294118 0 0.845588235294118 117 0.971277749749971 0.757025304952183 0.971277749749971 0.757025304952183 2 - 0 2299 N N 3.47911741325579 3.55401162459584 3.47911741325579 7 0 0.0155783015673810 N 0 0 N N 2 3223 ENSG00000196844 ENSG00000175928 - + 11 3 125153924 3864387 utr3p upstream PATE2 LRRN1 125151268 3816121 - + 0 125151456 3745219 + + Y - - N HCC1954 483 447.428571428571 420 14 1 N - - N LINE SINE 1 1 1 14 0.449930134075354 0.299953422716903 0.449930134075354 0.299953422716903 1 - - 28737 N Y 3.56911164413597 3.42783536197374 3.42783536197374 0 0 0.301566693141211 N 0.818178977627797 0.873515810523685 N N 7722 1710 ENSG00000090661 ENSG00000187535 - - 19 16 8233302 1600859 coding intron LASS4 IFT140 8180257 1500429 + - 0 8221961 1597789 - + Y - 3.90437934458788 N HCC1954 20 12.6666666666667 6 6 1 N - - N - SINE 0 1 1 6 0.535631111994469 0.442788385915428 0.535631111994469 0.442788385915428 1 - 0 17419 Y N 2.53993790609239 3.52680574168821 2.53993790609239 0 0.0508440447024867 0.0849576106814085 Y 0.303151323958788 0 N N 9281 0 ENSG00000213240 ENSG00000201789 - - 1 1 144003011 143861197 coding upstream NOTCH2NL U6 143920462 143861097 + - 0 143920676 143887811 - + N - - N HCC1954 4 2.57142857142857 2 7 1 N - - Y - LTR 0 0.00980392156862745 0.00980392156862745 7 0.778450549431962 0.657040830713216 0.778450549431962 0.657040830713216 2 - - 34287 Y Y 3.39168383545536 3.48167806633553 3.39168383545536 0 0 0.586852516873912 Y 0 0 N N 0 0 ENSG00000210611 ENSG00000217739 - - 9 9 32059981 31635158 upstream upstream AL589825.8 RP11-402B2.1 32059823 31634578 + - 0 31963015 31838907 - + N - - N HCC1954 2 1.2 1 1 1 N - - Y - LTR 0 1 1 5 0.328520415356608 0.442788385915428 0.442788385915428 0.328520415356608 2 - - 18358 N N 3.60103760561896 3.10654011282762 3.10654011282762 0 0 0.0908418170817094 Y 0.620219918756128 0 N N 16 0 ENSG00000162723 ENSG00000216758 + - 1 1 158190668 145062731 upstream intron SLAMF9 RP11-325P15.3 158187911 144959503 - - 0 158215012 144997649 - + N - 1 N HCC1954 20 20 20 4 1 N - - N - Simple_repeat 0 0.918918918918919 0.918918918918919 4 0.592765097273879 0.264244681917271 0.592765097273879 0.264244681917271 1 - 0 34186 Y Y 3.60785432895764 3.27677112823916 3.27677112823916 318 0 0.0323052622194281 Y 0 0.992828378806389 N N 0 0 ENSG00000165023 ENSG00000105061 + + 9 9 92444928 92035243 downstream downstream DIRAS2 RP11-389K14.2 92411934 92034287 - + 0 92235536 92185826 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.620689655172414 0.620689655172414 50 0.971277749749971 1.24266417982717 1.24266417982717 0.971277749749971 1 - - 47353 Y Y 3.39384326095097 3.57063922744582 3.39384326095097 0 0 0.651102431997797 Y 0.992932257275618 0.985864514551235 N N 3272 17901 ENSG00000141971 ENSG00000130303 - - 19 19 17397140 17377401 coding upstream FAM125A BST2 17391856 17374750 + - 0 17392122 17378105 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.0069864905496 0.771308801272036 1.0069864905496 0.771308801272036 4 - - 18952 Y Y 3.46807512488172 3.46192074895235 3.46192074895235 225 0 0.0193921942007415 Y 0 0.986900584795322 N N 0 25182 ENSG00000218745 ENSG00000116539 - - 1 1 153838612 153798948 intron upstream RP11-29H23.2 ASH1L 153823059 153571677 + - 0 153835258 153799803 - + N 1 - N HCC1954 2 1.25 1 1 1 N - - Y - - 0 0 0 4 0.442788385915428 0.528489363834543 0.528489363834543 0.442788385915428 1 0 - 27152 Y Y 3.37295958784206 3.2875921495814 3.2875921495814 168 0 0.00792983894116328 Y 0 0 N N 1207 571 ENSG00000196155 ENSG00000135740 - + 16 16 65880883 65863594 utr5p intron PLEKHG4 SLC9A5 65868914 65840356 + + 0 65869067 65857486 - + N - 1.07991449974805 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.492780623034912 1.04269523134923 1.04269523134923 0.492780623034912 1 - 0 20289 N N 3.68105312311849 3.5016965035439 3.5016965035439 0 0 0.129085766328274 N 0 0 N N 49089 0 ENSG00000117450 ENSG00000207173 - - 1 16 45760196 56674573 coding upstream PRDX1 Y_RNA 45749295 56674473 - - 0 45757265 56686128 + + Y - - N HCC1954 40 5.54901960784314 2 51 1 N - - N - SINE 0 1 1 51 1.15696320190805 0.278528178237124 1.15696320190805 0.278528178237124 3 - - 20655 N N 3.3241983368464 3.31489131844487 3.31489131844487 8 0 0.0400154208165348 N 0 0 N N 0 50640 ENSG00000165583 ENSG00000175793 - + X 1 47941143 27063534 utr3p downstream SSX5 SFN 47930600 27062240 - + 0.00225733634311498 47930929 27063538 + + Y - - N HCC1954 33 32.8 32 5 1 N - - N Simple_repeat - 0.972222222222222 0 0.972222222222222 5 0.257102933757345 0.364229156156239 0.364229156156239 0.257102933757345 1 - - 18263 Y Y 3.68783934123363 3.43937216388778 3.43937216388778 261 0 0.00583938488544111 Y 0.980273889457911 0.990136944728956 N N 145 959 ENSG00000187010 ENSG00000117616 - - 1 1 25529523 25446572 upstream utr5p RHD C1orf63 25471568 25441328 + - 0 25466817 25446106 - + N - 1.22646974895899 N HCC1954 2 2 2 6 1 N - - Y - - 0 0 0 6 0.557056356474248 0.764167053112109 0.764167053112109 0.557056356474248 1 - 0 26993 Y Y 3.45447218342791 3.55401162459584 3.45447218342791 0 0 0.478965744631677 Y 0 0.991558920077712 N N 0 1307 ENSG00000205014 ENSG00000170100 - + 16 16 87828005 87822471 upstream coding AC009113.8-1 ZNF778 87826786 87811612 + + 0 87826572 87820603 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LINE 0.973451327433628 0.408805031446541 0.973451327433628 7 0.792734045751814 1.0069864905496 1.0069864905496 0.792734045751814 1 - - 36573 Y Y 3.52680574168822 3.45976132345673 3.45976132345673 0 0 0.99757911696994 Y 0.851641273380404 0.994884181840704 N Y 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6313671 6328154 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 225 1.47120012094481 1.62117683230326 1.62117683230326 1.47120012094481 4 - - 48033 N N 3.41576000382978 3.61464054707278 3.41576000382978 0 0.0227450980392156 0.9926838752488 N 0.33187675070028 0.0127731092436975 N N 10798 0 ENSG00000113761 ENSG00000212451 - - 5 8 176426349 127753081 coding downstream ZNF346 U11 176382303 127752949 + + 0 176410541 128113175 - - Y - - N HCC1954 1 1 1 0 5 N - - N - SINE,SINE 0 1 1 45 1.55690109886392 0.764167053112109 1.55690109886392 0.764167053112109 2 - - 27235 Y Y 3.60785432895764 3.49744043328497 3.49744043328497 0 0 0.833334714977992 Y 0.669706516332283 0.993883454006153 N Y 10006 5916 ENSG00000132612 ENSG00000168807 - + 16 16 67916446 67900456 coding coding VPS4A SNTB2 67895081 67778533 + + 0 67907412 67891178 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.87843502367093 0.87843502367093 0.87843502367093 0.87843502367093 4 - - 31432 Y Y 3.33464863582806 3.54036883034868 3.33464863582806 367 0 0.257388181072109 Y 0.266155981697599 0.993727828903398 N N 18718 1907 ENSG00000160796 ENSG00000160799 - - 3 3 47026197 46993242 intron upstream AC094020.2 CCDC12 46996177 46938225 + - 0 46998427 46993338 - + N 0.283672096413374 - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 12 1.13553795742827 1.33550690590621 1.33550690590621 1.13553795742827 1 0 - 29436 Y Y 3.38440310380026 3.29123930559352 3.29123930559352 0 0 0.713571663585595 Y 0.992981863785452 0.978945591356357 N N 7875 4552 ENSG00000010017 ENSG00000137420 + + 6 6 13819932 13729105 coding utr3p RANBP9 NOL7 13729714 13723538 - + 0 13740604 13729067 - + N 0.757415991172966 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.921285512630487 0.956994253430118 0.956994253430118 0.921285512630487 4 0 - 9357 N Y 3.58697065584872 3.39483647792751 3.39483647792751 309 0 0.264326211788316 Y 0.951207368683097 0.979088872292756 N N 0 8390 ENSG00000207064 ENSG00000120071 + - 17 17 41648314 41625943 upstream utr5p Y_RNA KIAA1267 41648213 41463181 - - 0 41656814 41605375 - + N - 30.0463502853045 N HCC1954 2 1.825 1 33 2 N - - N - - 0 0 0 40 1.07126222398894 1.23552243166724 1.23552243166724 1.07126222398894 4 - 0 19832 N Y 3.20174893582312 3.52105259334297 3.20174893582312 205 0.170182841068917 0.00760934025750049 N 0.225503984997656 0.133302078449758 N N 10339 0 ENSG00000177200 ENSG00000217333 + - 16 1 51918914 169680726 intron upstream CHD9 RP1-81F6.1 51646446 169680447 + - 0.778715424285044 51784739 169691434 + + Y 1.27613943306093 - N HCC1954 168 75.3333333333333 20 6 1 N - - N SINE SINE 1 0.925 1 6 0.278528178237124 0.28566992639705 0.28566992639705 0.278528178237124 1 0 - 43542 N N 3.48418371977919 3.57592836747465 3.48418371977919 0 0 0.0218426695660149 N 0.245564892623716 0.15126050420168 N N 191 282831 ENSG00000168878 ENSG00000099194 - + 2 10 85749375 102114577 utr3p downstream SFTPB SCD 85737954 102096762 - + 0.15126050420168 85738610 102131186 + + Y - - N HCC1954 44 24.4285714285714 21 35 1 N - - N LTR LTR 1 1 1 35 0.371370904316165 0.671324327033068 0.671324327033068 0.371370904316165 0 - - 8449 N Y 3.67593181695901 3.4944157718888 3.4944157718888 0 0.551875 0.532427826511031 N 0.937760416666667 0.9253125 N N 0 103859 ENSG00000213643 ENSG00000108953 + + 7 17 63542489 1250267 downstream coding AC022202.12 YWHAE 63541578 1194595 - - 0.66390625 63531709 1250091 - - Y - - N HCC1954 2 1.05882352941176 1 1 1 N - - N - - 0 0 0 17 0.428504889595575 0.592765097273879 0.592765097273879 0.428504889595575 3 - - 26863 Y Y 3.81554318716558 3.20869364023779 3.20869364023779 252 0 0.0168751726110515 Y 0.989624669312169 0.989624669312169 N N 12 2292 ENSG00000150281 ENSG00000099385 - - 16 16 30822381 30812900 intron intron CTF1 BCL7C 30811875 30753770 + - 0 30813371 30794941 - + N 0.646833013435701 0.0622758297526604 N HCC1954 1 1 1 0 1 N - - Y LINE,LINE SINE 0.744186046511628 0.776315789473684 0.776315789473684 6 0.614190341753658 0.542772860154395 0.614190341753658 0.542772860154395 1 0 0 7517 Y Y 3.33680806132368 3.34615493251855 3.33680806132368 161 0.0244866071428571 0.638715014266643 Y 0.0743303571428572 0.992879464285714 N N 17694 466 ENSG00000153827 ENSG00000153832 - - 2 2 230494912 230586068 utr5p intron TRIP12 FBXO36 230340174 230495262 - + 0 230494840 230495843 + - N - 0.600688791064477 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 39 1.28551466878673 0.949852505270192 1.28551466878673 0.949852505270192 1 - 0 766 Y Y 3.04164577252194 3.43721273839216 3.04164577252194 109 0 0.364505932682886 Y 0.935380933386518 0.978460311128839 N N 1172 1543 ENSG00000174165 ENSG00000174483 + + 11 11 66070247 66057660 coding intron ZDHHC24 BBS1 66063311 66034666 - + 0 66067830 66048264 - + N - 1.76344442768481 N HCC1954 20 3.22222222222222 1 2 4 N - - Y - SINE 0 1 1 9 0.971277749749971 0.664182578873142 0.971277749749971 0.664182578873142 2 - 0 19188 Y Y 3.54292948342842 3.42779550918039 3.42779550918039 0 0 0.281400929470442 Y 0.708694083694084 0.993526535193202 N N 0 6723 ENSG00000201987 ENSG00000185630 - + 1 1 163090193 163082933 downstream coding Y_RNA PBX1 163090092 162795684 + + 0 163120404 163082445 - + N - - N HCC1954 1 1 1 0 1 N - - Y RNA,RNA - 0.401197604790419 0 0.401197604790419 24 1.19267194270768 1.07126222398894 1.19267194270768 1.07126222398894 2 - - 7872 N Y 3.31319590126568 3.59169073442408 3.31319590126568 0 0 0.452667259155945 N 0 0.831761209458586 N N 12251 5683 ENSG00000134851 ENSG00000144136 - + 4 2 55987095 113137869 coding utr5p TMEM165 SLC20A1 55956877 113119998 + + 0.831761209458586 55972761 113130547 - + Y - - N HCC1954 33 31.25 30 4 1 N - - N - SINE 0 1 1 4 0.421363141435649 0.271386430077198 0.421363141435649 0.271386430077198 1 - - 18117 Y Y 3.46807512488172 3.44768596531277 3.44768596531277 299 0.455530781617738 0.00247439192398657 Y 0.990771708163013 0.990771708163013 N N 198 293 ENSG00000212919 ENSG00000197959 + + 1 1 170679811 170648480 intron intron Z97195.1-1 DNM3 170629356 170077261 - + 0 170654045 170624573 - + N 1.98384233051846 2.14709267096208 N HCC1954 1 1 1 0 1 N - - Y Simple_repeat - 0.0495867768595041 0 0.0495867768595041 27 0.864151527351077 1.14982145374813 1.14982145374813 0.864151527351077 1 0 0 17085 N N 3.23999710710482 3.49272035470961 3.23999710710482 1 0 0.70792670587627 N 0.339658112184672 0 N N 1649619 2043 ENSG00000141736 ENSG00000197056 + + 17 1 35138441 35354047 coding intron ERBB2 ZMYM1 35104766 35317559 + + 0 35122225 35349116 + + Y - 1.80081736146951 N HCC1954 3 1.54545454545455 1 5 1 N - - N - SINE 0 1 1 11 0.657040830713216 0.249961185597419 0.657040830713216 0.249961185597419 3 - 0 34727 N Y 3.36976709257655 3.67849247003875 3.36976709257655 0 0 0.995913004909563 Y 0 0.992029962546816 N N 12832 1085 ENSG00000181090 ENSG00000203993 - - 9 9 139850397 139633086 utr5p upstream EHMT1 C9orf37 139711440 139629606 + - 0 139725238 139634339 - + N - - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 5 0.742741808632331 0.742741808632331 0.742741808632331 0.742741808632331 3 - - 10027 N N 3.49640736351508 3.21232721588077 3.21232721588077 0 0.00680848548147117 0.0670207493958328 N 0.0351853858962864 0.0351853858962864 Y N 313916 1649619 ENSG00000131748 ENSG00000141736 - + 17 17 35073248 35138441 coding coding STARD3 ERBB2 35046938 35104766 + + 0.0351853858962864 35070845 35126170 - + N - - N HCC1954 1 1 1 0 1 Y 520 12.148 N - - 0 0 0 4 0.928427260790413 0.842726282871298 0.928427260790413 0.842726282871298 1 - - 46194 N N 3.5010341561346 3.65384724021086 3.5010341561346 0 0 0.120929799371138 N 0 0.00653594771241828 N N 40617 11502 ENSG00000130164 ENSG00000159921 + + 19 9 11105490 36248450 utr3p utr3p LDLR GNE 11061132 36204430 + - 0.00653594771241828 11104135 36206920 + - Y - - N HCC1954 40 38.4 36 5 1 N - - N SINE SINE 0.274509803921569 1 1 5 0.364229156156239 0.299953422716903 0.364229156156239 0.299953422716903 3 - - 5774 N N 3.57912086274016 3.34528969661801 3.34528969661801 0 0 0.0827705845274775 N 0 0.18304378989044 N N 2859 10428 ENSG00000152056 ENSG00000114346 + + 2 3 224410563 174021957 utr3p intron AP1S3 ECT2 224325785 173951207 - + 0.18304378989044 224328559 173951477 - + Y - 0.443838089061747 N HCC1954 37 33.7777777777778 31 9 1 N - - N SINE - 1 0 1 9 0.357087407996313 0.542772860154395 0.542772860154395 0.357087407996313 2 - 0 4189 Y N 3.51935717616377 3.33676820853032 3.33676820853032 0 0 0.606945033860536 Y 0.235755813953488 0.710513565891473 N N 4592 22352 ENSG00000146828 ENSG00000196411 - - 7 7 100302567 100263079 upstream upstream SLC12A9 EPHB4 100288294 100238123 + - 0 100288064 100266025 - + N - - N HCC1954 2 1.07692307692308 1 1 2 N - - Y - SINE 0 0.866666666666667 0.866666666666667 13 0.414221393275723 0.749883556792257 0.749883556792257 0.414221393275723 3 - - 26485 N Y 3.44615838200292 3.45612774781375 3.44615838200292 0 0 0.388449679408808 N 0.0182329906999511 0.88937836514929 N N 4108 13271 ENSG00000006194 ENSG00000081923 - - 16 18 3281456 53550037 upstream upstream ZNF263 ATP8B1 3273488 53464656 + - 0 3266112 53550060 - + Y - - N HCC1954 20 16 12 4 1 N - - N SINE - 1 0 1 4 0.292811674556976 0.357087407996313 0.357087407996313 0.292811674556976 1 - - 31831 N N 3.44143830342756 2.88274380859372 2.88274380859372 4 0.00340136054421758 0.786289364164812 N 0.0411513090084518 0 N N 0 1131 ENSG00000207650 ENSG00000214116 + - 3 3 196911548 197173943 upstream coding hsa-mir-570 AC024937.21-2 196911452 197171055 + - 0 196911258 197171354 + + N - 1.93046968027974 Y HCC1954 2 1.75 1 3 1 N - - N - LINE 0 0.635220125786163 0.635220125786163 4 0.728458312312478 0.757025304952183 0.757025304952183 0.728458312312478 4 - 0 33137 Y N 3.40375919359932 2.99720337251751 2.99720337251751 0 0 0.998804256122959 N 0 0 Y N 247001 59837 ENSG00000198786 ENSG00000198695 - - MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 13291 14668 - + N 0.866182704432073 83.9529680782951 N HCC1954 3 1.5 1 8 7 N 189 4.09957 N - - 0 0 0 18 1.47834186910473 1.24266417982717 1.47834186910473 1.24266417982717 1 0 0 5770 N Y 3.40528677690917 3.30232144676095 3.30232144676095 11 0.0208373528844299 0.0701433779740313 N 0.0208373528844299 0.930059810920316 N N 676 0 ENSG00000144401 ENSG00000213113 + + 2 3 208198276 199332046 utr3p downstream FAM119A AC073135.3-1 208185086 199330983 - + 0.0488134285163033 208185155 199368867 - + Y - - N HCC1954 156 139.173913043478 105 23 1 N - - N SINE - 1 0 1 23 0.349945659836387 0.871293275511003 0.871293275511003 0.349945659836387 2 - - 31153 Y Y 3.67489874718912 3.52567938596249 3.52567938596249 274 0.0216018938646675 0.577558237325081 Y 0.946143223515486 0.982047741171829 N N 41283 6846 ENSG00000047457 ENSG00000163755 + + 3 3 150422519 150373995 coding intron CP HPS3 150373220 150330061 - + 0 150376727 150366527 - + N 0.138583464923563 1.33045161304183 N HCC1954 2 1.70121951219512 1 115 3 N - - Y - - 0 0 0 164 1.20695543902754 0.849868031031224 1.20695543902754 0.849868031031224 4 0 0 44799 Y Y 3.38292895365289 3.56129235625094 3.38292895365289 254 0 0.0237855206694199 Y 0.626476377952756 0.990422471229558 N N 0 338 ENSG00000218952 ENSG00000165338 - + 10 10 93294835 93264566 downstream downstream RPS27P1 HECTD2 93294589 93160082 + + 0 93304899 93274887 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE LTR 0.25 1 1 6 0.857009779191151 0.721316564152552 0.857009779191151 0.721316564152552 1 - - 33163 N Y 3.40215706237596 3.46657804679541 3.40215706237596 521 0 0.000108468498782099 Y 0 0.995823930484504 N N 0 151141 ENSG00000210191 ENSG00000198888 - + MT MT 12337 4264 intron coding AF347015.1-21 MT-ND1 12267 3308 + + 0 12292 4178 - + N 1 1.23059485440129 N HCC1954 2 1.6 1 3 1 N - - N - - 0 0 0 5 0.899860268150708 0.921285512630487 0.921285512630487 0.899860268150708 1 0 0 20493 N N 3.33680806132368 3.50000108636471 3.33680806132368 27 0 0.410697023291272 N 0.99250618239952 0.108235705542927 N N 2806 2601 ENSG00000143674 ENSG00000172197 + + 1 6 231587517 20320649 utr3p utr3p MAP3K19 MBOAT1 231530137 20208914 + - 0.108235705542927 231585767 20210044 + - Y - - N HCC1954 39 26.1875 22 16 1 N - - N - SINE 0 1 1 16 0.928427260790413 1.1141127129485 1.1141127129485 0.928427260790413 3 - - 38385 Y Y 3.13383928169109 3.60426060610801 3.13383928169109 10 0 0.751530670802533 Y 0 0.988925318761384 N N 333 438 ENSG00000181619 ENSG00000126790 - + 14 14 59001813 59020826 utr3p coding GPR135 C14orf149 58965493 59009159 - - 0 59000049 59012389 + - N - 0.432031894738066 N HCC1954 1 1 1 0 3 N - - Y SINE,SINE - 0.618320610687023 0 0.618320610687023 6 0.93556900895034 0.778450549431962 0.93556900895034 0.778450549431962 2 - 0 42651 N Y 3.74809754134998 3.45872825368684 3.45872825368684 0 0 0.460814246026109 N 0 0.744429882044561 N N 1184 47021 ENSG00000169435 ENSG00000130741 - + 4 X 74705151 24006846 utr3p utr3p RASSF6 EIF2S3 74657024 23982986 - + 0.616644823066841 74658002 24005373 + + Y - - N HCC1954 130 65.25 34 4 1 N - - N SINE SINE 1 1 1 4 0.528489363834543 0.678466075192994 0.678466075192994 0.528489363834543 3 - - 30440 N N 3.42572936964061 3.08359030017893 3.08359030017893 0 0 0.958880942664774 Y 0 0 N N 8617 441 ENSG00000221867 ENSG00000147402 - + X X 151621480 151576655 upstream upstream MAGEA6 GABRQ 151617901 151557293 + + 0 151617785 151494160 - + N - - N HCC1954 2 2 2 12 4 N - - N Low_complexity LTR 0.641025641025641 1 1 12 0.557056356474248 0.349945659836387 0.557056356474248 0.349945659836387 3 - - 31229 Y Y 3.56129235625094 3.74656995804013 3.56129235625094 266 0 0.205082478676015 Y 0 0 N N 2931 499 ENSG00000113812 ENSG00000056736 + + 3 3 53891227 53874866 utr3p coding ACTR8 IL17RB 53876195 53855617 - + 0 53877741 53874086 - + N 0.178700533431568 1.07137277249469 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.828442786551446 1.08554572030879 1.08554572030879 0.828442786551446 4 0 0 29384 Y Y 3.33420755545058 3.4780843434859 3.33420755545058 0 0 0.924847187590917 Y 0.965659732117413 0.988553244039137 N N 446 3909 ENSG00000111837 ENSG00000137210 + + 6 6 10946714 10865200 intron coding MAK TMEM14B 10870942 10856024 - + 0 10937222 10857913 - + N 1.45675219045357 - N HCC1954 2 2 2 7 3 N - - Y LTR,LTR - 0.863636363636364 0 0.863636363636364 7 0.685607823352921 0.521347615674617 0.685607823352921 0.521347615674617 1 0 - 40193 N N 3.59528445727371 3.32320511986986 3.32320511986986 11 0 0.297642992082263 N 0 0 N N 1 4041 ENSG00000124092 ENSG00000187720 + + 20 15 55534041 69862776 downstream intron CTCFL THSD4 55505630 69176345 - + 0 55503669 69244951 - + Y - 0.462355564430354 N HCC1954 6 3.75 3 4 1 N - - N - - 0 0 0 4 0.407079645115797 0.528489363834543 0.528489363834543 0.407079645115797 2 - 0 11050 N Y 3.12804628055249 3.68846183584958 3.12804628055249 1 0 0.232612626072068 N 0.880442804428044 0.946863468634686 N N 1649619 6539 ENSG00000141736 ENSG00000120253 - + 17 6 35138441 150109507 coding utr3p ERBB2 NUP43 35104766 150087147 + - 0 35122227 150089111 - - Y - - N HCC1954 23 21.9210526315789 21 38 1 N 194 18.9377 N - SINE 0 1 1 38 1.15696320190805 0.292811674556976 1.15696320190805 0.292811674556976 2 - - 33135 Y N 3.30331466373749 3.37192651807217 3.30331466373749 0 0 0.999747481351076 N 0 0 Y N 247001 59837 ENSG00000198786 ENSG00000198695 - - MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 13294 14612 - + N 0.867612121259097 1.63340493273755 N HCC1954 4 1.63157894736842 1 6 7 N 189 4.09957 N - - 0 0 0 19 1.10697096478857 1.14982145374813 1.14982145374813 1.10697096478857 3 0 0 46450 N N 3.44975210485255 3.44143830342756 3.44143830342756 98 0 0.0131586630190311 N 0 0 N N 33105 0 ENSG00000105372 ENSG00000217306 + + 19 20 47067322 2709687 coding upstream RPS19P3 RPL19P1 47055828 2709260 + + 0 47065658 2708348 + + Y - - N HCC1954 100 40 20 4 1 N - - N - SINE 0 1 1 4 0.599906845433805 0.349945659836387 0.599906845433805 0.349945659836387 1 - - 9416 Y Y 2.79678166559553 3.22167408707565 2.79678166559553 362 0 0.0656601396358427 Y 0.0789403007980355 0.993074739103745 N N 5477 1954 ENSG00000169992 ENSG00000205544 - - 17 17 7263903 7248142 upstream upstream NLGN2 C17orf61 7252226 7247038 + - 0 7252057 7249655 - + N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity,Low_complexity Low_complexity 0.296052631578947 0.4375 0.4375 73 1.08554572030879 1.48548361726466 1.48548361726466 1.08554572030879 1 - - 9454 N Y 3.55397177180249 3.70040921291755 3.55397177180249 217 0 0.137119154820137 Y 0 0 N N 11450 12 ENSG00000108244 ENSG00000187242 + - 17 17 36347362 36276988 downstream downstream KRT23 KRT12 36332478 36270956 - - 0 36328005 36260636 - + N - - N HCC1954 1 1 1 0 2 N - - N SINE - 1 0 1 11 0.892718519990782 0.521347615674617 0.892718519990782 0.521347615674617 2 - - 13724 Y Y 3.27448372166755 3.6623288755052 3.27448372166755 278 0 0.960167877744616 Y 0.961304742613676 0.980652371306838 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 intron intron AP000347.3 AP000347.4 22321400 22310865 - - 0 22324666 22311129 - + N 1 1 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 15 0.771308801272036 1.24266417982717 1.24266417982717 0.771308801272036 4 0 0 9469 Y Y 2.99293372188944 3.61207989399303 2.99293372188944 189 0 0.0134775480584191 Y 0 0.978608408715936 N N 1649619 109916 ENSG00000141736 ENSG00000161395 - - 17 17 35138441 35097836 upstream upstream ERBB2 PERLD1 35104766 35080902 + - 0 35103098 35098577 - + N - - N HCC1954 1 1 1 0 2 N - - Y DNA LINE 1 0.758620689655172 1 4 0.664182578873142 0.592765097273879 0.664182578873142 0.592765097273879 0 - - 48114 N N 3.54296933622177 3.59272380419397 3.54296933622177 0 0 0.999999781023675 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117944553 2608428 - + Y - - N HCC1954 2 1.10852713178295 1 14 12 N 282 1.61558 N - LINE 0 0.869565217391304 0.869565217391304 129 1.39264089118562 1.31408166142643 1.39264089118562 1.31408166142643 1 - - 30985 N N 3.21444678858304 1.99788396384033 1.99788396384033 1 0 0.0311896408100670 N 0 0 N N 41507 8332 ENSG00000188846 ENSG00000124788 + - 3 6 40478862 16869666 coding coding RPL14 ATXN1 40473834 16407322 + - 0 40478443 16435895 + + Y - 0.447134300216778 N HCC1954 40 21.6 8 5 1 Y - - N - Simple_repeat 0 1 1 5 0.385654400636018 0.34280391167646 0.385654400636018 0.34280391167646 1 - 0 44974 Y Y 3.57489529770476 3.20703807585194 3.20703807585194 11 0.00255754475703329 0.159524311355743 Y 0.994637406154608 0.994637406154608 N N 5786 1260 ENSG00000166272 ENSG00000156398 - + 10 10 104565987 104488930 coding downstream C10orf26 SFXN2 104525878 104464288 + + 0.747958089266562 104547741 104493891 - + N - - N HCC1954 10 1.25 1 21 1 N - - Y - Low_complexity,Low_complexity 0 0.572916666666667 0.572916666666667 116 1.52833410622422 1.37121564670584 1.52833410622422 1.37121564670584 1 - - 9536 Y Y 3.44615838200292 3.30704152533631 3.30704152533631 451 0 0.204186693290481 Y 0 0.963215384143787 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 utr3p intron C17orf37 ERBB2 35138937 35104766 - + 0 35138986 35133805 - + N 0.663546612455591 1.22302977699755 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 18 1.02841173502938 0.985561246069823 1.02841173502938 0.985561246069823 1 0 0 36142 N Y 3.3420972013525 3.33891851073686 3.33891851073686 102 0.690563725490196 0.00423443389587297 N 0.690563725490196 0.721507352941176 N N 614 2906 ENSG00000174099 ENSG00000214135 + + 12 3 64146945 196895854 utr3p downstream MSRB3 AC069513.28-1 63958755 196874647 + + 0.721507352941176 64144258 196896948 + + Y - - N HCC1954 44 35.5 21 6 1 N - - N SINE SINE 1 1 1 6 0.349945659836387 0.51420586751469 0.51420586751469 0.349945659836387 1 - - 18283 Y Y 3.62361669590707 3.73912139251568 3.62361669590707 0 0.736170212765958 0.461124535862016 Y 0.780141843971631 0.890070921985816 N N 0 0 ENSG00000223181 ENSG00000217260 + - 1 1 683579 653390 downstream upstream U6 RP11-206L10.1 683476 651474 - - 0.824113475177305 669187 661982 - + N - - N HCC1954 324 171.571428571429 102 7 4 N - - Y DNA DNA 1 1 1 7 0.499922371194838 0.499922371194838 0.499922371194838 0.499922371194838 1 - - 3339 Y Y 3.20487865035633 3.43824580816205 3.20487865035633 123 0.0388349514563107 0.378679079704356 Y 0.309385113268608 0.950161812297735 N Y 9381 29 ENSG00000159079 ENSG00000166984 + - 21 21 32906767 32879714 coding coding C21orf59 TCP10L 32895848 32870733 - - 0 32897342 32876596 - + N - 3.39148295475668 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 9 0.971277749749971 1.18553019454776 1.18553019454776 0.971277749749971 4 - 0 13741 Y Y 1.95021206491475 3.60103760561896 1.95021206491475 0 0 0.471937420828182 Y 0.752100840336134 0 N N 194 480 ENSG00000169325 ENSG00000159496 + + 22 22 22389508 22371363 downstream downstream AP000347.1 RGL4 22386399 22360329 - + 0 22382044 22377731 - + N - - N HCC1954 1 1 1 0 4 N - - Y LINE LINE 0.726027397260274 1 1 10 0.521347615674617 0.792734045751814 0.792734045751814 0.521347615674617 1 - - 26783 Y Y 3.38809011260573 3.6272104187567 3.38809011260573 183 0 0.0125175052719393 Y 0 0.986560330822626 N N 40802 568 ENSG00000205609 ENSG00000196877 + - 16 16 28322701 28275423 utr3p upstream EIF3CL NPIPL1 28298403 28262355 - - 0 28298582 28281630 - + N 0.0551412106077239 - N HCC1954 28 12.5 2 8 1 N - - Y - - 0 0 0 8 0.721316564152552 1.12839620926835 1.12839620926835 0.721316564152552 1 0 - 31903 Y Y 3.46551447180198 3.19872427442695 3.19872427442695 0 0 0.586663283334327 Y 0.994301902063942 0.994301902063942 N N 8254 0 ENSG00000163812 ENSG00000188990 + - 3 3 44992618 44935005 coding intron ZDHHC3 AC098649.2-2 44941663 44934497 - - 0 44943342 44934637 - + N - 1 N HCC1954 2 1.09090909090909 1 4 2 N - - Y - - 0 0 0 44 1.29979816510658 1.31408166142643 1.31408166142643 1.29979816510658 1 - 0 42512 Y Y 3.29231222815676 3.5319270478477 3.29231222815676 0 0 0.995670849874599 Y 0.0103494460002435 0.984536710093754 N N 25208 10761 ENSG00000138757 ENSG00000138768 - - 4 4 76817629 76954388 utr5p upstream G3BP2 USO1 76786991 76869028 - + 0 76806257 76868264 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 12 1.01412823870953 1.14982145374813 1.14982145374813 1.01412823870953 4 - - 29246 Y Y 3.26104861408308 3.33461813060452 3.26104861408308 303 0 0.00416315096399389 Y 0.990685049813392 0.990685049813392 N N 3388 788 ENSG00000198315 ENSG00000196812 - + 6 6 28233215 28205833 upstream upstream ZNF192 ZNF435 28217695 28200366 + + 0 28212503 28198969 - + N - - N HCC1954 2 1.0625 1 1 2 N - - Y - LINE,SINE 0 0.6484375 0.6484375 16 0.835584534711372 0.914143764470561 0.914143764470561 0.835584534711372 1 - - 26633 N Y 3.40016547074969 3.3984700535705 3.3984700535705 272 0 0.00975317428209155 Y 0 0.983113160518445 N N 0 0 ENSG00000203581 ENSG00000209499 - + 16 16 3206544 3186226 intron upstream OR1F2P AJ003147.1-2 3205613 3186154 + + 0 3205691 3181316 - + N 1 - N HCC1954 2 1.88888888888889 1 8 1 N - - N - - 0 0 0 9 0.899860268150708 1.32122340958636 1.32122340958636 0.899860268150708 3 0 - 28823 N N 3.2233083338141 3.60785432895764 3.2233083338141 0 0 0.0432235443840119 N 0 0 N N 1953 0 ENSG00000181027 ENSG00000209495 + - 19 16 51953581 3142681 intron upstream FKRP AC108134.3-1 51941143 3142610 + - 0.0526315789473685 51952889 3151262 + + Y - - N HCC1954 23 22.2 22 5 1 N - - N SINE - 1 0 1 5 0.307095170876829 0.649899082553289 0.649899082553289 0.307095170876829 1 - - 47933 N N 2.46144997190271 3.7297745213208 2.46144997190271 0 0 0.999951627969493 N 0 0.0226620243112819 N N 0 86504 ENSG00000182152 ENSG00000104408 + + 5 8 117142614 109330135 downstream coding AC114322.2 EIF3E 117142420 109283149 - - 0.0226620243112819 116890300 109296012 - - Y - - N HCC1954 2 1.13636363636364 1 24 7 N 241 0.00319582 N LINE - 1 0 1 176 1.16410495006798 1.20695543902754 1.20695543902754 1.16410495006798 4 - - 9463 Y Y 3.39271690522525 3.6623288755052 3.39271690522525 264 0 0.00927223536403743 Y 0.98027302730273 0.990136513651365 N N 0 473 ENSG00000204383 ENSG00000154251 + - 17 17 63677958 63635979 downstream downstream AC005332.1-2 AC005332.1-1 63677569 63633345 - - 0 63668724 63622258 - + N - - N HCC1954 4 1.625 1 3 1 N - - Y - - 0 0 0 8 0.678466075192994 0.764167053112109 0.764167053112109 0.678466075192994 1 - - 18352 Y Y 3.69209541149257 3.30062602958175 3.30062602958175 253 0 0.0842849286337096 Y 0.988281794931411 0.988281794931411 N N 11036 0 ENSG00000116161 ENSG00000208302 - + 1 1 173247786 173232388 utr5p downstream CACYBP Z99127.2 173235194 173232284 + + 0.988281794931411 173235356 173233495 - + N 0.0856065085552727 - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 5 0.485638874874985 0.507064119354764 0.507064119354764 0.485638874874985 3 0 - 43177 N Y 3.41103992525442 3.45823374014688 3.41103992525442 0 0 0.0667631437624817 N 0.903700189753321 0.989300021083702 N N 18316 6443 ENSG00000215136 ENSG00000168014 - + 10 11 45259678 73559712 intron coding AL731567.6 C2CD3 45189635 73423128 + - 0 45206911 73521540 - - Y - - N HCC1954 25 20.375 9 8 1 N - - N Other - 1 0 1 8 0.87843502367093 0.835584534711372 0.87843502367093 0.835584534711372 2 - - 36271 Y Y 3.42680229220385 3.39487633072086 3.39487633072086 262 0.0127914173715699 0.158121487361297 N 0.982050753043119 0.99102537652156 Y N 1240 120 ENSG00000139725 ENSG00000212694 + - 12 12 120715977 120718831 upstream coding RHOF AC084018.28-3 120700045 120718106 - - 0 120722138 120718533 - + N - 1.25268512365287 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 16 0.771308801272036 0.828442786551446 0.828442786551446 0.771308801272036 2 - 0 47354 Y Y 3.75169126419961 3.47548383761281 3.47548383761281 274 0 0.135900727219755 Y 0.961381768799864 0.984552707519946 N N 156 711 ENSG00000161551 ENSG00000198093 - + 19 19 57083009 57100059 utr5p coding ZNF577 ZNF649 57066367 57084301 - - 0 57075942 57085898 + - N - 0.2758375214674 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.0649350649350649 0 0.0649350649350649 13 1.09982921662864 0.971277749749971 1.09982921662864 0.971277749749971 4 - 0 25429 N N 3.33151892129485 3.52783881145811 3.33151892129485 0 0 0.0714627534130893 N 0.00231481481481466 0 N N 1325 86504 ENSG00000204977 ENSG00000104408 - + 13 8 49490604 109330135 utr3p coding TRIM13 EIF3E 49469144 109283149 + - 0 49485812 109321449 - - Y - - N HCC1954 38 32.375 30 8 1 N - - N SINE - 1 0 1 8 0.371370904316165 0.335662163516534 0.371370904316165 0.335662163516534 2 - - 29179 Y Y 3.68577320169385 3.01972902964314 3.01972902964314 276 0 0.736078693345916 Y 0.41950220541903 0.982671707624449 N N 11566 0 ENSG00000130338 ENSG00000188451 - - 6 6 158852842 158583817 upstream downstream TULP4 RP1-274L14.2 158653680 158578356 + - 0 158653071 158573323 - + N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity Simple_repeat 0.0632183908045977 0.403361344537815 0.403361344537815 42 1.24266417982717 0.849868031031224 1.24266417982717 0.849868031031224 4 - - 21776 N N 3.51832410639388 3.59425138750382 3.51832410639388 73 0 0.0207431466786248 N 0.849149338374291 0.116446124763705 N N 5950 18530 ENSG00000028203 ENSG00000198793 + - 12 1 94219075 11245176 utr5p intron VEZT FRAP1 94135715 11089179 + - 0.116446124763705 94135744 11103279 + + Y 0.734700439382263 0.976102348473042 N HCC1954 21 13.8 7 5 1 N - - N - SINE 0 1 1 5 0.421363141435649 0.314236919036755 0.421363141435649 0.314236919036755 3 0 0 41704 Y Y 3.59681204058356 3.0961203190695 3.0961203190695 0 0 0.0784335237483884 Y 0 0 N N 35 28808 ENSG00000079112 ENSG00000164951 + + 8 8 95289986 95007470 intron coding CDH17 PPM2C 95208566 94998338 - + 0 95225544 94998424 - + N 2.22378307942739 - N HCC1954 1 1 1 0 1 N - - Y DNA - 1 0 1 4 0.499922371194838 0.521347615674617 0.521347615674617 0.499922371194838 2 0 - 31660 Y Y 3.37767966641742 3.35207591473315 3.35207591473315 0 0 0.615189457762051 Y 0.884366925064599 0.98843669250646 N N 2709 98 ENSG00000163947 ENSG00000186451 - - 3 3 57044217 57084500 coding downstream ARHGEF3 SPATA12 56736489 57069509 - + 0 56967914 57088290 + - N - - N HCC1954 11 1.28571428571429 1 1 3 N - - Y - Simple_repeat,Low_complexity 0 0.270833333333333 0.270833333333333 35 1.10697096478857 0.685607823352921 1.10697096478857 0.685607823352921 3 - - 18136 Y Y 3.51207644450867 3.43614916339873 3.43614916339873 0 0 0.618121008534203 Y 0.818757192174914 0.993029122775958 N N 18522 3 ENSG00000179403 ENSG00000205116 - + 1 1 1366008 1353030 upstream downstream VWA1 AL391244.11-1 1360772 1351371 + + 0 1359425 1355909 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 1.06412047582901 0.928427260790413 1.06412047582901 0.928427260790413 1 - - 46793 Y Y 3.47336426491055 3.24057974892742 3.24057974892742 304 0 0.00582562724718805 Y 0.9839240237691 0.99196201188455 N N 351 1692 ENSG00000171119 ENSG00000141994 - - 19 19 5779334 5742194 upstream upstream NRTN DUS3L 5774818 5736155 + - 0 5774776 5756459 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE Low_complexity 1 0.73134328358209 1 42 1.24266417982717 0.956994253430118 1.24266417982717 0.956994253430118 1 - - 48828 Y Y 3.5010341561346 3.65384724021086 3.5010341561346 318 0 0.812938439097117 Y 0 0.991178271275115 N N 26477 14691 ENSG00000161011 ENSG00000161013 - - 5 5 179197681 179166547 intron upstream SQSTM1 MGAT4B 179180503 179156711 + - 0 179192637 179171287 - + N 1.14107388782732 - N HCC1954 6 1.64356435643564 1 17 5 N - - Y - LTR,LTR 0 0.680327868852459 0.680327868852459 101 1.36407389854591 0.871293275511003 1.36407389854591 0.871293275511003 1 0 - 20784 N N 3.38855412092215 3.09343168491377 3.09343168491377 0 0 0.116414903851872 N 0.00312500000000016 0 N N 8096 23977 ENSG00000010404 ENSG00000160691 - - X 1 148394714 153213476 utr3p utr5p IDS SHC1 148368206 153201398 - - 0 148368646 153213464 + + Y - - N HCC1954 33 23.2222222222222 13 9 1 N - - N SINE - 1 0 1 9 0.449930134075354 0.735600060472404 0.735600060472404 0.449930134075354 3 - - 41623 Y N 3.57592836747465 3.18188898491428 3.18188898491428 0 0 0.628136270580166 N 0 0 Y N 0 0 ENSG00000221176 ENSG00000221261 - + 8 8 129130666 129231616 downstream downstream hsa-mir-1207 hsa-mir-1208 129130580 129231544 + + 0 129180696 129248054 - + N - - N HCC1954 1 1 1 0 1 N 152 5.88226 N - SINE 0 0.381818181818182 0.381818181818182 7 1.07126222398894 1.1426797055882 1.1426797055882 1.07126222398894 2 - - 27040 Y Y 3.17780074852469 3.353603498043 3.17780074852469 0 0.00318471337579618 0.958292811537255 Y 0.134708952583156 0 N N 23054 0 ENSG00000131149 ENSG00000220991 - + 16 16 84267311 83906889 coding downstream KIAA0182 AC092275.3 84202524 83906768 + + 0 84239660 83962386 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 35 1.25694767614702 0.914143764470561 1.25694767614702 0.914143764470561 1 - - 14883 N Y 3.50000108636471 3.26824964015148 3.26824964015148 0 0 0.369069320859971 N 0.857723577235772 0.800813008130081 N N 187 8014 ENSG00000188783 ENSG00000149084 - - 1 11 201727098 43834736 utr3p utr3p PRELP HSD17B12 201711506 43658719 + + 0 201723985 43834016 - - Y - 1.56799368003871 N HCC1954 74 51.25 38 4 1 N - - N SINE,SINE - 0.77027027027027 0 0.77027027027027 4 0.528489363834543 0.899860268150708 0.899860268150708 0.528489363834543 2 - 0 41747 Y N 3.26249649180623 3.21063179870157 3.21063179870157 6 0.0388555841025152 0.974384395394685 Y 0.426840485932693 0 N N 9799 0 ENSG00000076554 ENSG00000222697 - - 8 8 81155565 81279688 coding upstream TPD52 SRP_euk_arch 81109662 81279396 - + 0 81139385 81245870 + - N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 19 1.22123893534739 1.19267194270768 1.22123893534739 1.19267194270768 1 - - 46957 Y Y 3.51576345331414 3.30657751701988 3.30657751701988 249 0 0.912364784079748 Y 0.223470151793615 0.99155945817167 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 intron upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10597928 10574236 - + N 0.303647347663951 - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.175438596491228 0.175438596491228 10 0.678466075192994 0.814159290231593 0.814159290231593 0.678466075192994 1 0 - 29134 Y Y 3.36464578641707 3.20613298715805 3.20613298715805 341 0 0.714407200139417 Y 0 0.988130149420472 N N 30978 0 ENSG00000112245 ENSG00000213312 - - 6 6 64351447 64317378 utr5p upstream PTP4A1 RPL7AP34 64339879 64316572 + - 0 64344300 64318357 - + N 0.363404336258786 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 65 1.27123117246687 1.22838068350732 1.27123117246687 1.22838068350732 4 0 - 25107 N N 3.55081912933034 3.06572194089636 3.06572194089636 0 0 0.139737592379923 N 0 0.175596816976127 N N 0 8146 ENSG00000214266 ENSG00000128283 - + 13 22 64782480 36295358 downstream intron AL139088.11 CDC42EP1 64782119 36286446 - + 0.175596816976127 64767980 36286619 + + Y - 0.579006632793134 N HCC1954 20 20 20 5 1 N - - N SINE - 1 0 1 5 0.349945659836387 0.335662163516534 0.349945659836387 0.335662163516534 1 - 0 9244 Y N 3.41952156054875 3.39024953810134 3.39024953810134 0 0.0561761372834712 0.539928512012065 N 0 0 N N 109916 1649619 ENSG00000161395 ENSG00000141736 + - 17 17 35097836 35138441 upstream utr5p PERLD1 ERBB2 35080902 35104766 - + 0 35098525 35104810 - - N - 0.0131376688666282 Y HCC1954 1 1 1 0 2 N 298 9.39526 N LINE - 0.682692307692308 0 0.682692307692308 6 0.721316564152552 0.921285512630487 0.921285512630487 0.721316564152552 1 - 0 26739 Y Y 3.59528445727371 3.684245618384 3.59528445727371 268 0 0.893632539689687 Y 0 0 N N 0 0 ENSG00000209496 ENSG00000209495 + - 16 16 3161032 3142681 downstream upstream AJ003147.1-1 AC108134.3-1 3160962 3142610 - - 0 3154070 3151304 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 5 0.771308801272036 0.564198104634174 0.771308801272036 0.564198104634174 3 - - 18475 Y Y 3.7297745213208 3.22593015733458 3.22593015733458 323 0 0.0389002404705365 Y 0.993526597241767 0.987053194483535 N N 0 8677 ENSG00000221225 ENSG00000134686 + - 1 1 33680299 33613781 downstream utr5p AL138837.12 PHC2 33680213 33561811 - - 0 33668369 33613781 - + N - 150.74126359639 N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.309941520467836 0.309941520467836 24 1.23552243166724 1.22123893534739 1.23552243166724 1.22123893534739 4 - 0 24010 N N 3.51156839350228 3.09719324163274 3.09719324163274 16 0 0.0404099864728368 N 0 0.155686660111439 N N 2833 13 ENSG00000133019 ENSG00000152495 + + 1 5 238139338 110848645 utr5p intron CHRM3 CAMK4 237858996 110587981 + + 0.155686660111439 237859357 110663685 + + Y - 1.03487135990953 N HCC1954 23 22.5 22 4 1 N - - N LINE - 1 0 1 4 0.492780623034912 0.557056356474248 0.557056356474248 0.492780623034912 1 - 0 38274 Y Y 3.24740581983591 3.13999365762046 3.13999365762046 234 0 0.0269635698765290 Y 0.783537718320327 0.989176885916016 N N 95 0 ENSG00000186615 ENSG00000213641 + + 14 14 55116581 55080646 downstream upstream C14orf33 AL138499.4-1 55113662 55079856 - + 0 55097563 55036270 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE LTR 0.0555555555555556 1 1 7 0.51420586751469 0.549914608314322 0.549914608314322 0.51420586751469 1 - - 38471 Y Y 3.29297457556607 2.99256299952886 2.99256299952886 0 0 0.689351893055488 Y 0 0 N N 31 6382 ENSG00000213145 ENSG00000182809 - + 14 14 105026173 105017543 coding utr3p CRIP1 CRIP2 105024249 105012176 + + 0 105025629 105017106 - + N - 0.999239679195046 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 4 0.649899082553289 0.914143764470561 0.914143764470561 0.649899082553289 2 - 0 2670 N Y 3.43209143223268 3.56232542602083 3.43209143223268 0 0 0.182153625069429 N 0 0.8512 N N 1 4 ENSG00000165457 ENSG00000103569 + + 11 15 71610632 56265402 upstream downstream FOLR2 AQP9 71605476 56217700 + + 0.3552 71600780 56339667 + + Y - - N HCC1954 120 30.4 20 10 1 N 250 29.001 N SINE LTR 1 1 1 10 0.257102933757345 0.471355378555133 0.471355378555133 0.257102933757345 3 - - 18176 Y Y 3.7297745213208 3.39640391403071 3.39640391403071 366 0 0.105962968013878 Y 0.679241363883297 0.994168024797878 N N 0 1472 ENSG00000212577 ENSG00000117543 - - 1 1 101371483 101263950 upstream upstream SCARNA16 DPH5 101371297 101227773 + - 0 101324997 101264206 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 19 1.28551466878673 1.35693215038599 1.35693215038599 1.28551466878673 1 - - 36425 N N 2.39581023261858 3.40016547074969 2.39581023261858 0 0 0.409768112192765 Y 0 0 N N 4442 597 ENSG00000139116 ENSG00000110799 + - 12 12 38123190 6104097 downstream intron KIF21A VWF 37973298 5928301 - - 0 37950678 6072043 - + N - 6.31786071851319 N HCC1954 4 2 1 3 1 N 344 7.16511 N LTR SINE 1 1 1 5 0.321378667196682 0.414221393275723 0.414221393275723 0.321378667196682 1 - 0 930 N Y 3.22536109588112 3.67320333000993 3.22536109588112 247 0 0.145396412482921 N 0.979674460877468 0.959348921754937 N N 99790 8369 ENSG00000186676 ENSG00000106554 + - 11 7 62106622 132417390 intron intron EEF1G CHCHD3 62083651 132120170 - - 0.959348921754937 62097879 132371208 - + Y 28.5706997546715 1.20501934687855 N HCC1954 2 1.18421052631579 1 7 1 N - - N - - 0 0 0 38 0.578481600954027 0.414221393275723 0.578481600954027 0.414221393275723 3 0 0 36762 N N 3.19975734419684 3.41423242051993 3.19975734419684 0 0 0.260818488298606 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000209388 + - 12 12 6517797 7664324 utr3p downstream GAPDH AC006927.27-1 6513918 7664262 + - 0 6517677 7611340 + + N - - Y HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.307095170876829 0.235677689277566 0.307095170876829 0.235677689277566 3 - - 14077 Y Y 3.63552422018169 3.21013728516161 3.21013728516161 175 0 0.139251784342611 Y 0.0885714285714285 0.979285714285714 N N 4030 855 ENSG00000185214 ENSG00000099910 + - 22 22 19180122 19122146 coding intron KLHL22 SCARF2 19125806 19108874 - - 0 19130771 19116279 - + N - 17.4140766496619 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 5 0.956994253430118 0.864151527351077 0.956994253430118 0.864151527351077 1 - 0 33153 N Y 3.01079273360219 3.30484224704734 3.01079273360219 303 0 0.00997290092764747 Y 0 0.991896750650675 N N 247001 1291380 ENSG00000198786 ENSG00000198804 - + MT MT 14149 7446 coding coding MT-ND5 MT-CO1 12338 5905 + + 0 14111 7176 - + N 2.97411851194636 1.1751433341563 N HCC1954 2 2 2 6 1 N - - N - - 0 0 0 6 0.799875793911741 0.771308801272036 0.799875793911741 0.771308801272036 2 0 0 9347 Y Y 3.40129182647542 3.29912895149544 3.29912895149544 444 0 0.883351577166044 N 0 0.994130895601484 Y N 317991 1482 ENSG00000171346 ENSG00000171345 + - 17 17 36932191 36938167 upstream utr5p KRT15 KRT19 36923523 36933396 - - 0 36946570 36938109 - + N - 31.5276649710027 N HCC1954 2 1.1875 1 3 8 N - - N - - 0 0 0 16 0.642757334393363 1.16410495006798 1.16410495006798 0.642757334393363 2 - 0 42062 N N 3.34359427943881 2.68847799505532 2.68847799505532 0 0 0.104638618497553 N 0 0 N N 20636 71032 ENSG00000196526 ENSG00000160932 - + 4 8 7992553 144175199 intron intron AFAP LY6E 7811341 144171300 - + 0 7965930 144171537 + + Y 2.59206211035713 1.33866756416173 N HCC1954 20 20 20 7 1 N - - N SINE Low_complexity 1 0.0930232558139535 1 7 0.28566992639705 0.614190341753658 0.614190341753658 0.28566992639705 3 0 0 648 Y Y 3.75016368088976 3.31273189294925 3.31273189294925 281 0 0.171197492320966 Y 0.983928366433245 0.983928366433245 N N 175 7069 ENSG00000149489 ENSG00000149499 - - 11 11 62139162 62136813 coding intron ROM1 EML3 62137199 62126267 + - 0 62138306 62135968 - + N - 3.57837221730661 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 19 0.771308801272036 1.15696320190805 1.15696320190805 0.771308801272036 4 - 0 37105 N Y 2.31424653518228 3.45504124488137 2.31424653518228 74 0.461916461916462 0.0115602552122102 N 0.461916461916462 0.461916461916462 N N 7722 1532 ENSG00000090661 ENSG00000123427 - + 19 12 8233302 56462588 coding utr3p LASS4 FAM119B 8180257 56452650 + + 0.461916461916462 8222081 56461185 - + Y - - N HCC1954 24 22.25 21 4 1 N - - N - SINE 0 1 1 4 0.335662163516534 0.321378667196682 0.335662163516534 0.321378667196682 2 - - 31190 Y Y 3.43421100493494 3.61464054707278 3.43421100493494 290 0 0.254703099759447 Y 0 0 N N 1708 0 ENSG00000114812 ENSG00000216013 - - 3 3 42554064 42444308 upstream upstream VIPR1 AC092047.3 42519121 42444214 + - 0 42490090 42476776 - + N - - N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 19 1.29979816510658 0.864151527351077 1.29979816510658 0.864151527351077 4 - - 9056 N N 3.41588798490577 3.63296356710195 3.41588798490577 0 0 0.0763427388376778 N 0 0 N N 0 1992 ENSG00000217690 ENSG00000003436 - - 17 2 15708192 188127464 downstream intron AC015922.5 TFPI 15673408 188037202 + - 0 15710893 188120722 - + Y - 11.2383441972674 N HCC1954 20 17.2857142857143 1 6 1 N - - N Other - 1 0 1 7 0.299953422716903 0.5713398527941 0.5713398527941 0.299953422716903 2 - 0 49491 Y Y 3.68783934123363 3.54040868314203 3.54040868314203 8 0.00225733634311498 0.193308155748218 Y 0.00225733634311498 0.994487609593056 N N 551733 46607 ENSG00000204628 ENSG00000146063 + + 5 5 180603512 180595414 utr3p downstream GNB2L1 TRIM41 180596536 180582912 - + 0.994487609593056 180596575 180595557 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.621332089913584 0.542772860154395 0.621332089913584 0.542772860154395 2 - - 22218 N N 3.59528445727371 3.25256697878875 3.25256697878875 1 0 0.0731535525891136 N 0 0 N N 1831 49089 ENSG00000156232 ENSG00000117450 - - 15 1 81300667 45760196 utr3p coding WHAMM PRDX1 81275027 45749295 + - 0 81299911 45757275 - + Y - - N HCC1954 29 12 2 9 1 N - - N SINE - 1 0 1 9 0.357087407996313 0.785592297591888 0.785592297591888 0.357087407996313 2 - - 198 Y Y 3.39487633072086 3.37232774565629 3.37232774565629 334 0 0.022035937518725 Y 0 0 N N 2405 10 ENSG00000142102 ENSG00000174885 - + 11 11 285688 275359 upstream intron ATHL1 NALP6 279135 268365 + + 0 278187 273248 - + N - 1.19018018223105 N HCC1954 1 1 1 0 1 N - - Y LINE SINE 0.202453987730061 0.572222222222222 0.572222222222222 6 0.657040830713216 0.721316564152552 0.721316564152552 0.657040830713216 1 - 0 7245 Y Y 3.49268050191626 3.61464054707278 3.49268050191626 213 0 0.916002389161495 Y 0 0.979478244034655 N Y 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 coding coding VAMP5 VAMP8 85665042 85658227 + + 0 85672359 85658283 - + N 0.0482059455852917 1.80954203171579 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.692749571512847 0.578481600954027 0.692749571512847 0.578481600954027 4 0 0 31322 Y Y 3.485365075141 2.93855246129772 2.93855246129772 262 0 0.990176378684395 Y 0 0.991337537338201 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 intron upstream LPP AC022498.18 189413415 189379637 + + 0 189425859 189354461 - + N 0.0161234218687541 - N HCC1954 1 1 1 0 7 N - - Y SINE - 0.233870967741935 0 0.233870967741935 29 0.885576771830856 1.10697096478857 1.10697096478857 0.885576771830856 4 0 - 6240 N N 2.33366642038406 2.6718368118362 2.33366642038406 0 0.177458481059899 0.208564245870351 N 0.69695838775891 0.177458481059899 N N 11 11502 ENSG00000179915 ENSG00000159921 + - 2 9 51113178 36248450 utr3p utr3p NRXN1 GNE 50000992 36204430 - - 0.177458481059899 50001367 36206342 - + Y - 0.659918255598569 N HCC1954 38 36.3333333333333 34 6 1 N - - N Simple_repeat LINE 1 0.514563106796116 1 6 0.307095170876829 0.735600060472404 0.735600060472404 0.307095170876829 1 - 0 2683 N N 3.42783536197374 3.58593758607883 3.42783536197374 0 0.0230694980694981 0.358113094723721 N 0 0.57554054054054 N N 0 22 ENSG00000220309 ENSG00000150672 + + 20 11 40061451 85015962 downstream coding RP5-1121H13.1 DLG2 40059185 82843701 - - 0 40008260 84500353 - - Y - - N HCC1954 1 1 1 0 1 N - - N SINE - 1 0 1 6 0.642757334393363 1.09982921662864 1.09982921662864 0.642757334393363 4 - - 29093 N N 3.74337746277462 3.39487633072086 3.39487633072086 6 0 0.866571798065925 N 0 0 N N 0 568998 ENSG00000219374 ENSG00000156508 + + 6 6 49436052 74288344 intron coding RP1-142O9.1 EEF1A1 49433818 74282194 - - 0 49434164 74284803 - - N 1 0.261325232866751 Y HCC1954 10 5.85714285714286 3 21 2 N - - N - - 0 0 0 21 0.257102933757345 0.792734045751814 0.792734045751814 0.257102933757345 2 0 0 22441 N N 3.18192883770763 3.51990257979396 3.18192883770763 3 0 0.106068039591704 N 0 0 N N 2406 17904 ENSG00000104381 ENSG00000180198 - + 8 1 75441888 28738194 intron utr5p GDAP1 RCC1 75425173 28705083 + + 0 75434857 28707228 - + Y 0.215954723148888 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.949852505270192 0.357087407996313 0.949852505270192 0.357087407996313 2 0 - 43114 N N 3.53296011761759 3.46600898534194 3.46600898534194 0 0 0.997530261504563 N 0 0 N N 9848 13 ENSG00000164134 ENSG00000152495 + + 4 5 140531972 110848645 coding intron NARG1 CAMK4 140442126 110587981 + + 0 140442435 110653601 + + Y 1.3634306974875 1.03487135990953 N HCC1954 1 1 1 0 5 N 370 4.32528 N - LTR 0 1 1 5 0.792734045751814 0.849868031031224 0.849868031031224 0.792734045751814 4 0 0 31309 Y Y 3.24103017687471 3.57167229721571 3.24103017687471 226 0 0.811990137969424 Y 0 0.989059612953418 N N 168 73312 ENSG00000113946 ENSG00000163347 - - 3 3 191611027 191522909 upstream coding CLDN16 CLDN1 191588535 191506197 + - 0 191558126 191513507 - + N - 0.861792730466097 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.464213630395207 0.714174815992626 0.714174815992626 0.464213630395207 2 - 0 49075 Y Y 3.1458747870417 3.29024608861698 3.1458747870417 311 0 0.0129914814476604 Y 0.143937961036505 0.976546245507849 N N 322 226 ENSG00000215068 ENSG00000177721 - - 5 5 43081249 43079029 downstream intron AC025171.8 C5orf39 43077952 43075258 + - 0 43086416 43077878 - + N - 9.50550804087227 N HCC1954 1 1 1 0 2 N - - Y LTR - 0.648148148148148 0 0.648148148148148 6 0.385654400636018 0.478497126715059 0.478497126715059 0.385654400636018 2 - 0 31852 Y N 3.70040921291755 3.54975555433691 3.54975555433691 0 0 0.546820722462923 Y 0 0 N N 6846 41283 ENSG00000163755 ENSG00000047457 + + 3 3 150373995 150422519 coding coding HPS3 CP 150330061 150373220 + - 0 150367578 150374205 + - N - - N HCC1954 2 1.04545454545455 1 1 3 N - - Y - - 0 0 0 22 0.749883556792257 0.971277749749971 0.971277749749971 0.749883556792257 1 - - 38983 N N 3.35463656781289 3.53824925764641 3.35463656781289 0 0 0.902367570704477 N 0 0 N N 0 5111 ENSG00000184565 ENSG00000181827 + - Y 15 19698690 54322775 intron downstream TTTY14 RFX7 19553973 54170024 - - 0 19613045 54152442 - + Y 1 - N HCC1954 2 1.4 1 2 3 N - - N - - 0 0 0 5 0.485638874874985 0.364229156156239 0.485638874874985 0.364229156156239 2 0 - 47266 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 0 0 0.761101483729596 Y 0 0.993521594684385 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 118 1.49262536542459 1.09982921662864 1.49262536542459 1.09982921662864 4 - - 24294 N N 3.68105312311849 3.36613351693357 3.36613351693357 6 0 0.0694022153128633 N 0.00793650793650802 0 N N 49089 0 ENSG00000117450 ENSG00000201368 - + 1 5 45760196 35465135 coding upstream PRDX1 U3 45749295 35464923 - + 0 45757265 35405525 + + Y - - N HCC1954 42 18.8181818181818 1 10 1 N - - N - SINE 0 1 1 11 0.771308801272036 0.507064119354764 0.771308801272036 0.507064119354764 2 - - 23813 N Y 3.60000453584907 3.63655728995158 3.60000453584907 10 0 0.44668618454771 N 0.123793103448276 0 N N 699 4473 ENSG00000188295 ENSG00000145817 - + 1 5 245334251 143530409 utr3p utr3p ZNF669 YIPF5 245328029 143517924 - - 0 245330183 143519740 + - Y - - N HCC1954 4 1.625 1 3 1 N - - N SINE,SINE - 0.682926829268293 0 0.682926829268293 8 0.292811674556976 0.378512652476092 0.378512652476092 0.292811674556976 1 - - 29614 Y N 2.81330723590509 3.28296535696188 2.81330723590509 0 0.161616161616161 0.120770186498999 Y 0.161616161616161 0.161616161616161 N N 2215 315 ENSG00000124588 ENSG00000215076 - + 6 6 2964995 2936302 coding utr5p NQO2 AL133351.34-1 2939231 2933881 + + 0.161616161616161 2951733 2933930 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.333333333333333 0 0.333333333333333 8 0.642757334393363 0.39993789695587 0.642757334393363 0.39993789695587 3 - - 45285 N N 3.57800808738356 3.40744620240479 3.40744620240479 0 0 0.269774981324689 N 0 0 N N 17943 710 ENSG00000105141 ENSG00000138336 + + 19 10 15027900 70124244 downstream intron CASP14 TET1 15024015 69990123 + + 0.00427350427350437 15029502 70065185 + + Y - 0.677999173194094 N HCC1954 14 12.5555555555556 1 8 1 N - - N SINE SINE 0.208 1 1 9 0.885576771830856 0.271386430077198 0.885576771830856 0.271386430077198 3 - 0 307 Y Y 3.36976709257655 3.64081336021051 3.36976709257655 282 0 0.0732902011026625 Y 0.985453227726873 0.992726613863436 N N 63500 30347 ENSG00000085733 ENSG00000131626 - + 11 11 69960337 69908148 upstream intron CTTN PPFIA1 69922292 69794471 + + 0 69921850 69899356 - + N - 2.16712280561002 N HCC1954 1 1 1 0 3 N - - Y LINE SINE 0.27972027972028 0.6796875 0.6796875 4 0.785592297591888 0.757025304952183 0.785592297591888 0.757025304952183 2 - 0 8630 N N 3.48271113610543 3.51310951427856 3.48271113610543 0 0 0.127505340075297 N 0 0 N N 8421 0 ENSG00000012048 ENSG00000177418 - - 17 7 38530994 65659784 utr5p downstream BRCA1 AC006001.2-1 38449840 65659267 - - 0 38530374 65657216 + + Y - - N HCC1954 26 24.25 21 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.378512652476092 0.378512652476092 0.321378667196682 3 - - 16066 N Y 3.45976132345673 3.43039601505348 3.43039601505348 40 0.839944379391101 0.318135055048188 N 0.822160421545667 0.839944379391101 N N 3364 52936 ENSG00000115946 ENSG00000179051 + - 2 1 68256593 17638807 utr3p upstream PNO1 RCC2 68238509 17605866 + - 0.839944379391101 68256032 17679096 + + Y - - N HCC1954 2 1.125 1 1 1 N - - N SINE SINE 0.426829268292683 1 1 8 0.585623349113953 0.264244681917271 0.585623349113953 0.264244681917271 2 - - 32265 N N 3.6035982586987 3.68527868815389 3.6035982586987 0 0 0.0775331081922119 N 0 0 N N 12271 312 ENSG00000177479 ENSG00000197343 + + 3 7 48997971 99012008 utr5p utr3p ARIH2 ZNF655 48931285 98993981 + + 0 48935226 99010997 + + Y - - N HCC1954 38 28.3181818181818 25 22 1 N - - N - SINE 0 1 1 22 0.907002016310634 0.34280391167646 0.907002016310634 0.34280391167646 2 - - 31758 N N 3.71720464963688 3.0935889136994 3.0935889136994 8 0.181916817359855 0.090571052531791 N 0.181916817359855 0.15370705244123 N N 89 172 ENSG00000196345 ENSG00000178917 - + 3 3 44599975 44527113 coding upstream ZNF167 AC099669.2-2 44571717 44516023 + - 0.15370705244123 44584477 44527126 - - N - - Y HCC1954 2 1.5 1 2 1 N - - N - Low_complexity 0 0.0925925925925926 0.0925925925925926 4 0.578481600954027 0.742741808632331 0.742741808632331 0.578481600954027 2 - - 42372 Y Y 3.22167408707565 3.30128837699106 3.22167408707565 300 0 0.239269246802328 Y 0 0.960133333333333 N N 2010 0 ENSG00000138735 ENSG00000209291 + - 4 4 120769429 120574710 utr3p upstream PDE5A AC093752.2-3 120635000 120574608 - - 0 120635032 120603719 - + N 0.357352256961623 - N HCC1954 5 1.75 1 2 4 N - - Y - LTR 0 0.848837209302326 0.848837209302326 8 0.464213630395207 0.614190341753658 0.614190341753658 0.464213630395207 3 0 - 43425 N Y 3.5816815158199 3.63296356710195 3.5816815158199 234 0.730324074074074 0.00245531348125028 N 0.751068376068376 0.771812678062678 N N 0 249 ENSG00000163046 ENSG00000150076 - + 2 10 132635998 33211797 upstream intron AC098826.3 C10orf68 132621950 32896657 - + 0.771812678062678 132676020 33113488 + + Y - 13.7178929359707 N HCC1954 160 55 20 4 1 N - - N LINE LINE 1 1 1 4 0.28566992639705 0.271386430077198 0.28566992639705 0.271386430077198 0 - 0 704 Y Y 3.58320909912975 3.62617734898681 3.58320909912975 89 0 0.424595527859978 Y 0.972834224598931 0.990944741532977 N N 5553 2214 ENSG00000176973 ENSG00000173465 - + 11 11 65098245 65095793 utr5p coding FAM89B SSSCA1 65096396 65094519 + + 0.990944741532977 65096492 65095439 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.678466075192994 0.871293275511003 0.871293275511003 0.678466075192994 2 - - 27134 N Y 3.33680806132368 3.32060461399677 3.32060461399677 0 0 0.660710120219123 N 0.9502 0.93775 N Y 152 6304 ENSG00000196993 ENSG00000196696 - + 16 16 28691577 68657352 coding utr3p AC145285.2-3 PDXDC2 28677526 68567713 + - 0 28689410 68573754 - - N - - Y HCC1954 54 10.8947368421053 7 19 1 N - - N - - 0 0 0 19 0.671324327033068 0.842726282871298 0.842726282871298 0.671324327033068 4 - - 30262 N N 3.60426060610801 3.16808731503482 3.16808731503482 0 0 0.0883201677356723 Y 0.905743740795287 0.198821796759941 N N 0 650 ENSG00000199920 ENSG00000170965 + - X X 133722044 133620179 upstream utr5p U4 PLAC1 133721904 133527539 - - 0.198821796759941 133725942 133563758 - + N - 2.77329434843417 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 35 0.685607823352921 0.564198104634174 0.685607823352921 0.564198104634174 1 - 0 47289 Y Y 3.55128313764676 2.87423653001532 2.87423653001532 0 0.00476190476190452 0.245954221984380 Y 0.781047619047619 0.980095238095238 N N 8931 13148 ENSG00000099622 ENSG00000167470 - + 19 19 1224169 1210139 utr5p downstream CIRBP MIDN 1220336 1199552 + + 0 1221928 1217701 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.292811674556976 0.578481600954027 0.578481600954027 0.292811674556976 1 - - 6730 Y Y 2.96163025502241 3.20959872893168 2.96163025502241 0 0 0.923417089946253 Y 0.994168803096567 0.994168803096567 N N 676 2952 ENSG00000144401 ENSG00000118260 + + 2 2 208198276 208171806 coding intron FAM119A CREB1 208185086 208102917 - + 0 208194776 208154916 - + N - 3.86540137913076 N HCC1954 1 1 1 0 3 N - - Y - LINE 0 1 1 9 1.0069864905496 0.842726282871298 1.0069864905496 0.842726282871298 1 - 0 21457 N Y 3.46448140203209 3.55231620741665 3.46448140203209 5 0 0.279007758460318 N 0 0.0202124015073656 N N 7771 3709 ENSG00000165304 ENSG00000152022 - + 9 1 36667678 144213026 utr5p utr3p MELK LIX1L 36562873 144188516 + + 0.0202124015073656 36571641 144211522 - + Y - - N HCC1954 34 30.8 23 5 1 N - - N - SINE 0 1 1 5 1.06412047582901 0.357087407996313 1.06412047582901 0.357087407996313 2 - - 9329 Y Y 3.65128658713112 3.46448140203209 3.46448140203209 333 0 0.0170345796264160 Y 0 0.993883454006153 N N 5878 966 ENSG00000129255 ENSG00000129226 - + 17 17 7432532 7426152 coding downstream MPDU1 CD68 7427854 7423529 + + 0.993883454006153 7427958 7426571 - + N 1.06488787999145 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 35 1.09982921662864 1.08554572030879 1.09982921662864 1.08554572030879 1 0 - 27311 Y Y 3.46079439322662 3.20145276137604 3.20145276137604 272 0 0.0357072182939826 Y 0.955053073861123 0 N N 10234 69736 ENSG00000141101 ENSG00000181019 + - 16 16 68346330 68318034 utr3p upstream NOB1 NQO1 68333276 68300808 - - 0 68333533 68318577 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.785592297591888 0.735600060472404 0.785592297591888 0.735600060472404 2 - - 30883 N N 3.329991337985 3.48593413659447 3.329991337985 7 0 0.140052694383624 N 0 0 N N 439 975 ENSG00000187715 ENSG00000198487 - + 3 6 129189204 42218335 utr3p intron KLHDC6 AL512274.9 129116765 42183124 + - 0 129188152 42204381 - - Y - 0.755947860259476 N HCC1954 37 28.2307692307692 21 39 2 N - - N SINE - 1 0 1 39 0.371370904316165 0.628473838073511 0.628473838073511 0.371370904316165 1 - 0 10078 Y Y 3.1840484104099 3.26616992024256 3.1840484104099 121 0.00289855072463774 0.687175936236158 Y 0 0 N N 9613 185 ENSG00000132510 ENSG00000183914 - + 17 17 7698831 7677783 utr5p downstream JMJD3 DNAH2 7683947 7562746 + + 0 7683950 7680623 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 7 0.964136001590045 0.557056356474248 0.964136001590045 0.557056356474248 1 - - 4478 Y Y 3.44611852920956 3.4398361722042 3.4398361722042 281 0 0.00742901676503438 Y 0 0.98576512455516 N N 7033 349 ENSG00000146834 ENSG00000078487 - - 7 7 99869676 99864238 coding upstream MEPCE ZCWPW1 99865190 99836432 + - 0 99866644 99864571 - + N 0.639434935940276 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.371370904316165 0.728458312312478 0.728458312312478 0.371370904316165 2 0 - 41862 N N 3.11700399217841 3.35616415112274 3.11700399217841 0 0 0.95879135455861 N 0.368540433925049 0 N N 29840 0 ENSG00000164830 ENSG00000212451 + + 8 8 107834093 127753081 utr5p downstream OXR1 U11 107739270 127752949 + + 0 107739489 128113267 + + N 1.01618091025984 - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - SINE,SINE 0 1 1 82 2.00683123293928 0.907002016310634 2.00683123293928 0.907002016310634 4 0 - 5 Y Y 3.18929769764537 3.46182746299651 3.18929769764537 395 0 0.0362189721207778 Y 0.994396245199829 0.994396245199829 N N 8 13917 ENSG00000150676 ENSG00000137501 - - 11 11 85308699 85146692 upstream upstream CCDC83 SYTL2 85243792 85082915 + - 0 85199643 85146803 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE - 0.0471204188481675 0 0.0471204188481675 8 0.621332089913584 1.14982145374813 1.14982145374813 0.621332089913584 2 - - 42180 Y Y 3.39657174790006 3.61513506061274 3.39657174790006 296 0 0.109983821167237 Y 0 0.989509246088193 N N 3331 439 ENSG00000138785 ENSG00000138784 + + 4 4 106849714 106772285 downstream downstream INTS12 AC105391.1 106823233 106693226 - + 0 106799661 106796329 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.942710757110266 0.614190341753658 0.942710757110266 0.614190341753658 1 - - 36775 Y N 3.67849247003875 3.57233464462502 3.57233464462502 0 0 0.0727581507066106 N 0 0 N N 23800 55227 ENSG00000067182 ENSG00000111319 + + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6313265 6327676 - - N - - Y HCC1954 1 1 1 0 1 N 442 20.5238 N - - 0 0 0 6 0.93556900895034 0.792734045751814 0.93556900895034 0.792734045751814 1 - - 30537 N N 3.65657572715995 3.11382084448272 3.11382084448272 0 0 0.629655416061742 Y 0 0 N N 6043 0 ENSG00000123130 ENSG00000210537 + - X X 23694513 23435351 downstream upstream ACOT9 AC096507.7 23631698 23435249 - - 0 23630483 23448064 - + N - - N HCC1954 20 6.5 1 2 1 N - - N SINE,SINE - 0.571428571428571 0 0.571428571428571 4 1.06412047582901 0.635615586233437 1.06412047582901 0.635615586233437 1 - - 30205 N Y 3.48912663185998 3.40744620240479 3.40744620240479 2 0 0.0156768410133391 N 0 0.922329215116279 N N 6539 0 ENSG00000009413 ENSG00000214908 - - 6 9 111911125 88180441 coding upstream REV3L AL353678.11 111726927 88179178 - - 0.0524164244186047 111736102 88198150 + + Y - - N HCC1954 640 620 600 5 1 N - - N LINE LINE 1 1 1 5 0.307095170876829 0.292811674556976 0.307095170876829 0.292811674556976 1 - - 48936 Y Y 3.61720120015252 3.46232197653647 3.46232197653647 195 0 0.102998159875600 Y 0 0.975435264324153 N N 3185 0 ENSG00000145740 ENSG00000222762 - - 5 5 68461635 68302335 upstream upstream SLC30A5 7SK 68425638 68302062 + - 0 68375026 68361746 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.607048593593732 0.535631111994469 0.607048593593732 0.535631111994469 4 - - 14085 Y Y 3.44768596531277 3.2059651532887 3.2059651532887 0 0 0.611523588072409 Y 0 0.944676894467689 N N 11861 4829 ENSG00000100241 ENSG00000100239 + + 22 22 49260330 49230380 coding downstream SBF1 SAPS2 49232050 49128599 - + 0.944676894467689 49232472 49231088 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.685607823352921 0.742741808632331 0.742741808632331 0.685607823352921 1 - - 45844 N Y 3.6052936758779 3.234707967076 3.234707967076 1 0 0.366782879862828 N 0 0.889348025711662 N N 671 0 ENSG00000187650 ENSG00000209951 - + 19 7 5861864 86960 utr3p upstream AC104532.2 AC097646.2-1 5855885 86858 + - 0 5860566 126103 - - Y - - N HCC1954 152 138.5 84 8 1 N - - N SINE - 1 0 1 8 0.328520415356608 0.51420586751469 0.51420586751469 0.328520415356608 3 - - 34235 Y Y 3.49847350305486 3.30380917727745 3.30380917727745 198 0 0.0252929722591134 Y 0.914718614718615 0.985786435786436 N N 333 14753 ENSG00000214654 ENSG00000119402 - - 9 9 122601666 122595561 intron upstream AL161911.17 FBXW2 122600367 122559075 + - 0 122600677 122595677 - + N 0.0469635433514239 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.649899082553289 0.299953422716903 0.649899082553289 0.299953422716903 2 0 - 47254 Y Y 3.44977610258113 3.30232144676095 3.30232144676095 0 0.350731382978723 0.211390687273115 Y 0.350731382978723 0.969082446808511 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 16 0.835584534711372 0.685607823352921 0.835584534711372 0.685607823352921 4 - - 46433 N Y 3.64809409186561 3.36447795254773 3.36447795254773 103 0.0296232192783916 0.216723203093528 N 0.931300758886966 0.931300758886966 N N 0 689 ENSG00000204554 ENSG00000196761 - + 20 19 25949568 41955556 intron coding AL450124.7 AC020928.7 25938471 41931454 + - 0.931300758886966 25949510 41944388 - - Y 1 - N HCC1954 2 2 2 7 1 N - - N - - 0 0 0 7 0.592765097273879 0.349945659836387 0.592765097273879 0.349945659836387 2 0 - 4006 Y Y 3.66016945000958 3.2802368700128 3.2802368700128 284 0 0.0193895312017549 Y 0 0.989510748702743 N N 11 0 ENSG00000164707 ENSG00000212303 + - 7 7 135063474 135000990 coding downstream SLC13A4 U6 135016579 135000887 - - 0 135026887 134997953 - + N 1.90358333333333 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.649899082553289 0.521347615674617 0.649899082553289 0.521347615674617 1 0 - 36415 Y Y 3.69359248957888 3.4033579660152 3.4033579660152 276 0 0.443051344125412 Y 0.362972202423378 0.991832976954146 N N 3074 122756 ENSG00000135477 ENSG00000135480 + + 12 12 50938438 50928976 downstream downstream AC021066.37 KRT7 50932079 50913221 - + 0 50931827 50929478 - + N - - N HCC1954 1 1 1 0 3 N - - Y DNA - 1 0 1 5 0.849868031031224 0.899860268150708 0.899860268150708 0.849868031031224 1 - - 20060 N Y 3.51679652308403 3.51782959285392 3.51679652308403 1 0 0.108765093293661 N 0 0.822046465645082 N N 2 75177 ENSG00000219073 ENSG00000125107 - + 1 16 22188432 57221251 upstream utr5p ELA3B CNOT1 22175999 57111359 + - 0 22156886 57190783 - - Y - - N HCC1954 20 20 20 17 1 N - - N SINE - 1 0 1 17 0.349945659836387 0.642757334393363 0.642757334393363 0.349945659836387 2 - - 18752 Y Y 3.73552766966605 3.63399663687184 3.63399663687184 182 0 0.031299986491927 Y 0 0.981583231583232 N N 18306 3709 ENSG00000131795 ENSG00000152022 - + 1 1 144222801 144213026 upstream intron RBM8A LIX1L 144218990 144188516 + + 0 144218821 144204524 - + N - 0.736589869841989 N HCC1954 26 4.5 1 2 2 N - - Y - SINE 0 1 1 8 0.435646637755502 0.749883556792257 0.749883556792257 0.435646637755502 1 - 0 47941 N N 3.67952553980864 3.61720120015252 3.61720120015252 3 0 0.666032536086913 N 0 0 N N 8397 70215 ENSG00000113716 ENSG00000008988 - + 5 8 149412883 57149623 intron coding HMGXB3 RPS20 149360491 57148169 + - 0 149381392 57148293 - - Y 0.918614116178153 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.257102933757345 0.385654400636018 0.385654400636018 0.257102933757345 3 0 - 26476 N N 3.50744965188915 3.19293127328835 3.19293127328835 0 0.00645161290322571 0.071017688389753 N 0.00645161290322571 0.00645161290322571 N N 36111 136 ENSG00000099917 ENSG00000103023 + - 22 16 19271918 56886444 coding upstream MED15 AC009107.11-2 19191886 56871403 + - 0.00645161290322571 19191994 56919643 + + Y - - N HCC1954 21 18.3636363636364 1 10 1 N - - N - SINE 0 1 1 11 0.449930134075354 0.307095170876829 0.449930134075354 0.307095170876829 2 - - 33126 N Y 3.18871505582277 3.08507803069543 3.08507803069543 485 0 8.99263196182387e-05 Y 0 0.995108146351324 N N 247001 0 ENSG00000198786 ENSG00000210117 - + MT MT 14149 5580 coding intron MT-ND5 AF347015.1-9 12338 5513 + + 0 14009 5524 - + N 1.47594752497229 1 N HCC1954 4 2 1 6 1 N - - N - - 0 0 0 8 0.885576771830856 0.771308801272036 0.885576771830856 0.771308801272036 0 0 0 17963 Y Y 3.6533527266709 3.46340847946885 3.46340847946885 134 0 0.050226005872765 Y 0 0.995622807017544 N N 21819 0 ENSG00000143162 ENSG00000218805 + + 1 1 165789684 165756447 coding downstream CREG1 RP3-455J7.1 165776877 165755397 - + 0 165782015 165766281 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR,LTR 0 0.295454545454545 0.295454545454545 5 1.07840397214886 0.628473838073511 1.07840397214886 0.628473838073511 3 - - 6891 Y Y 3.55976477294109 3.64656650855576 3.55976477294109 373 0 0.0272061319102251 Y 0.994520225083228 0.994520225083228 N N 2842 3966 ENSG00000204588 ENSG00000175772 - + 2 2 110111006 110111006 intron upstream AC013268.5-2 AC013268.5-1 110108526 110103138 + + 0 110109264 110102053 - + N 0.126801530543669 - N HCC1954 24 5.82513661202186 4 183 2 N - - Y - - 0 0 0 183 1.35693215038599 1.42834963198525 1.42834963198525 1.35693215038599 1 0 - 12178 N N 3.32593360681895 3.63552422018169 3.32593360681895 3 0 0.271948977551246 N 0 0 N N 5835 208974 ENSG00000034152 ENSG00000164924 - + 17 8 21159118 102034745 upstream utr3p MAP2K3 YWHAZ 21128561 101999980 + - 0 21125110 102000174 - - Y - - N HCC1954 4 3.5 3 4 1 N - - N LINE - 1 0 1 4 0.249961185597419 0.371370904316165 0.371370904316165 0.249961185597419 1 - - 6580 Y Y 3.74081680969488 3.57696143724454 3.57696143724454 0 0 0.865503677202532 Y 0.216931216931217 0.921693121693122 N N 1692 5068 ENSG00000144040 ENSG00000135631 - + 2 2 73152473 73193654 coding coding SFXN5 RAB11FIP5 73022673 73154019 - - 0 73139233 73156217 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.93556900895034 0.778450549431962 0.93556900895034 0.778450549431962 4 - - 35925 N Y 3.20128492750669 3.57063922744582 3.20128492750669 300 0 0.00429678748932261 N 0 0.975691056910569 N N 173 0 ENSG00000127720 ENSG00000219553 - - 12 6 81397069 149855118 coding intron C12orf26 RP1-281H8.3 81276455 149854399 + - 0.975691056910569 81276484 149854912 - + Y - 1 N HCC1954 2 1.85714285714286 1 6 1 N - - N - - 0 0 0 7 0.557056356474248 0.607048593593732 0.607048593593732 0.557056356474248 2 - 0 38118 Y Y 3.37448717115191 3.25252712599539 3.25252712599539 258 0 0.172352147697605 Y 0 0.98046815625475 N N 4 4 ENSG00000181552 ENSG00000181562 - + 14 14 20308947 20286379 upstream downstream FAM12B FAM12A 20306426 20283939 + + 0 20301962 20294367 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR LTR 1 0.34020618556701 1 4 0.685607823352921 0.621332089913584 0.685607823352921 0.621332089913584 1 - - 13783 Y Y 3.2875921495814 3.38440310380026 3.2875921495814 295 0 0.776418767480588 Y 0 0.985556374355195 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 intron upstream AP000347.3 AP000347.4 22321400 22310865 - - 0 22325057 22312740 - + N 1 - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 7 0.471355378555133 0.707033067832699 0.707033067832699 0.471355378555133 1 0 - 10749 N Y 3.6272104187567 3.36663737804334 3.36663737804334 344 0.800581395348837 0.00425716697786727 N 0.800581395348837 0.43390847711928 N N 78560 272 ENSG00000112493 ENSG00000204277 - - 6 17 33390114 73786168 utr3p utr3p TAPBP AC087645.19-2 33375449 73769025 - - 0.43390847711928 33377154 73769228 + + Y - - N HCC1954 37 36.5 35 4 1 N - - N DNA,SINE SINE 0.252336448598131 1 1 4 0.635615586233437 0.528489363834543 0.635615586233437 0.528489363834543 3 - - 29161 N Y 3.51207644450867 3.36551102231762 3.36551102231762 320 0 0.0118626923060644 Y 0.987053571428572 0.987053571428572 N N 7 345 ENSG00000124657 ENSG00000203813 - + 6 6 28033939 27969644 coding downstream OR2B6 HIST1H3H 28032998 27885821 + + 0 28033756 27969738 - + N 0.50721206782647 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 13 0.985561246069823 0.849868031031224 0.985561246069823 0.849868031031224 4 0 - 16055 N Y 3.51952501003312 3.58743466416515 3.51952501003312 22 0.0433835962291247 0.0181819004398476 N 0.845968545155537 0.0433835962291247 N N 810 0 ENSG00000154309 ENSG00000184565 - + 1 Y 221245958 19698690 intron intron DISP1 TTTY14 221112236 19553973 + - 0.0433835962291247 221190448 19612795 - - Y 4.55926832279471 1 N HCC1954 4 2.46153846153846 1 9 1 N - - N SINE SINE 1 0.131782945736434 1 13 0.271386430077198 0.921285512630487 0.921285512630487 0.271386430077198 1 0 0 49539 Y Y 2.57912767437607 3.46807512488172 2.57912767437607 0 0 0.310800746076338 Y 0 0.975078369905956 N N 1543 4630 ENSG00000134480 ENSG00000145715 + + 5 5 86744592 86723488 utr3p downstream CCNH RASA1 86725844 86599838 - + 0 86725910 86724405 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.964136001590045 0.557056356474248 0.964136001590045 0.557056356474248 3 - - 14379 N N 3.2233083338141 3.52105259334297 3.2233083338141 2 0 0.075183135441107 N 0 0.0071942446043165 N N 821 14402 ENSG00000203995 ENSG00000156689 - + 1 11 53133258 58368833 utr3p intron ZYG11A GLYATL2 53080771 58358118 + - 0.0071942446043165 53132217 58368481 - - Y - 0.958134545874787 N HCC1954 40 33.6 30 5 1 N 509 24.5521 N SINE - 1 0 1 5 0.292811674556976 0.435646637755502 0.435646637755502 0.292811674556976 2 - 0 33915 N N 3.21804051143267 2.65506430305583 2.65506430305583 1 0 0.614519000078549 N 0 0 N N 544065 59837 ENSG00000198744 ENSG00000198695 + - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8706 14655 + + N 0.551278888780803 9.36362635228759 Y HCC1954 3 2 1 2 3 N 316 3.86643 N - - 0 0 0 4 0.485638874874985 0.828442786551446 0.828442786551446 0.485638874874985 2 0 0 33916 N N 3.26720299001245 3.30847582269032 3.26720299001245 4 0.012987012987013 0.825442861953398 N 0 0 N N 544065 59837 ENSG00000198744 ENSG00000198695 + - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8818 14192 + + N 0.595329437551416 0.577069123119692 Y HCC1954 2 1.25 1 1 3 N 316 3.86643 N - - 0 0 0 4 0.778450549431962 0.821301038391519 0.821301038391519 0.778450549431962 2 0 0 48018 N N 3.24831090852981 3.34359427943881 3.24831090852981 0 0 0.999917686092097 N 0 0 N N 86504 0 ENSG00000104408 ENSG00000182152 + + 8 5 109330135 117142614 intron downstream EIF3E AC114322.2 109283149 117142420 - - 0 109290104 116868566 - - Y 0.54481186694143 - N HCC1954 1 1 1 0 7 N 241 0.00319582 N - LINE 0 0.15702479338843 0.15702479338843 6 0.785592297591888 0.864151527351077 0.864151527351077 0.785592297591888 3 0 - 35759 N N 3.47336426491055 3.64231043829683 3.47336426491055 6 0 0.08333682642781 N 0 0.0199934447722059 N N 4364 13811 ENSG00000139178 ENSG00000182149 + + 12 16 7153069 70520407 intron intron C1RL KIAA0174 7138294 70486946 - + 0.0199934447722059 7142570 70517100 - + Y 0.796143328047562 1.78722638847245 N HCC1954 21 20.25 20 4 1 N - - N LINE,SINE SINE 0.713114754098361 1 1 4 0.521347615674617 0.335662163516534 0.521347615674617 0.335662163516534 2 0 0 37229 N Y 3.62088820895798 3.46192074895235 3.46192074895235 0 0 0.107472662651588 N 0 0.792205638474295 N N 1390 16017 ENSG00000131732 ENSG00000018236 - - 5 12 80644872 39750361 utr5p utr5p ZCCHC9 CNTN1 80633178 39588423 + + 0 80633781 39588446 - - Y - 0.0694111112616335 N HCC1954 32 25 22 8 1 N - - N SINE - 1 0 1 8 0.314236919036755 0.485638874874985 0.485638874874985 0.314236919036755 2 - 0 34361 Y Y 2.79674181280218 3.35719722089263 2.79674181280218 322 0 0.0204496376661133 Y 0 0.989722738041878 N N 7771 4429 ENSG00000165304 ENSG00000137075 - - 9 9 36667678 36391195 upstream intron MELK RNF38 36562873 36326401 + - 0 36477310 36380720 - + N - 4.66746019765606 N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.0769230769230769 0 0.0769230769230769 7 0.557056356474248 0.671324327033068 0.671324327033068 0.557056356474248 1 - 0 28504 N N 3.35463656781289 3.43681151080804 3.35463656781289 1 0 0.0731252546804444 N 0 0 N N 19343 75177 ENSG00000163694 ENSG00000125107 + + 4 16 40326640 57221251 intron utr5p RBM47 CNOT1 40120029 57111359 - - 0 40287667 57190762 - - Y 1.31300695157071 - N HCC1954 35 23 20 5 1 N 578 25.124 N SINE - 1 0 1 5 0.28566992639705 0.335662163516534 0.335662163516534 0.28566992639705 2 0 - 7187 N Y 3.46232197653647 3.00041279263742 3.00041279263742 340 0 0.00118683178490331 Y 0 0.987051184110008 N N 0 3165 ENSG00000208925 ENSG00000163013 - - 2 2 73379382 73351551 upstream upstream AC069404.5 FBXO41 73379320 73335308 + - 0.987051184110008 73366439 73365199 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE - 0.533980582524272 0 0.533980582524272 6 0.699891319672773 0.442788385915428 0.699891319672773 0.442788385915428 1 - - 42644 N N 3.54296933622177 3.38552945952599 3.38552945952599 0 0 0.500711957933869 N 0.00218818380743979 0.746501862913241 N N 4574 42670 ENSG00000188917 ENSG00000128050 - - X 4 100193758 57022291 utr3p utr3p TRMT2B PAICS 100150992 56996672 - + 0 100151997 57020869 + - Y - 1.585128975859 N HCC1954 35 33.5 30 4 1 N - - N SINE SINE,LINE 1 0.826315789473684 1 4 0.392796148795944 0.664182578873142 0.664182578873142 0.392796148795944 2 - 0 7518 Y Y 3.353603498043 3.39959640929622 3.353603498043 149 0 0.877801139366116 Y 0.379413413039417 0.981194345849679 N N 17694 466 ENSG00000153827 ENSG00000153832 - - 2 2 230494912 230586068 utr5p intron TRIP12 FBXO36 230340174 230495262 - + 0 230453088 230496108 + - N - 0.600688791064477 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 1.10697096478857 0.757025304952183 1.10697096478857 0.757025304952183 4 - 0 28013 N N 3.50421730383029 3.41952156054875 3.41952156054875 1 0 0.104248675453104 N 0.882310084904867 0.748928181130384 N N 45068 201 ENSG00000205336 ENSG00000173698 + - 16 X 56256445 19050676 upstream intron GPR56 GPR64 56220023 18917348 + - 0 56211295 19034950 + + Y - 3.36503073775745 N HCC1954 21 20.0526315789474 20 19 2 N - - N - SINE 0 1 1 19 0.428504889595575 0.349945659836387 0.428504889595575 0.349945659836387 0 - 0 29623 Y Y 3.54296933622177 3.37345410138202 3.37345410138202 0 0 0.376421501814379 Y 0.986528066528066 0.993264033264033 N N 387 8928 ENSG00000164674 ENSG00000146425 - - 6 6 159105889 158985759 utr5p upstream SYTL3 DYNLT1 158991034 158977494 + - 0 158992774 158986255 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.0523255813953488 0.0523255813953488 10 1.07126222398894 1.20695543902754 1.20695543902754 1.07126222398894 1 - - 39987 Y Y 3.3478104969044 3.03014882340126 3.03014882340126 349 0 0.00763441211577442 Y 0 0.989042476148493 N N 5454 5834 ENSG00000166716 ENSG00000140612 - - 15 15 83150663 83060678 coding upstream ZNF592 SEC11A 83126889 83013781 + - 0 83126966 83093051 - + N 0.848752374975591 - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat 0 1 1 6 0.907002016310634 0.642757334393363 0.907002016310634 0.642757334393363 2 0 - 25378 N Y 3.27502227789748 3.44785379918211 3.27502227789748 317 0.19433040923037 0.00226073688326178 N 0.139708742059548 0.836134998487533 N N 1328 936 ENSG00000102781 ENSG00000151338 + - 13 14 29779584 37090214 intron downstream KATNAL1 MIPOL1 29674768 36736907 - + 0.235296659608487 29741308 37105946 - - Y 0.790951167900013 - N HCC1954 21 20.125 20 8 1 N 87 22.756 N Other SINE 1 1 1 8 0.857009779191151 0.728458312312478 0.857009779191151 0.728458312312478 1 0 - 31896 Y Y 3.50000108636471 3.42936294528359 3.42936294528359 0 0.140909090909091 0.364552162754799 Y 0.153359683794466 0.987549407114625 N N 4553 9271 ENSG00000136522 ENSG00000136518 + + 3 3 180805128 180788882 coding intron MRPL47 ACTL6A 180788951 180763402 - + 0 180793129 180782984 - + N - 2.20176635922485 N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.722222222222222 0.722222222222222 6 0.914143764470561 0.51420586751469 0.914143764470561 0.51420586751469 1 - 0 30871 N Y 2.84535093662244 3.48064499656564 2.84535093662244 182 0.171245421245421 0.0151697192899490 N 0.58562271062271 0.58562271062271 N N 0 12481 ENSG00000219699 ENSG00000177565 + + 6 3 128023417 178397734 intron coding RP11-325O24.2 TBL1XR1 128022528 178212163 - - 0 128022595 178226902 - - Y 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.357087407996313 0.828442786551446 0.828442786551446 0.357087407996313 2 0 - 48801 N Y 3.67320333000993 3.09462324098319 3.09462324098319 0 0 0.467894448028241 Y 0.993568177320404 0.980704531961211 N N 397 4794 ENSG00000145779 ENSG00000172869 - + 5 5 118756975 118612721 coding downstream TNFAIP8 DMXL1 118752897 118434983 + + 0 118756410 118632501 - + N 0.0250352751461399 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 183 1.26408942430695 1.08554572030879 1.26408942430695 1.08554572030879 4 0 - 31161 N Y 3.44768596531277 3.61513506061274 3.44768596531277 0 0 0.768547078890756 Y 0.335449735449736 0.909379509379509 N N 763 95 ENSG00000205814 ENSG00000215837 - + 3 3 196924416 196900773 upstream downstream AC069513.28-3 AC069513.28-2 196912000 196900191 + + 0.184415584415585 196908486 196901620 - + N - - N HCC1954 6 1.34615384615385 1 3 4 N - - N LINE - 1 0 1 26 0.871293275511003 0.542772860154395 0.871293275511003 0.542772860154395 1 - - 15539 N N 3.81145495077599 3.51001030496889 3.51001030496889 35 0.291609938733832 0.428215813004646 N 0.349046970728387 0.387338325391423 N N 0 0 ENSG00000216979 ENSG00000205871 + + 1 7 119471437 97853832 intron intron RP4-610L12.1 AC093799.2-1 119470685 97853042 - - 0.387338325391423 119471002 97853377 - - Y 1 1 N HCC1954 11 4.78571428571429 3 14 1 N - - N - - 0 0 0 14 0.271386430077198 0.471355378555133 0.471355378555133 0.271386430077198 2 0 0 29220 Y Y 3.69681549006792 3.33680806132367 3.33680806132367 242 0 0.0696549823715847 Y 0 0 N N 0 8087 ENSG00000218143 ENSG00000137269 + + 6 6 53989534 53896878 downstream downstream RP11-411K7.2 LRRC1 53989240 53767737 - + 0 53955516 53902336 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 0.699891319672773 1.02126998686945 1.02126998686945 0.699891319672773 1 - - 18479 N N 3.38548960673263 3.47439733468044 3.38548960673263 0 0 0.155830970513998 Y 0 0 N N 3863 1843 ENSG00000219481 ENSG00000142794 - + 1 1 146862781 21684085 upstream intron NBPF15 NBPF3 146827614 21639217 + + 0 146824712 21639930 - + N - 0.707256802427417 N HCC1954 18 4.06666666666667 1 12 1 N - - N SINE,SINE - 1 0 1 15 0.778450549431962 0.428504889595575 0.778450549431962 0.428504889595575 1 - 0 33044 N Y 3.19446820416802 3.17407904459906 3.17407904459906 300 0 0.164495593031802 Y 0 0.99085626911315 N N 171855 539404 ENSG00000198886 ENSG00000198712 - + MT MT 12138 8270 coding coding MT-ND4 MT-CO2 10761 7587 + + 0 10904 8253 - + N 0.411787399530623 3.11599246263018 N HCC1954 2 1.4 1 2 3 N - - N - - 0 0 0 5 0.907002016310634 0.892718519990782 0.907002016310634 0.892718519990782 2 0 0 19187 Y Y 3.54292948342842 3.42779550918039 3.42779550918039 6 0.0140955682233627 0.291978926242585 Y 0.0140955682233627 0.994096380648044 N N 0 6723 ENSG00000201987 ENSG00000185630 - + 1 1 163090193 163082933 downstream coding Y_RNA PBX1 163090092 162795684 + + 0 163120404 163082445 - + N - - N HCC1954 1 1 1 0 1 N - - Y RNA,RNA - 0.401197604790419 0 0.401197604790419 23 1.19267194270768 1.48548361726466 1.48548361726466 1.19267194270768 2 - - 35621 N N 3.26764481531067 3.32948747687522 3.26764481531067 0 0.0045871559633025 0.765221887611246 N 0.285344624794166 0.0045871559633025 N N 0 712661 ENSG00000216315 ENSG00000111640 + + 22 12 39400402 6517797 intron coding CTA-229A8.6 GAPDH 39399439 6513918 - + 0.0045871559633025 39399921 6516760 - + Y 1 - N HCC1954 4 2.6 1 3 2 N - - N - - 0 0 0 5 0.278528178237124 0.485638874874985 0.485638874874985 0.278528178237124 2 0 - 46961 N N 3.79465951405667 3.6035982586987 3.6035982586987 0 0 0.641949914650052 Y 0.198518061129978 0.319954718534527 N N 0 155 ENSG00000213904 ENSG00000079435 + - 19 19 47681706 47623418 intron downstream AC011497.6 LIPE 47681065 47597499 - - 0.319954718534527 47681139 47593259 - + N 1 - N HCC1954 2 1.2 1 1 2 N - - N - - 0 0 0 5 0.771308801272036 0.585623349113953 0.771308801272036 0.585623349113953 2 0 - 49326 Y Y 3.46704205511183 3.72146071989581 3.46704205511183 2 0 0.322322966417685 Y 0 0 N N 5788 4938 ENSG00000134986 ENSG00000129595 - + 5 5 111137815 111782909 coding downstream C5orf13 EPB41L4A 111092408 111507433 - - 0 111119367 111472650 + - N - - N HCC1954 3 1.57142857142857 1 3 1 N - - Y - LINE 0 0.488372093023256 0.488372093023256 7 1.19267194270768 0.921285512630487 1.19267194270768 0.921285512630487 1 - - 41698 N N 3.35823029066252 3.72717401544771 3.35823029066252 0 0 0.626129803641389 N 0 0 N N 249 79632 ENSG00000155897 ENSG00000182197 + + 8 8 132123854 119193119 upstream coding ADCY8 EXT1 131861736 118875910 - - 0 132357382 119191505 - - N - - Y HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 8 0.87843502367093 1.05697872766909 1.05697872766909 0.87843502367093 3 - - 22523 N N 3.45868840089349 3.69784855983781 3.45868840089349 0 0 0.0772391103074105 N 0 0 N N 462279 2351 ENSG00000070756 ENSG00000186501 - + 8 1 101803491 27535477 coding intron PABPCP5 TMEM222 101784320 27521276 - + 0 101791022 27524394 + + Y - 0.725964722344023 N HCC1954 20 20 20 4 1 N - - N - snRNA 0 1 1 4 0.864151527351077 0.442788385915428 0.864151527351077 0.442788385915428 2 - 0 48736 N Y 3.69255941980899 3.6491271616355 3.6491271616355 5 0 0.66270309922799 N 0.944048597789349 0.932858317347218 N N 8136 1459 ENSG00000164346 ENSG00000165244 - - 5 9 74108490 98220490 coding intron TINP1 ZNF367 74098859 98190057 + - 0.272631771261533 74105449 98210011 - + Y - 1.86288217314499 N HCC1954 3 2.4 1 4 1 N - - N - SINE 0 0.559322033898305 0.559322033898305 5 0.678466075192994 0.421363141435649 0.678466075192994 0.421363141435649 4 - 0 13689 Y Y 3.31125774280189 3.30591516961058 3.30591516961058 365 0 0.00891632367152517 Y 0 0.986878154289834 N N 4357 1260 ENSG00000100216 ENSG00000100211 - + 22 22 37410709 37399795 upstream intron TOMM22 CBY1 37407900 37382604 + + 0 37407734 37394444 - + N - 0.895294809181644 N HCC1954 1 1 1 0 2 N - - Y DNA DNA 0.509803921568627 1 1 4 0.721316564152552 0.792734045751814 0.792734045751814 0.721316564152552 3 - 0 41955 N N 3.66592259835483 3.56079784271098 3.56079784271098 17 0 0.97450014593588 N 0 0.0498737373737375 N N 86504 559 ENSG00000104408 ENSG00000102290 + + 8 X 109330135 91764885 coding upstream EIF3E PCDH11X 109283149 90920960 - + 0.0838068181818182 109309672 90823313 - + Y 0.593852950305209 - N HCC1954 2 1.5 1 2 3 N - - N - LTR 0 1 1 4 0.657040830713216 0.849868031031224 0.849868031031224 0.657040830713216 4 0 - 9121 N Y 3.12804628055249 3.60422075331465 3.12804628055249 1 0 0.220661119358373 N 0.897485965340493 0.809616792775201 N N 1649619 2643 ENSG00000141736 ENSG00000003402 - + 17 2 35138441 201737246 coding intron ERBB2 CFLAR 35104766 201689135 + + 0 35122227 201735212 - + Y - 1.71079594210933 N HCC1954 22 10.5 1 7 1 N - - N - SINE 0 1 1 8 0.857009779191151 0.378512652476092 0.857009779191151 0.378512652476092 2 - 0 19119 Y Y 3.55081912933034 3.67849247003875 3.55081912933034 246 0 0.232288100620466 Y 0 0 N Y 169 24350 ENSG00000134256 ENSG00000134247 - + 1 1 117380690 117334495 intron coding IGSF2 PTGFRN 117345905 117254207 + + 0 117353995 117318468 - + N 0.209124552569314 1.24207939815101 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.592765097273879 0.699891319672773 0.699891319672773 0.592765097273879 4 0 0 27060 Y Y 2.6465826677615 3.23697244570866 2.6465826677615 3 0.00916962902196716 0.954396241839639 Y 0.00916962902196716 0.987457843405341 N N 4999 5945 ENSG00000141013 ENSG00000003249 - - 16 16 88638880 88613438 coding upstream GAS8 DBNDD1 88616509 88598782 + - 0 88621545 88613677 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.153846153846154 0.153846153846154 61 1.4426331283051 1.02126998686945 1.4426331283051 1.02126998686945 4 - - 20357 N Y 3.25256697878875 3.66592259835483 3.25256697878875 0 0 0.0733538489359409 N 0 0 N N 49089 52571 ENSG00000117450 ENSG00000096433 - + 1 6 45760196 33772324 coding intron PRDX1 ITPR3 45749295 33697139 - + 0 45757275 33736634 + + Y - 0.736425527458909 N HCC1954 21 13.1 6 10 1 N - - N - SINE 0 1 1 10 0.5713398527941 0.264244681917271 0.5713398527941 0.264244681917271 2 - 0 37615 N N 3.41423242051993 2.92867122376953 2.92867122376953 0 0 0.0867728631375066 N 0 0 N N 443941 0 ENSG00000172057 ENSG00000200312 - + 17 14 35337380 89248922 utr3p intron ORMDL3 7SK 35330822 89248608 - + 0 35331488 89248730 + + Y 2.06937151288757 1 N HCC1954 5 4.25 4 4 1 N - - N - RNA 0 1 1 4 0.871293275511003 0.557056356474248 0.871293275511003 0.557056356474248 2 0 0 1730 N N 3.58217602935986 3.64553343878587 3.58217602935986 0 0 0.535826764781221 N 0 0 N N 5754 57665 ENSG00000168461 ENSG00000166441 - + 18 11 9852547 8667978 upstream utr3p RAB31 RPL27A 9764874 8660571 + + 0 9724787 8663953 - + Y - - N HCC1954 2 1.375 1 3 1 N - - N - - 0 0 0 8 0.349945659836387 1.20695543902754 1.20695543902754 0.349945659836387 2 - - 44667 Y Y 3.55760534744548 3.40744620240479 3.40744620240479 316 0 0.0296726828116769 Y 0.975883013474888 0.991961004491629 N N 0 282831 ENSG00000212325 ENSG00000099194 + + 10 10 102148193 102114577 downstream downstream Y_RNA SCD 102148099 102096762 - + 0 102144855 102131194 - + N - - N HCC1954 8 2 1 2 2 N - - Y LINE LTR,LTR 1 0.73936170212766 1 8 0.835584534711372 1.22123893534739 1.22123893534739 0.835584534711372 1 - - 5314 N N 2.94972647754617 3.47655676017605 2.94972647754617 0 0.0550964187327821 0.038290977729629 N 0.280073461891644 0.505050505050505 N N 3968 511 ENSG00000124496 ENSG00000170417 - + 6 2 42527767 102800311 utr3p intron TRERF1 TMEM182 42300647 102719799 - + 0.505050505050505 42302800 102721389 + + Y - 2.52655060430884 N HCC1954 21 20.8333333333333 20 6 1 N - - N DNA SINE 1 1 1 6 0.378512652476092 0.314236919036755 0.378512652476092 0.314236919036755 1 - 0 48397 N N 3.39231567764112 3.42424163912411 3.39231567764112 7 0 0.542201752476041 N 0 0 N N 850768 0 ENSG00000075624 ENSG00000176183 + + 7 5 5536758 97702893 utr3p downstream ACTB AC094106.3-1 5533313 97702584 - + 0 5533540 97703823 - + Y 0.816623488654224 - N HCC1954 5 1.19148936170213 1 4 1 N - - N - - 0 0 0 47 1.24980592798709 0.278528178237124 1.24980592798709 0.278528178237124 1 0 - 35148 N Y 3.73080759109069 3.39959640929622 3.39959640929622 0 0 0.87477782317546 N 0.722046511627907 0.768372093023256 N N 542 0 ENSG00000135482 ENSG00000157680 - - 12 7 54802545 137182149 upstream intron ZC3H10 DGKI 54798297 136724925 + - 0.768372093023256 54796830 136849135 - + Y - 1 N HCC1954 6 2.06040268456376 2 149 1 N - - N - - 0 0 0 149 1.18553019454776 0.421363141435649 1.18553019454776 0.421363141435649 4 - 0 32993 N N 2.96319769112561 3.49272035470961 2.96319769112561 0 0 0.999498346054782 N 0 0.1140642303433 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0.1140642303433 8593 14908 - + N 0.65879648337433 0.647784255393754 N HCC1954 9 4.875 1 15 8 Y 189 4.09957 N - - 0 0 0 16 0.642757334393363 0.928427260790413 0.928427260790413 0.642757334393363 2 0 0 4542 N Y 3.44871903508266 3.54552998930151 3.44871903508266 389 0.967996920665906 0.000227730819356453 Y 0.914658455109083 0.983998460332953 N N 0 7862 ENSG00000196898 ENSG00000091073 + + 7 7 76436410 75973241 upstream utr5p AC114737.3-1 DTX2 76435514 75928954 - + 0 76445777 75937666 - + N - - N HCC1954 2 1.66666666666667 1 4 1 N 11 9.55262 N - - 0 0 0 6 0.421363141435649 0.87843502367093 0.87843502367093 0.421363141435649 2 - - 38097 Y Y 3.55231620741665 3.41679307359967 3.41679307359967 255 0 0.216901531512773 Y 0 0 N N 1740 16 ENSG00000066427 ENSG00000212924 + + 14 14 91642707 91576617 utr3p coding ATXN3 AL049872.3 91598883 91576287 - + 0 91599328 91576400 - + N 0.107182427307181 1.05188822426569 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 47 0.542772860154395 0.764167053112109 0.764167053112109 0.542772860154395 4 0 0 47510 Y Y 2.97316705693644 3.36398343900777 2.97316705693644 0 0 0.997076466282569 Y 0 0 N N 6250 3492 ENSG00000105245 ENSG00000123815 - + 19 19 45888396 45914440 coding utr3p NUMBL ADCK4 45863650 45889274 - - 0 45884740 45889337 + - N - 0.230459120047516 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 16 1.28551466878673 1.37121564670584 1.37121564670584 1.28551466878673 4 - 0 3386 N N 3.44871903508266 3.35253057547976 3.35253057547976 0 0 0.909790489771687 N 0 0 Y N 542 9455 ENSG00000160191 ENSG00000160299 - + 21 21 43068688 46690106 downstream coding PDE9A PCNT 42946931 46568483 + + 0 43084600 46579110 - + N - 1.42897890447035 N HCC1954 3 1.05714285714286 1 1 1 N 580 8.94009 N LINE,LTR - 0.875 0 0.875 35 0.685607823352921 1.09268746846872 1.09268746846872 0.685607823352921 4 - 0 10023 Y Y 3.32064446679012 3.30165909935164 3.30165909935164 0 0 0.999999932299086 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 coding coding GSDMB ORMDL3 35314374 35330822 - - 0 35326991 35332961 + - N - - N HCC1954 1 1 1 0 14 Y - - Y - - 0 0 0 4 0.692749571512847 0.707033067832699 0.707033067832699 0.692749571512847 2 - - 10958 N Y 3.12328634918378 2.99930936485065 2.99930936485065 103 0 0.429638576554924 N 0.953064690443106 0.958931604137718 N N 4310 2906 ENSG00000183011 ENSG00000079819 - - 17 6 7701897 131426017 coding downstream LSMD1 EPB41L2 7700730 131202180 - - 0 7701426 131164595 + + Y - - N HCC1954 4 2.96503496503496 1 282 2 N - - N - - 0 0 0 286 1.27123117246687 1.28551466878673 1.28551466878673 1.27123117246687 2 - - 38153 Y Y 3.55504469436573 3.5246463161926 3.5246463161926 323 0 0.0148287390980596 Y 0.992390045612459 0.984780091224919 N N 3478 0 ENSG00000182512 ENSG00000212530 - - 14 14 95080808 95069719 upstream downstream GLRX5 SCARNA13 95071076 95069445 + - 0.984780091224919 95070683 95069151 - + N - - N HCC1954 2 1.02325581395349 1 1 1 N - - Y - - 0 0 0 43 1.18553019454776 0.978419497909897 1.18553019454776 0.978419497909897 4 - - 37418 N Y 3.47233119514066 3.37126417066287 3.37126417066287 2 0 0.0932203900044716 N 0 0.909652076318743 N N 20739 0 ENSG00000143951 ENSG00000212071 - + 2 14 63669355 35735525 utr3p downstream C2orf86 AL162511.5-2 63202041 35735437 - - 0 63309485 35660864 + - Y - - N HCC1954 640 520 400 4 1 N - - N LINE LINE 1 1 1 4 0.349945659836387 0.385654400636018 0.385654400636018 0.349945659836387 4 - - 42572 N Y 3.11613875627787 3.18552256055726 3.11613875627787 225 0 0.0212918001979076 Y 0.783574879227053 0.985571658615137 N N 177 177 ENSG00000215375 ENSG00000215375 - + 4 4 665817 665817 coding upstream MYL5 MYL5 661711 661711 + + 0 661818 659997 - + N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 5 0.899860268150708 0.764167053112109 0.899860268150708 0.764167053112109 3 - - 45742 N Y 3.40488554932505 3.19872427442695 3.19872427442695 323 0 0.0318854975069284 N 0 0.947531367117484 N N 6657 9146 ENSG00000163428 ENSG00000104960 + + 3 19 121550876 55055802 downstream utr3p LRRC58 PTOV1 121526266 55045950 - + 0.947531367117484 121509546 55055402 - + Y - 8.17863059935085 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 19 0.407079645115797 0.728458312312478 0.728458312312478 0.407079645115797 2 - 0 9090 N Y 3.07101108092519 3.48590363137093 3.07101108092519 0 0 0.144899678940264 N 0.790256309919781 0.832205047935825 N N 1649619 3677 ENSG00000141736 ENSG00000115355 - + 17 2 35138441 55500467 coding intron ERBB2 CCDC88A 35104766 55368482 + - 0 35125066 55373375 - - Y - 0.224931415773513 N HCC1954 2 2 2 8 1 N - - N - SINE 0 1 1 8 0.735600060472404 0.28566992639705 0.735600060472404 0.28566992639705 1 - 0 33093 N Y 3.76951977068882 3.16316473730098 3.16316473730098 544 0 0.00454777170085896 Y 0 0.996219084224599 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0 11177 5428 - + N 0.790069325830896 1.20099545258328 N HCC1954 2 1.2 1 1 4 N - - N - - 0 0 0 5 1.17838844638783 0.771308801272036 1.17838844638783 0.771308801272036 1 0 0 16734 N Y 3.12804628055249 3.65913638023969 3.12804628055249 1 0 0.136029519332001 N 0.926206509539843 0.926206509539843 N N 1649619 8122 ENSG00000141736 ENSG00000134717 - + 17 1 35138441 52328976 coding intron ERBB2 BTF3L4 35104766 52294385 + + 0 35122227 52300042 - + Y - 0.49887053871844 N HCC1954 9 4.4 1 5 1 N - - N - SINE 0 1 1 10 0.564198104634174 0.357087407996313 0.564198104634174 0.357087407996313 2 - 0 42605 Y Y 3.1808652627142 3.30331466373749 3.1808652627142 107 0 0.164026070412122 Y 0.00395256916996045 0.989173397490978 N N 26328 2446 ENSG00000205403 ENSG00000123739 + - 4 4 110942783 110870660 coding upstream CFI PLA2G12A 110881297 110854140 - - 0 110883099 110875404 - + N - - N HCC1954 20 8.5 1 4 1 N - - Y - SINE 0 1 1 6 1.14982145374813 0.614190341753658 1.14982145374813 0.614190341753658 1 - - 44685 N Y 2.89831269838974 3.6727393216935 2.89831269838974 0 0 0.722772225212578 Y 0.957549099836334 0.994693637479542 N N 253 6115 ENSG00000203780 ENSG00000089876 - - 10 10 127688151 127559874 upstream upstream FANK1 DHX32 127575098 127514896 + - 0 127574780 127564238 - + N - - N HCC1954 1 1 1 0 2 N - - N - LTR 0 1 1 44 1.48548361726466 1.34264865406614 1.48548361726466 1.34264865406614 2 - - 41496 Y Y 3.56335849579072 3.71464399655714 3.56335849579072 301 0 0.0234419366207455 Y 0.0515486014360733 0 N N 2237 1798 ENSG00000147408 ENSG00000104611 + + 8 8 19584374 19297594 coding intron CSGALNACT1 SH2D4A 19305952 19215483 - + 0 19307617 19295336 - + N 0.662802924584521 1.73580809453999 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 1.09268746846872 0.921285512630487 1.09268746846872 0.921285512630487 1 0 0 40162 Y Y 2.99926951205729 3.41103992525442 2.99926951205729 165 0 0.127712864853767 Y 0.988680408738548 0.93208245243129 N Y 2587 4948 ENSG00000214446 ENSG00000157823 + - 15 15 88257163 88238206 coding coding C15orf38 AP3S2 88244836 88177793 - - 0 88247452 88233376 - + N - 1.64305934929519 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 18 1.03555348318931 0.628473838073511 1.03555348318931 0.628473838073511 4 - 0 27428 Y Y 3.58846773393504 3.56911164413597 3.56911164413597 0 0 0.250977949517865 Y 0 0.990119340476142 N N 8701 10526 ENSG00000213853 ENSG00000186261 + - 16 16 10582040 10534118 coding intron EMP2 AC027277.5 10533550 10529936 - - 0 10539306 10531200 - + N - 0.784030487870489 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.12621359223301 0.12621359223301 4 0.499922371194838 0.728458312312478 0.728458312312478 0.499922371194838 2 - 0 34473 Y Y 3.16783138271386 3.57696143724454 3.16783138271386 235 0 0.00766714664388335 Y 0.544802431610942 0 N N 34750 10783 ENSG00000197694 ENSG00000119392 - + 9 9 130435762 130344398 upstream downstream SPTAN1 GLE1 130354687 130306792 + + 0 130354470 130345786 - + N - - N HCC1954 9 2.33333333333333 1 1 1 N - - Y - SINE 0 1 1 6 0.535631111994469 0.464213630395207 0.535631111994469 0.464213630395207 2 - - 9679 Y Y 3.18296190747752 3.45293525254824 3.18296190747752 149 0.00805934242181239 0.381138179570788 Y 0.00805934242181239 0.994266238973536 N N 18893 6556 ENSG00000141551 ENSG00000141526 + + 17 17 77824862 77790658 intron coding CSNK1D SLC16A3 77795535 77779582 - + 0 77812063 77788036 - + N 1.53392144218755 - N HCC1954 1 1 1 0 3 N - - Y SINE - 0.8125 0 0.8125 9 1.02126998686945 0.814159290231593 1.02126998686945 0.814159290231593 1 0 - 21748 N Y 3.53871326596283 3.65488030998075 3.53871326596283 1 0 0.250107458347580 N 0.569151569151569 0.973071973071973 N N 1186 0 ENSG00000137968 ENSG00000187950 - - 1 12 75849389 29541886 coding downstream SLC44A5 OVCH1 75440404 29471771 - - 0 75634856 29456311 + + Y - - N HCC1954 21 18.2857142857143 2 7 1 N - - N - LINE 0 1 1 7 1.1141127129485 0.485638874874985 1.1141127129485 0.485638874874985 2 - - 2071 N N 3.27870928670295 3.47023455037734 3.27870928670295 24 0.0448979591836737 0.462633692987344 N 0.512288319583152 0.0448979591836737 N N 78560 1788 ENSG00000112493 ENSG00000184937 - + 6 11 33390114 32413663 utr3p downstream TAPBP WT1 33375449 32365897 - - 0.0448979591836737 33376424 32331425 + - Y - - N HCC1954 42 19.4 1 4 1 N - - N SINE SINE,SINE 1 0.765957446808511 1 5 0.642757334393363 0.335662163516534 0.642757334393363 0.335662163516534 2 - - 7630 N Y 3.47233119514066 3.37126417066287 3.37126417066287 2 0 0.091004351447119 N 0 0.92234563253012 N N 20739 0 ENSG00000143951 ENSG00000219531 - + 2 20 63669355 21417263 utr3p downstream C2orf86 RP5-984P4.1 63202041 21416882 - - 0 63309485 21411352 + - Y - - N HCC1954 660 530 420 4 1 N - - N LINE LINE 1 1 1 4 0.385654400636018 0.257102933757345 0.385654400636018 0.257102933757345 4 - - 29188 Y Y 3.15993238924212 3.59425138750382 3.15993238924212 312 0 0.00191701882282291 Y 0 0 N N 2712 784 ENSG00000185127 ENSG00000184465 - - 6 6 169848326 169844084 coding intron C6orf120 WDR27 169844182 169599232 + - 0 169844767 169831497 - + N 1.5909211421559 0.542395977263072 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 6 0.542772860154395 0.549914608314322 0.549914608314322 0.542772860154395 2 0 0 31482 Y Y 3.3184850412945 3.37977631118074 3.3184850412945 256 0 0.3412103084541 Y 0 0.987852515243902 N N 3882 5040 ENSG00000120756 ENSG00000175054 - - 3 3 143915191 143780358 intron upstream PLS1 ATR 143825034 143650770 + - 0 143853955 143798038 - + N 0.0233330598934899 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.578481600954027 0.599906845433805 0.599906845433805 0.578481600954027 2 0 - 26416 N Y 3.62464976567696 3.46653819400206 3.46653819400206 0 0 0.382871806165027 N 0.767567567567567 0.684555984555985 N N 3776 18076 ENSG00000128271 ENSG00000168411 - - 22 16 23168324 73258280 downstream intron ADORA2A RFWD3 22996866 73212798 + - 0 23182634 73252852 - + Y - 2.94744463310958 N HCC1954 4 1.5 1 3 1 N - - N SINE - 1 0 1 10 0.314236919036755 0.692749571512847 0.692749571512847 0.314236919036755 1 - 0 33062 N Y 3.53039946453785 3.41273534243362 3.41273534243362 422 0 0.279248338805082 Y 0 0.994457609268036 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding coding MT-CO3 MT-ND1 8367 3308 + + 0 8753 4223 - + N 0.558737747784603 1.43362340929214 N HCC1954 6 3.66666666666667 2 6 6 N - - N - - 0 0 0 6 0.828442786551446 1.12125446110842 1.12125446110842 0.828442786551446 1 0 0 49469 Y Y 3.32679884271949 3.43681151080804 3.32679884271949 0 0 0.976913539609585 Y 0 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883894 140816150 - + N - 0.194212665568841 N HCC1954 7 1.25954198473282 1 20 2 N - - Y - LTR 0 1 1 131 1.45691662462496 1.4140661356654 1.45691662462496 1.4140661356654 4 - 0 25174 Y Y 3.02804283106813 3.33896748681929 3.02804283106813 185 0 0.00938173287685662 Y 0.810553410553411 0.905276705276705 N N 3 1423 ENSG00000120664 ENSG00000133104 - - 13 13 35840547 35818453 intron intron RP11-251J8.3 SPG20 35818569 35773777 + - 0 35818777 35808492 - + N 0.696629213483146 4.70975515971942 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.642757334393363 0.549914608314322 0.642757334393363 0.549914608314322 3 0 0 13776 Y Y 3.4985040082784 3.29396779254261 3.29396779254261 268 0 0.0556587893323408 Y 0 0.992394895750256 N N 0 3368 ENSG00000218527 ENSG00000215193 - + 22 22 16964654 16952207 upstream coding XXbac-B476C20.10 PEX26 16964378 16940705 + + 0 16963414 16948023 - + N - 1.20195729197157 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.778450549431962 0.757025304952183 0.778450549431962 0.757025304952183 1 - 0 31952 N N 3.51377186168787 3.39930023484915 3.39930023484915 1 0 0.504923234072851 N 0 0 N N 8 850768 ENSG00000157152 ENSG00000075624 - - 3 7 12208532 5536758 intron coding SYN2 ACTB 12020862 5533313 + - 0 12087288 5534665 - + Y 0.808139534883721 1.2931632563077 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.278528178237124 0.564198104634174 0.564198104634174 0.278528178237124 0 0 0 45598 N Y 3.12449241049621 2.39788152983156 2.39788152983156 15 0 0.065622390748592 N 0 0.887307032590052 N N 297 0 ENSG00000204655 ENSG00000182225 - + 6 19 29748128 5527949 utr3p downstream MOG AC011533.6 29732788 5527671 + - 0 29747854 5518621 - - Y - - N HCC1954 39 34.5 32 6 1 N - - N SINE - 1 0 1 6 0.307095170876829 0.39993789695587 0.39993789695587 0.307095170876829 1 - - 43753 N Y 3.61257440753299 3.00762316627563 3.00762316627563 2 0 0.0317921515325496 N 0.811733684904417 0.905866842452208 N N 9 3891 ENSG00000213373 ENSG00000166295 + + 17 10 38304247 73665622 utr3p intron AC016889.28-2 C10orf104 38280217 73645812 - + 0 38280299 73645904 - + Y - 0.744979490524871 N HCC1954 37 28.75 21 4 1 N - - N SINE - 1 0 1 4 0.407079645115797 0.535631111994469 0.535631111994469 0.407079645115797 1 - 0 9741 Y Y 3.16567195721824 3.16038281718941 3.16038281718941 288 0 0.0118603785672133 Y 0 0.991258528265107 N N 520 14964 ENSG00000108352 ENSG00000108349 - + 17 17 35605426 35581957 upstream coding RAPGEFL1 CASC3 35588133 35550033 + + 0 35586704 35579223 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 1.22838068350732 1.20695543902754 1.22838068350732 1.20695543902754 2 - - 3556 N N 3.42783536197374 3.15951758128887 3.15951758128887 0 0 0.122694712812811 N 0 0 N N 0 10271 ENSG00000199698 ENSG00000159200 + + 21 21 23726473 34909303 upstream coding Y_RNA DSCR1 23726372 34810652 - - 0 23726990 34817876 - - N - - Y HCC1954 1 1 1 0 1 N - - N LTR,LTR - 1 0 1 9 0.964136001590045 0.907002016310634 0.964136001590045 0.907002016310634 2 - - 4309 Y N 3.64022392894185 3.30587531681723 3.30587531681723 0 0 0.129805001070645 Y 0 0 N N 2592 14326 ENSG00000187257 ENSG00000127947 - + 7 7 77247056 77107324 upstream downstream RSBN1L PTPN12 77163679 77004351 + + 0 77152546 77128497 - + N - - N HCC1954 3 1.22222222222222 1 1 1 N - - Y - SINE 0 1 1 9 0.678466075192994 0.707033067832699 0.707033067832699 0.678466075192994 3 - - 14847 N N 3.25256697878875 3.44975210485255 3.25256697878875 0 0.00531914893617003 0.0745122051781762 N 0.00531914893617003 0.00531914893617003 N N 49089 3831 ENSG00000117450 ENSG00000165490 - - 1 11 45760196 82323345 coding downstream PRDX1 C11orf82 45749295 82303402 - + 0 45757275 82327160 + - Y - - N HCC1954 12 4.28947368421053 1 34 1 N - - N - SINE 0 1 1 38 1.02841173502938 0.328520415356608 1.02841173502938 0.328520415356608 2 - - 17260 N N 3.17245817533338 3.25144062306302 3.17245817533338 0 0.464127218934911 0.472721404242027 N 0.578957100591716 0.540680473372781 N N 17278 21 ENSG00000100106 ENSG00000132688 - - 22 1 36502509 154913813 utr3p upstream TRIOBP NES 36422957 154905182 + - 0.540680473372781 36499945 154914409 - + Y - - N HCC1954 20 5.8 1 3 1 N 612 24.7212 N - Simple_repeat 0 1 1 5 0.521347615674617 0.271386430077198 0.521347615674617 0.271386430077198 3 - - 30295 Y Y 3.16254224268503 3.42424163912411 3.16254224268503 281 0 0.0341056629185303 Y 0.586841420015623 0.975696554118566 N N 22309 3794 ENSG00000002586 ENSG00000169084 - - X X 2669348 2428975 upstream upstream CD99 DHRSX 2619228 2147557 + - 0 2537147 2495333 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 44 0.614190341753658 1.04983697950916 1.04983697950916 0.614190341753658 4 - - 41563 Y N 3.44040523365767 3.36804242257272 3.36804242257272 7 0 0.895898463702244 Y 0.640151515151515 0.23532196969697 N N 3297 2237 ENSG00000104613 ENSG00000147408 - - 8 8 19753864 19584374 upstream utr5p INTS10 CSGALNACT1 19719198 19305952 + - 0.23532196969697 19659649 19487061 - + N - 8.81350450665804 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 4 0.421363141435649 0.378512652476092 0.421363141435649 0.378512652476092 1 - 0 10094 Y Y 3.58424216889964 3.51273879191798 3.51273879191798 236 0 0.913003334989842 Y 0 0 N N 252027 170868 ENSG00000141738 ENSG00000141741 - - 17 17 35157070 35140314 utr5p coding GRB7 C17orf37 35147713 35138937 + - 0 35152032 35140043 - + N - 1.90403885026224 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 5 0.5713398527941 0.607048593593732 0.607048593593732 0.5713398527941 1 - 0 10469 Y Y 3.50848272165904 3.4780843434859 3.4780843434859 0 0 0.608394441956663 Y 0 0.979656419529837 N N 1046 0 ENSG00000173805 ENSG00000201920 + + 17 17 37144422 37128038 coding upstream HAP1 5S_rRNA 37130591 37127932 - + 0 37135637 37127804 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.333333333333333 0.333333333333333 5 0.942710757110266 0.771308801272036 0.942710757110266 0.771308801272036 4 - - 24067 N Y 3.56439156556061 3.65760879692984 3.56439156556061 0 0 0.0731938479224725 N 0.879321852890135 0.879321852890135 N N 16 38037 ENSG00000081985 ENSG00000131446 - - 1 5 67635171 180175147 intron upstream IL12RB2 MGAT1 67545635 180150147 + - 0 67621023 180191413 - + Y 0.590803747534517 - N HCC1954 11 5 1 3 1 N 617 27.1664 N SINE - 1 0 1 4 0.357087407996313 0.828442786551446 0.828442786551446 0.357087407996313 1 0 - 12168 N N 3.39483647792751 3.54719490125717 3.39483647792751 5 0 0.0891797474534695 N 0 0.355327868852459 N N 252027 5 ENSG00000141738 ENSG00000183117 - - 17 8 35157070 3258996 utr5p intron GRB7 CSMD1 35147713 2780282 + - 0.355327868852459 35147875 2976620 - + Y 0.410465831783318 1.03912193001521 N HCC1954 21 20.1666666666667 20 6 1 N - - N - SINE 0 1 1 6 0.471355378555133 0.321378667196682 0.471355378555133 0.321378667196682 2 0 0 11642 N Y 3.74590761063082 3.2338028783821 3.2338028783821 284 0 0.00428865149055146 N 0.892851734060276 0.892851734060276 N N 3009 1772 ENSG00000188419 ENSG00000187451 - - X 17 85189222 42483361 coding downstream CHM AC068152.11-2 85002841 42480430 - + 0 85120432 42499785 + - Y - - N HCC1954 24 17.125 1 7 1 N - - N LTR - 0.983957219251337 0 0.983957219251337 8 0.792734045751814 0.585623349113953 0.792734045751814 0.585623349113953 0 - - 13446 N N 1.9566353188789 3.27870928670295 1.9566353188789 38 0.173192444090613 0.128501911362195 N 0.173192444090613 0.173192444090613 N N 850768 0 ENSG00000075624 ENSG00000213857 - - 7 22 5536758 39801189 utr3p downstream ACTB AL080243.21-3 5533313 39800114 - - 0.173192444090613 5533812 39800059 + + Y 0.965100862734119 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.607048593593732 0.22853594111764 0.607048593593732 0.22853594111764 2 0 - 20452 N Y 3.38486711211668 3.66745018166468 3.38486711211668 0 0 0.92500712413754 N 0.91739051606204 0.93509254833446 N N 0 8888 ENSG00000202394 ENSG00000112159 - - 1 6 172100206 90586163 downstream intron SNORD47 MDN1 172100130 90409952 - - 0.93509254833446 172100067 90488016 + + Y - 1.96227421382155 N HCC1954 3 2.45 1 17 2 N - - N - - 0 0 0 20 0.942710757110266 1.29979816510658 1.29979816510658 0.942710757110266 2 - 0 48872 Y Y 3.61464054707278 3.35781971550858 3.35781971550858 270 0 0.0465668750399675 Y 0.607757363662875 0.992155147273258 N N 0 0 ENSG00000208333 ENSG00000222533 - + 5 5 180661677 180661677 downstream downstream AC138036.2-1 U6 180661575 180661574 + + 0.293963254593176 180670534 180666257 - + N - - N HCC1954 240 137.733333333333 6 15 1 N - - Y SINE SINE,LTR 1 0.576 1 15 1.01412823870953 0.892718519990782 1.01412823870953 0.892718519990782 2 - - 36121 N N 3.18192883770763 3.0756913067072 3.0756913067072 0 0 0.181119157549397 N 0 0 N N 38048 41507 ENSG00000111676 ENSG00000188846 - - 12 3 6921743 40478862 coding coding ATN1 RPL14 6903887 40473834 + + 0 6915979 40477984 - - Y - - N HCC1954 52 25.75 1 3 1 N - - N Simple_repeat - 0.614583333333333 0 0.614583333333333 4 0.578481600954027 0.371370904316165 0.578481600954027 0.371370904316165 3 - - 30619 Y Y 3.64656650855576 3.51104337473878 3.51104337473878 0 0 0.337513193448185 Y 0 0.981413994169096 N N 8096 26 ENSG00000010404 ENSG00000176289 - - X X 148394714 148415449 coding downstream IDS AF011889.1-1 148368206 148414420 - + 0 148392747 148418790 + - N - - N HCC1954 1 1 1 0 1 N - - Y - LINE,LINE 0 1 1 10 0.971277749749971 1.07126222398894 1.07126222398894 0.971277749749971 1 - - 46399 N N 2.78051543753633 3.21166486847146 2.78051543753633 0 0.0633608815426997 0.336186019655988 N 0 0.252199413489736 N N 131026 108833 ENSG00000115053 ENSG00000179218 - + 2 19 232037449 12916303 coding coding NCL CALR 232027706 12910423 - + 0.252199413489736 232034657 12915575 + + Y - - N HCC1954 1 1 1 0 1 Y - - N Simple_repeat,Simple_repeat,Simple_repeat - 0.276190476190476 0 0.276190476190476 4 0.792734045751814 0.764167053112109 0.792734045751814 0.764167053112109 2 - - 4151 Y Y 3.08615095325867 3.1703920357936 3.08615095325867 252 0 0.0044622506028017 Y 0.940712396069539 0.988142479213908 N N 2897 1806 ENSG00000164713 ENSG00000205356 - - 7 7 97758775 97719404 coding upstream BRI3P1 TECPR1 97748923 97683993 + - 0 97749600 97719777 - + N 0.261364897574815 - N HCC1954 2 1.04347826086957 1 1 1 N - - Y - - 0 0 0 23 0.685607823352921 0.871293275511003 0.871293275511003 0.685607823352921 1 0 - 37913 N Y 3.51104337473878 3.40744620240479 3.40744620240479 1 0 0.0201052731405238 N 0 0.926888368983957 N N 8304 1 ENSG00000087299 ENSG00000165259 - - 14 X 49848697 83644117 utr3p upstream L2HGDH HDX 49774064 83459541 - - 0.883021390374332 49780571 83716645 + + Y - - N HCC1954 640 615 600 4 1 N 574 23.1726 N LINE,LINE LINE 1 1 1 4 0.307095170876829 0.34280391167646 0.34280391167646 0.307095170876829 1 - - 9899 N Y 3.49847350305486 3.29231222815676 3.29231222815676 0 0 0.080992259969967 Y 0 0 N N 1649619 313916 ENSG00000141736 ENSG00000131748 - + 17 17 35138441 35073248 coding utr5p ERBB2 STARD3 35104766 35046938 + + 0 35116831 35063265 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.899860268150708 0.51420586751469 0.899860268150708 0.51420586751469 1 - - 30303 Y Y 3.40125197368207 3.57063922744582 3.40125197368207 0 0 0.893550346901844 Y 0.991258848876577 0.973776546629732 N N 0 153 ENSG00000173954 ENSG00000129682 - - X X 138272206 137894912 upstream coding CXorf19 FGF13 138271925 137541401 + - 0 138113887 137767507 - + N - 4.78789796608532 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 1.14982145374813 0.842726282871298 1.14982145374813 0.842726282871298 4 - 0 2119 N Y 3.70144228268744 3.33168675516419 3.33168675516419 227 0.0496595915098116 0.00712291804686793 N 0.939660926445067 0.939660926445067 N N 4574 3567 ENSG00000188917 ENSG00000177951 + - X 11 100193758 197428 intron intron TRMT2B BET1L 100150992 157784 - - 0 100155274 170406 - + Y 0.908101447029568 2.87394543524002 N HCC1954 105 65 8 5 1 N - - N SINE - 1 0 1 5 0.407079645115797 0.807017542071667 0.807017542071667 0.407079645115797 2 0 0 33351 N N 3.42680229220385 3.6581033104698 3.42680229220385 0 0.0418353149506703 0.999966975250734 N 0.00708322792815586 0.00708322792815586 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.00708322792815586 8549 13735 - + N - 1.04464883352071 N HCC1954 6 2.875 1 5 10 Y 189 4.09957 N - - 0 0 0 8 1.24980592798709 1.19981369086761 1.24980592798709 1.19981369086761 2 - 0 9471 Y Y 3.34884356667429 3.24831090852981 3.24831090852981 0 0 0.608922369364161 Y 0.896576151121606 0.974144037780402 N N 0 4 ENSG00000213330 ENSG00000131484 - + 17 17 41020078 40967414 upstream downstream AC126544.5-1 AC091132.16-1 41019020 40936493 + + 0 41017721 40978825 - + N - - N HCC1954 8 6.25 5 4 1 N - - Y Low_complexity - 0.0666666666666667 0 0.0666666666666667 4 0.428504889595575 0.478497126715059 0.478497126715059 0.428504889595575 4 - - 47058 Y Y 3.02808268386148 3.4561676006071 3.02808268386148 0 0 0.570339422158502 Y 0.00328947368421073 0 N N 14641 253 ENSG00000125753 ENSG00000213889 - + 19 19 50722076 50697608 upstream intron VASP AC138534.3 50702528 50683875 + + 0 50701785 50696647 - + N - 0.449543730162142 N HCC1954 1 1 1 0 1 N - - Y Low_complexity LTR 0.173410404624277 0.392857142857143 0.392857142857143 7 0.678466075192994 0.871293275511003 0.871293275511003 0.678466075192994 2 - 0 30647 Y Y 3.47076375903745 3.66336194527509 3.47076375903745 39 0.133369201339072 0.840764368616992 Y 0.993483978957437 0.986967957914873 N N 111946 0 ENSG00000147065 ENSG00000219305 - - X X 64878517 64689026 coding upstream MSN RP3-475B7.3 64804283 64687503 + - 0.107305117168819 64853405 64725217 - + N - - N HCC1954 2 1.19444444444444 1 7 2 N - - Y SINE - 0.00571428571428571 0 0.00571428571428571 36 1.24980592798709 1.15696320190805 1.24980592798709 1.15696320190805 4 - - 31918 N Y 3.43209143223268 3.4797797606651 3.43209143223268 0 0 0.165645447729949 N 0 0.470990813243726 N N 49 10428 ENSG00000214148 ENSG00000114346 + + 3 3 191858537 174021957 intron intron AC108747.5-1 ECT2 191846266 173951207 + + 0.470990813243726 191858460 173951474 + + N - 0.443838089061747 Y HCC1954 38 35.5 34 4 1 N - - N SINE - 1 0 1 4 0.528489363834543 0.328520415356608 0.528489363834543 0.328520415356608 3 - 0 49239 Y Y 3.5010341561346 3.40591861909494 3.40591861909494 0 0 0.98818709450343 Y 0 0.986198462613557 N N 26477 14691 ENSG00000161011 ENSG00000161013 - - 5 5 179197681 179166547 coding upstream SQSTM1 MGAT4B 179180503 179156711 + - 0 179192638 179166735 - + N - - N HCC1954 1 1 1 0 5 N - - Y - Low_complexity 0 0.208333333333333 0.208333333333333 10 0.364229156156239 0.51420586751469 0.51420586751469 0.364229156156239 3 - - 39991 Y Y 3.43105836246279 3.20078106639692 3.20078106639692 261 0.00383141762452099 0.322064000542763 Y 0 0.968207385668868 N N 64 4136 ENSG00000214701 ENSG00000137868 - - 15 15 72300722 72288419 coding intron AC023300.19 STRA6 72296666 72258863 + - 0 72297891 72282492 - + N 0.341243738446377 77.7654973618439 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.471355378555133 0.39993789695587 0.471355378555133 0.39993789695587 4 0 0 17448 Y Y 3.37192651807217 2.67267154251321 2.67267154251321 0 0 0.974008110775234 Y 0 0.878321758594961 N N 2873 0 ENSG00000127124 ENSG00000216933 - - 1 1 42156965 42279987 utr5p upstream HIVEP3 RP1-21K4.1 41744623 42278855 - + 0 42156785 42274068 + - N - - N HCC1954 1 1 1 0 3 N - - Y - Low_complexity 0 0.138461538461538 0.138461538461538 22 0.907002016310634 0.928427260790413 0.928427260790413 0.907002016310634 2 - - 10791 N Y 3.2274272354209 3.81401560385573 3.2274272354209 0 0 0.327529444289505 N 0 0.885060885060885 N N 1649619 0 ENSG00000141736 ENSG00000218806 + - 17 6 35138441 24859831 coding downstream ERBB2 RP3-369A17.2 35104766 24858879 + - 0 35122227 24856231 + + Y - - N HCC1954 21 18.6363636363636 3 11 1 N - - N - SINE 0 1 1 11 0.721316564152552 0.307095170876829 0.721316564152552 0.307095170876829 2 - - 39962 Y N 3.59165088163073 3.41952156054875 3.41952156054875 1 0 0.604296800710202 Y 0.583171395258453 0 N N 0 0 ENSG00000180987 ENSG00000215302 + - 15 15 30678304 30608228 downstream upstream AC123768.8-1 AC135983.4-1 30677791 30606298 - - 0 30655085 30616445 - + N - - N HCC1954 16 6 2 4 3 N - - Y SINE - 1 0 1 4 0.364229156156239 0.464213630395207 0.464213630395207 0.364229156156239 3 - - 27170 Y Y 3.5465630590714 3.25360004855864 3.25360004855864 0 0 0.900128270714418 Y 0 0.988280717692482 N N 354 5009 ENSG00000151006 ENSG00000167397 - + 16 16 31007631 31014802 coding downstream AC135050.5 VKORC1 31002246 31009664 - - 0 31006646 31009595 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.585623349113953 1.08554572030879 1.08554572030879 0.585623349113953 2 - - 9538 Y Y 3.69103183649914 3.36716658670346 3.36716658670346 0 0 0.342252278710041 Y 0 0.990429547088426 N N 5791 0 ENSG00000133195 ENSG00000211264 + + 17 17 68600427 67836854 downstream downstream SLC39A11 AC005243.1 68153684 67836654 - + 0 68099938 67928770 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.578481600954027 0.764167053112109 0.764167053112109 0.578481600954027 2 - - 47231 Y Y 3.59528445727371 2.81973147824423 2.81973147824423 131 0.0130752004623275 0.201838055629445 Y 0.734992414938958 0.990861807411688 N N 602 16304 ENSG00000053501 ENSG00000099331 - + 19 19 17191638 17185093 upstream coding USE1 MYO9B 17187155 17073466 + + 0 17186266 17183580 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.628473838073511 0.735600060472404 0.735600060472404 0.628473838073511 2 - - 38810 N Y 3.6769648867289 3.45976132345673 3.45976132345673 1 0 0.305305588520284 N 0 0.971548117154812 N N 1367 4657 ENSG00000175898 ENSG00000198252 - - 19 14 10202948 52311409 utr3p coding S1PR2 STYX 10193109 52266675 - + 0 10194978 52266999 + - Y - - N HCC1954 37 34.2857142857143 32 7 1 N - - N SINE,SINE - 1 0 1 7 0.307095170876829 0.471355378555133 0.471355378555133 0.307095170876829 1 - - 47989 N N 3.71720464963688 3.78465029545248 3.71720464963688 0 0 0.99982664082076 N 0 0.0302275960170697 N N 86504 0 ENSG00000104408 ENSG00000182152 + + 8 5 109330135 117142614 intron downstream EIF3E AC114322.2 109283149 117142420 - - 0.0302275960170697 109296011 116869230 - - Y 0.54481186694143 - N HCC1954 2 1.26905829596413 1 60 7 N 241 0.00319582 N - Unknown 0 0.364532019704433 0.364532019704433 223 0.864151527351077 1.44977487646503 1.44977487646503 0.864151527351077 1 0 - 30765 Y Y 3.37080016234644 2.88425761686467 2.88425761686467 0 0.0403923086849913 0.36303044362519 Y 0 0.0403923086849913 N N 4921 315 ENSG00000065923 ENSG00000147119 + + X X 46503551 46342781 coding downstream SLC9A7 CHST7 46351081 46318136 - + 0 46387657 46346577 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.892718519990782 0.692749571512847 0.892718519990782 0.692749571512847 1 - - 46905 Y Y 3.03533291029304 2.97995327505158 2.97995327505158 240 0 0.970353200873134 Y 0 0.987705761316872 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 intron upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10602665 10574228 - + N 0.550675653368877 - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.642757334393363 0.499922371194838 0.642757334393363 0.499922371194838 2 0 - 47446 N N 3.2496867133392 3.51104337473878 3.2496867133392 0 0 0.0418232052969765 Y 0.209876543209877 0.407407407407407 N N 1635 92 ENSG00000127220 ENSG00000167555 - - 19 19 17275282 57647004 coding utr3p ABHD8 ZNF534 17263941 57592933 - + 0 17264522 57613112 + - N - - N HCC1954 25 24 23 5 1 N 569 19.4271 N - SINE 0 1 1 5 0.39993789695587 0.271386430077198 0.39993789695587 0.271386430077198 1 - - 37189 N Y 3.30094695668127 3.6272104187567 3.30094695668127 250 0.967870967741935 0.00999167701964476 N 0.967870967741935 0.518064516129032 N N 0 119704 ENSG00000208978 ENSG00000111057 - + 5 12 123018910 51632951 upstream coding AC008541.6 KRT18P19 123018501 51628922 + + 0.64658064516129 123000667 51632182 - + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.271386430077198 0.307095170876829 0.307095170876829 0.271386430077198 1 - - 29896 N N 3.51832410639388 2.78061807106198 2.78061807106198 258 0.619661733615222 0.00274511065046479 N 0.746441155743481 0.257434813248767 N N 78560 0 ENSG00000112493 ENSG00000217035 + + 6 X 33390114 44379422 utr3p downstream TAPBP CHTF8P 33375449 44377882 - + 0.311768851303735 33376421 44385736 - + Y 0.849508719738468 - N HCC1954 9 3.77777777777778 1 6 1 N 184 25.9721 N SINE SINE 1 0.65625 1 9 0.549914608314322 0.22853594111764 0.549914608314322 0.22853594111764 2 0 - 4298 Y Y 3.58271458558979 3.54292948342842 3.54292948342842 7 0.032624962586052 0.478724231225592 Y 0.674348997306196 0.990422029332535 N N 16361 188 ENSG00000198420 ENSG00000159860 + + 7 7 143230181 143146099 downstream downstream FAM115B AC099548.6 143180984 143138257 - + 0 143164667 143161907 - + N - - N HCC1954 2 2 2 6 2 N - - Y Simple_repeat - 0.478260869565217 0 0.478260869565217 6 0.328520415356608 0.749883556792257 0.749883556792257 0.328520415356608 1 - - 35898 N N 3.0783011601501 3.31319590126568 3.0783011601501 0 0 0.72570080636106 N 0 0 N N 0 712661 ENSG00000218582 ENSG00000111640 + + 6 12 80720444 6517797 intron coding RP3-357D13.1 GAPDH 80719441 6513918 - + 0 80719609 6517304 - + Y 1 - N HCC1954 4 1.6 1 1 2 N - - N - - 0 0 0 5 0.271386430077198 0.535631111994469 0.535631111994469 0.271386430077198 4 0 - 29276 N N 3.3974369838006 3.58999531724489 3.3974369838006 0 0.300274851122309 0.97463168281426 Y 0 0.273362345396244 N N 343 52571 ENSG00000178729 ENSG00000096433 + + 6 6 48144384 33772324 intron coding C6orf138 ITPR3 47953998 33697139 - + 0.273362345396244 48114525 33697446 - + N 5.08738813241339 0.342852548401221 N HCC1954 1 1 1 0 4 N 104 11.3593 N - - 0 0 0 9 0.421363141435649 1.07126222398894 1.07126222398894 0.421363141435649 4 0 0 44347 N N 3.425274708894 3.21279122419719 3.21279122419719 14 0 0.141754039371535 N 0 0 N N 2591 3891 ENSG00000111696 ENSG00000166295 + + 12 10 102759064 73665622 utr3p intron NT5DC3 C10orf104 102690219 73645812 - + 0 102694263 73645955 - + Y - 0.744979490524871 N HCC1954 35 30.2903225806452 17 31 1 N - - N SINE - 1 0 1 31 0.378512652476092 1.0069864905496 1.0069864905496 0.378512652476092 1 - 0 22511 N N 3.78208964237274 2.51516888508513 2.51516888508513 0 0 0.0218881938842422 N 0 0 N N 2833 27 ENSG00000133019 ENSG00000164749 - - 1 8 238139338 76641600 utr5p upstream CHRM3 HNF4G 237858996 76482732 + + 0 237859411 76412582 - - Y - - N HCC1954 23 21.4 13 10 1 N - - N LINE LINE 1 1 1 10 0.385654400636018 0.542772860154395 0.542772860154395 0.385654400636018 0 - - 9580 Y Y 3.53768019619294 3.25252712599539 3.25252712599539 335 0 0.0968574649029181 Y 0 0.989505106048704 N N 0 12836 ENSG00000222777 ENSG00000167258 + + 17 17 34955984 34941095 upstream coding U6 CRKRS 34955883 34871265 - + 0 34956245 34940805 - + N - 3.15775540163771 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.635615586233437 0.664182578873142 0.664182578873142 0.635615586233437 1 - 0 12562 N Y 3.57800808738356 3.37614273553776 3.37614273553776 0 0 0.446994689219298 N 0 0 N N 17943 14151 ENSG00000105141 ENSG00000185722 + - 19 17 15027900 4114023 downstream intron CASP14 ANKFY1 15024015 4013414 + - 0.771436281454497 15029502 4061740 + + Y - 0.791103648665349 N HCC1954 20 20 20 9 1 N 179 26.7215 N - SINE 0 1 1 9 0.51420586751469 0.264244681917271 0.51420586751469 0.264244681917271 3 - 0 18725 Y Y 3.33317448568069 3.27767621693306 3.27767621693306 282 0 0.0551708918248246 Y 0.929936835106383 0.984430407801418 N N 253 0 ENSG00000196407 ENSG00000201134 + - 1 1 150092797 150080937 intron upstream THEM5 Y_RNA 150081603 150080836 - - 0 150083145 150081131 - + N 1.15319841531513 - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 10 1.01412823870953 0.956994253430118 1.01412823870953 0.956994253430118 4 0 - 636 N N 3.47911741325579 3.56079784271098 3.47911741325579 6 0 0.0158227130221434 N 0 0 Y N 2 25107 ENSG00000196844 ENSG00000182704 - - 11 11 125153924 76186845 utr3p upstream PATE2 TSKU 125151268 76171933 - + 0 125151456 76143820 + - N - - N HCC1954 462 446.142857142857 420 7 1 N - - N LINE SINE 1 1 1 7 0.449930134075354 0.335662163516534 0.449930134075354 0.335662163516534 1 - - 18506 Y Y 3.02019303795956 3.64400585547602 3.02019303795956 332 0 0.00839410669433971 Y 0 0.969479960658962 N N 0 0 ENSG00000208053 ENSG00000218362 + - 1 1 245434586 245439418 upstream intron AL390728.37-2 RP11-488L18.4 245434504 245419776 - - 0 245440551 245430111 - + N - 1 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 15 1.25694767614702 0.785592297591888 1.25694767614702 0.785592297591888 2 - 0 33921 N N 3.43528392749819 3.14160936921295 3.14160936921295 0 0 0.0707720761106163 N 0 0 N N 0 544065 ENSG00000210127 ENSG00000198744 - + MT MT 5656 9988 intron coding AF347015.1-10 MT-CO3 5588 8367 - + 0 5625 8677 + + N 1 0.567956504381133 Y HCC1954 2 1.42857142857143 1 3 1 N 301 4.17858 N - - 0 0 0 7 0.93556900895034 0.621332089913584 0.93556900895034 0.621332089913584 1 0 0 7120 Y Y 3.20972671000768 3.67593181695901 3.20972671000768 279 0 0.00448824754070709 Y 0.257217334636689 0.990941674812643 N N 0 719 ENSG00000208176 ENSG00000189362 + - 2 2 191111031 191107693 upstream upstream AC108047.4 TMEM194B 191110890 191077313 - - 0 191141045 191108093 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 7 0.828442786551446 1.09268746846872 1.09268746846872 0.828442786551446 1 - - 48083 N N 3.64081336021051 3.41592783769912 3.41592783769912 0 0 0.99900805140772 N 0 0 N N 12549 0 ENSG00000087206 ENSG00000212451 + + 5 8 176366358 127753081 coding downstream UIMC1 U11 176264612 127752949 - + 0 176270998 128113265 - + Y - - N HCC1954 1 1 1 0 5 N 573 7.11156 N Low_complexity SINE,SINE 0.0111731843575419 0.786127167630058 0.786127167630058 114 1.2783729206268 1.23552243166724 1.2783729206268 1.23552243166724 3 - - 29163 Y Y 3.41423242051993 3.6035982586987 3.41423242051993 179 0 0.564566764803974 Y 0.475170701427685 0.986188702669149 N N 1789 0 ENSG00000204599 ENSG00000203481 - - 6 6 30419485 30360468 upstream upstream TRIM39 AL662795.5 30402600 30360104 + - 0 30401847 30370718 - + N - - N HCC1954 1 1 1 0 5 N - - Y LINE - 0.273224043715847 0 0.273224043715847 5 0.835584534711372 0.392796148795944 0.835584534711372 0.392796148795944 1 - - 28978 N N 3.73233517440054 3.48809356209009 3.48809356209009 0 0 0.0977634713776425 N 0 0.00389105058365768 N N 7 45068 ENSG00000186952 ENSG00000205336 - + 5 16 110090271 56256445 intron upstream AC012622.6 GPR56 109931539 56220023 - + 0.00389105058365768 110043913 56211646 + + Y 1.39612807148176 - N HCC1954 21 19.1379310344828 8 29 1 N - - N SINE - 1 0 1 29 0.385654400636018 0.742741808632331 0.742741808632331 0.385654400636018 1 0 - 44737 Y Y 3.48639814491089 3.61360747730288 3.48639814491089 298 0 0.0773477339886794 Y 0.993030459473412 0.986060918946825 N N 6 1878 ENSG00000173088 ENSG00000138185 - + 10 10 97783497 97627013 upstream utr3p C10orf131 ENTPD1 97657655 97461526 + + 0 97647275 97626407 - + N - 12.0576925818999 N HCC1954 20 7.33333333333333 1 2 2 N - - Y SINE - 1 0 1 6 0.799875793911741 0.999844742389676 0.999844742389676 0.799875793911741 4 - 0 19520 N Y 3.5920919620082 3.36079094374226 3.36079094374226 303 0.865524647702866 0.0269742593483981 N 0.928807166430929 0.968358740635968 N N 29204 2251 ENSG00000203832 ENSG00000186275 - + 1 1 146713675 143541658 utr5p upstream NBPF10 NBPF8 146616873 143326471 - + 0 146713672 143318418 + + N - - Y HCC1954 20 12.2857142857143 4 7 1 N - - N - SINE 0 0.234782608695652 0.234782608695652 7 0.621332089913584 0.821301038391519 0.821301038391519 0.621332089913584 4 - - 24734 N Y 3.47125827257741 3.40744620240479 3.40744620240479 214 0 0.00672991896725306 Y 0 0.983130049105022 N N 0 1258 ENSG00000202093 ENSG00000177576 + - 18 18 45269676 45267602 upstream coding SNORD58 C18orf32 45269613 45262027 - - 0.156502455251069 45269732 45264074 - + N - 0.580346647678466 N HCC1954 8 4.66666666666667 1 5 1 N - - N - - 0 0 0 6 1.10697096478857 0.807017542071667 1.10697096478857 0.807017542071667 1 - 0 16254 N N 3.0447984149941 3.43105836246279 3.0447984149941 17 0 0.218548328207629 N 0 0.00273224043715836 N N 1391 4212 ENSG00000064933 ENSG00000218839 - + 2 1 190450599 178113539 utr3p intron PMS1 AL359853.18-1 190357355 178100200 + - 0.00273224043715836 190379277 178101194 - - Y - 0.520641249909699 N HCC1954 21 21 21 5 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.392796148795944 0.392796148795944 0.299953422716903 4 - 0 33262 N N 3.45976132345673 3.09616017186285 3.09616017186285 15 0 0.99999567724497 N 0 0.0766436858920465 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.0766436858920465 8757 10887 - + N 0.56110518273874 - N HCC1954 4 2.5 1 2 12 N 189 4.09957 N - - 0 0 0 4 0.385654400636018 0.87843502367093 0.87843502367093 0.385654400636018 1 0 - 30339 N Y 3.54975555433691 3.48593413659447 3.48593413659447 199 0 0.0158953199155502 Y 0.771424691022681 0.959663180768708 N N 0 0 ENSG00000208964 ENSG00000209002 - + X X 101951770 101914855 downstream upstream AL590407.8-9 AL035427.17-1 101951702 101914785 + + 0 101967580 101911993 - + N - - N HCC1954 17 2.6 1 1 2 N - - N - LINE 0 1 1 10 0.892718519990782 0.585623349113953 0.892718519990782 0.585623349113953 2 - - 8658 N N 3.62568283544685 3.48743121468078 3.48743121468078 0 0 0.135554188527170 N 0.303097345132743 0 N N 9989 811 ENSG00000160916 ENSG00000136480 - - 7 17 98901744 59923631 coding intron ATP5J2 POLG2 98893721 59904366 - - 0 98894822 59918114 + + Y - 0.55577137779398 N HCC1954 3 1.6 1 2 1 N - - N - SINE 0 0.027027027027027 0.027027027027027 5 0.807017542071667 0.264244681917271 0.807017542071667 0.264244681917271 2 - 0 1721 N N 3.33420755545058 3.47233119514066 3.33420755545058 0 0 0.743210314173 N 0 0.0582952815829528 N N 12635 4030 ENSG00000109919 ENSG00000185214 + - 11 22 47620640 19180122 coding upstream MTCH2 KLHL22 47595444 19125806 - - 0.0582952815829528 47612859 19180440 - + Y - - N HCC1954 1 1 1 0 3 N 341 20.4969 N - - 0 0 0 4 0.414221393275723 0.507064119354764 0.507064119354764 0.414221393275723 1 - - 36929 N N 3.56232542602083 3.37345410138202 3.37345410138202 0 0 0.55933425775176 N 0 0 N N 1977 16017 ENSG00000196074 ENSG00000018236 + + 20 12 57942105 39750361 coding coding SYCP2 CNTN1 57872016 39588423 - + 0 57889438 39619514 - + Y 0.703866208810466 1.33369441840304 N HCC1954 1 1 1 0 3 N 470 0.598344 N - - 0 0 0 15 0.771308801272036 0.785592297591888 0.785592297591888 0.771308801272036 1 0 0 19142 N Y 3.54872248456702 3.58217602935986 3.54872248456702 12 0 0.792407269585718 N 0.302880658436214 0.715461493239271 Y N 49 2833 ENSG00000186973 ENSG00000133019 - + 1 1 43394654 238139338 upstream utr5p FAM183A CHRM3 43382616 237858996 + + 0.0610229276895944 43374043 237859193 - + N - - N HCC1954 25 23.8235294117647 21 17 3 N - - N LTR LINE 0.568965517241379 1 1 17 0.414221393275723 0.499922371194838 0.499922371194838 0.414221393275723 2 - - 48073 N N 3.59425138750382 3.56079784271098 3.56079784271098 0 0 0.537482902500978 N 0 0.161395741092136 N N 86504 0 ENSG00000104408 ENSG00000182152 + - 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0.161395741092136 109296013 116871247 - + Y - - N HCC1954 2 1.66666666666667 1 8 3 N - - N - DNA 0 0.478723404255319 0.478723404255319 12 0.742741808632331 0.671324327033068 0.742741808632331 0.671324327033068 1 - - 19179 N Y 3.0742035761907 2.31441296411064 2.31441296411064 0 0 0.607118062163862 Y 0 0.967858812529219 N N 0 582 ENSG00000213037 ENSG00000153363 - + 1 1 209682923 209638102 upstream coding AL590101.9 C1orf97 209682219 209622768 + + 0 209672198 209636822 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 27 0.692749571512847 0.714174815992626 0.714174815992626 0.692749571512847 1 - - 44045 N Y 3.68577320169385 3.19343513439813 3.19343513439813 20 0.197496222749838 0.170904956076065 N 0.00294985250737467 0.11238218576876 N N 906 78560 ENSG00000148814 ENSG00000112493 - - 10 6 134109058 33390114 utr3p utr3p LRRC27 TAPBP 133995648 33375449 + - 0.331246852291532 134041405 33377057 - + Y - - N HCC1954 37 35.25 32 4 1 N - - N SINE,SINE DNA,SINE 1 0.278350515463918 1 4 0.621332089913584 0.671324327033068 0.671324327033068 0.621332089913584 3 - - 2179 N Y 3.26824964015148 3.5319270478477 3.26824964015148 26 0 0.196793974903396 N 0.969206633796504 0.917884356790677 N N 8014 0 ENSG00000149084 ENSG00000121871 - + 11 3 43834736 166397163 utr3p upstream HSD17B12 SLITRK3 43658719 166387227 + - 0.230165844912595 43834016 166502254 - - Y 1.56799368003871 - N HCC1954 38 8.66666666666667 4 12 1 N - - N - SINE 0 1 1 12 0.671324327033068 0.364229156156239 0.671324327033068 0.364229156156239 2 0 - 39546 N Y 3.33424740824393 3.3550912285595 3.33424740824393 19 0.501893939393939 0.0570063658137928 N 0.557239057239057 0.520342312008979 N N 0 0 ENSG00000213138 ENSG00000212769 - + 6 15 121771639 27811302 downstream intron AL139098.15-1 AC022613.13 121771387 27810108 + + 0.520342312008979 121771677 27810512 - + Y - 1 N HCC1954 13 9.25 6 8 1 N - - N - - 0 0 0 8 0.242819437437493 0.407079645115797 0.407079645115797 0.242819437437493 1 - 0 31343 Y Y 3.33528047801382 3.44256465915329 3.33528047801382 290 0 0.0143242612123934 Y 0 0.988275862068965 N N 1974 0 ENSG00000172113 ENSG00000199476 + + 3 3 48317852 48305188 intron downstream NME6 Y_RNA 48310595 48305081 - + 0 48311495 48306076 - + N 1.4774807474971 - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.115384615384615 0.115384615384615 5 0.942710757110266 0.914143764470561 0.942710757110266 0.914143764470561 1 0 - 31710 Y Y 3.72721386824106 3.46977054206091 3.46977054206091 219 0.00456621004566216 0.210572430835261 Y 0.964448793215916 0.982224396607958 N N 1033 0 ENSG00000196639 ENSG00000213964 - - 3 3 11280243 11251366 utr5p downstream HRH1 AC083855.3 11269385 11250939 + - 0 11269902 11242742 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR LINE 0.242857142857143 1 1 5 0.671324327033068 0.678466075192994 0.678466075192994 0.671324327033068 2 - - 24805 N Y 3.24637275006602 3.30016202126533 3.24637275006602 120 0.0545482133373796 0.0346828602145776 Y 0.837341628101055 0.989833851756316 N N 2212 1884 ENSG00000141759 ENSG00000101546 - - 18 18 75849520 75907373 coding upstream TXNL4A C18orf22 75833857 75895346 - + 0 75849229 75894841 + - N - - N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.112359550561798 0.112359550561798 16 1.03555348318931 0.635615586233437 1.03555348318931 0.635615586233437 1 - - 48360 N Y 3.23034293992665 3.46657804679541 3.23034293992665 234 0.0991045991045987 0.0271061515588851 N 0.146520146520147 0.0991045991045987 N N 0 0 ENSG00000213763 ENSG00000217920 + - 5 X 77117595 46033507 intron intron AC035147.4 RP1-30G7.1 77116467 46032395 + - 0.620675620675621 77117240 46032739 + + Y 1 1 N HCC1954 8 2.8 2 10 1 N - - N - - 0 0 0 10 0.557056356474248 0.357087407996313 0.557056356474248 0.357087407996313 2 0 0 26747 Y Y 3.36084437690474 3.3070415253363 3.3070415253363 417 0 0.0936170344877185 Y 0 0.994199988846132 N N 1747 10006 ENSG00000157312 ENSG00000132612 + + 16 16 67921999 67916446 downstream intron COG8 VPS4A 67920025 67895081 - + 0 67919777 67914348 - + N - 1.05622450190527 N HCC1954 1 1 1 0 4 N - - Y - SINE 0 0.147058823529412 0.147058823529412 5 0.899860268150708 0.728458312312478 0.899860268150708 0.728458312312478 3 - 0 12819 N Y 3.12804628055249 3.60422075331465 3.12804628055249 0 0 0.220170786729647 N 0.943858271580704 0.943858271580704 N N 1649619 1942 ENSG00000141736 ENSG00000171295 - + 17 19 35138441 11807016 coding utr3p ERBB2 ZNF440 35104766 11786107 + + 0 35122227 11806083 - + Y - - N HCC1954 23 21.6979166666667 1 95 1 N - - N - SINE 0 1 1 96 1.32836515774628 0.364229156156239 1.32836515774628 0.364229156156239 2 - - 6808 Y Y 3.0431827034016 3.684245618384 3.0431827034016 7 0 0.0811865238937334 Y 0.657186206896552 0.992027586206897 N N 2153 13273 ENSG00000115540 ENSG00000115541 - + 2 2 198125750 198076351 upstream coding MOBKL3 HSPE1 198088550 198073109 + + 0 198083370 198076059 - + N - - N HCC1954 6 4.4 3 5 1 N - - Y SINE - 1 0 1 5 0.785592297591888 0.721316564152552 0.785592297591888 0.721316564152552 1 - - 29657 Y Y 3.76273355257368 3.18871505582277 3.18871505582277 0 0 0.81737298305255 Y 0 0 N N 37845 3999 ENSG00000204463 ENSG00000204439 - + 6 6 31728461 31736528 utr5p intron BAT3 C6orf47 31714784 31734054 - - 0 31727532 31736077 + - N - 0.931815999673143 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 1.2783729206268 1.31408166142643 1.31408166142643 1.2783729206268 4 - 0 30345 Y Y 3.43205157943933 3.73080759109069 3.43205157943933 187 0 0.209186499069777 Y 0.868837045307634 0.978139507551272 N N 0 0 ENSG00000188441 ENSG00000182707 - + X X 73168380 73013524 upstream downstream RP13-36G14.2 FXYD8 73168022 73011598 + + 0 73131426 73081224 - + N - - N HCC1954 20 5.42857142857143 1 6 4 N - - Y SINE - 1 0 1 14 0.821301038391519 0.628473838073511 0.821301038391519 0.628473838073511 2 - - 33922 N N 2.99190065211955 3.14160936921295 2.99190065211955 0 0 0.082988380804053 N 0 0 N N 275222 544065 ENSG00000198763 ENSG00000198744 + + MT MT 5512 9988 coding coding MT-ND2 MT-CO3 4471 8367 + + 0 5435 8677 + + N 1.24760530096795 0.567956504381133 Y HCC1954 4 2.16666666666667 1 5 1 N 301 4.17858 N - - 0 0 0 6 1.02841173502938 1.07840397214886 1.07840397214886 1.02841173502938 1 0 0 34666 Y Y 3.66336194527509 3.66641711189479 3.66336194527509 326 0 0.144712200216624 Y 0 0.987052824476137 N N 17291 0 ENSG00000070159 ENSG00000213539 - + 9 9 111300407 111336541 utr5p upstream PTPN3 AL162733.9 111177800 111334974 - - 0 111265552 111340332 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 75 1.16410495006798 1.2783729206268 1.2783729206268 1.16410495006798 4 - - 29856 Y Y 3.40169305405954 3.01927436889653 3.01927436889653 0 0 0.714288275332211 Y 0 0.994029536235447 N N 4334 3813 ENSG00000013375 ENSG00000083097 + + 6 6 83959690 83934909 coding intron PGM3 DOPEY1 83935349 83834104 - + 0 83935677 83932901 - + N - 0.633661025247976 N HCC1954 8 1.64 1 4 1 N - - Y - DNA,DNA 0 1 1 25 1.23552243166724 1.32836515774628 1.32836515774628 1.23552243166724 1 - 0 43937 N Y 3.46551447180198 2.87268267428126 2.87268267428126 0 0 0.0575656518683964 N 0 0.838897721250662 N N 5350 75177 ENSG00000078403 ENSG00000125107 - + 10 16 22072560 57221251 intron utr5p MLLT10 CNOT1 21863108 57111359 + - 0 21875599 57221169 - - Y 0.51055733572302 - N HCC1954 20 17.5714285714286 3 7 1 N - - N SINE - 1 0 1 7 0.364229156156239 0.335662163516534 0.364229156156239 0.335662163516534 1 0 - 27383 N Y 3.69528790675807 3.67952553980864 3.67952553980864 0 0 0.493329683166646 Y 0.979648369042908 0.989824184521454 N N 7487 568 ENSG00000188603 ENSG00000196877 + - 16 16 28411124 28275423 coding intron CLN3 NPIPL1 28396101 28262355 - - 0 28396560 28271884 - + N - 22.22221131631 N HCC1954 20 9.85714285714286 5 7 2 N - - N - SINE 0 0.656862745098039 0.656862745098039 7 0.949852505270192 0.728458312312478 0.949852505270192 0.728458312312478 1 - 0 6203 N Y 3.44975210485255 3.13636008197748 3.13636008197748 0 0 0.0718132612235096 N 0 0 N N 11330 0 ENSG00000072135 ENSG00000214121 + - 2 9 130849446 12963437 intron intron PTPN18 AL161449.7 130830088 12962842 + - 0 130845808 12963410 + + Y 0.684569644059298 1 N HCC1954 40 13 2 6 1 N - - N SINE - 1 0 1 6 0.278528178237124 0.28566992639705 0.28566992639705 0.278528178237124 2 0 0 8050 N N 3.53615261288309 3.04999942674028 3.04999942674028 17 0 0.151630153182775 N 0 0 N N 4010 26328 ENSG00000152683 ENSG00000205403 - + 2 4 32302672 110942783 utr3p intron SLC30A6 CFI 32244437 110881297 + - 0 32299854 110883017 - - Y - 0.342753129624331 N HCC1954 38 26.8181818181818 22 11 1 N - - N SINE - 1 0 1 11 0.357087407996313 0.542772860154395 0.542772860154395 0.357087407996313 2 - 0 18566 N Y 3.660633458326 3.60000453584907 3.60000453584907 260 0 0.287711329956288 Y 0.0320391872278664 0 N N 0 10857 ENSG00000218025 ENSG00000085832 + - 1 1 51833157 51757583 intron intron RP11-191G24.2 EPS15 51800126 51592523 - - 0 51812253 51756706 - + N 1 1.29050686031236 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.692749571512847 0.956994253430118 0.956994253430118 0.692749571512847 4 0 0 8294 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.745605842018725 N 0.238972118185602 0.958489388264669 N N 0 3966 ENSG00000164512 ENSG00000175772 + + 5 2 55564943 110111006 intron upstream ANKRD55 AC013268.5-1 55431264 110103138 - + 0 55556630 110102056 - + Y 1 - N HCC1954 40 38.3846153846154 8 26 1 N - - N LINE - 1 0 1 26 0.428504889595575 0.892718519990782 0.892718519990782 0.428504889595575 3 0 - 48074 N N 3.7297745213208 3.16423765986423 3.16423765986423 3 0 0.744639665628909 N 0.0574563895376976 0 N N 86504 0 ENSG00000104408 ENSG00000182152 + - 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0 109296012 116869447 - + Y - - N HCC1954 3 1.45454545454545 1 4 3 N - - N - Unknown 0 0.104477611940299 0.104477611940299 11 1.21409718718746 0.956994253430118 1.21409718718746 0.956994253430118 3 - - 5706 N N 2.43069440883542 3.5963175270436 2.43069440883542 15 0 0.0979753348437187 N 0 0.0470421820028291 N N 122511 0 ENSG00000187514 ENSG00000213178 - + 2 3 232286495 170684502 coding intron PTMA AC074033.18 232280638 170684153 + - 0.0722860977113633 232284897 170684169 - - Y - 1 N HCC1954 35 12.2 2 5 1 N - - N Low_complexity - 0.236453201970443 0 0.236453201970443 5 0.835584534711372 0.621332089913584 0.835584534711372 0.621332089913584 1 - 0 21819 N N 3.09616017186285 3.26104861408308 3.09616017186285 6 0 0.459958022912321 N 0 0 N N 0 712661 ENSG00000220620 ENSG00000111640 + + 1 12 119941325 6517797 downstream utr3p AL109966.2 GAPDH 119940313 6513918 - + 0 119940216 6517675 - + Y - - N HCC1954 20 12.4444444444444 3 9 1 N - - N - - 0 0 0 9 0.378512652476092 0.492780623034912 0.492780623034912 0.378512652476092 2 - - 6339 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.102165698340740 N 0 0.910990502035278 N N 20739 1315 ENSG00000143951 ENSG00000164989 - - 2 9 63669355 15964031 utr3p intron C2orf86 C9orf93 63202041 15543005 - + 0.896155585707824 63309485 15664070 + - Y - 1.64579865543476 N HCC1954 620 565 420 4 1 N - - N LINE LINE 1 1 1 4 0.349945659836387 0.349945659836387 0.349945659836387 0.349945659836387 4 - 0 6722 Y Y 3.13805549915667 3.52105259334297 3.13805549915667 339 0 0.124368322991969 Y 0 0.994065177693496 N N 603 2838 ENSG00000163126 ENSG00000168763 + + 2 2 96873485 96864848 utr3p utr3p ANKRD23 CNNM3 96867379 96845718 - + 0 96867966 96863007 - + N - 0.862187867848867 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 13 1.26408942430695 1.12839620926835 1.26408942430695 1.12839620926835 1 - 0 39788 Y Y 3.61464054707278 3.51104337473878 3.51104337473878 360 0 0.0765545851392925 Y 0 0.988404392764858 N N 1136 38799 ENSG00000104147 ENSG00000187446 + + 15 15 39412111 39361377 downstream downstream OIP5 AC012652.1 39388762 39310729 - + 0 39377350 39364843 - + N - - N HCC1954 18 2.17948717948718 1 63 4 N - - Y - LTR 0 0.464646464646465 0.464646464646465 78 0.614190341753658 0.707033067832699 0.707033067832699 0.614190341753658 2 - - 46257 N N 3.53039946453785 3.48656597878024 3.48656597878024 8 0 0.254038774500486 N 0 0 N N 1819 0 ENSG00000160439 ENSG00000184565 + + 19 Y 60272709 19698690 intron intron RDH13 TTTY14 60247523 19553973 - - 0 60255444 19612778 - - Y 1.29505610042428 1 N HCC1954 13 10 6 5 1 N - - N SINE,SINE SINE 0.75 0.403846153846154 0.75 5 0.314236919036755 0.371370904316165 0.371370904316165 0.314236919036755 1 0 0 42989 N N 3.54872248456702 3.59681204058356 3.54872248456702 0 0 0.873854813121955 N 0 0 N N 0 1969 ENSG00000220996 ENSG00000109390 + + 5 4 115406857 140443155 upstream utr5p AC034236.5-1 NDUFC1 115406767 140430521 - - 0 115417610 140441206 - - Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.949852505270192 0.999844742389676 0.999844742389676 0.949852505270192 4 - - 46754 Y Y 2.59633368624933 3.56013549530168 2.59633368624933 276 0 0.208550851286189 Y 0.937726449275362 0.98443161231884 N N 65965 17 ENSG00000108107 ENSG00000160472 - + 19 19 60595261 60581424 upstream downstream RPL28 TMEM190 60589112 60580016 + + 0 60586902 60582547 - + N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity,Low_complexity - 0.513157894736842 0 0.513157894736842 119 1.08554572030879 0.821301038391519 1.08554572030879 0.821301038391519 4 - - 22983 N Y 3.62295434849776 3.25256697878875 3.25256697878875 0 0 0.0736188051248042 N 0 0 N N 11845 49089 ENSG00000148735 ENSG00000117450 + - 10 1 115533178 45760196 downstream coding C10orf81 PRDX1 115501203 45749295 + - 0 115546648 45757275 + + Y - 3.11556065904221 N HCC1954 42 11 4 7 1 N - - N SINE - 1 0 1 7 0.264244681917271 0.392796148795944 0.392796148795944 0.264244681917271 2 - 0 46276 N N 3.62295434849776 3.37448717115191 3.37448717115191 0 0 0.226596083421246 N 0 0 N N 2827 52 ENSG00000119574 ENSG00000214164 - - 19 2 63722733 110569923 coding downstream ZBTB45 AC112229.4-2 63716711 110569013 - - 0 63719586 110545927 + + Y - - N HCC1954 60 56 20 10 2 N - - N - LINE 0 1 1 10 0.407079645115797 0.5713398527941 0.5713398527941 0.407079645115797 2 - - 34214 Y Y 3.13424050927521 3.63146648901564 3.13424050927521 299 0 0.154432493198890 Y 0 0 N N 179 30778 ENSG00000196366 ENSG00000148396 - - 9 9 138500339 138491962 utr5p utr5p C9orf163 SEC16A 138497768 138454370 + - 0 138497803 138491962 - + N 0.319085286777889 196.010469436001 N HCC1954 1 1 1 0 3 N - - Y Simple_repeat - 0.152866242038217 0 0.152866242038217 20 1.12125446110842 1.1141127129485 1.12125446110842 1.1141127129485 2 0 0 40759 N N 3.48230056095149 3.37808089400154 3.37808089400154 27 0 0.266689220558912 N 0.942350332594235 0.110547988596769 N N 56 695 ENSG00000181092 ENSG00000149531 - + 3 20 188058944 28265815 downstream coding ADIPOQ FRG1B 188043157 28225518 + + 0.110547988596769 188073792 28246382 - + Y - - N HCC1954 44 31.5 20 4 1 N - - N Other tRNA 1 0.0396825396825397 1 4 0.664182578873142 0.771308801272036 0.771308801272036 0.664182578873142 2 - - 42240 N Y 3.62361669590707 3.21075977977757 3.21075977977757 0 0 0.929327383458064 Y 0 0.984304637505596 N N 1192 1975 ENSG00000109265 ENSG00000174799 - + 4 4 56891647 56594283 utr5p downstream KIAA1211 CEP135 56731118 56509794 + + 0 56740207 56610222 - + N 0.0771658512363107 - N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.259668508287293 0.259668508287293 10 0.956994253430118 1.29265641694665 1.29265641694665 0.956994253430118 4 0 - 47571 Y Y 3.56488607910057 3.25724720457075 3.25724720457075 0 0.337051867316891 0.469098015297985 Y 0.550348223049717 0 N N 1761 6705 ENSG00000104899 ENSG00000104897 - + 19 19 2203072 2199677 coding coding AMH SF3A2 2200113 2187816 + + 0 2200743 2198867 - + N - - N HCC1954 2 1.08333333333333 1 3 1 N - - Y - - 0 0 0 36 1.3069399132665 1.45691662462496 1.45691662462496 1.3069399132665 2 - - 5074 N Y 3.63193049733206 3.03383583220673 3.03383583220673 0 0 0.314040212527059 N 0 0.915785369657391 N N 3838 0 ENSG00000154710 ENSG00000201515 + - 7 7 65913881 65653116 coding downstream RABGEF1 5S_rRNA 65843078 65652992 + - 0 65907751 65648180 + + N - - Y HCC1954 2 1.75 1 3 1 N - - N - SINE 0 0.21259842519685 0.21259842519685 4 0.671324327033068 0.714174815992626 0.714174815992626 0.671324327033068 1 - - 33950 N N 3.19343513439813 3.14160936921295 3.14160936921295 0 0 0.0645861505639496 N 0 0 N N 336285 544065 ENSG00000198868 ENSG00000198744 + + MT MT 12138 9988 downstream coding MT-ND4 MT-CO3 10471 8367 + + 0 12146 8678 + + N - 0.567198009783091 Y HCC1954 4 2 1 3 1 N 316 3.86643 N - - 0 0 0 5 0.928427260790413 0.671324327033068 0.928427260790413 0.671324327033068 1 - 0 34557 N Y 3.58999531724489 3.47449062063627 3.47449062063627 132 0 0.520097316747494 N 0 0.970119521912351 N N 0 262 ENSG00000165121 ENSG00000165113 - + 9 9 87654248 85622477 upstream utr5p AL353743.22-1 GKAP1 87634198 85544156 + - 0 87627613 85621733 - - N - - Y HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.671324327033068 0.828442786551446 0.828442786551446 0.671324327033068 2 - - 41716 N N 3.38552945952599 3.48593413659447 3.38552945952599 0 0.0503165529534699 0.477110553424246 N 0 0 N N 0 8783 ENSG00000221261 ENSG00000147697 - + 8 8 129231616 130868316 upstream coding hsa-mir-1208 GSDMC 129231544 130829625 + - 0 129182406 130844056 - - N - - Y HCC1954 3 1.09285714285714 1 12 1 N 397 4.17426 N LTR - 1 0 1 140 1.34979040222606 1.37835739486577 1.37835739486577 1.34979040222606 2 - - 25197 Y Y 3.38759559906577 3.55504469436573 3.38759559906577 254 0 0.0344376397729067 Y 0.896959000814553 0.988551000090506 N N 2546 3633 ENSG00000136159 ENSG00000136143 - - 13 13 47519283 47473463 utr5p upstream NUDT15 SUCLA2 47509704 47414792 + - 0 47509742 47487384 - + N - - N HCC1954 21 5 1 1 2 N - - Y - SINE 0 1 1 5 0.607048593593732 0.51420586751469 0.607048593593732 0.51420586751469 1 - - 12650 N N 3.34728128824428 3.234707967076 3.234707967076 0 0.24720417509852 0.609736092306695 N 0.368622856534242 0.24720417509852 N N 1892 12272 ENSG00000108306 ENSG00000105355 + + 17 19 34811424 4818676 intron utr3p FBXL20 M6PRBP1 34670374 4789346 - - 0.24720417509852 34731253 4789600 - - Y 3.7981894810182 - N HCC1954 18 12.6 2 5 1 N - - N SINE SINE 0.923076923076923 1 1 5 0.371370904316165 0.535631111994469 0.535631111994469 0.371370904316165 2 0 - 24391 N N 3.24893340314576 3.65384724021086 3.24893340314576 17 0 0.632648113093327 N 0.863357843137255 0.00446428571428581 N N 0 2527 ENSG00000206696 ENSG00000186001 + + 18 3 45272097 199082851 upstream intron SNORD58 LRCH3 45272032 199002542 - + 0.00446428571428581 45272639 199062232 - + Y - 1.31517858497148 N HCC1954 8 3.45454545454545 1 9 2 N - - N - - 0 0 0 11 0.814159290231593 0.928427260790413 0.928427260790413 0.814159290231593 3 - 0 39826 Y Y 3.57080706131517 3.46448140203209 3.46448140203209 284 0 0.233183101531622 Y 0 0.992507677644816 N N 7 1228 ENSG00000206125 ENSG00000186031 + - 15 15 31274189 31147377 downstream upstream AC019278.6 FMN1 31229284 30853637 - - 0 31212094 31168468 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.864151527351077 0.899860268150708 0.899860268150708 0.864151527351077 1 - - 20345 N Y 3.41679307359967 3.50529022639353 3.41679307359967 1 0 0.581894462701316 N 0.833994708994709 0.81739417989418 N N 49089 4090 ENSG00000117450 ENSG00000112578 - - 1 6 45760196 42008762 utr5p intron PRDX1 BYSL 45749295 41996943 - + 0 45759868 41999047 + - Y - 0.834173037592588 N HCC1954 6 2 1 5 2 N - - N - SINE 0 1 1 17 0.842726282871298 0.335662163516534 0.842726282871298 0.335662163516534 2 - 0 3799 N Y 3.45720067037699 3.80297331548166 3.45720067037699 0 0 0.53132788421517 N 0 0 N N 30 0 ENSG00000215386 ENSG00000069018 - - 21 5 16901413 135720974 downstream intron C21orf34 TRPC7 16364713 135577022 + - 0 17197175 135667445 - + Y - 1 N HCC1954 20 20 20 4 1 N - - N LTR LTR 0.964912280701754 1 1 4 0.407079645115797 0.428504889595575 0.428504889595575 0.407079645115797 4 - 0 19100 Y Y 3.3828009725769 3.45343911365801 3.3828009725769 231 0 0.00676556213513835 Y 0 0 N N 0 2647 ENSG00000189245 ENSG00000070785 + - 1 1 45226984 45224869 upstream upstream RP5-882O7.4 EIF2B3 45226493 45089037 - - 0 45228183 45225219 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 4 0.449930134075354 0.478497126715059 0.478497126715059 0.449930134075354 1 - - 18112 Y Y 3.19872427442695 3.50744965188915 3.19872427442695 260 0.0137090632140138 0.177584001079101 Y 0.98027418126428 0.99013709063214 N N 43044 10731 ENSG00000143570 ENSG00000160741 + - 1 1 152206812 152197725 coding intron SLC39A1 CRTC2 152198210 152186775 - - 0 152199673 152194267 - + N 3.91332747527344 2.04002046287997 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 19 0.835584534711372 0.764167053112109 0.835584534711372 0.764167053112109 1 0 0 4399 Y Y 3.35356364524965 3.55553920790569 3.35356364524965 283 0 0.526198515145818 Y 0 0 N N 0 0 ENSG00000219101 ENSG00000213783 + - 7 7 27335677 27275855 upstream upstream AC004996.1 AC004996.1 27334732 27275497 - - 0 27339993 27303721 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.949852505270192 0.857009779191151 0.949852505270192 0.857009779191151 4 - - 655 Y Y 3.26663392855898 3.40847927217468 3.26663392855898 223 0 0.892889891384389 Y 0 0.987556053811659 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 coding utr3p C11orf66 C11orf79 61005168 60954173 + + 0 61005865 60970178 - + N - 1.9768768266545 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.535631111994469 0.971277749749971 0.971277749749971 0.535631111994469 1 - 0 9632 Y Y 3.14484171727181 3.30232144676095 3.14484171727181 0 0 0.423717469481393 Y 0.984434185606061 0.99221709280303 N N 160 1722 ENSG00000121068 ENSG00000141376 - + 17 17 56841607 56824973 upstream downstream TBX2 BCAS3 56832039 56109998 + + 0 56831383 56825891 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.871293275511003 0.39993789695587 0.871293275511003 0.39993789695587 1 - - 11134 N N 3.42953077915294 3.23999710710482 3.23999710710482 1 0 0.402246312847987 N 0.486217489248413 0 N N 0 1649619 ENSG00000206531 ENSG00000141736 + + 3 17 114047487 35138441 upstream coding CD200R1L ERBB2 114017246 35104766 - + 0 114083900 35122226 - + Y - - N HCC1954 10 3.2 1 3 1 N 560 26.871 N SINE - 1 0 1 5 0.299953422716903 0.45707188223528 0.45707188223528 0.299953422716903 1 - - 42449 N N 3.43358851031899 3.4415315893834 3.43358851031899 14 0.0324448529411764 0.989203212336302 N 0.0324448529411764 0 N N 0 2269 ENSG00000174473 ENSG00000056050 - + 4 4 174199266 170915637 upstream coding GALNTL6 C4orf27 172971229 170887205 + - 0 172839869 170895386 - - N - - Y HCC1954 1 1 1 0 3 N - - N - - 0 0 0 10 1.0069864905496 1.21409718718746 1.21409718718746 1.0069864905496 4 - - 32963 N Y 3.37291973504871 3.72824693801095 3.37291973504871 370 0.0383204633204635 0.00210564948632319 Y 0.0442567567567568 0.994063706563707 N N 59837 539404 ENSG00000198695 ENSG00000198712 + + MT MT 14674 8270 coding coding MT-ND6 MT-CO2 14150 7587 - + 0 14648 8017 - + N 4.47709083203842 - N HCC1954 2 1.25 1 1 1 N - - N - - 0 0 0 4 0.585623349113953 0.628473838073511 0.628473838073511 0.585623349113953 3 0 - 13680 Y Y 3.52039024593366 3.50848272165904 3.50848272165904 235 0 0.489124752947603 Y 0.931914893617021 0.991489361702128 N N 194 480 ENSG00000169325 ENSG00000159496 + + 22 22 22389508 22371363 downstream downstream AP000347.1 RGL4 22386399 22360329 - + 0.31063829787234 22381315 22377726 - + N - - N HCC1954 1 1 1 0 4 N - - Y LINE LINE 1 1 1 55 0.921285512630487 0.949852505270192 0.949852505270192 0.921285512630487 1 - - 21851 N Y 3.425274708894 3.43105836246279 3.425274708894 1 0 0.545820193032867 N 0 0 N N 4 4212 ENSG00000214700 ENSG00000218839 + + 12 1 27126679 178113539 upstream intron C12orf71 AL359853.18-1 27125257 178100200 - - 0 27201399 178101194 - - Y - 0.520641249909699 N HCC1954 1 1 1 0 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.714174815992626 0.714174815992626 0.271386430077198 3 - 0 47702 N N 3.2793317813189 3.45976132345673 3.2793317813189 0 0 0.199196869559976 N 0 0.0767973856209148 N N 1814 43495 ENSG00000178229 ENSG00000105220 + + 19 19 62533956 39583076 utr3p downstream ZNF543 GPI 62523689 39547909 + + 0 62532956 39584382 + + N - - Y HCC1954 37 35.8 34 5 1 N 82 15.1954 N SINE SINE 1 1 1 5 0.378512652476092 0.39993789695587 0.39993789695587 0.378512652476092 3 - - 29145 Y Y 3.55760534744548 3.35616415112274 3.35616415112274 246 0 0.179144355935784 Y 0 0 N N 0 61 ENSG00000183239 ENSG00000181577 + + 6 6 44165423 44080864 downstream downstream AL109615.42-1 C6orf223 44164963 44076317 - + 0 44150211 44119399 - + N - - N HCC1954 1 1 1 0 3 N - - Y - SINE 0 0.510204081632653 0.510204081632653 6 0.542772860154395 0.699891319672773 0.699891319672773 0.542772860154395 1 - - 35794 N N 3.71823771940677 3.40591861909494 3.40591861909494 0 0 0.202692922728555 N 0 0 N N 712661 17333 ENSG00000111640 ENSG00000169180 - - 12 16 6517797 28130691 coding upstream GAPDH XPO6 6513918 28016817 + - 0 6516386 28159208 - + Y - - N HCC1954 5 3.75 3 4 1 N - - N - - 0 0 0 4 0.714174815992626 0.557056356474248 0.714174815992626 0.557056356474248 1 - - 36522 Y Y 3.7061623612628 3.43209143223268 3.43209143223268 0 0 0.975540497511864 Y 0 0.79321868690385 N N 2401 16105 ENSG00000120647 ENSG00000073614 - - 12 12 422065 368881 utr5p utr5p CCDC77 JARID1A 381084 259484 + - 0 381100 368822 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 12 0.914143764470561 0.471355378555133 0.914143764470561 0.471355378555133 2 - - 44611 N Y 3.63296356710195 3.49847350305486 3.49847350305486 230 0.732351566152408 0.00253640396898624 N 0.743057503506312 0.807293127629733 N N 249 2 ENSG00000150076 ENSG00000163288 + + 10 4 33211797 47123202 intron intron C10orf68 GABRB1 32896657 46728336 + + 0.764469378214119 33113488 46996699 + + Y 13.7178929359707 0.888817065287653 N HCC1954 20 20 20 5 1 N - - N LINE LINE 1 1 1 5 0.264244681917271 0.321378667196682 0.321378667196682 0.264244681917271 0 0 0 47982 N N 3.48656597878024 3.44615838200292 3.44615838200292 0 0 0.872319118360558 N 0 0 N N 0 51629 ENSG00000208525 ENSG00000165671 - + 8 5 130372654 176655369 downstream coding AC103833.2-1 NSD1 130372411 176493532 + + 0 130419871 176571802 - + Y - - N HCC1954 1 1 1 0 1 N 57 8.55269 N LINE - 0.150537634408602 0 0.150537634408602 281 1.32836515774628 1.37835739486577 1.37835739486577 1.32836515774628 4 - - 40987 N N 3.55657227767559 3.73552766966605 3.55657227767559 0 0 0.977597278272332 N 0 0 Y N 9407 7469 ENSG00000101346 ENSG00000126001 - + 20 20 30290125 33563218 downstream coding POFUT1 CEP250 30259357 33506564 + + 0 30306813 33527834 - + N - 0.95791209663739 N HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 5 0.685607823352921 0.778450549431962 0.778450549431962 0.685607823352921 4 - 0 33308 N N 2.94806716636195 0.494089294346095 0.494089294346095 0 0 0.99974040254639 Y 0 0 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding downstream MT-CO3 MT-ND2 8367 4471 + + 0 8497 5562 - + N 0.603627792848188 - N HCC1954 3 1.75 1 16 9 Y - - N - - 0 0 0 28 1.03555348318931 1.28551466878673 1.28551466878673 1.03555348318931 1 0 - 36715 Y Y 3.47336426491055 3.29806537650201 3.29806537650201 4 0 0.293984784593314 Y 0.0883056284631089 0.996070282881306 N N 4974 4945 ENSG00000152556 ENSG00000079387 - - 12 12 46826154 46785886 coding upstream PFKM SENP1 46787424 46722948 + - 0 46787487 46786328 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.671324327033068 0.749883556792257 0.749883556792257 0.671324327033068 1 - - 1024 N N 3.39384326095097 3.68680627146374 3.39384326095097 0 0 0.0264911864911342 N 0 0 N N 309 2325 ENSG00000157214 ENSG00000174915 - + 7 11 89708027 481386 utr3p coding STEAP2 PTDSS2 89678936 440280 + + 0 89701931 476970 - + Y - - N HCC1954 34 24.6666666666667 22 6 1 N - - N SINE - 1 0 1 6 0.392796148795944 0.407079645115797 0.407079645115797 0.392796148795944 0 - - 40353 N Y 3.61360747730288 3.54296933622177 3.54296933622177 0 0 0.177095545549058 N 0.736375 0.907375 N N 27074 216 ENSG00000137804 ENSG00000179284 - + 15 19 39460535 12946567 coding utr3p NUSAP1 DAND5 39412361 12936973 + + 0 39445077 12945816 - + Y - - N HCC1954 37 29 22 24 1 N 389 22.6782 N - SINE 0 1 1 24 1.2783729206268 0.34280391167646 1.2783729206268 0.34280391167646 1 - - 3174 N N 3.01671371581679 1.94975536667293 1.94975536667293 8 0 0.332824633625636 N 0.566956521739131 0 N N 5996 2425 ENSG00000187678 ENSG00000134954 + + 5 11 141684750 127948235 utr3p utr3p SPRY4 ETS1 141670189 127833874 - - 0.133913043478261 141671692 127835202 - - Y 1.15558210629949 - N HCC1954 38 37 36 4 1 N - - N - Simple_repeat 0 1 1 4 0.314236919036755 0.278528178237124 0.314236919036755 0.278528178237124 1 0 - 4822 Y Y 3.91914035949957 3.1677915299205 3.1677915299205 0 0 0.998823428936517 Y 0 0.977842003853564 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding downstream CRCP ASL 65216341 65178207 + + 0 65230127 65202613 - + N - - N HCC1954 1 1 1 0 6 N - - Y - Simple_repeat,Simple_repeat 0 0.202614379084967 0.202614379084967 6 0.592765097273879 1.03555348318931 1.03555348318931 0.592765097273879 1 - - 48757 N N 3.47758982994594 3.26936241550807 3.26936241550807 0 0 0.0841382083299654 N 0 0.337526205450734 N N 11502 11413 ENSG00000159921 ENSG00000112877 + + 9 5 36248450 706664 utr3p coding GNE CEP72 36204430 665405 - + 0 36205266 665504 - + Y - - N HCC1954 38 33 31 5 1 N 583 24.9172 N SINE,SINE - 0.951219512195122 0 0.951219512195122 5 0.292811674556976 0.299953422716903 0.299953422716903 0.292811674556976 2 - - 9434 Y Y 3.41319935075004 3.40847927217468 3.40847927217468 260 0 0.064633117279061 Y 0.102058504875406 0.985969664138678 N N 37605 105 ENSG00000131771 ENSG00000214546 - + 17 17 35046404 35032292 intron coding PPP1R1B AC087491.2 35036705 35029392 + + 0 35038138 35031982 - + N 0.00076455330258651 0.694419305798148 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 0.378512652476092 0.928427260790413 0.928427260790413 0.378512652476092 2 0 0 41908 N N 3.00869608883888 3.3991324009798 3.00869608883888 0 0 0.948533372132893 N 0 0 N N 29840 0 ENSG00000164830 ENSG00000212451 + + 8 8 107834093 127753081 coding downstream OXR1 U11 107739270 127752949 + + 0 107760614 128113266 + + N - - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - SINE,SINE 0 0.730337078651685 0.730337078651685 74 1.32836515774628 1.27123117246687 1.32836515774628 1.27123117246687 1 - - 31928 Y Y 3.49528100778935 3.4267624394105 3.4267624394105 245 0 0.428321150060361 Y 0.988419553868059 0.976839107736118 N N 14776 20207 ENSG00000065534 ENSG00000206527 + - 3 3 125085868 124786616 coding upstream MYLK PTPLB 124811586 124693087 - - 0 124831031 124787331 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.607048593593732 0.521347615674617 0.607048593593732 0.521347615674617 4 - - 45393 N N 3.004029443426 3.04426920633398 3.004029443426 0 0 0.0967894560634598 N 0 0 N N 20 551733 ENSG00000185532 ENSG00000204628 - + 10 5 53728116 180603512 intron utr3p PRKG1 GNB2L1 52421124 180596536 + - 0 53076789 180596548 - - Y 1.44769471035294 - N HCC1954 20 13.8333333333333 1 5 1 N - - N - - 0 0 0 6 0.257102933757345 0.714174815992626 0.714174815992626 0.257102933757345 2 0 - 9382 Y Y 2.69468157134785 2.98933999903981 2.69468157134785 0 0 0.984097967827435 Y 0 0.973780605359553 N N 1312 5490 ENSG00000120093 ENSG00000173917 + - 17 17 44006809 43977392 utr3p upstream HOXB3 HOXB2 43981232 43975020 - - 0 43982252 43979204 - + N 0.859810433175983 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 57 0.45707188223528 0.635615586233437 0.635615586233437 0.45707188223528 1 0 - 48958 N N 3.53039946453785 3.56129235625094 3.53039946453785 0 0 0.0747537325988101 Y 0 0 N N 0 1051 ENSG00000206958 ENSG00000164180 - - 5 5 87714480 87600421 downstream upstream SNORA70 TMEM161B 87714345 87526779 + - 0 87767897 87600849 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.264244681917271 0.521347615674617 0.521347615674617 0.264244681917271 1 - - 30852 N N 3.71145150129163 2.50564148646865 2.50564148646865 0 0.248550191946418 0.465912484919993 N 0.304908927550437 0.248550191946418 N N 0 32064 ENSG00000209103 ENSG00000134107 + + 6 3 17333325 5001861 downstream utr3p AL136305.14 BHLHE40 17333229 4996208 - + 0.248550191946418 17311456 5000540 - + Y - - N HCC1954 2 1.25 1 1 1 N 417 23.3004 N - - 0 0 0 4 0.321378667196682 0.535631111994469 0.535631111994469 0.321378667196682 2 - - 34457 Y Y 3.57489529770476 3.329991337985 3.329991337985 263 0 0.0176450843207085 Y 0.989513708224935 0.989513708224935 N N 16658 15197 ENSG00000136930 ENSG00000119408 + + 9 9 126217542 126155407 intron coding PSMB7 NEK6 126155566 126059706 - + 0 126177869 126149921 - + N 0.945414057446564 1.52752562266127 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.871293275511003 0.707033067832699 0.871293275511003 0.707033067832699 1 0 0 40295 N N 2.97466413502276 3.36447795254773 2.97466413502276 7 0 0.0835991469173802 N 0 0.00483091787439605 N N 221 26328 ENSG00000185823 ENSG00000205403 - + 15 4 22479686 110942783 upstream coding C15orf2 CFI 22471634 110881297 + - 0.00483091787439605 22418971 110883158 - - Y - - N HCC1954 20 19.5 18 4 1 N - - N SINE - 1 0 1 4 0.378512652476092 0.521347615674617 0.521347615674617 0.378512652476092 1 - - 26445 N Y 3.49847350305486 3.61616813038263 3.49847350305486 0 0.0640517241379311 0.368643798280043 N 0.870560344827586 0.860603448275862 N N 36111 6656 ENSG00000099917 ENSG00000131153 - + 22 16 19271918 84280089 coding intron MED15 GINS2 19191886 84268782 + - 0 19221404 84275316 - - Y - 1.42585972785488 N HCC1954 21 20.1111111111111 20 9 1 N 293 16.8972 N - SINE 0 1 1 9 0.664182578873142 0.307095170876829 0.664182578873142 0.307095170876829 4 - 0 13978 Y Y 3.62464976567696 3.34472063516454 3.34472063516454 1 0.00289855072463785 0.363834627339691 Y 0.0459831812488818 0 N N 24 26397 ENSG00000100053 ENSG00000197077 - + 22 22 23933324 23923415 utr5p utr3p CRYBB3 CTA-221G9.5 23925825 23753158 + + 0 23925869 23918662 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.749883556792257 0.764167053112109 0.764167053112109 0.749883556792257 4 - - 24743 Y Y 3.50848272165904 3.54552998930151 3.50848272165904 305 0 0.097466521730939 Y 0.976820434616851 0.992273478205617 N N 12709 2050 ENSG00000141458 ENSG00000141452 + + 18 18 19420468 19365744 coding intron NPC1 C18orf8 19365463 19337460 - + 0 19367319 19340606 - + N 0.503164889808938 0.66113285614209 N HCC1954 1 1 1 0 2 N - - Y - SINE,SINE,LINE 0 0.341772151898734 0.341772151898734 23 0.985561246069823 1.12839620926835 1.12839620926835 0.985561246069823 3 0 0 42600 Y Y 3.131238775818 3.44785379918211 3.131238775818 262 0 0.00786183896241488 Y 0.99102537652156 0.99102537652156 N N 682 0 ENSG00000109667 ENSG00000209883 + - 4 4 9650970 9403583 coding upstream SLC2A9 AC098976.2-1 9436948 9403494 - - 0 9437157 9409963 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA,LTR 0 0.397058823529412 0.397058823529412 4 0.799875793911741 0.642757334393363 0.799875793911741 0.642757334393363 2 - - 28292 N N 3.71890006681607 2.68846441468618 2.68846441468618 0 0 0.0724700935216238 N 0.970409540954095 0.0333783378337834 N N 3 27 ENSG00000150394 ENSG00000164749 + + 16 8 60628240 76641600 intron upstream CDH8 HNF4G 60244866 76482732 - + 0.0333783378337834 60373484 76299149 - + Y 0.920588235294118 - N HCC1954 22 5.2 1 1 1 N - - N LINE LINE 0.918181818181818 0.79646017699115 0.918181818181818 5 0.542772860154395 0.592765097273879 0.592765097273879 0.542772860154395 1 0 - 31727 Y Y 3.09756396399333 3.52936639476796 3.09756396399333 0 0 0.999881766287195 Y 0.0669399872764544 0.858627270799463 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 utr5p upstream LPP AC022498.18 189413415 189379637 + + 0 189425889 189354505 - + N - - N HCC1954 1 1 1 0 7 N - - Y Low_complexity,SINE - 0.154362416107383 0 0.154362416107383 32 1.06412047582901 1.09982921662864 1.09982921662864 1.06412047582901 1 - - 40087 Y Y 3.32320511986986 3.73825615661514 3.32320511986986 238 0 0.0850155958135519 Y 0.976290516206483 0.988145258103241 N Y 1083 360 ENSG00000136371 ENSG00000180953 - + 15 15 77976425 78003132 coding utr5p MTHFS ST20 77924375 77978240 - - 0 77968751 78002849 + - N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.201923076923077 0.201923076923077 4 0.528489363834543 0.714174815992626 0.714174815992626 0.528489363834543 4 - - 1411 N Y 3.50000108636471 3.26824964015148 3.26824964015148 1 0 0.302804091090403 N 0.941419543023821 0.882839086047642 N N 534 8014 ENSG00000141576 ENSG00000149084 - - 17 11 71747985 43834736 utr3p utr3p RNF157 HSD17B12 71651451 43658719 - + 0 71652282 43834016 + - Y - - N HCC1954 74 52.3333333333333 38 6 1 N - - N SINE - 0.757142857142857 0 0.757142857142857 6 0.499922371194838 1.25694767614702 1.25694767614702 0.499922371194838 1 - - 25300 N N 3.42424163912411 3.1761496919349 3.1761496919349 0 0 0.363624496530041 N 0 0 N N 2774 0 ENSG00000188342 ENSG00000219004 - + 13 X 44756237 39532334 intron downstream GTF2F2 CTD-2324A24.1 44592656 39531330 + - 0 44596052 39531251 - - Y 1.33038624388049 - N HCC1954 5 2.25 1 2 1 N - - N - - 0 0 0 4 0.557056356474248 0.549914608314322 0.557056356474248 0.549914608314322 1 0 - 47760 N N 2.72029709021333 2.96682191919878 2.72029709021333 0 0 0.401962173158642 N 0.430866322432588 0 N N 5996 141 ENSG00000187678 ENSG00000160117 + + 5 19 141684750 17259455 utr3p utr3p SPRY4 ANKLE1 141670189 17253454 - + 0 141671688 17258473 - + Y 1.14614386371356 - N HCC1954 37 32.8181818181818 31 11 1 N - - N - Simple_repeat 0 0.928571428571429 0.928571428571429 11 0.421363141435649 0.299953422716903 0.421363141435649 0.299953422716903 1 0 - 18816 Y Y 3.62398741826765 3.40744620240479 3.40744620240479 294 0 0.0462982060831006 Y 0.993030778745064 0.993030778745064 N N 1013 1125 ENSG00000164011 ENSG00000164010 - + 1 1 43090735 43083247 upstream utr3p ZNF691 ERMAP 43084867 43055363 + + 0.993030778745064 43084515 43082942 - + N - 2.56195976414258 N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 4 0.657040830713216 0.599906845433805 0.657040830713216 0.599906845433805 3 - 0 7092 Y Y 3.43408302385895 3.62464976567696 3.43408302385895 237 0 0.138113652850052 Y 0.917994539587987 0.976569868453711 N N 53 2713 ENSG00000125551 ENSG00000222041 - + 2 2 87840110 87687439 upstream utr3p PLGLB2 AC133644.1 87828721 87536002 + + 0 87781618 87687403 - + N - 48.7858294269144 N HCC1954 10 4 2 6 2 N - - Y - LINE 0 1 1 6 0.557056356474248 1.07126222398894 1.07126222398894 0.557056356474248 4 - 0 14463 N N 3.2948728812365 3.06320114060997 3.06320114060997 5 0 0.34199098645873 N 0 0 N N 0 95337 ENSG00000218206 ENSG00000172757 + + 1 11 51396731 65382380 intron utr3p CFLP2 CFL1 51396048 65378884 - - 0 51396199 65379365 - - Y 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.485638874874985 0.599906845433805 0.599906845433805 0.485638874874985 1 0 - 6721 Y Y 3.33424740824393 2.77742557579647 2.77742557579647 316 0 0.0328401993114507 Y 0.993172359979192 0.993172359979192 N N 812 603 ENSG00000213337 ENSG00000163126 + - 2 2 96887475 96873485 utr3p intron ANKRD39 ANKRD23 96877505 96867379 - - 0 96877734 96871976 - + N - 15.7890876065391 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 58 1.2783729206268 1.02841173502938 1.2783729206268 1.02841173502938 1 - 0 9950 Y Y 3.56910229656616 3.04426920633398 3.04426920633398 3 0 0.999999985068424 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 utr5p utr3p GSDMB ORMDL3 35314374 35330822 - - 0 35328406 35332279 + - N - 3.47756524163568 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 12 1.52119235806429 1.02841173502938 1.52119235806429 1.02841173502938 1 - 0 41823 Y Y 3.4797797606651 3.16150917291514 3.16150917291514 0 0 0.280373008734614 Y 0 0.977369439071567 N N 3818 2525 ENSG00000175305 ENSG00000156170 - - 8 8 95976660 96140114 coding intron CCNE2 C8orf38 95951746 95977217 - + 0 95975460 95977755 + - N - 0.126696524681592 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.592765097273879 0.621332089913584 0.621332089913584 0.592765097273879 1 - 0 17825 Y Y 3.52361324642271 3.56232542602083 3.52361324642271 289 0 0.00587295612431615 Y 0 0 N N 17463 10895 ENSG00000155366 ENSG00000155363 + + 1 1 113051548 113044884 coding coding RHOC MOV10 113045251 113018632 - + 0.991625716030357 113045723 113044385 - + N - 0.889066329733219 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.778450549431962 0.421363141435649 0.778450549431962 0.421363141435649 2 - 0 29096 N N 3.21488786896051 3.55976477294109 3.21488786896051 2 0.00446428571428559 0.77330321958496 N 0.00446428571428559 0.00446428571428559 N N 0 568998 ENSG00000219374 ENSG00000156508 + + 6 6 49436052 74288344 downstream utr3p RP1-142O9.1 EEF1A1 49433818 74282194 - - 0.00446428571428559 49433665 74284128 - - N - 0.0254093200594288 Y HCC1954 14 10.0833333333333 5 12 2 N - - N - - 0 0 0 12 0.278528178237124 0.93556900895034 0.93556900895034 0.278528178237124 2 - 0 33047 N N 3.15678909433978 3.28296535696188 3.15678909433978 2 0 0.332205174535877 N 0 0 Y N 275222 59837 ENSG00000198763 ENSG00000198695 - - MT MT 5512 14674 coding coding MT-ND2 MT-ND6 4471 14150 + - 0 5201 14312 - + N 0.980550559228209 0.852476921038053 N HCC1954 2 1.5 1 2 2 N 106 8.09281 N - - 0 0 0 4 0.899860268150708 0.771308801272036 0.899860268150708 0.771308801272036 2 0 0 41989 N Y 3.64553343878587 3.08505510275648 3.08505510275648 90 0 0.0158495551123071 N 0.576190476190476 0.576190476190476 N N 1692 27 ENSG00000013619 ENSG00000164749 + + X 8 149433106 76641600 utr5p upstream MAMLD1 HNF4G 149282209 76482732 + + 0.576190476190476 149340049 76388469 + + Y - - N HCC1954 25 23.2 21 5 1 N - - N LINE LTR 1 1 1 5 0.292811674556976 0.414221393275723 0.414221393275723 0.292811674556976 2 - - 21370 N Y 2.94802731356859 3.2216342342823 2.94802731356859 0 0 0.754890249015209 N 0 0.980064935064935 N N 1238 1842 ENSG00000121310 ENSG00000164051 + - 1 3 53159986 48456533 intron upstream ECHDC2 CCDC51 53134492 48448174 - - 0.980064935064935 53158736 48456873 - + Y 1.92942435745801 - N HCC1954 2 1.75 1 3 1 N - - N - - 0 0 0 4 0.335662163516534 0.649899082553289 0.649899082553289 0.335662163516534 1 0 - 42301 Y N 3.27870928670295 3.54643934467102 3.27870928670295 0 0 0.88193988100379 Y 0 0.248253968253968 N N 2010 0 ENSG00000138735 ENSG00000209291 + - 4 4 120769429 120574710 downstream upstream PDE5A AC093752.2-3 120635000 120574608 - - 0.248253968253968 120633994 120603512 - + N - - N HCC1954 4 2.30769230769231 1 6 4 N - - Y - LTR 0 0.795918367346939 0.795918367346939 13 0.792734045751814 0.699891319672773 0.792734045751814 0.699891319672773 2 - - 47272 Y Y 3.35719722089263 3.52680574168821 3.35719722089263 0 0.161099615725687 0.35189217529929 Y 0.161099615725687 0.94147206621342 N N 617 302 ENSG00000197863 ENSG00000167637 - - 19 19 42021124 42062306 utr5p intron ZNF790 ZNF345 42000176 42033103 - + 0 42008427 42033487 + - N - 0.191267882868105 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 22 1.06412047582901 0.692749571512847 1.06412047582901 0.692749571512847 2 - 0 26574 Y Y 3.45823374014688 3.38755574627242 3.38755574627242 182 0 0.0320908809522924 Y 0.68507326007326 0.933699633699634 N N 438 5 ENSG00000140660 ENSG00000048462 - + 16 16 12054642 11969426 upstream upstream RUNDC2A TNFRSF17 11978103 11966465 + + 0 11977955 11965364 - + N - - N HCC1954 6 1.2962962962963 1 2 2 N - - Y - SINE 0 1 1 27 0.635615586233437 1.01412823870953 1.01412823870953 0.635615586233437 3 - - 3484 N N 3.33784113109357 3.49640736351508 3.33784113109357 0 0 0.967688196672563 N 0 0 N N 24125 166846 ENSG00000157557 ENSG00000142192 - + 21 21 39118749 26465003 upstream coding ETS2 APP 39099101 26174733 + - 0 39027834 26384131 - - N - - Y HCC1954 1 1 1 0 3 N - - N - - 0 0 0 25 1.17838844638783 1.24266417982717 1.24266417982717 1.17838844638783 1 - - 2825 N N 3.57912086274016 3.09512710209296 3.09512710209296 0 0 0.453039143285919 N 0 0.0431059401647639 N N 0 9885 ENSG00000200521 ENSG00000020922 + + 4 11 158908715 93866688 downstream coding Y_RNA MRE11A 158908615 93790123 - - 0 158859045 93833850 - - Y - - N HCC1954 2 1.38095238095238 1 8 1 N - - N - - 0 0 0 21 1.1426797055882 1.59260983966356 1.59260983966356 1.1426797055882 1 - - 3312 N Y 2.42122408509758 3.14232091698542 2.42122408509758 10 0 0.0685681693557845 N 0.985238862050456 0.247181964573269 N N 12188 8014 ENSG00000168724 ENSG00000149084 + + 5 11 34994825 43834736 coding utr3p DNAJA5 HSD17B12 34965455 43658719 + + 0.21027911969941 34991937 43834024 + + Y - 1.56153208144737 N HCC1954 37 29.5714285714286 24 49 1 N 584 19.9177 N SINE - 1 0 1 49 0.864151527351077 1.07840397214886 1.07840397214886 0.864151527351077 2 - 0 1296 N Y 3.26824964015148 3.20397356166243 3.20397356166243 1 0 0.0280751422832091 N 0.263444235195648 0 N N 8014 754 ENSG00000149084 ENSG00000196208 - + 11 2 43834736 11700365 utr3p utr3p HSD17B12 AC110754.4 43658719 11591693 + + 0 43834016 11699318 - + Y 1.56799368003871 - N HCC1954 105 66.2 36 20 1 N - - N - SINE 0 1 1 20 0.685607823352921 0.507064119354764 0.685607823352921 0.507064119354764 1 0 - 46895 Y Y 3.28126993978269 3.66745018166468 3.28126993978269 241 0 0.0609720612815515 Y 0.872623757599151 0.988420341599923 N N 1092 8931 ENSG00000222015 ENSG00000099622 - + 19 19 1230227 1224169 upstream intron C19orf24 CIRBP 1226438 1220336 + + 0 1225307 1223051 - + N - 2.82283334788733 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.757025304952183 0.521347615674617 0.757025304952183 0.521347615674617 1 - 0 3415 N N 3.47233119514066 3.52936639476796 3.47233119514066 0 0 0.52327644554234 Y 0 0 N N 5 49 ENSG00000183844 ENSG00000186842 - - 21 21 41651524 32870062 intron intron FAM3B C21orf77 41610526 32866420 + - 0 41632334 32868401 - + N 0.768768578837518 3.7798074459128 N HCC1954 1 1 1 0 1 N 425 8.27458 N - - 0 0 0 37 0.785592297591888 1.07126222398894 1.07126222398894 0.785592297591888 2 0 0 24606 N N 3.45553575842133 3.45720067037699 3.45553575842133 0 0 0.141343003306164 N 0 0 N N 13271 9 ENSG00000081923 ENSG00000172955 - + 18 4 53550037 100359426 coding intron ATP8B1 ADH6 53464656 100342818 - - 0 53549977 100354447 + - Y - 1.24090492204219 N HCC1954 2 1.25 1 1 1 N 322 23.2271 N - SINE 0 1 1 4 0.335662163516534 0.278528178237124 0.335662163516534 0.278528178237124 3 - 0 25298 N N 3.54040868314203 3.20807114562183 3.20807114562183 6 0 0.118058330345339 N 0 0 N N 0 3160 ENSG00000218877 ENSG00000151846 + + X 13 73720106 24570705 intron coding CTD-2530H13.2 PABPC3 73719648 24568276 - + 0 73719652 24570196 - + Y 1 - N HCC1954 2 2 2 5 1 N 392 25.9311 N - - 0 0 0 5 0.271386430077198 0.292811674556976 0.292811674556976 0.271386430077198 2 0 - 36338 Y Y 3.63080414160633 3.49065421516983 3.49065421516983 252 0 0.665274947873 Y 0 0.990945165945166 N Y 2025 1204 ENSG00000176894 ENSG00000176876 - + 12 12 131805819 131791649 coding intron PGAM5 PXMP2 131797509 131774265 + + 0 131801517 131777035 - + N 0.421077361904013 0.667347527491825 N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 4 0.792734045751814 0.707033067832699 0.792734045751814 0.707033067832699 4 0 0 38705 N N 3.67423639977982 3.34049715675232 3.34049715675232 0 0 0.171691123574471 N 0 0 N N 169845 519 ENSG00000080824 ENSG00000205100 + + 14 4 101675494 190633338 coding coding HSP90AA2 HSP90AA4P 101617139 190631295 - + 0 101620500 190632283 - + Y 0.772620530251608 - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 4 0.357087407996313 0.271386430077198 0.357087407996313 0.271386430077198 1 0 - 21156 N Y 3.39128260787123 3.63655728995158 3.39128260787123 8 0 0.06720691284264 N 0.898929266709929 0 N N 12271 74 ENSG00000177479 ENSG00000116701 - - 3 1 48997971 181826634 intron upstream ARIH2 NCF2 48931285 181791321 + - 0 48939897 181827381 - + Y 0.963247002497696 - N HCC1954 21 20.5 20 8 1 N - - N Simple_repeat SINE 0.18705035971223 1 1 8 0.956994253430118 0.378512652476092 0.956994253430118 0.378512652476092 1 0 - 25855 N Y 3.51782959285392 3.38486711211668 3.38486711211668 0 0 0.104681557172373 N 0 0.764413875598086 N N 75177 269 ENSG00000125107 ENSG00000154997 + - 16 7 57221251 55897976 utr5p intron CNOT1 SEPT14 57111359 55828731 - - 0 57190783 55868412 - + Y - 8.21329264157341 N HCC1954 20 20 20 6 1 N - - N - SINE 0 1 1 6 0.407079645115797 0.321378667196682 0.407079645115797 0.321378667196682 2 - 0 48967 Y Y 3.48652612598689 3.62192127872787 3.48652612598689 314 0 0.0263075202369539 Y 0.974440633676303 0.991480211225434 N N 1390 1 ENSG00000131732 ENSG00000131730 - + 5 5 80644872 80597970 upstream intron ZCCHC9 CKMT2 80633178 80564895 + + 0 80632864 80567699 - + N - 0.951677852348993 N HCC1954 1 1 1 0 2 N - - Y LINE,LINE,LINE - 0.862903225806452 0 0.862903225806452 10 0.871293275511003 1.15696320190805 1.15696320190805 0.871293275511003 2 - 0 10077 Y Y 3.00190987072374 3.09190410160392 3.00190987072374 118 0 0.67887979483234 Y 0 0 N N 9613 185 ENSG00000132510 ENSG00000183914 - + 17 17 7698831 7677783 utr5p downstream JMJD3 DNAH2 7683947 7562746 + + 0 7683952 7678379 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 7 0.778450549431962 0.864151527351077 0.864151527351077 0.778450549431962 1 - - 29935 N Y 3.50744965188915 3.31957154422688 3.31957154422688 7 0 0.233976992366735 N 0.00452488687782804 0.732558924832849 N N 128 47021 ENSG00000204385 ENSG00000130741 - + 6 X 31954802 24006846 utr3p utr3p SLC44A4 EIF2S3 31938948 23982986 - + 0 31939111 24005443 + + Y - - N HCC1954 60 41.75 34 4 1 N - - N SINE SINE 1 1 1 4 0.299953422716903 0.421363141435649 0.421363141435649 0.299953422716903 3 - - 41048 Y Y 3.79040344379773 3.43937216388778 3.43937216388778 278 0 0.022703106565638 Y 0 0 N N 2742 6703 ENSG00000088836 ENSG00000125877 + + 20 20 3166812 3152516 downstream coding SLC4A11 ITPA 3156063 3138056 - + 0 3155328 3147277 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.0529801324503311 0 0.0529801324503311 16 1.07840397214886 1.2783729206268 1.2783729206268 1.07840397214886 1 - - 44259 N Y 3.37704782423165 3.62977107183644 3.37704782423165 246 0.776422764227642 0.0220781116464412 N 0.776422764227642 0.776422764227642 N N 0 0 ENSG00000217094 ENSG00000219149 + - 10 9 32517745 78354504 intron intron AL445071.15 AL161626.20-1 32517254 78354018 - - 0.878048780487805 32517417 78354177 - + Y 1 1 N HCC1954 38 24.8333333333333 18 12 1 N 376 22.211 N - - 0 0 0 12 0.371370904316165 0.278528178237124 0.371370904316165 0.278528178237124 2 0 0 19602 N N 3.55401162459584 3.61464054707278 3.55401162459584 0 0 0.163071439984775 N 0 0.628902195608782 N N 2833 0 ENSG00000133019 ENSG00000215401 - - 1 18 238139338 1353874 utr5p upstream CHRM3 AP005119.2 237858996 1352441 + - 0 237859380 1504367 - + Y 12.30285677733 - N HCC1954 22 21.5 21 4 1 N - - N LINE - 1 0 1 4 0.314236919036755 0.428504889595575 0.428504889595575 0.314236919036755 3 0 - 42203 Y Y 3.74913061111987 3.48912663185998 3.48912663185998 380 0 0.053572829278796 Y 0.994133126934984 0.982399380804953 N N 73 5741 ENSG00000109743 ENSG00000118564 - - 4 4 15343508 15266111 upstream upstream BST1 FBXL5 15313739 15215252 + - 0 15292001 15278761 - + N - - N HCC1954 28 6.50980392156863 1 26 3 N - - Y - SINE 0 1 1 51 1.02126998686945 0.971277749749971 1.02126998686945 0.971277749749971 4 - - 40968 Y Y 3.20654356231198 3.78105657260285 3.20654356231198 264 0 0.091269451174284 Y 0.990136513651365 0.98027302730273 N Y 10175 1340 ENSG00000088888 ENSG00000125843 - + 20 20 3795973 3753954 utr5p coding RP11-119B16.1 C20orf29 3775484 3749178 + + 0 3783205 3750940 - + N 0.847646667126807 0.99430918700577 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.642757334393363 0.907002016310634 0.907002016310634 0.642757334393363 4 0 0 8768 N N 3.41952156054875 3.30977001228539 3.30977001228539 16 0.0199023199023197 0.357680379020672 N 0.76989010989011 0.0284249084249084 N N 9881 153380 ENSG00000008294 ENSG00000185275 + + 17 Y 46553204 19614093 intron utr3p SPAG9 CD24L4 46397083 19611898 - - 0.0284249084249084 46546575 19612790 - - Y 1.4836300114869 - N HCC1954 4 2.78571428571429 2 14 1 N 331 17.1899 N SINE SINE 1 0.329341317365269 1 14 0.271386430077198 0.964136001590045 0.964136001590045 0.271386430077198 4 0 - 20700 N N 2.72548055699787 3.65591337975064 2.72548055699787 0 0 0.0822870601219204 N 0 0 N N 2833 0 ENSG00000133019 ENSG00000198354 + - 1 X 238139338 125127615 utr5p upstream CHRM3 WDR40C 237858996 125126195 + - 0.0121951219512196 237859311 125244636 + + Y - - N HCC1954 44 27.5 22 4 1 N - - N LINE LTR 1 1 1 4 0.328520415356608 0.407079645115797 0.407079645115797 0.328520415356608 2 - - 24636 Y Y 3.48593413659447 3.67167574670008 3.48593413659447 201 0 0.348366437930588 Y 0 0.980489708321139 N N 10593 4475 ENSG00000134779 ENSG00000134775 + + 18 18 32663156 32614016 coding downstream C18orf10 FHOD3 32630033 32131700 - + 0 32632415 32617024 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 5 0.635615586233437 0.692749571512847 0.692749571512847 0.635615586233437 1 - - 45525 N Y 3.31233066536513 3.58743466416515 3.31233066536513 2 0 0.619328512912016 N 0 0.925333333333333 N N 19274 6845 ENSG00000179134 ENSG00000112294 - - 19 6 44567375 24645414 utr5p intron SAMD4B ALDH5A1 44524948 24603176 + + 0.925333333333333 44536545 24607048 - - Y - 0.575322907991453 N HCC1954 22 20.75 20 4 1 N - - N - SINE 0 1 1 4 0.642757334393363 0.39993789695587 0.642757334393363 0.39993789695587 1 - 0 6662 N Y 3.67320333000993 3.23640338425519 3.23640338425519 1 0 0.865057388985739 N 0.987688331122675 0.975376662245349 N N 5406 95 ENSG00000153561 ENSG00000183281 + - 2 2 86855943 87102486 coding upstream RMND5A PLGLB1 86800948 87083193 + - 0 86821703 87133626 + + N - - Y HCC1954 8 5.11111111111111 1 44 1 N - - N - - 0 0 0 45 1.45691662462496 1.20695543902754 1.45691662462496 1.20695543902754 4 - - 13652 Y Y 3.03123532633363 3.39909254818645 3.03123532633363 332 0 0.00314268438995269 Y 0.171517054132021 0.985957916171729 N N 10093 0 ENSG00000183963 ENSG00000209058 - + 22 22 29830609 29786271 upstream downstream SMTN AC005005.1-1 29807305 29785975 + + 0 29806433 29790170 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.457983193277311 0 0.457983193277311 15 1.39264089118562 0.442788385915428 1.39264089118562 0.442788385915428 1 - - 14192 N Y 3.73808832274579 3.59272380419397 3.59272380419397 173 0 0.0133642554941075 N 0 0.972761105392351 N N 10 0 ENSG00000205550 ENSG00000220101 + - 5 22 70529370 22325521 intron intron AC145138.2-1 AP000347.3 70471472 22321400 - - 0.0330192414284584 70529227 22324747 - + Y 0.495249721059202 1 N HCC1954 8 7.85714285714286 7 7 1 N - - N - - 0 0 0 7 0.728458312312478 0.578481600954027 0.728458312312478 0.578481600954027 1 0 0 27148 N Y 3.52720696927234 3.75016368088976 3.52720696927234 156 0.0149589277993948 0.186659116682850 Y 0.0592304366623432 0 N N 12911 0 ENSG00000103479 ENSG00000210272 - + 16 16 52083060 51926076 coding downstream RBL2 AC079416.4-1 52025862 51925975 + + 0 52030430 51970018 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.735600060472404 0.578481600954027 0.735600060472404 0.578481600954027 1 - - 37730 N N 3.24161281869731 3.45976132345673 3.24161281869731 134 0.55301685891748 0.00547698092122706 N 0.855811889973381 0.394409937888199 N N 2947 18458 ENSG00000100578 ENSG00000166530 - + 14 16 58085299 82400529 intron coding KIAA0586 HSBP1 57963351 82399094 + + 0.394409937888199 58000504 82399198 - + Y 0.866568530265679 1.79335694891267 N HCC1954 1 1 1 0 1 N 30 25.2576 N - - 0 0 0 7 0.314236919036755 0.749883556792257 0.749883556792257 0.314236919036755 2 0 0 4284 Y Y 3.28702308812794 3.21228736308742 3.21228736308742 391 0 0.0346824021024125 Y 0 0.994027290687168 N N 12472 5664 ENSG00000161057 ENSG00000105821 - - 7 7 102795891 102772556 upstream intron PSMC2 DNAJC2 102775325 102740157 + - 0 102775205 102772206 - + N - 1.98634028849029 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.864151527351077 0.928427260790413 0.928427260790413 0.864151527351077 3 - 0 48679 N N 3.69784855983781 3.28139792085868 3.28139792085868 2 0 0.73868165704156 N 0 0 N N 27 850768 ENSG00000184188 ENSG00000075624 + + 5 7 79631912 5536758 coding coding AC026410.5-4 ACTB 79631253 5533313 - - 0 79631780 5534672 - - Y - - N HCC1954 10 3.33333333333333 1 2 3 Y - - N - - 0 0 0 6 0.249961185597419 0.778450549431962 0.778450549431962 0.249961185597419 1 - - 7367 Y Y 3.49268050191626 3.52567938596249 3.49268050191626 207 0 0.80189684900376 Y 0.690690690690691 0.97310353832093 N Y 176 4881 ENSG00000168899 ENSG00000118640 - + 2 2 85674020 85662665 coding coding VAMP5 VAMP8 85665042 85658227 + + 0 85672359 85659801 - + N 0.0482059455852917 - N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 8 0.799875793911741 1.02126998686945 1.02126998686945 0.799875793911741 4 0 - 49241 Y Y 3.44611852920956 3.6272104187567 3.44611852920956 0 0 0.996921679024624 Y 0 0.994458987783595 N N 26477 14691 ENSG00000161011 ENSG00000161013 - - 5 5 179197681 179166547 coding utr5p SQSTM1 MGAT4B 179180503 179156711 + - 0 179192639 179166198 - + N - 3.13211081034331 N HCC1954 1 1 1 0 5 N - - Y - Low_complexity 0 0.0241545893719807 0.0241545893719807 25 0.864151527351077 1.40692438750547 1.40692438750547 0.864151527351077 1 - 0 49143 Y Y 3.4325554405491 3.20699822305859 3.20699822305859 133 0 0.236653860395150 Y 0 0.980847088134538 N N 7 5148 ENSG00000177453 ENSG00000172262 - + 5 5 43316708 43211578 upstream coding AC114947.1 ZNF131 43228084 43157399 + + 0 43227612 43209307 - + N - - N HCC1954 2 1.4 1 2 1 N - - Y - - 0 0 0 5 0.771308801272036 1.07840397214886 1.07840397214886 0.771308801272036 4 - - 33145 N Y 3.00190987072374 2.97572771001618 2.97572771001618 344 0.00290697674418583 0.368253514294395 Y 0.00290697674418583 0.979008567931457 N N 247001 275222 ENSG00000198786 ENSG00000198763 - + MT MT 14149 5512 coding coding MT-ND5 MT-ND2 12338 4471 + + 0.0763769889840881 12391 5459 - + N 1.21310056846492 1.95596712074578 N HCC1954 2 2 2 5 5 N - - N - - 0 0 0 5 0.735600060472404 0.764167053112109 0.764167053112109 0.735600060472404 2 0 0 34455 Y Y 3.37080016234644 3.30694823938047 3.30694823938047 135 0 0.00639086942568223 Y 0.555044699872286 0.965772669220945 N N 45208 11655 ENSG00000119335 ENSG00000119333 - - 9 9 130498488 130458950 intron utr5p SET WDR34 130485996 130435761 + - 0 130486514 130458885 - + N 0.138517976927999 132.182584385432 N HCC1954 1 1 1 0 1 N - - Y LINE,LINE - 1 0 1 7 0.535631111994469 0.628473838073511 0.628473838073511 0.535631111994469 1 0 0 7266 Y Y 3.62464976567696 3.50272957331379 3.50272957331379 0 0 0.594579841503217 Y 0 0.977110582639715 N N 1872 2755 ENSG00000172965 ENSG00000153094 + + 2 2 111969088 111642493 downstream downstream AC068491.4 BCL2L11 111903370 111594962 - + 0 111818108 111721684 - + N - - N HCC1954 2 2 2 5 2 N - - Y LINE - 1 0 1 5 0.535631111994469 0.742741808632331 0.742741808632331 0.535631111994469 1 - - 772 Y Y 3.61253455473964 3.34984194132402 3.34984194132402 0 0 0.66659934457437 Y 0 0.991105377512221 N N 1658 129 ENSG00000149743 ENSG00000149781 + + 11 11 63750257 63747930 coding intron TRPT1 FERMT3 63747848 63730782 - + 0.991105377512221 63748337 63746793 - + N - 0.439096559465417 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.714174815992626 0.592765097273879 0.714174815992626 0.592765097273879 2 - 0 37585 N Y 3.4937534244795 2.81623104135043 2.81623104135043 13 0 0.0379068047218643 N 0.949441129108648 0.0249360613810742 N N 3866 544 ENSG00000198740 ENSG00000186960 - + 17 14 44794834 28332126 utr3p utr3p ZNF652 C14orf23 44727485 28311661 - + 0.176612674055129 44727763 28331558 + + Y - - N HCC1954 37 25.3846153846154 20 13 1 N - - N - SINE 0 1 1 13 0.871293275511003 1.12125446110842 1.12125446110842 0.871293275511003 0 - - 49447 N N 3.15526151102993 3.49424793801946 3.15526151102993 1 0.00298507462686581 0.991841449028684 N 0.0117308195862791 0 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 coding intron TICAM2 AC034236.1 114942238 115326170 - + 0 114984189 115380417 - + N - 0.505191337881934 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 9 0.942710757110266 0.99270299422975 0.99270299422975 0.942710757110266 3 - 0 31662 Y N 2.98152071115478 3.58441000276898 2.98152071115478 0 0 0.196867614485758 Y 0 0 N N 5799 417 ENSG00000163605 ENSG00000172986 - + 3 3 73199031 73107077 coding intron PPP4R2 GLT8D4 73128651 73020075 + + 0 73128912 73099619 - + N - 1.031753226604 N HCC1954 6 4.75 1 3 1 Y - - Y - - 0 0 0 4 0.392796148795944 0.792734045751814 0.792734045751814 0.392796148795944 3 - 0 49189 Y Y 3.40847927217468 3.508977235199 3.40847927217468 75 0 0.458040490506823 Y 0 0 N N 2781 5 ENSG00000082196 ENSG00000215159 - - 5 5 34160396 34232139 coding intron AMACR AC138409.1-1 34023069 34210910 - + 0 34160353 34211721 + - N - 0.899963885879379 N HCC1954 9 5.57142857142857 2 7 3 N - - Y LTR - 0.574850299401198 0 0.574850299401198 7 1.02126998686945 0.892718519990782 1.02126998686945 0.892718519990782 2 - 0 32962 N N 3.47080361183081 3.8552884365336 3.47080361183081 0 0 0.120353459692852 N 0 0 Y N 0 1291380 ENSG00000211459 ENSG00000198804 - + MT MT 1603 7446 intron coding AF347015.1-2 MT-CO1 650 5905 + + 0 1548 7058 - + N 1 - N HCC1954 8 5.5 2 4 1 N 368 9.72153 N - - 0 0 0 4 0.264244681917271 0.51420586751469 0.51420586751469 0.264244681917271 2 0 - 2032 N N 3.35087501109391 3.49381805691774 3.35087501109391 0 0 0.0277347574251284 N 0.376030437539632 0 N N 138 975 ENSG00000176697 ENSG00000198487 + + 11 6 27700181 42218335 intron coding BDNF AL512274.9 27633016 42183124 - - 0.0120481927710846 27640256 42204454 - - Y 2.15412002483155 - N HCC1954 22 18.2 6 5 1 N 113 24.6235 N SINE - 1 0 1 5 0.271386430077198 0.549914608314322 0.549914608314322 0.271386430077198 1 0 - 13645 N Y 3.28080593146627 3.29652844562235 3.28080593146627 229 0 0.00369241150351973 Y 0.68943551941028 0.990865750570891 N N 0 3076 ENSG00000217793 ENSG00000093100 - - 22 22 16882966 16769601 upstream utr5p XXbac-B476C20.12 MICAL3 16881980 16697104 + - 0 16864161 16769579 - + N - 4.46768093274563 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 72 0.864151527351077 1.04269523134923 1.04269523134923 0.864151527351077 2 - 0 13144 N Y 2.42680847320244 2.17391195130055 2.17391195130055 0 0.234521575984991 0.140215132338434 N 0.655534709193246 0 N N 5996 46217 ENSG00000187678 ENSG00000131746 - + 5 17 141684750 35911380 utr3p utr3p SPRY4 TNS4 141670189 35885606 - - 0.234521575984991 141671703 35886189 + - Y - - N HCC1954 38 28.25 3 4 1 N - - N - Simple_repeat 0 0.769230769230769 0.769230769230769 4 0.428504889595575 0.464213630395207 0.464213630395207 0.428504889595575 1 - - 31619 Y Y 3.51001030496889 3.40914161958398 3.40914161958398 0 0 0.93031800742424 Y 0.981537260151718 0.990768630075859 N N 3882 5040 ENSG00000120756 ENSG00000175054 - - 3 3 143915191 143780358 utr5p upstream PLS1 ATR 143825034 143650770 + - 0 143825091 143798037 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 238 1.52833410622422 0.857009779191151 1.52833410622422 0.857009779191151 2 - - 33289 N N 2.98272161479402 3.28569384391097 2.98272161479402 6 0 0.99996599499682 N 0 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8408 15658 - + N 1.00286059173194 - N HCC1954 2 1.1 1 2 8 N 189 4.09957 N - - 0 0 0 20 1.47834186910473 1.56404284702385 1.56404284702385 1.47834186910473 3 0 - 13712 Y Y 3.67017866861376 3.51104337473878 3.51104337473878 287 0 0.00698808458628475 Y 0.95729218516675 0.992882030861125 N N 12 1045 ENSG00000205704 ENSG00000100162 - - 22 22 40684597 40673094 upstream upstream Z99716.4-3 CENPM 40684142 40654116 + - 0 40683621 40673907 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE,LTR 0 0.847826086956522 0.847826086956522 5 0.785592297591888 0.985561246069823 0.985561246069823 0.785592297591888 1 - - 41827 Y Y 3.21804051143267 3.23999710710482 3.21804051143267 0 0 0.296266502544108 Y 0.261809377063614 0.994364957076821 N N 1458 0 ENSG00000158856 ENSG00000158815 - + 8 8 21995982 21962263 utr5p downstream EPB49 FGF17 21971322 21956374 + + 0 21980294 21962680 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity,Low_complexity,Low_complexity 0 0.381395348837209 0.381395348837209 25 1.67116906942274 1.12839620926835 1.67116906942274 1.12839620926835 1 - - 13082 N Y 3.12804628055249 3.54296933622177 3.12804628055249 1 0 0.177312412379206 N 0.868413696715584 0.943605870020965 N N 1649619 905 ENSG00000141736 ENSG00000174132 - - 17 5 35138441 99950341 coding upstream ERBB2 FAM174A 35104766 99898943 + + 0 35122227 99841891 - - Y - - N HCC1954 21 6.33333333333333 4 9 1 N - - N - SINE 0 1 1 9 0.45707188223528 0.257102933757345 0.45707188223528 0.257102933757345 2 - - 39837 Y Y 3.329991337985 3.54872248456702 3.329991337985 344 0 0.0210228969647233 Y 0.970146915471383 0.988058766188553 N N 18 542 ENSG00000188869 ENSG00000172345 + - 15 15 79453510 79403579 downstream upstream TMC3 STARD5 79411746 79392069 - - 0 79411741 79403957 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 36 1.22123893534739 1.22838068350732 1.22838068350732 1.22123893534739 4 - - 11777 N N 3.45872825368684 3.40591861909494 3.40591861909494 0 0 0.0384135377605189 N 0.615844155844156 0 N N 1140 5530 ENSG00000161570 ENSG00000148154 + + 17 9 31231910 113735168 utr3p coding CCL5 UGCG 31222608 113698867 - + 0 31223129 113728589 - + Y - - N HCC1954 36 32.625 29 8 1 N - - N SINE - 1 0 1 8 0.499922371194838 0.599906845433805 0.599906845433805 0.499922371194838 1 - - 30287 Y Y 3.29976079368121 3.70719543103269 3.29976079368121 318 0 0.95936912624998 Y 0.867085953878407 0.99335429769392 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62653513 62569094 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 50 1.17124669822791 1.17124669822791 1.17124669822791 1.17124669822791 1 - - 4866 Y Y 3.43677165801469 3.60426060610801 3.43677165801469 0 0 0.211117706002578 Y 0 0.98972168044333 N N 6667 6258 ENSG00000062582 ENSG00000106608 - + 7 7 43875670 43932521 coding coding MRPS24 AC004985.2-1 43872682 43882030 - - 0 43875446 43885310 + - N - - N HCC1954 1 1 1 0 1 N - - Y - LINE,LINE 0 0.255172413793103 0.255172413793103 8 0.871293275511003 0.892718519990782 0.892718519990782 0.871293275511003 2 - - 2677 N Y 3.40631984667906 3.49640736351508 3.40631984667906 0 0 0.194918542447258 N 0.862595419847328 0.95706106870229 N N 4017 2846 ENSG00000214482 ENSG00000175348 + - 15 11 83018061 8942565 utr3p upstream AC115102.7 TMEM9B 83013781 8925416 - - 0 83016557 8946162 - + Y - - N HCC1954 23 22.25 20 8 1 N - - N Other - 1 0 1 8 0.649899082553289 0.971277749749971 0.971277749749971 0.649899082553289 1 - - 5439 N N 3.64553343878587 3.40119854051958 3.40119854051958 0 0 0.0590430999826262 N 0 0 N N 1992 7560 ENSG00000003436 ENSG00000065060 - + 2 6 188127464 34953265 utr5p upstream TFPI UHRF1BP1 188037202 34867772 - + 0 188127391 34861733 + + Y - - N HCC1954 20 10.8 4 5 1 N - - N - Other 0 1 1 5 0.421363141435649 0.321378667196682 0.421363141435649 0.321378667196682 1 - - 28584 N N 3.65488030998075 3.50744965188915 3.50744965188915 0 0 0.228483898752329 N 0 0 N N 42670 45068 ENSG00000128050 ENSG00000205336 + + 4 16 57022291 56256445 utr3p upstream PAICS GPR56 56996672 56220023 + + 0 57021807 56211648 + + Y - - N HCC1954 28 22.14 2 50 2 N - - N SINE - 1 0 1 50 0.499922371194838 0.657040830713216 0.657040830713216 0.499922371194838 1 - - 31582 Y Y 3.15379097658604 3.45872825368684 3.15379097658604 0 0.0947603121516163 0.163613715229944 Y 0.439613526570048 0.870680044593088 N N 457 82015 ENSG00000168038 ENSG00000168036 + + 3 3 41978664 41256943 downstream coding ULK4 CTNNB1 41263097 41211405 - + 0 41261483 41255769 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.435646637755502 0.507064119354764 0.507064119354764 0.435646637755502 2 - - 22020 N N 3.37287988225536 3.44785379918211 3.37287988225536 30 0.0437828994167022 0.0261174488550500 N 0.204829990041258 0.194764546877223 N N 7282 936 ENSG00000157216 ENSG00000151338 + - 1 14 54644680 37090214 intron downstream SSBP3 MIPOL1 54464783 36736907 - + 0.194764546877223 54470943 37105946 - - Y 2.23029013878574 - N HCC1954 20 17.625 1 7 1 N - - N Other SINE 1 1 1 8 0.628473838073511 0.449930134075354 0.628473838073511 0.449930134075354 1 0 - 38160 N N 3.28934652957335 3.45400817511148 3.28934652957335 0 0.340579710144928 0.233403064169658 Y 0.439492753623188 0.439492753623188 N N 0 1187 ENSG00000214385 ENSG00000215394 + + 14 14 18790591 18754290 downstream utr5p AL589743.4-1 AL589743.4-2 18789543 18720037 - + 0.439492753623188 18788413 18720094 - + N - 2.35007641019667 N HCC1954 12 10 6 6 2 N - - N - - 0 0 0 6 0.599906845433805 0.707033067832699 0.707033067832699 0.599906845433805 2 - 0 27737 N Y 3.59425138750382 3.29553522864581 3.29553522864581 6 0 0.0613290777972828 N 0 0.917117117117117 N N 928 45068 ENSG00000144559 ENSG00000205336 + + 3 16 11863355 56256445 intron upstream C3orf31 GPR56 11806920 56220023 - + 0 11828499 56211562 - + Y 0.446900287742621 - N HCC1954 24 22.1111111111111 21 9 1 N - - N SINE - 1 0 1 9 0.307095170876829 0.442788385915428 0.442788385915428 0.307095170876829 1 0 - 31818 N N 3.25 3.49487978020523 3.25 0 0 0.0705394182942717 Y 0.477647058823529 0.361568627450981 N N 45 0 ENSG00000114279 ENSG00000200184 - + 3 3 193609532 193930200 coding downstream FGF12 U1 193342424 193930038 - - 0.361568627450981 193560957 193927757 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.485638874874985 0.51420586751469 0.51420586751469 0.485638874874985 1 - - 41867 Y N 3.4561676006071 2.73814433474487 2.73814433474487 0 0 0.0456718611681260 N 0 0 N N 0 0 ENSG00000221176 ENSG00000221261 + + 8 8 129130666 129231616 downstream upstream hsa-mir-1207 hsa-mir-1208 129130580 129231544 + + 0 129178084 129182588 + + N - - Y HCC1954 1 1 1 0 1 N 462 19.8895 N - LTR 0 1 1 4 0.671324327033068 0.414221393275723 0.671324327033068 0.414221393275723 1 - - 30613 Y Y 3.46128890676658 3.27039548527796 3.27039548527796 0 0 0.696417577304913 Y 0.939391664664905 0.988980302666346 N N 294 1934 ENSG00000147003 ENSG00000186312 - - X X 15593075 15631393 coding intron TMEM27 CA5BP 15555372 15602976 - + 0 15592763 15603462 + - N - 0.0419537976485248 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.99270299422975 0.93556900895034 0.99270299422975 0.93556900895034 2 - 0 33051 N Y 3.00463835767282 2.89211846966702 2.89211846966702 384 0.110430743243243 0.997276638806786 Y 0.101445195195195 0.95507225975976 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8414 5443 - + N 1.08080409485149 1.36651119851212 N HCC1954 4 2.36842105263158 1 18 9 N - - N - - 0 0 0 19 0.914143764470561 1.49262536542459 1.49262536542459 0.914143764470561 2 0 0 44240 N N 3.39657174790006 3.09087103183403 3.09087103183403 7 0 0.152641338541447 N 0 0 N N 1555 3891 ENSG00000148153 ENSG00000166295 + + 9 10 114520250 73665622 upstream intron C9orf80 C10orf104 114488618 73645812 - + 0 114530274 73645953 - + Y - 0.744979490524871 N HCC1954 28 22.75 15 4 1 N - - N SINE - 1 0 1 4 0.592765097273879 0.471355378555133 0.592765097273879 0.471355378555133 1 - 0 24665 Y Y 3.56232542602083 3.53039946453785 3.53039946453785 0 0 0.8557174488101 Y 0 0.9706853038245 N N 4614 2590 ENSG00000134490 ENSG00000134508 + + 18 18 19271923 19092614 coding downstream C18orf45 CABLES1 19129975 18969725 - + 0 19143687 19092906 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.785592297591888 0.635615586233437 0.785592297591888 0.635615586233437 2 - - 31756 N N 3.79040344379773 3.2656754067026 3.2656754067026 0 0 0.373238710857982 Y 0.389742910151074 0.379571958653591 N N 37 0 ENSG00000189283 ENSG00000212211 - + 3 3 60497735 60817317 coding downstream FHIT U3 59712992 60817102 - - 0 60497673 60782544 + - N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.999844742389676 0.714174815992626 0.999844742389676 0.714174815992626 2 - - 31248 Y Y 3.35087501109391 3.36361271664718 3.35087501109391 311 0 0.0413481755243488 Y 0 0 N N 1892 667 ENSG00000163611 ENSG00000206530 + - 3 3 114716693 114643030 utr3p upstream CCDC52 WDR52 114644262 114493094 - - 0 114646281 114643194 - + N 0.074306383342022 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 1.0069864905496 1.34979040222606 1.34979040222606 1.0069864905496 3 0 - 24281 N Y 3.78208964237274 3.37080016234644 3.37080016234644 0 0 0.865479983697094 N 0 0.821254503072685 N N 11413 658 ENSG00000112877 ENSG00000180758 - + 5 1 706664 9111837 coding upstream CEP72 GPR157 665405 9086668 + - 0.821254503072685 672105 9120905 - - Y - - N HCC1954 20 14 8 4 1 N - - N - SINE 0 1 1 4 0.442788385915428 0.299953422716903 0.442788385915428 0.299953422716903 4 - - 9378 Y Y 3.46295381872224 3.08035795212007 3.08035795212007 354 0 0.000273596754262750 Y 0 0 N N 12 443941 ENSG00000204913 ENSG00000172057 - - 17 17 35354622 35337380 downstream utr5p AC090844.7 ORMDL3 35353259 35330822 + - 0 35358871 35334003 - + N - 23.468902184199 N HCC1954 1 1 1 0 1 N - - Y DNA,LINE - 0.547826086956522 0 0.547826086956522 22 0.821301038391519 1.17124669822791 1.17124669822791 0.821301038391519 0 - 0 49348 N Y 3.43887765034782 3.03440489366019 3.03440489366019 4 0 0.323926001179028 Y 0.994167476739342 0.994167476739342 N N 60434 0 ENSG00000155506 ENSG00000221552 - + 5 5 154177354 154045614 coding upstream LARP1 hsa-mir-1303 154072655 154045529 + + 0 154115944 154042787 - + N - - N HCC1954 1 1 1 0 1 N - - N - Low_complexity 0 0.622222222222222 0.622222222222222 37 1.50690886174444 1.22838068350732 1.50690886174444 1.22838068350732 2 - - 20610 N Y 2.93023865987273 3.48383749183115 2.93023865987273 242 0.810310901219992 0.00695815877119932 N 0.952577725304998 0.541584677948314 N N 0 78560 ENSG00000217333 ENSG00000112493 + + 1 6 169680726 33390114 upstream utr3p RP1-81F6.1 TAPBP 169680447 33375449 - - 0.52577725304998 169691296 33376425 - - Y - - N HCC1954 91 27.9 1 9 1 N - - N SINE SINE 0.96 0.976047904191617 0.976047904191617 10 0.357087407996313 1.1141127129485 1.1141127129485 0.357087407996313 2 - - 26589 Y Y 3.4439989565073 3.52361324642271 3.4439989565073 222 0 0.0370724678602802 Y 0 0.98739879119626 N N 1 1140 ENSG00000167194 ENSG00000149927 - - 16 16 29943524 29930243 upstream upstream AC093512.2 DOC2A 29942156 29924338 + - 0 29940073 29934015 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat,Simple_repeat 0 0.150234741784038 0.150234741784038 27 0.778450549431962 1.15696320190805 1.15696320190805 0.778450549431962 2 - - 5766 N N 2.47179079997317 2.90509891650488 2.47179079997317 0 0.110843373493976 0.165615661160570 N 0.209638554216868 0.308433734939759 N N 676 0 ENSG00000144401 ENSG00000182447 - + 2 3 208198276 162704424 downstream downstream FAM119A AC104471.6 208185086 162697290 - + 0.357831325301205 208184572 163650995 + + Y - - N HCC1954 63 46 21 4 1 N 542 18.1672 N Other LINE 1 1 1 4 0.685607823352921 0.51420586751469 0.685607823352921 0.51420586751469 3 - - 31625 Y Y 3.45041445226185 3.34934742778406 3.34934742778406 335 0 0.0113231245499753 Y 0.993993885991728 0.993993885991728 N N 14912 30 ENSG00000114353 ENSG00000188338 - + 3 3 50271775 50233404 coding downstream GNAI2 SLC38A3 50248640 50217696 + + 0 50264538 50239631 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 63 1.24266417982717 1.09982921662864 1.24266417982717 1.09982921662864 1 - - 40860 N Y 3.12804628055249 3.44143830342756 3.12804628055249 0 0 0.115754195662742 N 0 0 N N 0 62 ENSG00000149617 ENSG00000136928 + - 20 9 51925503 100511300 downstream intron AC005220.1 GABBR2 51925198 100090187 - - 0 51897834 100388498 - + Y - 1.93647622852577 N HCC1954 20 20 20 6 1 N - - N SINE SINE 0.557377049180328 1 1 6 0.435646637755502 0.314236919036755 0.435646637755502 0.314236919036755 3 - 0 24506 N N 3.48280442206126 3.3478104969044 3.3478104969044 9 0.0194909993792675 0.0326513075928866 N 0.415037243947859 0.442892613283675 N N 153380 5654 ENSG00000185275 ENSG00000153339 - + Y 18 19614093 27777089 utr3p intron CD24L4 KIAA1012 19611898 27663135 - - 0.442892613283675 19612654 27766564 + - Y - 1.35434413700117 N HCC1954 13 6.6 2 5 1 N - - N - SINE 0 1 1 5 0.45707188223528 0.271386430077198 0.45707188223528 0.271386430077198 1 - 0 24746 Y Y 3.43718223316862 3.55760534744548 3.43718223316862 0 0 0.50057616355924 Y 0 0.987555066079295 N N 0 0 ENSG00000200872 ENSG00000206944 + - 18 18 44255969 43950259 downstream upstream 5S_rRNA U6 44255856 43950153 - - 0 44118547 43965871 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 4 0.521347615674617 0.542772860154395 0.542772860154395 0.521347615674617 2 - - 26087 N Y 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.084374430921274 N 0 0 N N 8831 45068 ENSG00000004897 ENSG00000205336 + + 17 16 42621664 56256445 intron upstream CDC27 GPR56 42552625 56220023 - + 0 42592694 56211646 - + Y 0.755428248231296 - N HCC1954 24 21.0833333333333 20 12 1 N - - N SINE - 1 0 1 12 0.357087407996313 0.599906845433805 0.599906845433805 0.357087407996313 1 0 - 49158 Y Y 3.47336426491055 3.7825841559127 3.47336426491055 0 0 0.268677735882266 Y 0.993883734849618 0.993883734849618 N N 27719 6604 ENSG00000129625 ENSG00000153037 + + 5 5 112285930 112231502 intron coding REEP5 SRP19 112239980 112224892 - + 0 112255201 112231001 - + N 0.261135326182625 - N HCC1954 3 1.7 1 5 1 N - - Y - - 0 0 0 10 1.23552243166724 1.18553019454776 1.23552243166724 1.18553019454776 1 0 - 342 Y Y 3.54400240599166 3.38127338926705 3.38127338926705 273 0 0.00720158839161289 N 0 0.986535986535987 Y N 0 0 ENSG00000222048 ENSG00000129586 + - 11 11 10836196 10836165 intron downstream ZBED5 AC069360.7 10830827 10830921 - - 0 10835987 10813113 - + N 1 - N HCC1954 15 5.25 1 3 1 N - - N - LTR 0 1 1 4 0.478497126715059 0.349945659836387 0.478497126715059 0.349945659836387 1 0 - 27046 Y Y 3.17780074852469 3.353603498043 3.17780074852469 0 0.0031446540880502 0.95590979153352 Y 0.134674178895877 0 N N 23054 0 ENSG00000131149 ENSG00000220991 - + 16 16 84267311 83906889 coding downstream KIAA0182 AC092275.3 84202524 83906768 + + 0 84239660 83962386 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 36 1.19981369086761 1.06412047582901 1.19981369086761 1.06412047582901 1 - - 31200 Y Y 3.47655676017605 3.4267624394105 3.4267624394105 263 0 0.544429252555322 Y 0 0.980273312502353 N N 14776 20207 ENSG00000065534 ENSG00000206527 + - 3 3 125085868 124786616 utr3p upstream MYLK PTPLB 124811586 124693087 - - 0 124812772 124787331 - + N 0.0279545152456471 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 15 0.757025304952183 1.18553019454776 1.18553019454776 0.757025304952183 4 0 - 18372 Y Y 3.61633596425197 3.68783934123363 3.61633596425197 0 0 0.101820057630074 Y 0.991623400952738 0.991623400952738 N N 0 16684 ENSG00000220509 ENSG00000162923 - - 1 1 222829714 222688624 upstream upstream RP11-100E13.2 WDR26 222828759 222639728 + - 0 222770067 222689513 - + N - - N HCC1954 1 1 1 0 1 N - - Y DNA - 1 0 1 13 0.907002016310634 1.16410495006798 1.16410495006798 0.907002016310634 1 - - 2883 N Y 3.26824964015148 3.54193626645188 3.26824964015148 24 0 0.180360737616366 N 0.968553182118476 0.916141818982603 N N 8014 2 ENSG00000149084 ENSG00000138653 - + 11 4 43834736 116254481 utr3p upstream HSD17B12 NDST4 43658719 115968378 + - 0.119489099317331 43834016 116323922 - - Y - - N HCC1954 69 51.75 46 4 1 N 212 18.9249 N - SINE 0 1 1 4 0.549914608314322 0.385654400636018 0.549914608314322 0.385654400636018 1 - - 31900 Y Y 3.46551447180198 3.19872427442695 3.19872427442695 0 0 0.519383849919695 Y 0.879322753607543 0.993648565979344 N N 8254 0 ENSG00000163812 ENSG00000188990 + - 3 3 44992618 44935005 coding intron ZDHHC3 AC098649.2-2 44941663 44934497 - - 0 44943342 44934637 - + N - 1 N HCC1954 2 1.12903225806452 1 4 2 N - - Y - - 0 0 0 31 1.15696320190805 1.24266417982717 1.24266417982717 1.15696320190805 1 - 0 48126 N N 3.66016945000958 3.67849247003875 3.66016945000958 0 0 0.884397111053014 N 0 0 N Y 8224 110930 ENSG00000171444 ENSG00000147677 + - 5 8 112852010 117837243 coding intron MCC EIF3H 112385695 117726237 - - 0 112506814 117740400 - + Y - 0.735060423462682 N HCC1954 1 1 1 0 1 N 528 14.4716 N - - 0 0 0 8 1.05697872766909 0.985561246069823 1.05697872766909 0.985561246069823 4 - 0 24246 N Y 3.51104337473878 3.25256697878875 3.25256697878875 0 0 0.0749165824547932 N 0 0 N N 0 49089 ENSG00000222560 ENSG00000117450 - - 5 1 26048892 45760196 downstream coding U4 PRDX1 26048755 45749295 + - 0 26266849 45757275 - + Y - 3.11556065904221 N HCC1954 5 3.25 1 3 1 N - - N SINE - 1 0 1 4 0.257102933757345 0.292811674556976 0.292811674556976 0.257102933757345 2 - 0 33061 N Y 2.96059718525252 2.97670734662359 2.96059718525252 390 0 0.982831289588247 Y 0 0.992875457875458 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8449 4763 - + N 0.830587017366512 0.925680050044508 N HCC1954 4 2.33333333333333 2 6 9 Y - - N - - 0 0 0 6 1.06412047582901 0.928427260790413 1.06412047582901 0.928427260790413 2 0 0 34951 N N 3.43091076507078 3.6344911504118 3.43091076507078 10 0 0.0707337707341141 N 0.43754565376187 0.142926710494278 N N 7291 0 ENSG00000147996 ENSG00000217091 - - 9 9 169078 67904016 upstream intron CBWD1 RP11-764K9.2 111039 67903302 - - 0.250060871682493 182260 67903404 + + N - 1 Y HCC1954 15 8.125 5 8 1 N 481 5.15597 N - - 0 0 0 8 0.364229156156239 0.635615586233437 0.635615586233437 0.364229156156239 2 - 0 38110 N N 2.84752516064765 3.46232197653647 2.84752516064765 0 0 0.97890015991071 Y 0 0.065201729106628 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 upstream upstream SIPA1L1 SNORD56 71065795 70934807 + + 0.065201729106628 71049039 70856935 - + N - - N HCC1954 1 1 1 0 6 N - - N LTR Low_complexity 1 0.271317829457364 1 38 0.807017542071667 0.921285512630487 0.921285512630487 0.807017542071667 1 - - 8134 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.6391843466231 N 0.235749833256375 0.959058026781591 N N 188 3966 ENSG00000152503 ENSG00000175772 - + 5 2 114544142 110111006 downstream upstream TRIM36 AC013268.5-1 114488377 110103138 - + 0 114280712 110102056 + + Y - - N HCC1954 60 40.36 18 50 1 N 3 26.2442 N LINE - 1 0 1 50 0.442788385915428 1.35693215038599 1.35693215038599 0.442788385915428 3 - - 64 Y Y 3.51207644450867 3.05890521755769 3.05890521755769 267 0 0.166950593473800 Y 0.118358688807133 0.982367173776143 N N 0 20278 ENSG00000223272 ENSG00000186174 - - 11 11 118307394 118286823 upstream upstream SRP_euk_arch BCL9L 118307130 118272059 + - 0 118301182 118294798 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.821301038391519 0.942710757110266 0.942710757110266 0.821301038391519 4 - - 48448 N Y 3.26191384998362 3.48593413659447 3.26191384998362 0 0 0.0269485383068626 N 0.779033270558694 0.803585129385506 N N 81 116 ENSG00000152380 ENSG00000174469 - - 5 7 79873962 147749019 upstream intron FAM151B CNTNAP2 79819556 145444902 + + 0 79817047 147645153 - - Y - 0.502750939666558 N HCC1954 20 17.3333333333333 4 6 1 N - - N LINE SINE 1 1 1 6 0.549914608314322 0.357087407996313 0.549914608314322 0.357087407996313 1 - 0 18969 Y Y 3.66016945000958 3.33680806132368 3.33680806132368 269 0 0.00549653114508564 Y 0 0 N N 10 7970 ENSG00000117507 ENSG00000007933 - + 1 1 169397326 169353583 upstream downstream FMO6P FMO3 169373503 169326660 + + 0 169365480 169356451 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR 1 1 1 4 0.278528178237124 0.39993789695587 0.39993789695587 0.278528178237124 2 - - 31866 Y Y 3.34785034969775 3.65016023140539 3.34785034969775 0 0 0.824413642238908 Y 0.993920164492343 0.987840328984685 N N 3580 0 ENSG00000080822 ENSG00000181828 + + 3 3 99724600 99700165 coding downstream CLDND1 OR5K2 99717008 99699215 - + 0 99718586 99708281 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 9 1.26408942430695 1.25694767614702 1.26408942430695 1.25694767614702 4 - - 6975 N Y 3.2420632466446 3.80400638525155 3.2420632466446 0 0 0.488929369603294 Y 0.195974373685217 0.951998470070759 N N 43 3966 ENSG00000163492 ENSG00000175772 + + 2 2 179623031 110111006 intron upstream CCDC141 AC013268.5-1 179407145 110103138 - + 0 179474292 110102058 - + N 1.34421870013828 - N HCC1954 60 41.4285714285714 40 14 1 N 379 25.2094 N LINE - 1 0 1 14 0.428504889595575 0.949852505270192 0.949852505270192 0.428504889595575 1 0 - 32890 N Y 3.30744275292043 3.49744043328497 3.30744275292043 6 0 0.0573642698620379 N 0 0.627586206896552 N N 0 0 ENSG00000222261 ENSG00000222867 - + 5 3 34562163 78247296 downstream upstream AC114302.3 SRP_euk_arch 34562016 78246999 - + 0.0224137931034483 34454529 78187564 + + Y - - N HCC1954 5 4.42105263157895 2 19 1 N 34 23.3109 N LTR LTR 1 1 1 19 0.39993789695587 0.392796148795944 0.39993789695587 0.392796148795944 1 - - 39933 Y Y 3.50575423470996 3.29383981146661 3.29383981146661 325 0 0.00735883712083985 Y 0 0 N N 4041 0 ENSG00000187720 ENSG00000214727 - - 15 15 69862776 69143405 upstream upstream THSD4 AC013752.10 69176345 69142491 + - 0 69172468 69159385 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.978419497909897 1.02841173502938 1.02841173502938 0.978419497909897 3 - - 1733 N Y 3.49168728493972 3.38759559906577 3.38759559906577 0 0 0.552307214232643 N 0.619806576402321 0.0676208897485493 N N 14402 4 ENSG00000156689 ENSG00000170579 + - 11 18 58368833 3870135 utr5p intron GLYATL2 DLGAP1 58358118 3486030 - - 0.0676208897485493 58368484 3591836 - + Y 0.956449640258661 0.984037726305767 N HCC1954 2 1.2 1 1 1 N - - N - SINE 0 1 1 5 0.678466075192994 0.364229156156239 0.678466075192994 0.364229156156239 2 0 0 39872 Y Y 3.2875921495814 3.52361324642271 3.2875921495814 264 0 0.0441892107280666 Y 0 0.98951355661882 N N 110 5989 ENSG00000166813 ENSG00000140534 + + 15 15 87992583 87972255 coding utr3p KIF7 C15orf42 87972211 87919822 - + 0 87973666 87971418 - + N 1.34983714765012 1.79556254225306 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.621332089913584 0.642757334393363 0.642757334393363 0.621332089913584 1 0 0 44367 N N 3.18615440274303 3.21063179870157 3.18615440274303 1 0 0.247970863708148 N 0 0 N N 0 70 ENSG00000218380 ENSG00000198732 + - 10 14 33387341 69568836 downstream intron RPL7AP53 SMOC1 33386549 69415896 - + 0 33386530 69421822 - - Y - 0.805534767733355 N HCC1954 11 5.875 4 8 1 N - - N - - 0 0 0 8 0.257102933757345 0.34280391167646 0.34280391167646 0.257102933757345 1 - 0 9404 Y Y 3.51952501003312 3.49168728493972 3.49168728493972 369 0 0.0558398128679637 N 0 0.978781064406389 Y N 136 1495 ENSG00000132141 ENSG00000198783 + + 17 17 30312619 30314177 upstream downstream CCT6B ZNF830 30279053 30312678 - + 0 30320640 30314242 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE - 0.532467532467532 0 0.532467532467532 5 0.549914608314322 0.685607823352921 0.685607823352921 0.549914608314322 4 - - 17403 N Y 3.7527243339695 3.32952732966858 3.32952732966858 20 0.079140461215933 0.394212614790845 N 0.0415543575920934 0.859052111410602 N N 548 23977 ENSG00000162654 ENSG00000160691 - - 1 1 89437150 153213476 utr3p utr5p GBP4 SHC1 89420044 153201398 - - 0 89420986 153213349 + + N - - Y HCC1954 39 38.25 37 4 1 N 112 28.782 N SINE - 1 0 1 4 0.278528178237124 0.349945659836387 0.349945659836387 0.278528178237124 2 - - 31925 Y Y 3.31319590126568 3.11761290642523 3.11761290642523 0 0 0.79578860059876 Y 0 0 N N 3918 418 ENSG00000175193 ENSG00000180834 + - 3 3 185085387 185026059 coding upstream PARL MAP6D1 185029870 185016364 - - 0 185033974 185027214 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.949852505270192 1.07840397214886 1.07840397214886 0.949852505270192 4 - - 29342 Y Y 3.48743121468078 3.3414348539432 3.3414348539432 237 0.015535097813579 0.0725738468253955 Y 0.0268507863444573 0 N N 0 3765 ENSG00000210078 ENSG00000007944 + + 6 6 16256655 16256458 upstream intron AL021407.1-1 MYLIP 16256582 16237296 - + 0 16259085 16253528 - + N - 1.80579891325375 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.628473838073511 0.857009779191151 0.857009779191151 0.628473838073511 1 - 0 24703 Y Y 3.64759957832565 3.53039946453785 3.53039946453785 340 0 0.0223039586775828 Y 0.981871657754011 0.987914438502674 N N 2121 3500 ENSG00000075643 ENSG00000134759 - + 18 18 32102682 32008609 upstream downstream MOCOS STATIP1 32021478 31963881 + + 0 32021196 32014351 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 97 1.28551466878673 1.23552243166724 1.28551466878673 1.23552243166724 4 - - 19482 N N 3.61360747730288 3.38296880644625 3.38296880644625 0 0 0.0456698272571974 N 0 0 N N 49089 47 ENSG00000117450 ENSG00000183780 - + 1 1 45760196 232526872 coding intron PRDX1 SLC35F3 45749295 232107447 - + 0 45757256 232524506 + + N - 1.16926786023461 Y HCC1954 21 11.24 1 24 1 N - - N - SINE 0 1 1 25 0.664182578873142 0.378512652476092 0.664182578873142 0.378512652476092 1 - 0 21581 N N 2.89378609696779 3.04596733885829 2.89378609696779 0 0.173558682223748 0.255641287103479 N 0.40665751544269 0.173558682223748 N N 9281 11502 ENSG00000213240 ENSG00000159921 + + 1 9 144003011 36248450 utr3p utr3p NOTCH2NL GNE 143920462 36204430 + - 0.173558682223748 143995500 36206334 + - Y - - N HCC1954 851 812.5 756 4 1 N - - N Simple_repeat SINE 0.977777777777778 1 1 4 0.321378667196682 0.392796148795944 0.392796148795944 0.321378667196682 3 - - 34387 Y Y 2.71782972308943 3.5816815158199 2.71782972308943 321 0 0.0477375542037071 Y 0 0.978638184245661 N N 18794 86 ENSG00000196642 ENSG00000213213 - + 9 9 138855460 138822013 intron intron C9orf86 AL355987.31-3 138822195 138810623 + + 0.978638184245661 138822692 138821475 - + N 0.463032385926216 1.63853719409275 N HCC1954 1 1 1 0 1 N - - Y Low_complexity LTR 0.22289156626506 0.13013698630137 0.22289156626506 5 0.664182578873142 0.549914608314322 0.664182578873142 0.549914608314322 4 0 0 26513 N Y 3.23065023590994 3.18615440274303 3.18615440274303 0 0 0.0666896231319657 N 0 0.980059880239521 N N 11435 0 ENSG00000141429 ENSG00000210272 + + 18 16 31545792 51926076 intron downstream GALNT1 AC079416.4-1 31415001 51925975 + + 0 31485003 51970199 + + Y 0.00997943928545466 - N HCC1954 21 20.5 20 4 1 N - - N LTR - 1 0 1 4 0.442788385915428 0.407079645115797 0.442788385915428 0.407079645115797 1 0 - 34656 Y Y 3.33577499155378 2.92079850272202 2.92079850272202 151 0.00429184549356232 0.0161253243210182 Y 0.149122122512681 0 N N 15728 0 ENSG00000148344 ENSG00000217808 - - 9 9 131555165 131593937 coding upstream PTGES RP11-5J2.2 131540433 131593296 - + 0 131555105 131579402 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 1.1426797055882 0.942710757110266 1.1426797055882 0.942710757110266 2 - - 30446 Y N 3.485365075141 2.85381686522283 2.85381686522283 0 0 0.592785454735694 Y 0 0 N N 57 0 ENSG00000177324 ENSG00000218530 + + X X 18148924 17862864 downstream downstream BEND2 RP1-272E8.1 18090974 17861390 - + 0 18032591 17924107 - + N - - N HCC1954 20 3.26666666666667 1 10 3 N - - Y LINE - 1 0 1 15 0.921285512630487 0.578481600954027 0.921285512630487 0.578481600954027 2 - - 37942 N N 3.44785379918211 3.37287988225536 3.37287988225536 31 0.107440922730683 0.0264655985263486 N 0.0913587771942985 0.107440922730683 N N 936 5254 ENSG00000151338 ENSG00000170142 - + 14 3 37090214 23907792 downstream intron MIPOL1 UBE2E1 36736907 23822443 + + 0.107440922730683 37105946 23888796 - + Y - 1.41324494024521 N HCC1954 20 17.25 9 4 1 N - - N SINE Other 1 1 1 4 0.778450549431962 0.528489363834543 0.778450549431962 0.528489363834543 1 - 0 33075 N N 3.00931858345483 3.56335849579072 3.00931858345483 0 0.490553469783214 0.996321165804738 Y 0.479714181906261 0.533910621291026 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0.533910621291026 13857 9155 - + N 1.02927469145911 0.515874194736157 N HCC1954 2 1.25 1 1 7 N - - N - - 0 0 0 4 1.0069864905496 0.628473838073511 1.0069864905496 0.628473838073511 2 0 0 19514 N Y 3.52208566311286 3.40587876630159 3.40587876630159 249 0 0.119732791107661 N 0.985353177415544 0.956059532246633 N N 1725 2064 ENSG00000196369 ENSG00000196550 - - 1 1 142805834 204321697 coding upstream SRGAP2P2 FAM72A 142627547 204303958 + + 0 142725258 204301916 - - N - - Y HCC1954 2 2 2 7 1 N - - N - - 0 0 0 7 0.528489363834543 0.39993789695587 0.528489363834543 0.39993789695587 4 - - 27411 N Y 3.02030743866642 3.57808779297027 3.02030743866642 0 0 0.913155933717523 Y 0 0.993126059920859 N N 4968 37 ENSG00000104731 ENSG00000154118 + + 16 16 86357056 86289263 utr3p coding KLHDC4 JPH3 86298920 86194000 - + 0 86299182 86287762 - + N - 0.510708934642837 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 9 1.02126998686945 1.04269523134923 1.04269523134923 1.02126998686945 1 - 0 16034 N N 3.34822107205833 2.9920684859889 2.9920684859889 56 0.0678028584392014 0.450317531335184 N 0 0.0109081972171809 N N 154774 0 ENSG00000122566 ENSG00000220375 - - 7 1 26206942 558984 coding intron HNRPA2B1 RP5-857K21.14 26196081 558778 - + 0.0109081972171809 26199795 558821 + - Y - 1 N HCC1954 2 2 2 5 3 N - - N - - 0 0 0 5 0.885576771830856 0.871293275511003 0.885576771830856 0.871293275511003 1 - 0 17801 Y Y 3.5727053669856 3.51576345331414 3.51576345331414 0 0.43910146582905 0.335037232861055 N 0.43910146582905 0.990329335617742 Y N 3984 0 ENSG00000053371 ENSG00000200403 + - 1 1 19511227 19504263 coding downstream AKR7A2 U6 19503046 19504157 - - 0 19505101 19498190 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 11 0.871293275511003 0.621332089913584 0.871293275511003 0.621332089913584 1 - - 6496 Y Y 3.54040868314203 3.60785432895764 3.54040868314203 9 0 0.327768365574943 Y 0.918786549707602 0.992616959064328 N N 138 22339 ENSG00000123999 ENSG00000124006 - - 2 2 220148671 220144430 coding intron INHA OBSL1 220145198 220123708 + - 0 220145590 220142384 - + N - 1.07815621166713 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.857009779191151 0.728458312312478 0.857009779191151 0.728458312312478 3 - 0 3570 N N 3.04790278197696 3.49424793801946 3.04790278197696 0 0 0.609849011437257 N 0 0 N N 49 0 ENSG00000186842 ENSG00000184029 + + 21 21 32870062 38415324 intron intron C21orf77 DSCR4 32866420 38245598 - - 0 32868129 38313454 - - N 4.02835923235156 1 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 38 1.22123893534739 1.10697096478857 1.22123893534739 1.10697096478857 1 0 0 32214 N Y 3.33168675516419 3.70144228268744 3.33168675516419 284 0 0.00509732502427673 N 0.957776318930532 0.983110527572213 N N 0 0 ENSG00000209951 ENSG00000222792 - + 7 3 86960 199408117 upstream upstream AC097646.2-1 U6 86858 199408014 - + 0 116554 199373711 + + Y - - N HCC1954 144 31.8636363636364 9 22 1 N 65 1.11453 N - SINE 0 1 1 22 1.28551466878673 0.635615586233437 1.28551466878673 0.635615586233437 2 - - 399 Y Y 3.55297855482595 3.47695798776018 3.47695798776018 0 0 0.997567397904896 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0 1816504 1814664 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 76 1.32836515774628 1.24266417982717 1.32836515774628 1.24266417982717 1 - - 41695 N N 3.48908677906663 3.3012485241977 3.3012485241977 4 0.00249999999999984 0.0615658642708837 N 0.027753164556962 0 N N 1370 6625 ENSG00000180694 ENSG00000153317 + + 8 8 91727309 131483399 upstream coding TMEM64 ASAP1 91704778 131133535 - - 0 91768766 131318373 - - N - - Y HCC1954 1 1 1 0 1 N - - N LTR - 1 0 1 4 0.871293275511003 0.857009779191151 0.871293275511003 0.857009779191151 1 - - 49443 N N 3.59681204058356 3.59169073442408 3.59169073442408 0 0 0.993530223436654 N 0 0 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 coding downstream TICAM2 AC034236.1 114942238 115326170 - + 0 114989197 115391486 - + N - - N HCC1954 1 1 1 0 5 N - - N - LTR 0 1 1 5 0.507064119354764 0.614190341753658 0.614190341753658 0.507064119354764 4 - - 19506 N N 3.5074097990958 3.47076375903745 3.47076375903745 11 0 0.903849009410586 Y 0.00306748466257678 0.062585843787199 N Y 13137 1725 ENSG00000163486 ENSG00000196369 - + 1 1 204704406 142805834 coding coding SRGAP2 SRGAP2P2 204582820 142627547 + + 0 204623992 142627649 - + N - 0.856895206795462 N HCC1954 6 5.37254901960784 1 152 1 Y - - N - - 0 0 0 153 1.06412047582901 1.03555348318931 1.06412047582901 1.03555348318931 4 - 0 11842 N Y 3.07101108092519 3.54296933622177 3.07101108092519 3 0.00386100386100374 0.37861570336459 N 0.769412269412269 0.870870870870871 N N 1649619 8375 ENSG00000141736 ENSG00000138835 - - 17 9 35138441 115399839 coding intron ERBB2 RGS3 35104766 115262358 + + 0 35125066 115364452 - - Y - 0.284980541367053 N HCC1954 20 11.25 4 16 1 N - - N - SINE 0 1 1 16 0.664182578873142 0.349945659836387 0.664182578873142 0.349945659836387 1 - 0 35094 Y Y 3.3478104969044 3.38805025981237 3.3478104969044 0 0.0855240401245244 0.522062758830404 Y 0.989839156001384 0.979678312002767 N N 636 10592 ENSG00000136936 ENSG00000136937 + + 9 9 99499512 99475851 coding intron XPA NCBP1 99477013 99435526 - + 0 99477592 99456827 - + N - 2.04821698224695 N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.644444444444444 0.644444444444444 5 0.564198104634174 0.642757334393363 0.642757334393363 0.564198104634174 4 - 0 213 N Y 3.40587876630159 3.04587133755734 3.04587133755734 289 0 0.00605646985493524 Y 0.986159169550173 0.993079584775086 N N 34 1353 ENSG00000205867 ENSG00000184545 + - 11 11 1576056 1550035 downstream upstream KRTAP5-2 DUSP8 1575523 1531857 - - 0 1575053 1550873 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.857009779191151 0.949852505270192 0.949852505270192 0.857009779191151 1 - - 3011 N N 2.70587329418536 3.14232091698542 2.70587329418536 2 0.00473933649289093 0.0182186548253018 N 0.931831461403623 0.00473933649289093 N N 10 8014 ENSG00000169169 ENSG00000149084 + + 19 11 54908800 43834736 intron utr3p CPT1C HSD17B12 54886205 43658719 + + 0.00473933649289093 54889159 43834024 + + Y 0.766513995664045 1.56153208144737 N HCC1954 18 6.54545454545455 1 7 1 N - - N SINE - 1 0 1 11 0.499922371194838 0.842726282871298 0.842726282871298 0.499922371194838 1 0 0 568 Y Y 3.57336771439491 3.3022815939676 3.3022815939676 0 0 0.835333144535992 Y 0 0 N Y 4289 193 ENSG00000110497 ENSG00000180423 - + 11 11 46572145 46595353 coding utr5p AMBRA1 HARBI1 46374540 46581124 - - 0 46472330 46595250 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 0.928427260790413 0.778450549431962 0.928427260790413 0.778450549431962 4 - - 10881 N Y 3.70144228268745 3.40129182647542 3.40129182647542 0 0 0.368616929799438 N 0 0.953448559670782 N N 0 317991 ENSG00000218014 ENSG00000171346 - + 6 17 72352330 36932191 intron upstream RP11-263F15.1 KRT15 72351145 36923523 + - 0 72351554 36946570 - - Y 1 - N HCC1954 2 1.14285714285714 1 1 2 N - - N - - 0 0 0 7 0.664182578873142 1.04269523134923 1.04269523134923 0.664182578873142 1 0 - 35133 N Y 3.41103992525442 3.63759035972147 3.41103992525442 4 0.0440917923568057 0.682858711811595 N 0.724067733876191 0.832469695567688 N N 34637 0 ENSG00000197111 ENSG00000220595 + - 12 21 52159872 39465902 coding intron PCBP2 AF129408.11 52132161 39464926 + - 0.7536319052466 52142616 39465258 + + Y - 1 N HCC1954 2 1.28571428571429 1 4 2 N - - N SINE SINE 0.373626373626374 0.2578125 0.373626373626374 14 1.10697096478857 0.657040830713216 1.10697096478857 0.657040830713216 2 - 0 36354 Y Y 2.77288691145959 3.58953130892846 2.77288691145959 220 0 0.116283209481506 Y 0 0 N N 2279 3360 ENSG00000051825 ENSG00000090975 + - 12 12 122272394 122160928 downstream upstream MPHOSPH9 PITPNM2 122203033 122033980 - - 0 122201254 122160989 - + N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.326315789473684 0 0.326315789473684 9 0.678466075192994 0.649899082553289 0.678466075192994 0.649899082553289 1 - - 6802 Y Y 3.07105093371854 3.31951811106439 3.07105093371854 7 0.151483984719366 0.106228157424301 Y 0.345430502497796 0.151483984719366 N N 829 466 ENSG00000163053 ENSG00000153832 + + 2 2 230641863 230586068 downstream coding SLC16A14 FBXO36 230607944 230495262 - + 0.151483984719366 230597911 230569848 - + N - - N HCC1954 2 1.4 1 2 1 N - - Y SINE - 1 0 1 5 0.414221393275723 0.899860268150708 0.899860268150708 0.414221393275723 3 - - 37243 N N 3.4503745994685 3.70466528317649 3.4503745994685 0 0 0.107185140027675 N 0 0.00301204819277123 N N 0 119704 ENSG00000208978 ENSG00000111057 + + 5 12 123018910 51632951 upstream coding AC008541.6 KRT18P19 123018501 51628922 + + 0.00301204819277123 123000650 51631890 + + Y - 0.934267292062685 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.271386430077198 0.442788385915428 0.442788385915428 0.271386430077198 1 - 0 44595 N N 3.59681204058356 3.50425715662364 3.50425715662364 5 0 0.309241950280481 N 0.0252117953730857 0 N N 18316 0 ENSG00000215136 ENSG00000214796 - + 10 4 45259678 125577725 coding downstream AL731567.6 AC097474.3 45189635 125576352 + - 0 45205394 125560869 - - Y - - N HCC1954 21 21 21 9 1 N - - N LINE LTR 1 1 1 9 0.45707188223528 0.671324327033068 0.671324327033068 0.45707188223528 2 - - 34180 Y Y 3.24099032408136 3.71401215437137 3.24099032408136 380 0.103555764411028 0.0547829215114252 Y 0.151049498746867 0 N N 179 30778 ENSG00000196366 ENSG00000148396 - - 9 9 138500339 138491962 coding utr5p C9orf163 SEC16A 138497768 138454370 + - 0 138498740 138491958 - + N 1.33925027930901 78.43 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 43 1.45691662462496 1.23552243166724 1.45691662462496 1.23552243166724 1 0 0 36199 Y Y 3.57696143724454 3.27767621693306 3.27767621693306 304 0 0.0123400482018390 Y 0.993399268037644 0.986798536075288 N N 22666 1823 ENSG00000111684 ENSG00000126749 + + 12 12 6996103 6955232 intron coding LPCAT3 EMG1 6955608 6950348 - + 0 6962424 6954801 - + N 1.21742472556179 3.35458609319782 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.525641025641026 0 0.525641025641026 7 1.05697872766909 1.03555348318931 1.05697872766909 1.03555348318931 4 0 0 5155 Y Y 3.13639993477083 3.62617734898681 3.13639993477083 242 0 0.0231692323103802 Y 0.703154799745709 0 N N 491 25117 ENSG00000153814 ENSG00000106052 + + 7 7 28186962 27835911 utr3p coding JAZF1 TAX1BP1 27836726 27746239 - + 0 27838849 27834923 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.699891319672773 0.649899082553289 0.699891319672773 0.649899082553289 1 - - 16501 N N 3.52271195568076 3.22332965146149 3.22332965146149 0 0 0.0311203790173313 N 0.295601851851852 0 N N 2228 5170 ENSG00000144535 ENSG00000116918 + + 2 1 232916529 229768890 utr3p upstream DIS3L2 TSNAX 232534537 229731022 + + 0 232704310 229725008 + + Y - - N HCC1954 31 23.6428571428571 22 14 1 N - - N SINE LTR 1 1 1 14 0.685607823352921 0.649899082553289 0.685607823352921 0.649899082553289 1 - - 4467 Y Y 2.95530804522369 3.51100352194543 2.95530804522369 273 0 0.0285488435461658 Y 0 0.989728484573845 N N 0 0 ENSG00000209951 ENSG00000223022 + - 7 7 86960 86961 upstream downstream AC097646.2-1 U6 86858 86858 - - 0 93336 84906 - + N - - N HCC1954 238 190.25 144 4 1 N - - Y SINE - 0.0194174757281553 0 0.0194174757281553 4 0.735600060472404 0.678466075192994 0.735600060472404 0.678466075192994 1 - - 18591 Y Y 3.36464578641707 3.2274272354209 3.2274272354209 301 0 0.00876328239392066 Y 0 0.993078626799557 N N 0 1414 ENSG00000201134 ENSG00000143365 + - 1 1 150080937 150070972 intron intron Y_RNA RORC 150080836 150045173 - - 0 150080840 150070259 - + N 1 2.05260414538498 N HCC1954 20 3.375 1 1 1 N - - Y scRNA,Low_complexity - 0.597222222222222 0 0.597222222222222 8 1.02841173502938 1.01412823870953 1.02841173502938 1.01412823870953 1 0 0 42170 Y Y 3.37977631118074 1.7115007445575 1.7115007445575 0 0 0.0414279489855857 Y 0 0 N N 1 4461 ENSG00000124875 ENSG00000169429 - + 4 4 74923340 74828295 upstream downstream CXCL6 IL8 74921277 74825122 + + 0.506493506493506 74899271 74862207 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE Low_complexity 0.634146341463415 0.186274509803922 0.634146341463415 56 0.87843502367093 0.728458312312478 0.87843502367093 0.728458312312478 1 - - 33134 N Y 3.37295958784206 3.20865378744444 3.20865378744444 282 0 0.00739649529170316 Y 0 0.98892828999212 N N 247001 38150 ENSG00000198786 ENSG00000198840 - + MT MT 14149 10405 coding coding MT-ND5 MT-ND3 12338 10060 + + 0 13894 10264 - + N 1.08418755299053 1.7004955602771 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.87843502367093 0.735600060472404 0.87843502367093 0.735600060472404 3 0 0 5145 N N 3.57273587220914 3.71976530271662 3.57273587220914 16 0 0.103308141086695 Y 0 0 N N 717 56725 ENSG00000198750 ENSG00000077809 + + 7 7 74705533 73812956 coding coding AC118138.2-2 GTF2I 74645565 73709966 - + 0 74705221 73782545 - + N - - N HCC1954 15 6.5 2 6 1 N - - N Low_complexity - 0.0458015267175573 0 0.0458015267175573 6 0.592765097273879 0.778450549431962 0.778450549431962 0.592765097273879 2 - - 8490 N Y 3.4944157718888 3.69255941980899 3.4944157718888 65 0.679414056412654 0.389414316709061 N 0.948013090229079 0.939348605267259 N N 103859 0 ENSG00000108953 ENSG00000213650 + - 17 7 1250267 56604450 coding intron YWHAE AC092447.5 1194595 56603093 - - 0.679414056412654 1250091 56604089 - + Y 1.2244694610651 1 N HCC1954 2 1.0625 1 2 1 N - - N - - 0 0 0 32 1.09268746846872 0.657040830713216 1.09268746846872 0.657040830713216 3 0 0 33766 N N 3.28296535696188 2.89930591536628 2.89930591536628 0 0 0.999975314671585 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8367 14362 - + N - 1.03536010558427 N HCC1954 4 1.85714285714286 1 12 10 N 189 4.09957 N - - 0 0 0 21 1.26408942430695 1.32836515774628 1.32836515774628 1.26408942430695 2 - 0 13747 Y Y 3.45653832296769 3.66592259835483 3.45653832296769 429 0 0.00859856414591942 Y 0 0.981409894453373 N N 10 238 ENSG00000211644 ENSG00000211643 - + 22 22 21007325 21003581 upstream downstream D87018.1-1 IGLV5-52 21006864 21003021 + + 0 21005750 21003734 - + N - - N HCC1954 2 1.1 1 1 1 N - - Y - - 0 0 0 10 1.34979040222606 1.48548361726466 1.48548361726466 1.34979040222606 4 - - 38141 N Y 3.61360747730289 2.56910487540276 2.56910487540276 0 0 0.999258654271503 Y 0.374149659863946 0.981034838177695 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 upstream upstream SIPA1L1 SNORD56 71065795 70934807 + + 0 71049213 70857651 - + N - - N HCC1954 1 1 1 0 6 N - - N LTR Low_complexity 1 0.377777777777778 1 22 0.749883556792257 0.964136001590045 0.964136001590045 0.749883556792257 4 - - 26802 Y Y 3.09552832967708 3.46657804679541 3.09552832967708 340 0 0.0267261566382659 Y 0.994100243647755 0.98820048729551 N N 1962 1644 ENSG00000140939 ENSG00000102878 - + 16 16 65767125 65761349 upstream downstream NOL3 HSF4 65765371 65754858 + + 0 65765266 65762861 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 6 1.02126998686945 0.956994253430118 1.02126998686945 0.956994253430118 4 - - 21677 N N 3.46448140203209 3.39487633072086 3.39487633072086 1 0 0.259250067470535 N 0 0 N N 2752 85100 ENSG00000162852 ENSG00000148303 - + 1 9 244898484 135208102 intron coding C1orf71 RPL7A 244796386 135204890 + + 0 244862163 135208030 - + Y 1.2443699952896 - N HCC1954 11 4.1304347826087 3 46 1 N - - N - - 0 0 0 46 0.271386430077198 0.599906845433805 0.599906845433805 0.271386430077198 1 0 - 19379 N Y 3.56658149627977 3.47080361183081 3.47080361183081 0 0 0.494917237032507 N 0.018308080808081 0.962242618492618 N N 0 0 ENSG00000207106 ENSG00000208696 + + 1 1 143022733 147554054 upstream upstream U1 AL356957.27-7 143022570 147553983 - - 0 143037387 147557824 - - N - - Y HCC1954 30 11.25 5 4 1 N 159 13.0875 N - LTR 0 1 1 4 0.628473838073511 0.678466075192994 0.678466075192994 0.628473838073511 2 - - 23071 N N 3.09087103183403 3.54040868314203 3.09087103183403 7 0 0.0916135934246785 N 0 0 N N 3891 5278 ENSG00000166295 ENSG00000143375 + + 10 1 73665622 149777789 intron upstream C10orf104 CGN 73645812 149750497 + + 0 73645953 149730437 + + Y 0.744979490524871 - N HCC1954 27 21.4 20 5 1 N - - N - SINE,SINE 0 1 1 5 0.471355378555133 0.521347615674617 0.521347615674617 0.471355378555133 1 0 - 36572 Y Y 3.45976132345673 3.45976132345673 3.45976132345673 77 0 0.985103475956958 Y 0.017228868202268 0.971305952356271 N N 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 utr5p coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6321453 6328155 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 16 1.52119235806429 1.03555348318931 1.52119235806429 1.03555348318931 1 - - 16242 N N 3.64127736852694 2.93446422490813 2.93446422490813 1 0 0.0224488713670492 N 0 0 N N 4543 30801 ENSG00000132680 ENSG00000144063 - + 1 2 154170814 110231432 utr3p utr3p KIAA0907 MALL 154149460 110198738 - - 0 154151826 110199546 + - Y - - N HCC1954 39 36.75 35 4 1 N - - N SINE Low_complexity 1 0.123188405797101 1 4 0.314236919036755 0.842726282871298 0.842726282871298 0.314236919036755 0 - - 46393 N Y 3.47076375903745 3.53146303953127 3.47076375903745 261 0 0.063816371682581 N 0.852419469277707 0.852419469277707 N N 3966 2827 ENSG00000175772 ENSG00000119574 - - 2 19 110111006 63722733 coding intron AC013268.5-1 ZBTB45 110103138 63716711 + - 0.594153540513694 110103264 63720853 - + Y 1.158319818327 8.55053704756341 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.278528178237124 0.385654400636018 0.385654400636018 0.278528178237124 2 0 0 42426 Y N 3.63296356710195 3.23999710710482 3.23999710710482 8 0.0821165566277298 0.0588271087550421 Y 0.0821165566277298 0.0594527679024887 N N 5644 31588 ENSG00000109686 ENSG00000145425 + + 4 4 152367022 152245252 intron coding SH3D19 RPS3AP47 152260886 152240204 - + 0.0594527679024887 152280187 152245087 - + N 0.510320692487037 - N HCC1954 6 5 3 5 1 N - - Y Simple_repeat - 0.0165289256198347 0 0.0165289256198347 5 0.835584534711372 0.871293275511003 0.871293275511003 0.835584534711372 1 0 - 18344 Y Y 2.79309465679006 3.42254622194492 2.79309465679006 313 0 0.00106176811270797 Y 0 0.983386581469648 N N 6790 67 ENSG00000066136 ENSG00000181295 - - 1 1 41009864 40930268 utr5p downstream NFYC AL031289.1-2 40929965 40929882 + - 0 40930284 40925962 - + N 0.775895646660875 - N HCC1954 4 1.5 1 4 1 N - - Y - SINE 0 1 1 18 0.821301038391519 0.892718519990782 0.892718519990782 0.821301038391519 1 0 - 48768 N N 3.33208798274832 3.44871903508266 3.33208798274832 0 0 0.0266865002209969 N 0 0 N N 5961 9344 ENSG00000113456 ENSG00000106780 + - 5 9 34954139 122516457 utr3p intron RAD1 MEGF9 34938268 122402912 - - 0 34944624 122510351 - + Y - 1.40544874458423 N HCC1954 21 13.5 9 4 1 N - - N - SINE,SINE 0 1 1 4 0.642757334393363 0.292811674556976 0.642757334393363 0.292811674556976 0 - 0 32714 N Y 2.96595182135875 3.48908677906663 2.96595182135875 124 0 0.416475651241203 N 0.944941249870022 0.938823610966691 N N 95 1157 ENSG00000215837 ENSG00000185986 - + 3 5 196900773 1646257 coding utr3p AC069513.28-2 AC091849.2 196900191 1625243 + - 0 196900585 1625297 - - Y 0.999453193350831 - N HCC1954 8 3.38775510204082 2 49 1 N - - N LINE - 0.738636363636364 0 0.738636363636364 49 1.25694767614702 1.2783729206268 1.2783729206268 1.25694767614702 4 0 - 36396 Y Y 3.08524586456477 3.44256465915329 3.08524586456477 236 0 0.00438632538670947 Y 0.961701434159061 0.987233811386354 N N 224 36 ENSG00000090612 ENSG00000214029 - - 12 12 132246120 132208490 upstream upstream ZNF10 AC026786.5 132217286 132206974 + - 0 132216887 132208684 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.707033067832699 0.978419497909897 0.978419497909897 0.707033067832699 1 - - 44331 N N 3.51952501003312 3.71720464963688 3.51952501003312 2 0 0.079307493962779 N 0 0 N N 3891 0 ENSG00000166295 ENSG00000213703 - - 10 12 73665622 31296800 utr5p downstream C10orf104 AC024940.39-1 73645812 31296190 + - 0 73653652 31284755 - + Y - - N HCC1954 20 16.6 3 5 1 N - - N - SINE 0 1 1 5 0.728458312312478 0.299953422716903 0.728458312312478 0.299953422716903 2 - - 5051 N N 3.46232197653647 3.66592259835483 3.46232197653647 0 0 0.987412583366956 Y 0 0 N N 28646 3396 ENSG00000164880 ENSG00000188191 + - 7 7 1510772 733813 coding intron INTS1 PRKAR1B 1476439 555361 - - 0 1500978 723009 - + N - 0.636992906513447 N HCC1954 1 1 1 0 3 N 22 4.15045 N - - 0 0 0 24 0.971277749749971 0.956994253430118 0.971277749749971 0.956994253430118 4 - 0 27109 N Y 3.63874722067073 3.60099775282561 3.60099775282561 0 0 0.292363113855109 N 0.814305084745763 0 N N 6328 24 ENSG00000167508 ENSG00000140678 - + 16 16 87257019 31301819 coding utr3p MVD ITGAX 87245849 31274010 - + 0 87252629 31301210 + + N - - Y HCC1954 35 30.4 23 5 1 N - - N - SINE 0 1 1 5 0.578481600954027 0.328520415356608 0.578481600954027 0.328520415356608 3 - - 24486 N N 3.54296933622177 3.60256518892881 3.54296933622177 0 0 0.121018269016032 N 0 0 N N 10593 168 ENSG00000134779 ENSG00000197646 - + 18 9 32663156 5565421 coding intron C18orf10 PDCD1LG2 32630033 5500579 - + 0 32634172 5525228 + + Y - 1.36099497117411 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.871293275511003 0.749883556792257 0.871293275511003 0.749883556792257 2 - 0 30533 Y Y 3.59784511035345 3.49015970162987 3.49015970162987 0 0 0.306364483949772 Y 0 0.990518145584225 N N 604 2324 ENSG00000168939 ENSG00000185973 - - X X 154665311 154495791 utr5p intron SPRY3 TMLHE 154650645 154372967 + - 0 154650815 154495499 - + N 1.27997993255586 0.628734583390829 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.428504889595575 0.807017542071667 0.807017542071667 0.428504889595575 1 0 0 30314 Y Y 3.04128439773117 3.329991337985 3.04128439773117 280 0 0.0863452971047095 Y 0.814225181598063 0.983111380145279 N N 6 0 ENSG00000102128 ENSG00000208964 - + X X 102079884 101951770 upstream downstream RAB40AL AL590407.8-9 102078856 101951702 + + 0 102025727 102006736 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 1.0069864905496 0.814159290231593 1.0069864905496 0.814159290231593 4 - - 9766 Y Y 3.33168675516419 3.43312450200257 3.33168675516419 340 0 0.214970182028837 Y 0 0.923303167420815 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron coding C17orf76 C17orf45 16286053 16283081 - + 0 16306993 16285115 - + N 3.43189971253672 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 5 0.435646637755502 0.642757334393363 0.642757334393363 0.435646637755502 1 0 - 30597 N Y 3.24471718568018 3.10187346741475 3.10187346741475 0 0 0.087015099742939 Y 0 0 N N 0 16 ENSG00000217748 ENSG00000198930 + + X X 151704649 151660174 upstream utr5p U82671.12 CSAG1 151703833 151653884 - + 0 151710571 151655146 - + N - - N HCC1954 2 1.125 1 1 1 N - - N LINE,LINE,LINE Low_complexity 0.756302521008403 0.24 0.756302521008403 8 0.849868031031224 0.357087407996313 0.849868031031224 0.357087407996313 2 - - 39812 Y Y 3.18465732465672 3.56591914887046 3.18465732465672 171 0 0.0245167492647305 Y 0.829573934837093 0.985797827903091 N N 3186 10214 ENSG00000092531 ENSG00000103994 - - 15 15 40612548 40537022 upstream upstream SNAP23 ZFP106 40575127 40492314 + - 0 40570492 40545596 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 39 0.942710757110266 0.507064119354764 0.942710757110266 0.507064119354764 2 - - 47631 N Y 3.34252135687557 3.25360004855864 3.25360004855864 0 0 0.23072653358492 N 0.848935786435786 0.987914862914863 N N 14186 770 ENSG00000171570 ENSG00000197446 + + 19 19 46006176 46326121 coding intron EGLN2 CYP2F1 45996959 46312193 + + 0 45999158 46319412 + + N 0.880817265657256 1.04469508096349 Y HCC1954 2 2 2 88 1 N - - N - - 0 0 0 88 1.24266417982717 1.26408942430695 1.26408942430695 1.24266417982717 1 0 0 5049 N N 3.29231222815676 3.45872825368684 3.29231222815676 0 0 0.82674432160205 Y 0 0.0437387387387387 N N 28646 9342 ENSG00000164880 ENSG00000164818 + + 7 7 1510772 795716 coding intron INTS1 HEATR2 1476439 732864 - + 0.0437387387387387 1499959 742216 - + N - 0.730643023203145 N HCC1954 7 1.60606060606061 1 8 1 N 22 4.15045 N - LINE 0 1 1 33 1.12839620926835 1.05697872766909 1.12839620926835 1.05697872766909 3 - 0 18119 N Y 3.53717633508317 3.60000453584907 3.53717633508317 0 0 0.88900224652626 Y 0.346571230662665 0.983664280766567 N N 0 10857 ENSG00000218025 ENSG00000085832 + - 1 1 51833157 51757583 downstream intron RP11-191G24.2 EPS15 51800126 51592523 - - 0 51799142 51756706 - + N - 1.29050686031236 N HCC1954 1 1 1 0 2 N - - N SINE,SINE - 0.436507936507937 0 0.436507936507937 29 0.899860268150708 1.02126998686945 1.02126998686945 0.899860268150708 4 - 0 41519 N Y 3.43358851031899 3.38912318237562 3.38912318237562 0 0 0.890510027494783 Y 0 0.984312305789363 N N 0 0 ENSG00000221176 ENSG00000207110 - + 8 8 129130666 129080722 downstream upstream hsa-mir-1207 U1 129130580 129080559 + + 0 129177946 129070719 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 16 0.942710757110266 0.985561246069823 0.985561246069823 0.942710757110266 4 - - 13322 N Y 3.33151892129485 3.63296356710195 3.33151892129485 0 0 0.483374865207414 N 0.730785472972973 0.825010557432432 N N 44336 9158 ENSG00000124486 ENSG00000100350 + - X 22 40980776 35233033 intron downstream USP9X FOXRED2 40829832 35214235 + - 0.825010557432432 40927320 35213918 + + Y 1.08887396144597 - N HCC1954 5 4.25 3 4 1 N - - N SINE SINE 1 0.207547169811321 1 4 0.357087407996313 0.378512652476092 0.378512652476092 0.357087407996313 1 0 - 4034 N Y 3.76170048280379 3.53039946453785 3.53039946453785 265 0 0.00767310579581548 Y 0.825660377358491 0.991698113207547 N N 5753 5753 ENSG00000136280 ENSG00000136280 - + 7 7 45082593 45082593 upstream upstream CCM2 CCM2 45006312 45006312 + + 0 45001155 44998975 - + N - - N HCC1954 3 1.11764705882353 1 1 1 N - - N LTR,LTR Other,LTR 0.627906976744186 0.952380952380952 0.952380952380952 17 0.921285512630487 0.899860268150708 0.921285512630487 0.899860268150708 2 - - 5282 N Y 3.51360402781852 3.56911164413597 3.51360402781852 0 0 0.680615287516532 N 0.901624945103206 0.877031181379007 N N 3120 147 ENSG00000128581 ENSG00000179082 + + 7 9 100751750 131127005 utr3p downstream RABL5 C9orf106 100743369 131123116 - + 0 100744043 131144143 - + Y - - N HCC1954 35 28.7222222222222 21 18 1 N - - N SINE - 1 0 1 18 0.371370904316165 0.814159290231593 0.814159290231593 0.371370904316165 4 - - 9942 Y Y 3.57167229721571 3.29545552305911 3.29545552305911 247 0 0.999993871872034 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 utr5p utr3p GSDMB ORMDL3 35314374 35330822 - - 0 35327102 35332219 + - N - - N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 30 1.19267194270768 1.44977487646503 1.44977487646503 1.19267194270768 1 - - 34240 Y Y 3.39065076568547 3.53871326596283 3.39065076568547 262 0.00381679389312972 0.361781437336567 Y 0.991485613623018 0.982971227246036 N N 96280 22394 ENSG00000099219 ENSG00000107036 + + 9 9 5823081 5766555 utr3p downstream ERMP1 KIAA1432 5774571 5619120 - + 0 5777061 5769055 - + N 0.714605616367404 - N HCC1954 1 1 1 0 2 N - - Y - SINE,LINE 0 0.5 0.5 13 0.949852505270192 0.828442786551446 0.949852505270192 0.828442786551446 4 0 - 41343 N Y 3.50000108636471 3.26824964015148 3.26824964015148 26 0 0.106438913821171 N 0.975715341569 0.805722732552001 N N 0 0 ENSG00000209923 ENSG00000219531 + - 5 20 8672285 21417263 downstream downstream AC091953.3-1 RP5-984P4.1 8672217 21416882 - - 0.295744905501003 8485633 21416224 - + Y - - N HCC1954 69 51.75 46 4 1 N 452 25.6411 N SINE - 1 0 1 4 0.45707188223528 0.421363141435649 0.45707188223528 0.421363141435649 1 - - 34259 Y Y 3.44359772892318 3.58486466351559 3.44359772892318 244 0 0.197765342025875 Y 0 0 N N 147 0 ENSG00000179082 ENSG00000220992 - - 9 9 131127005 131032817 upstream upstream C9orf106 AL158151.16-2 131123116 131032672 + - 0 131080509 131076329 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 0.528489363834543 0.742741808632331 0.742741808632331 0.528489363834543 2 - - 43944 N N 3.67849247003875 3.10078696448237 3.10078696448237 0 0.0421865715983364 0.088294320279323 N 0.0667458902753022 0 N N 0 6328 ENSG00000218641 ENSG00000167508 - + 10 16 28766013 87257019 upstream coding RP11-351M16.1 MVD 28765136 87245849 + - 0 28761605 87251345 - - Y - - N HCC1954 7 2.5 1 1 1 N - - N SINE - 1 0 1 4 0.292811674556976 0.549914608314322 0.549914608314322 0.292811674556976 2 - - 42153 Y Y 3.59784511035345 3.40016547074969 3.40016547074969 0 0 0.72177548078597 Y 0 0.142249284718656 N N 0 0 ENSG00000200521 ENSG00000221618 + - 4 4 158908715 158728837 upstream upstream Y_RNA AC093817.3 158908615 158728750 - - 0.142249284718656 158964404 158817935 - + N - - N HCC1954 2 1.02857142857143 1 1 1 N - - Y LINE LTR 1 1 1 35 1.15696320190805 0.985561246069823 1.15696320190805 0.985561246069823 4 - - 33316 N Y 3.49168728493972 3.1776727674487 3.1776727674487 340 0 0.992164195544788 Y 0 0.992023529411765 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8749 5253 - + N 0.556575370833566 - N HCC1954 4 3.11111111111111 2 9 9 N - - N - - 0 0 0 9 1.33550690590621 1.17838844638783 1.33550690590621 1.17838844638783 2 0 - 25120 Y Y 3.45400817511148 3.69106234172268 3.45400817511148 133 0 0.189690778210517 Y 0.993441358024691 0.993441358024691 N N 2873 2546 ENSG00000136146 ENSG00000136159 + + 13 13 47567268 47519283 coding downstream MED4 NUDT15 47548093 47509704 - + 0 47551982 47525629 - + N - - N HCC1954 4 1.5 1 1 2 N - - Y - SINE 0 0.727941176470588 0.727941176470588 6 0.985561246069823 0.778450549431962 0.985561246069823 0.778450549431962 1 - - 41871 N N 3.40847927217468 3.62568283544685 3.40847927217468 8 0 0.863324029930824 N 0.260818195244425 0.287697533599173 N N 29840 30 ENSG00000164830 ENSG00000212993 + + 8 8 107834093 128498621 intron upstream OXR1 POU5F1P1 107739270 128497039 + + 0.341456210308669 107754500 128196688 + + N 1.03655686692363 - Y HCC1954 20 4.8 1 1 4 N 607 3.86243 N LTR,LTR - 0.842105263157895 0 0.842105263157895 5 0.814159290231593 0.414221393275723 0.814159290231593 0.414221393275723 2 0 - 41535 Y Y 3.68680627146374 3.53362246502689 3.53362246502689 152 0 0.0127208952861804 Y 0.982872050816697 0.982872050816697 N N 971 118 ENSG00000176731 ENSG00000133740 + + 8 8 86319855 86314003 utr5p downstream AC011773.9 E2F5 86316756 86276871 - + 0 86319811 86314112 - + N 0.673894820018603 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 16 0.528489363834543 0.535631111994469 0.535631111994469 0.528489363834543 3 0 - 38176 N Y 2.94237016652429 3.485365075141 2.94237016652429 303 0 0.06771399991275 Y 0 0 N N 0 0 ENSG00000178069 ENSG00000178069 + - 14 14 91110709 91110709 upstream upstream AL133373.5 AL133373.5 91110277 91110277 - - 0 91113771 91111623 - + N - - N HCC1954 3 1.6 1 2 1 N - - N LTR,LTR LTR 0.655172413793103 1 1 5 0.985561246069823 0.964136001590045 0.985561246069823 0.964136001590045 4 - - 31273 N Y 3.329991337985 3.36460593362372 3.329991337985 216 0 0.361223604997626 Y 0.88940329218107 0.989945753834643 N N 763 95 ENSG00000205814 ENSG00000215837 - + 3 3 196924416 196900773 intron downstream AC069513.28-3 AC069513.28-2 196912000 196900191 + + 0 196920185 196900845 - + N 3.4479945631077 - N HCC1954 3 2.25 2 4 4 N - - N - LINE 0 0.885496183206107 0.885496183206107 4 0.657040830713216 0.792734045751814 0.792734045751814 0.657040830713216 3 0 - 31634 Y Y 3.47336426491055 3.51525959220437 3.47336426491055 0 0 0.516425703821244 Y 0.993609227651781 0.993609227651781 N Y 168 139 ENSG00000144649 ENSG00000206552 - + 3 3 43076707 42959283 utr5p coding C3orf41 C3orf41 42995833 42952856 + + 0 43048763 42958567 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 1.18553019454776 1.18553019454776 1.18553019454776 1.18553019454776 4 - - 7523 N N 3.70512929149291 3.41315949795669 3.41315949795669 0 0 0.905762294742812 Y 0.106124686716792 0 N Y 8684 2286 ENSG00000055044 ENSG00000082146 - + 2 2 202876627 202053819 coding coding NOP58 STRADB 202838760 202024637 + + 0 202870347 202046044 - + N - 3.07171143089077 N HCC1954 2 1.76536312849162 1 137 1 Y 512 4.03905 N - - 0 0 0 179 1.32122340958636 0.956994253430118 1.32122340958636 0.956994253430118 4 - 0 20462 N N 3.24165267149067 1.73922825884065 1.73922825884065 0 0 0.0404963141075625 N 0 0.00307692307692331 N N 0 4 ENSG00000207623 ENSG00000184486 + + 1 6 207672210 99393381 upstream coding hsa-mir-205 POU3F2 207672101 99389301 + + 0.00307692307692331 207670645 99389717 + + Y - 0.920642893018584 N HCC1954 2 1.1 1 1 1 N - - N - Simple_repeat 0 1 1 10 0.542772860154395 0.414221393275723 0.542772860154395 0.414221393275723 1 - 0 47912 N N 3.62824348852659 3.35616415112274 3.35616415112274 0 0 0.99907672806705 N 0 0 N N 12549 0 ENSG00000087206 ENSG00000212451 + + 5 8 176366358 127753081 coding downstream UIMC1 U11 176264612 127752949 - + 0 176302942 128113267 - + Y 0.856623788651406 - N HCC1954 1 1 1 0 5 N 573 7.11156 N - SINE,SINE 0 0.786127167630058 0.786127167630058 103 1.09982921662864 1.23552243166724 1.23552243166724 1.09982921662864 4 0 - 36607 Y Y 3.69937614314766 3.25616070163838 3.25616070163838 129 0 0.443855434764320 Y 0 0.926500143554407 N N 35326 55227 ENSG00000111321 ENSG00000111319 - - 12 12 6370994 6354976 coding upstream LTBR SCNN1A 6363595 6326276 + - 0 6364110 6355162 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.585623349113953 0.714174815992626 0.714174815992626 0.585623349113953 2 - - 2624 N N 3.49744043328497 3.8097595335968 3.49744043328497 0 0 0.23059853970529 N 0 0.0854845801143143 N N 10635 21198 ENSG00000048649 ENSG00000137815 + - 11 15 77209528 39563053 intron intron RSF1 RTF1 77054923 39496594 - + 0.0854845801143143 77123881 39506048 - - Y 1.29167088559693 0.624287980678544 N HCC1954 14 9 4 4 1 N - - N - SINE 0 1 1 4 0.314236919036755 0.28566992639705 0.314236919036755 0.28566992639705 2 0 0 29578 N N 3.4780843434859 3.62617734898681 3.4780843434859 3 0 0.675939158038785 N 0 0.0304307116104869 Y N 736 95833 ENSG00000204622 ENSG00000204525 - - 6 6 30085708 31432935 coding coding HLA-J HLA-C 30082339 31344505 + - 0.0304307116104869 30082717 31347756 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.385654400636018 0.707033067832699 0.707033067832699 0.385654400636018 3 - - 37986 N Y 3.35633198499208 3.54552998930151 3.35633198499208 1 0 0.0351603309272158 N 0.566330414921964 0.97202131709174 N N 1054 1294 ENSG00000187621 ENSG00000144681 - + 14 3 95228718 36564500 utr5p coding TCL6 STAC 95186588 36397101 + + 0 95186798 36460135 - + Y - 1.36990340242264 N HCC1954 23 21.6 14 10 1 N - - N LTR,LTR - 1 0 1 10 0.564198104634174 0.521347615674617 0.564198104634174 0.521347615674617 1 - 0 4079 Y Y 3.58849823915857 3.29855989004197 3.29855989004197 290 0 0.084036521404508 Y 0 0.985344827586207 N N 0 0 ENSG00000206634 ENSG00000203448 - - 7 7 64858081 64832435 upstream upstream SNORA22 AC104057.4 64857948 64830585 + - 0 64853312 64834503 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.392796148795944 1.04983697950916 1.04983697950916 0.392796148795944 2 - - 30986 N Y 3.6314359837921 3.4797797606651 3.4797797606651 0 0 0.114672358515601 N 0 0.911388888888889 N N 128 10428 ENSG00000204385 ENSG00000114346 + + 6 3 31954802 174021957 utr3p intron SLC44A4 ECT2 31938948 173951207 - + 0 31939077 173951474 - + Y - 0.443838089061747 N HCC1954 34 31.625 29 8 1 N - - N SINE - 1 0 1 8 0.39993789695587 0.642757334393363 0.642757334393363 0.39993789695587 2 - 0 38129 Y Y 3.28871850530713 3.64231043829683 3.28871850530713 337 0 0.00173752457964838 Y 0 0.985550251580441 N N 5143 9623 ENSG00000197119 ENSG00000100811 + + 14 14 99842613 99814557 utr3p downstream SLC25A29 YY1 99827201 99774855 - + 0 99827513 99816285 - + N 0.624684471519607 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.914143764470561 0.785592297591888 0.914143764470561 0.785592297591888 1 0 - 33136 Y N 3.42953077915294 3.11704384497176 3.11704384497176 0 0 0.99994668109323 N 0 0 Y N 247001 59837 ENSG00000198786 ENSG00000198695 - - MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 13062 14632 - + N 0.836448317744016 2.05254252436398 N HCC1954 2 1.11111111111111 1 4 7 N 189 4.09957 N - - 0 0 0 36 1.26408942430695 0.721316564152552 1.26408942430695 0.721316564152552 2 0 0 9267 N N 3.50744965188915 3.684245618384 3.50744965188915 0 0 0.852345392493067 N 0 0 N N 149 5791 ENSG00000161381 ENSG00000133195 + + 17 17 34561298 68600427 intron downstream PLXDC1 SLC39A11 34473083 68153684 - - 0 34520775 68099936 - - N 2.76147619998736 - Y HCC1954 1 1 1 0 2 N - - N LINE - 0.148936170212766 0 0.148936170212766 6 0.671324327033068 0.821301038391519 0.821301038391519 0.671324327033068 1 0 - 31387 N Y 3.15425894648358 3.55025006787687 3.15425894648358 301 0 0.0644035816975497 Y 0 0.980066445182724 N N 298 7313 ENSG00000182983 ENSG00000181061 - - 3 3 42933958 42820986 intron upstream ZNF662 HIGD1D 42922406 42800797 + - 0 42925150 42825988 - + N 0.335014920371209 - N HCC1954 1 1 1 0 3 N - - N - LTR 0 1 1 16 0.857009779191151 0.649899082553289 0.857009779191151 0.649899082553289 3 0 - 7016 Y Y 3.59528445727371 3.57489529770476 3.57489529770476 251 0 0.0357679852514905 Y 0.0132064335251587 0.990777630219861 N N 13698 5800 ENSG00000138031 ENSG00000138092 + + 2 2 24995559 24898749 coding intron ADCY3 CENPO 24895545 24869518 - + 0 24900776 24894215 - + N 0.644926614407127 1.31914077040737 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.771308801272036 0.471355378555133 0.771308801272036 0.471355378555133 1 0 0 23121 N Y 3.79209886097693 3.55401162459584 3.55401162459584 158 0.0521908471275561 0.00875554956184665 N 0.0521908471275561 0.908276533592989 N N 4675 182 ENSG00000117505 ENSG00000123243 - + 1 10 93600732 7748940 upstream utr3p DR1 ITIH5 93584066 7641641 + - 0.159201557935735 93575549 7641907 - - Y - - N HCC1954 22 20.6 18 5 1 N - - N SINE SINE 0.8 1 1 5 0.464213630395207 0.335662163516534 0.464213630395207 0.335662163516534 1 - - 29601 N Y 3.3755202409218 3.40744620240479 3.3755202409218 2 0 0.656717767501073 Y 0 0 N N 6455 0 ENSG00000118418 ENSG00000201464 - + 6 6 80001125 80068502 coding upstream HMGN3 Y_RNA 79967685 80068399 - - 0 79981458 80078804 + - N - - N HCC1954 2 1.5625 1 9 1 N - - N - LTR 0 1 1 16 1.23552243166724 0.785592297591888 1.23552243166724 0.785592297591888 4 - - 47431 N Y 3.61720120015252 3.03486890197662 3.03486890197662 275 0.836802507836991 0.0038345649927195 Y 0.93987460815047 0.836802507836991 N N 3678 2375 ENSG00000198466 ENSG00000178935 - - 19 19 63068299 63018093 utr5p upstream ZNF587 ZNF552 63053081 63010262 + - 0 63053203 63023076 - + N - - N HCC1954 3 2.16666666666667 2 6 2 N - - N - - 0 0 0 6 0.899860268150708 0.885576771830856 0.899860268150708 0.885576771830856 2 - - 12725 N Y 3.45972147066338 3.58527523866953 3.45972147066338 0 0 0.878466953040075 N 0.0662350597609564 0.750996015936255 N N 4483 10 ENSG00000121289 ENSG00000184650 + + 19 17 38154709 8190088 intron upstream CCDC123 ODF4 38061748 8183913 - + 0 38153644 8179443 - + Y 0.981511122534271 - N HCC1954 2 1.14285714285714 1 1 1 N - - N SINE,LINE SINE 0.566037735849057 1 1 7 0.378512652476092 0.299953422716903 0.378512652476092 0.299953422716903 3 0 - 3813 N Y 3.60256518892881 3.37808089400154 3.37808089400154 237 0.954737245876486 0.0473818741203712 N 0.954737245876486 0.93210586881473 N N 0 4749 ENSG00000208307 ENSG00000156162 - + 7 8 145325416 95873238 upstream coding AC073308.4 DPY19L4 145325354 95801327 + + 0.230533179900268 144911350 95807845 - + Y - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 14 0.478497126715059 0.535631111994469 0.535631111994469 0.478497126715059 3 - - 19040 Y Y 3.53568860456667 3.35872480420248 3.35872480420248 0 0 0.661904734012078 Y 0 0 N Y 132 2752 ENSG00000143653 ENSG00000162852 - + 1 1 244998060 244898484 coding utr5p SCCPDH C1orf71 244954001 244796386 + + 0 244956817 244796588 - + N 0.157133225458468 0.538702307158656 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 0.835584534711372 1.0069864905496 1.0069864905496 0.835584534711372 4 0 0 26902 Y Y 3.38759559906577 3.41319935075004 3.38759559906577 0 0 0.5723103421209 Y 0 0.992981618524708 N N 0 30870 ENSG00000207294 ENSG00000179889 - + 16 16 15152154 15140696 downstream coding Y_RNA PDXDC1 15152055 14976487 + + 0 15154193 15031413 - + N - - N HCC1954 10 6.07142857142857 4 14 1 N - - Y - - 0 0 0 14 1.10697096478857 1.1141127129485 1.1141127129485 1.10697096478857 3 - - 4531 Y Y 3.65488030998075 3.3697272397832 3.3697272397832 320 0 0.0214885346787317 Y 0.970894160583942 0.992723540145985 N N 5674 93 ENSG00000105983 ENSG00000105982 + + 7 7 156378663 156162585 downstream coding LMBR1 RNF32 156166332 156117523 - + 0 156164532 156162079 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 28 1.24266417982717 1.07840397214886 1.24266417982717 1.07840397214886 3 - - 29285 Y Y 3.52039024593366 3.51001030496889 3.51001030496889 22 0.0819185645272603 0.307132778477201 Y 0.991338854382333 0.991338854382333 N N 0 343 ENSG00000214653 ENSG00000178729 + - 6 6 48225620 48144384 downstream intron AL353138.10 C6orf138 48224673 47953998 - - 0 48186747 48084812 - + N - 5.08738813241339 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 6 0.778450549431962 0.51420586751469 0.778450549431962 0.51420586751469 2 - 0 31502 Y Y 3.27717235582328 3.39271690522525 3.27717235582328 258 0 0.91090895152127 Y 0 0.991412723870623 N N 168 73312 ENSG00000113946 ENSG00000163347 - - 3 3 191611027 191522909 upstream upstream CLDN16 CLDN1 191588535 191506197 + - 0 191558112 191527105 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.299953422716903 0.378512652476092 0.378512652476092 0.299953422716903 3 - - 35707 N N 3.56129235625094 3.50848272165904 3.50848272165904 40 0.282271241830065 0.106823687989847 N 0.296918767507003 0.282271241830065 N N 2774 712661 ENSG00000188342 ENSG00000111640 - + 13 12 44756237 6517797 intron coding GTF2F2 GAPDH 44592656 6513918 + + 0.282271241830065 44596221 6517244 - + Y 1.33038624388049 1.33615938423776 N HCC1954 4 2 1 3 1 N - - N - - 0 0 0 6 0.271386430077198 1.02841173502938 1.02841173502938 0.271386430077198 1 0 0 22112 N Y 3.53296011761759 3.35104284496326 3.35104284496326 0 0 0.612831606405234 N 0.940813269518834 0.921084359358445 N N 1 0 ENSG00000166206 ENSG00000208313 - - 15 1 24767329 172102129 intron downstream GABRB3 SNORD77 24339786 172102062 - - 0.921084359358445 24441802 172101967 + + Y 1.01325966850829 - N HCC1954 2 1.45454545454545 1 5 1 N - - N - - 0 0 0 11 0.907002016310634 0.864151527351077 0.907002016310634 0.864151527351077 3 0 - 30455 Y N 3.33464863582806 3.18989809546429 3.18989809546429 0 0 0.461294100194651 Y 0.00961538461538458 0 N N 0 7010 ENSG00000217748 ENSG00000213401 + - X X 151704649 151688896 upstream upstream U82671.12 MAGEA3 151703833 151685309 - - 0 151710709 151688955 - + N - - N HCC1954 2 2 2 5 3 N - - Y LINE Low_complexity 0.898989898989899 0.442307692307692 0.898989898989899 5 0.628473838073511 0.371370904316165 0.628473838073511 0.371370904316165 1 - - 37708 N Y 3.52936639476796 3.42783536197374 3.42783536197374 245 0 0.0438557954062662 N 0.852456538170824 0.889342403628118 N N 18458 2947 ENSG00000166530 ENSG00000100578 - + 16 14 82400529 58085299 downstream intron HSBP1 KIAA0586 82399094 57963351 + + 0.889342403628118 82402525 58000637 - + Y - 0.866568530265679 N HCC1954 2 1.16129032258065 1 10 1 N - - N - - 0 0 0 62 0.542772860154395 0.407079645115797 0.542772860154395 0.407079645115797 2 - 0 44715 Y Y 3.56960615767593 3.27192306858781 3.27192306858781 326 0 0.00596320292512087 Y 0 0 N N 535 9608 ENSG00000165816 ENSG00000095627 - + 10 10 116056184 115982053 upstream downstream VWA2 TDRD1 115989008 115929019 + + 0 115986860 115983599 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.749883556792257 0.99270299422975 0.99270299422975 0.749883556792257 1 - - 42374 Y Y 3.38127338926705 3.52617389950245 3.38127338926705 209 0 0.283555329194976 Y 0 0.966072205306655 N N 0 0 ENSG00000214796 ENSG00000213466 + + 4 4 125577725 125203592 downstream downstream AC097474.3 AC108075.3 125576352 125203103 - + 0 125448807 125351147 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 9 0.864151527351077 0.549914608314322 0.864151527351077 0.549914608314322 1 - - 19139 N N 3.08143087468331 3.37758638046158 3.08143087468331 3 0 0.250437702555981 N 0 0 Y N 0 1725 ENSG00000171943 ENSG00000196369 - + 1 1 120832672 142805834 intron coding SRGAP2P1 SRGAP2P2 120808677 142627547 + + 0 120817410 142725259 - + N 1 - N HCC1954 6 5.68468468468468 2 111 1 N - - N - - 0 0 0 111 0.899860268150708 0.764167053112109 0.899860268150708 0.764167053112109 4 0 - 29239 N Y 3.20384558058643 3.1735845310591 3.1735845310591 256 0 0.0642037695156589 Y 0.991629464285714 0.991629464285714 N N 26 13696 ENSG00000204364 ENSG00000204371 - - 6 6 32021428 31973433 intron upstream C2 EHMT2 32003473 31955515 + - 0 32009364 31973696 - + N 0.529353480307159 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.707033067832699 0.785592297591888 0.785592297591888 0.707033067832699 2 0 - 34627 Y Y 3.70512929149291 3.75065819442972 3.70512929149291 0 0 0.916264746070646 Y 0.0189337689337687 0.95968220968221 N N 11502 0 ENSG00000159921 ENSG00000222760 - - 9 9 36248450 36257919 coding downstream GNE U4 36204430 36257780 - + 0 36226884 36266877 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.678466075192994 0.349945659836387 0.678466075192994 0.349945659836387 2 - - 31202 Y Y 3.33151892129485 2.90679433368408 2.90679433368408 279 0 0.00392318662789493 N 0.981199702441334 0.990599851220667 Y N 0 763 ENSG00000207650 ENSG00000205814 - + 3 3 196911548 196924416 upstream upstream hsa-mir-570 AC069513.28-3 196911452 196912000 + + 0 196911082 196908641 - + N - - N HCC1954 20 8 1 12 1 N - - N LTR LINE 0.2 1 1 22 1.17838844638783 0.857009779191151 1.17838844638783 0.857009779191151 1 - - 33028 N N 3.63395678407849 2.93805794775776 2.93805794775776 2 0 0.0617779183236447 N 0 0 Y N 171855 339915 ENSG00000198886 ENSG00000198727 - + MT MT 12138 15882 coding coding MT-ND4 MT-CYB 10761 14748 + + 0 10987 15550 - + N 0.543149686424306 1.30623577009913 N HCC1954 1 1 1 0 1 Y 189 4.09957 N - - 0 0 0 4 0.857009779191151 0.949852505270192 0.949852505270192 0.857009779191151 1 0 0 29215 Y Y 3.40319013214585 3.28189243439864 3.28189243439864 305 0 0.0124141222517702 Y 0.99344262295082 0.99344262295082 N N 30335 48732 ENSG00000204388 ENSG00000204389 - + 6 6 31906010 31893702 upstream downstream HSPA1B HSPA1A 31903667 31891299 + + 0 31902956 31898054 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 38 1.02841173502938 1.05697872766909 1.05697872766909 1.02841173502938 1 - - 43021 N N 2.8988072119297 3.12747721909902 2.8988072119297 12 0.3746351567649 0.086932913117826 N 0.420958478486019 0 N N 0 551733 ENSG00000208635 ENSG00000204628 + + 4 5 160648060 180603512 upstream utr3p AC105423.4-2 GNB2L1 160647991 180596536 - - 0 160671568 180596544 - - Y - - N HCC1954 18 7.6 1 2 1 N - - N LINE - 1 0 1 5 0.357087407996313 0.742741808632331 0.742741808632331 0.357087407996313 2 - - 372 Y N 3.48140486803346 2.60221700146248 2.60221700146248 0 0 0.0675653320152744 Y 0.462017434620174 0 N N 5638 2 ENSG00000168005 ENSG00000188070 - - 11 11 63351727 63290008 upstream upstream C11orf84 AP006289.2 63337436 63287888 + - 0.462017434620174 63336828 63295146 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.421052631578947 0.421052631578947 4 0.521347615674617 0.628473838073511 0.628473838073511 0.521347615674617 2 - - 27087 N Y 3.24462389972434 3.38656252929588 3.24462389972434 0 0 0.524157117115637 N 0 0.934769064066098 Y N 6304 40802 ENSG00000196696 ENSG00000205609 - + 16 16 68657352 28322701 coding utr3p PDXDC2 EIF3CL 68567713 28298403 - - 0 68587870 28298549 + - N - 0.013634658472662 N HCC1954 28 22 2 5 1 N - - N SINE - 0.183673469387755 0 0.183673469387755 5 0.857009779191151 0.757025304952183 0.857009779191151 0.757025304952183 2 - 0 35973 N N 2.99542187481193 3.26616992024256 2.99542187481193 0 0.00467289719626196 0.275781847994577 N 0.00467289719626196 0.00467289719626196 N N 0 712661 ENSG00000219004 ENSG00000111640 + + X 12 39532334 6517797 downstream utr3p CTD-2324A24.1 GAPDH 39531330 6513918 - + 0.00467289719626196 39531232 6517673 - + Y - - N HCC1954 2 1.85714285714286 1 6 1 N - - N - - 0 0 0 7 0.378512652476092 0.471355378555133 0.471355378555133 0.378512652476092 2 - - 13346 N N 3.7533866813788 3.2044774227722 3.2044774227722 46 0 0.190465368927629 N 0 0.181451612903226 N N 36111 41507 ENSG00000099917 ENSG00000188846 - + 22 3 19271918 40478862 intron coding MED15 RPL14 19191886 40473834 + + 0.181451612903226 19250722 40478437 - + Y 1.06098463590531 - N HCC1954 3 2.5 1 3 1 N - - N Simple_repeat,Simple_repeat - 0.311557788944724 0 0.311557788944724 4 0.778450549431962 0.714174815992626 0.778450549431962 0.714174815992626 2 0 - 1661 N Y 3.45400817511148 3.45716081758364 3.45400817511148 1 0 0.154588621338865 N 0 0.929414872539955 N N 12320 6443 ENSG00000108587 ENSG00000168014 - + 17 11 25877957 73559712 utr3p coding GOSR1 C2CD3 25828552 73423128 + - 0 25874177 73511722 - - Y - - N HCC1954 22 21.5 21 4 1 N - - N Other,Other - 1 0 1 4 0.621332089913584 0.785592297591888 0.785592297591888 0.621332089913584 2 - - 42971 N N 3.41952156054875 3.57332786160156 3.41952156054875 0 0 0.041495776805493 N 0 0 N N 1139 0 ENSG00000132570 ENSG00000169744 - - 5 4 134326223 16509425 intron upstream PCBD2 LDB2 134268709 16112265 + - 0 134288911 16672813 - + Y 1.57189749691755 - N HCC1954 2 2 2 10 1 N - - N - - 0 0 0 10 0.414221393275723 0.392796148795944 0.414221393275723 0.392796148795944 0 0 - 41644 N N 3.49272035470961 3.57233464462502 3.49272035470961 0 0 0.0826056057028053 N 0 0 Y N 19339 4 ENSG00000177570 ENSG00000184090 + - 8 8 119703365 129029462 coding downstream SAMD12 TMEM75 119270880 129029046 - - 0 119460978 128996127 - + N 0.650810980173114 - N HCC1954 1 1 1 0 1 N - - N - LINE 0 1 1 7 0.93556900895034 0.899860268150708 0.93556900895034 0.899860268150708 1 0 - 9495 Y N 3.62559223734505 3.54872248456702 3.54872248456702 5 0 0.0767412285553117 Y 0 0 N N 149 27 ENSG00000161381 ENSG00000214553 + + 17 17 34561298 34462984 downstream downstream PLXDC1 AC091178.7-1 34473083 34439685 - + 0 34470953 34466876 - + N - - N HCC1954 2 1.2 1 1 1 N - - Y SINE - 1 0 1 5 0.449930134075354 0.364229156156239 0.449930134075354 0.364229156156239 2 - - 30331 N Y 3.89400061613173 3.50678730447985 3.50678730447985 297 0 0.0459547295546299 Y 0.992506518822308 0.985013037644617 N N 123 2220 ENSG00000198932 ENSG00000125962 - + X X 101800664 101745743 upstream downstream GPRASP1 ARMCX5 101792950 101740752 + + 0 101780985 101747238 - + N - - N HCC1954 1 1 1 0 2 N - - N LINE,LINE - 0.611510791366906 0 0.611510791366906 58 0.99270299422975 1.22838068350732 1.22838068350732 0.99270299422975 1 - - 27287 N Y 3.59528445727371 3.44934152969861 3.44934152969861 0 0 0.570578576744533 Y 0.851167670133187 0.919859514687101 N N 18192 77 ENSG00000157106 ENSG00000196908 + - 16 16 18844887 15371268 coding upstream SMG1 AC137803.2 18723677 15365326 - - 0 18776995 15382688 - + N - - N HCC1954 14 12.6153846153846 8 13 1 N 58 26.3695 N - SINE 0 0.56969696969697 0.56969696969697 13 0.385654400636018 0.828442786551446 0.828442786551446 0.385654400636018 2 - - 29261 N Y 3.31233066536513 3.50000108636471 3.31233066536513 0 0.361860242119142 0.415043196892701 Y 0.361860242119142 0.990331215789684 N N 174 0 ENSG00000111817 ENSG00000220105 - - 6 6 116866135 116686971 intron intron SART2 AL050331.11-1 116798214 116686349 + - 0 116827052 116686821 - + N 0.225010188042149 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.507064119354764 0.635615586233437 0.635615586233437 0.507064119354764 1 0 0 41910 N N 2.87064280716569 3.37126417066287 2.87064280716569 0 0 0.989460126575422 N 0 0 N N 29840 30 ENSG00000164830 ENSG00000212993 + + 8 8 107834093 128498621 utr5p upstream OXR1 POU5F1P1 107739270 128497039 + + 0 107739588 128160561 + + N - - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - LINE,LINE 0 0.542372881355932 0.542372881355932 91 1.82828752894112 1.26408942430695 1.82828752894112 1.26408942430695 1 - - 12014 N Y 3.58589773328548 3.37808089400154 3.37808089400154 0 0 0.204388567671761 N 0.988145048814505 0.97629009762901 N N 12320 695 ENSG00000108587 ENSG00000149531 - + 17 20 25877957 28265815 utr3p coding GOSR1 FRG1B 25828552 28225518 + + 0 25874010 28246382 - + Y - - N HCC1954 72 43.2820512820513 14 39 1 N - - N Other tRNA 1 1 1 39 0.721316564152552 1.23552243166724 1.23552243166724 0.721316564152552 2 - - 31649 Y Y 2.88274380859372 3.65488030998075 2.88274380859372 162 0 0.212495649760042 Y 0.979295267489712 0.958590534979424 N N 1131 2216 ENSG00000214116 ENSG00000185485 - + 3 3 197173943 197201530 coding coding AC024937.21-2 AC024937.21-3 197171055 197174603 - - 0 197171354 197176697 + - N - - N HCC1954 4 2.5 1 13 3 N - - Y LINE - 0.456896551724138 0 0.456896551724138 14 0.828442786551446 0.93556900895034 0.93556900895034 0.828442786551446 4 - - 4114 Y Y 3.44313372060675 3.36720643949681 3.36720643949681 0 0 0.157428227015295 Y 0.782069288389513 0.989622347066167 N N 827 0 ENSG00000146707 ENSG00000205485 + + 7 7 76094556 76018755 intron downstream POMZP3 AC004980.5-1 76077243 76016614 - + 0 76082741 76018773 - + N 0.357019946114005 - N HCC1954 10 9 6 4 1 N - - Y DNA - 0.647887323943662 0 0.647887323943662 4 0.507064119354764 0.499922371194838 0.507064119354764 0.499922371194838 1 0 - 36696 Y Y 3.22630087969517 3.16001209482883 3.16001209482883 387 0 0.00214650888773349 Y 0 0 N N 8908 1055 ENSG00000182196 ENSG00000111325 - + 12 12 122033413 122030541 coding utr3p ARL6IP4 OGFOD2 122030833 122025242 + + 0.987212615119592 122031630 122029878 - + N - 0.974691763488043 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.778450549431962 0.899860268150708 0.899860268150708 0.778450549431962 2 - 0 31399 Y Y 3.43421100493494 3.63552422018169 3.43421100493494 266 0 0.420157377607692 Y 0 0 N N 1708 0 ENSG00000114812 ENSG00000216013 - - 3 3 42554064 42444308 upstream upstream VIPR1 AC092047.3 42519121 42444214 + - 0 42490090 42460134 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.922480620155039 0.922480620155039 4 0.87843502367093 0.921285512630487 0.921285512630487 0.87843502367093 4 - - 46936 Y Y 3.49168728493972 3.59528445727371 3.49168728493972 328 0 0.0898567925938628 Y 0.0224699081406399 0.987052581564777 N N 6558 2469 ENSG00000104866 ENSG00000142252 - + 19 19 50341570 50286622 utr5p coding LRRC68 GEMIN7 50288058 50274370 + + 0 50288182 50285443 - + N 0.277762603000665 1.47406282394095 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 1.15696320190805 1.17838844638783 1.17838844638783 1.15696320190805 4 0 0 46748 N Y 3.13479264587427 3.53035961174449 3.13479264587427 387 0 0.0710782168243258 Y 0.994777926593341 0.984333779780024 N N 4351 16224 ENSG00000105127 ENSG00000141867 + - 19 19 15351603 15252262 downstream utr5p AKAP8 BRD4 15325341 15209301 - - 0 15304101 15244944 - + N - 121.978740415978 N HCC1954 1 1 1 0 2 N - - N Simple_repeat,Simple_repeat - 0.812182741116751 0 0.812182741116751 80 0.964136001590045 1.36407389854591 1.36407389854591 0.964136001590045 4 - 0 16952 N N 3.63655728995158 3.20807114562183 3.20807114562183 0 0 0.117433947457256 N 0 0.0126724006310756 N N 253 1649619 ENSG00000196407 ENSG00000141736 - + 1 17 150092797 35138441 utr3p intron THEM5 ERBB2 150081603 35104766 - + 0.0126724006310756 150085213 35116983 + + Y - 0.414298691005656 N HCC1954 37 33 29 12 1 N 490 24.3583 N SINE - 1 0 1 12 0.557056356474248 1.12125446110842 1.12125446110842 0.557056356474248 3 - 0 13414 N N 3.51463709758841 3.74337746277462 3.51463709758841 0 0 0.638456274983772 N 0 0 N N 0 850768 ENSG00000213857 ENSG00000075624 + + 22 7 39801189 5536758 intron coding AL080243.21-3 ACTB 39800114 5533313 - - 0 39800339 5534273 - - Y 1 - N HCC1954 4 4 4 6 2 N - - N - - 0 0 0 6 0.22853594111764 0.335662163516534 0.335662163516534 0.22853594111764 2 0 - 48815 Y Y 3.67849247003875 3.5816815158199 3.5816815158199 0 0 0.936126894709571 Y 0.567674891518422 0.994235665220246 N N 1658 551733 ENSG00000183718 ENSG00000204628 + - 5 5 180620725 180603512 utr3p upstream TRIM52 GNB2L1 180615994 180596536 - - 0 180616792 180606990 - + N 0.677684857654279 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 187 1.25694767614702 1.40692438750547 1.40692438750547 1.25694767614702 1 0 - 25292 N N 3.54400240599166 3.49744043328497 3.49744043328497 0 0 0.0806776153412545 N 0 0 N N 975 0 ENSG00000198487 ENSG00000222791 + - 6 13 42218335 82770303 coding downstream AL512274.9 U6 42183124 82770207 - - 0 42183238 82710614 - + Y - - N HCC1954 23 20.6 20 5 1 N - - N - SINE 0 1 1 5 0.507064119354764 0.371370904316165 0.507064119354764 0.371370904316165 2 - - 28972 N N 2.57019137833513 1.51522489708421 1.51522489708421 0 0.171707185548016 0.142119164380105 N 0.171707185548016 0.0681705837415177 N N 25305 1 ENSG00000153113 ENSG00000070915 - + 5 16 96136143 55504850 utr5p intron CAST SLC12A3 96023533 55456643 + + 0 96023781 55469480 - + Y - 0.965763195435093 N HCC1954 20 17.25 12 4 1 N - - N Low_complexity,Low_complexity Simple_repeat 0.55421686746988 1 1 4 0.592765097273879 0.28566992639705 0.592765097273879 0.28566992639705 2 - 0 36963 N N 3.78105657260285 3.51360402781852 3.51360402781852 0 0 0.999949921667025 N 0 0 N N 12084 3 ENSG00000177119 ENSG00000179242 + + 12 20 44112391 59945671 coding intron ANO6 CDH4 43896170 59260965 + + 0 44047841 59576424 + + Y - 0.929733246584255 N HCC1954 20 2.94117647058824 1 6 8 N 451 26.2081 N - SINE 0 1 1 17 0.885576771830856 0.942710757110266 0.942710757110266 0.885576771830856 1 - 0 9446 Y Y 3.46807512488172 3.57489529770476 3.46807512488172 279 0 0.968475881616463 Y 0 0.980462435870406 N N 1312 5490 ENSG00000120093 ENSG00000173917 + - 17 17 44006809 43977392 downstream upstream HOXB3 HOXB2 43981232 43975020 - - 0.980462435870406 43980736 43979100 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 35 0.799875793911741 1.12125446110842 1.12125446110842 0.799875793911741 4 - - 45095 N Y 3.59425138750382 3.25828027434064 3.25828027434064 109 0 0.0296153863275138 Y 0 0 N N 24224 0 ENSG00000151208 ENSG00000210466 - - 10 10 79356384 79383151 coding upstream DLG5 AL391421.27-2 79220555 79382947 - + 0 79286588 79370458 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.699891319672773 0.314236919036755 0.699891319672773 0.314236919036755 2 - - 44529 N Y 3.57336771439491 3.50529022639353 3.50529022639353 0 0.110878661087866 0.330474070171926 N 0.608786610878661 0.804393305439331 N N 2570 0 ENSG00000109466 ENSG00000222414 - - 4 10 166463748 103114782 intron intron KLHL2 U2 166348238 103114592 + - 0.804393305439331 166433865 103114735 - + Y 1.17413542739455 1 N HCC1954 14 9.17647058823529 1 16 1 N 122 25.4177 N snRNA snRNA 1 0.666666666666667 1 17 0.392796148795944 0.299953422716903 0.392796148795944 0.299953422716903 3 0 0 34157 Y Y 3.61889661733171 3.53568860456667 3.53568860456667 338 0 0.997995949737522 Y 0 0.987536982248521 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 intron downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5619567 5567511 - + N 0.517971726419133 - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 206 1.3069399132665 1.18553019454776 1.3069399132665 1.18553019454776 4 0 - 14456 N N 3.56232542602083 3.49528100778935 3.49528100778935 12 0 0.0604328283433215 N 0 0 N N 6443 18015 ENSG00000168014 ENSG00000127603 + + 11 1 73559712 39725376 coding intron C2CD3 MACF1 73423128 39322426 - + 0 73507042 39473480 - + Y - 0.0466782167588403 N HCC1954 22 21 20 4 1 N - - N - Other 0 1 1 4 0.471355378555133 0.971277749749971 0.971277749749971 0.471355378555133 1 - 0 24317 N Y 3.61360747730288 3.61616813038263 3.61360747730288 0 0 0.4257232637067 N 0.806817441178387 0.791957244345956 N N 33725 6117 ENSG00000143819 ENSG00000171368 - + 1 5 224099884 746510 utr5p upstream EPHX1 TPPP 224064459 712978 + - 0 224083049 755974 - - Y - - N HCC1954 21 17 1 4 1 N - - N - LTR 0 1 1 5 0.414221393275723 0.335662163516534 0.414221393275723 0.335662163516534 4 - - 7185 Y Y 3.4210491438586 3.57167229721571 3.4210491438586 237 0 0.0305091333654237 Y 0.0381664748753358 0.977368622938243 N N 3612 0 ENSG00000079308 ENSG00000118245 + - 2 2 218517041 217433027 downstream upstream TNS1 TNP1 218372757 217432431 - - 0 217904497 217901120 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 7 1.02126998686945 0.864151527351077 1.02126998686945 0.864151527351077 4 - - 47782 N N 3.27721220861664 3.4937534244795 3.27721220861664 0 0 0.146962523768837 N 0 0 N N 0 551733 ENSG00000209834 ENSG00000204628 - + 19 5 34184503 180603512 downstream coding AC011505.6 GNB2L1 34184414 180596536 + - 0 34250755 180597256 - - Y - 0.538527507822136 N HCC1954 18 13.5 1 3 1 N 111 27.0518 N - - 0 0 0 4 0.257102933757345 0.371370904316165 0.371370904316165 0.257102933757345 2 - 0 13694 Y Y 3.40591861909494 3.70719543103269 3.40591861909494 147 0 0.637642160147421 Y 0.503401360544218 0.903884134298881 N N 194 480 ENSG00000169325 ENSG00000159496 + + 22 22 22389508 22371363 downstream downstream AP000347.1 RGL4 22386399 22360329 - + 0 22381320 22373036 - + N - - N HCC1954 1 1 1 0 4 N - - Y LINE LINE 1 1 1 5 0.321378667196682 0.471355378555133 0.471355378555133 0.321378667196682 1 - - 9336 Y Y 3.16150917291514 3.44296588673741 3.16150917291514 225 0 0.0349635492737824 Y 0.96822695035461 0.989408983451537 N N 16 0 ENSG00000108370 ENSG00000211170 - + 17 17 60654281 60502890 upstream downstream RGS9 AC015821.9 60564011 60502725 + + 0 60537298 60527878 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 17 0.87843502367093 0.649899082553289 0.87843502367093 0.649899082553289 1 - - 14123 N Y 3.41423242051993 3.47233119514066 3.41423242051993 0 0 0.788131503980942 N 0 0 N N 523 0 ENSG00000100058 ENSG00000222502 - + 22 8 23957836 37885711 coding upstream CRYBB2 SRP_euk_arch 23945612 37885410 + + 0 23953820 37882905 - + Y - - N HCC1954 4 2.25 1 3 1 N - - N - SINE 0 1 1 4 0.478497126715059 0.271386430077198 0.478497126715059 0.271386430077198 3 - - 24285 N Y 3.41679307359967 3.62464976567696 3.41679307359967 1 0 0.125603335151272 N 0.85773562537048 0.85773562537048 N N 49089 5939 ENSG00000117450 ENSG00000113615 - - 1 5 45760196 134091500 utr5p intron PRDX1 SEC24A 45749295 134012378 - + 0 45759868 134052303 + - Y - 3.12504211582365 N HCC1954 6 3 1 6 1 N - - N - SINE 0 1 1 7 0.828442786551446 0.392796148795944 0.828442786551446 0.392796148795944 2 - 0 12765 N Y 3.67017866861376 3.62464976567696 3.62464976567696 0 0 0.680215455036949 N 0 0 N N 0 20747 ENSG00000214723 ENSG00000073605 - + 19 17 1154822 35328429 downstream coding AC011544.6 GSDMB 1154208 35314374 + - 0.9146166574738 1154996 35314656 - - Y - - N HCC1954 21 19.5 17 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.39993789695587 0.39993789695587 0.321378667196682 1 - - 30483 Y Y 3.52567938596249 3.76848670091893 3.52567938596249 249 0 0.063425804682076 Y 0.976837582889698 0.965256374334547 N N 4474 49 ENSG00000056998 ENSG00000124343 - + X X 2810858 2743955 upstream downstream GYG2 XG 2756859 2680115 + + 0 2752051 2747301 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 5 0.678466075192994 0.635615586233437 0.678466075192994 0.635615586233437 4 - - 1781 N Y 3.47911741325579 3.56079784271098 3.47911741325579 8 0 0.023438304968454 N 0 0.923455854490337 N N 2 2922 ENSG00000196844 ENSG00000126217 - - 11 13 125153924 112802054 utr3p intron PATE2 MCF2L 125151268 112596693 - + 0 125151456 112651151 + - Y - 0.183554794007263 N HCC1954 462 435.5 420 8 1 N - - N LINE SINE 1 1 1 8 0.449930134075354 0.321378667196682 0.449930134075354 0.321378667196682 1 - 0 34171 Y Y 3.17151839151932 3.71041843152174 3.17151839151932 319 0 0.0433628948588416 Y 0.987053698652445 0.993526849326222 N N 0 0 ENSG00000218062 ENSG00000215364 - + 9 9 98721421 98713998 upstream upstream RP11-330M2.3 RP11-330M2.4 98721031 98713138 + + 0 98720747 98705212 - + N - - N HCC1954 18 4.66666666666667 1 16 2 N - - Y - SINE,LINE 0 0.925 0.925 18 1.23552243166724 1.1426797055882 1.23552243166724 1.1426797055882 1 - - 40879 N Y 3.57912086274016 3.2656754067026 3.2656754067026 1 0 0.0646544826312951 N 0 0.870680044593088 N N 3725 17935 ENSG00000174306 ENSG00000148180 + + 20 9 39362153 123134942 utr3p utr5p ZHX3 GSN 39240502 123009896 - + 0 39241752 123070312 - + Y - 0.143006109932988 N HCC1954 36 32.25 26 4 1 N - - N SINE Low_complexity 1 0.0163934426229508 1 4 0.314236919036755 0.435646637755502 0.435646637755502 0.314236919036755 1 - 0 9289 Y Y 3.1923087786724 3.16935896602371 3.16935896602371 353 0 0.201117229933028 Y 0.890554826228149 0.99391971256823 N N 18893 6556 ENSG00000141551 ENSG00000141526 + + 17 17 77824862 77790658 intron coding CSNK1D SLC16A3 77795535 77779582 - + 0 77812062 77789056 - + N 1.53392144218755 0.765114504216815 N HCC1954 1 1 1 0 3 N - - Y SINE - 0.760479041916168 0 0.760479041916168 35 1.19267194270768 1.25694767614702 1.25694767614702 1.19267194270768 3 0 0 40203 N Y 3.48593413659447 2.70281953111478 2.70281953111478 0 0.0138888888888886 0.146924103420113 N 0 0.825980392156863 N N 1627 5111 ENSG00000101417 ENSG00000181827 - - 20 15 31771797 54322775 utr3p downstream PXMP4 RFX7 31754209 54170024 - - 0.0138888888888886 31756708 54152877 + + Y - - N HCC1954 70 43.4 29 5 1 N - - N SINE - 1 0 1 5 0.39993789695587 0.435646637755502 0.435646637755502 0.39993789695587 3 - - 12112 N Y 3.11080976345569 3.13073491470822 3.11080976345569 103 0 0.89766939551785 N 0.976535229476406 0.982401422107305 N N 1021 4310 ENSG00000104714 ENSG00000183011 + - 8 17 671226 7701897 upstream coding ERICH1 LSMD1 604201 7700730 - - 0.00274725274725274 913664 7701243 - + Y - 11.8312907194667 N HCC1954 4 2.78915662650602 1 312 3 N - - N Other - 0.0445544554455446 0 0.0445544554455446 332 1.4426331283051 1.28551466878673 1.4426331283051 1.28551466878673 2 - 0 26104 N N 1.8028709568244 1.87157582224653 1.8028709568244 0 0 0.085017106903618 N 0.529987760097919 0.634434924520604 N N 7973 22 ENSG00000157637 ENSG00000182885 + + 17 16 76883691 56281476 intron downstream SLC38A10 GPR97 76833396 56259658 - + 0.634434924520604 76837809 56282586 - + Y 0.58359421712609 - N HCC1954 3 1.71428571428571 1 4 1 N 240 6.97048 N Low_complexity Simple_repeat 1 0.890909090909091 1 7 0.521347615674617 0.392796148795944 0.521347615674617 0.392796148795944 2 0 - 41948 Y Y 2.91757550223297 3.54552998930151 2.91757550223297 124 0.00371747211895912 0.100932817112549 Y 0.983113855459643 0.991556927729822 N N 2710 13677 ENSG00000147804 ENSG00000071894 + - 8 8 145613081 145605541 coding upstream SLC39A4 CPSF1 145608607 145589254 - - 0 145608753 145606111 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.771308801272036 0.807017542071667 0.807017542071667 0.771308801272036 1 - - 24906 N N 2.71327421303014 3.67423639977982 2.71327421303014 0 0.276190476190476 0.0491289002316739 N 0.276190476190476 0.0129870129870132 N N 82 1328 ENSG00000106069 ENSG00000102781 - - 7 13 29520469 29779584 utr3p utr3p CHN2 KATNAL1 29200646 29674768 + - 0.276190476190476 29519051 29679811 - + Y - - N HCC1954 28 26.75 23 4 1 N - - N - SINE 0 1 1 4 0.471355378555133 0.314236919036755 0.471355378555133 0.314236919036755 2 - - 39792 Y Y 2.87316360745208 3.36079094374226 2.87316360745208 0 0 0.3660974007562 Y 0.987456519447665 0.993728259723833 N N 33005 9 ENSG00000166145 ENSG00000166143 - - 15 15 38937144 38908227 utr5p upstream SPINT1 PPP1R14D 38923538 38894943 + - 0 38923671 38915774 - + N 0.263427080343323 - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 26 1.34979040222606 1.07840397214886 1.34979040222606 1.07840397214886 1 0 - 22121 N Y 3.26720299001245 3.55231620741665 3.26720299001245 174 0 0.0210186659548079 N 0.00384615384615372 0.0152961980548186 N N 38799 49727 ENSG00000187446 ENSG00000142657 + + 15 1 39361377 10402788 coding upstream AC012652.1 PGD 39310729 10381668 + + 0.0152961980548186 39350050 10380478 + + Y - - N HCC1954 40 36.2 21 5 1 N - - N - SINE 0 1 1 5 0.521347615674617 0.335662163516534 0.521347615674617 0.335662163516534 2 - - 47400 Y Y 3.3012485241977 3.40744620240479 3.3012485241977 0 0 0.966636223143485 Y 0.926564878453803 0.993880406537817 N N 746 2845 ENSG00000126460 ENSG00000142546 - - 19 19 54785999 54775625 utr5p upstream PRRG2 NOSIP 54778280 54750782 + - 0.993880406537817 54778280 54776556 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 128 1.67831081758267 1.17838844638783 1.67831081758267 1.17838844638783 2 - - 9444 N Y 2.23592635062903 3.71976530271662 2.23592635062903 0 0 0.400455759365105 Y 0 0.0117647058823529 N N 11450 12 ENSG00000108244 ENSG00000187242 + - 17 17 36347362 36276988 downstream downstream KRT23 KRT12 36332478 36270956 - - 0.0117647058823529 36331261 36260637 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 8 0.528489363834543 0.464213630395207 0.528489363834543 0.464213630395207 3 - - 6866 Y N 3.78208964237274 3.62464976567696 3.62464976567696 0 0 0.150433944338654 N 0.0170156374238009 0 N N 2755 1872 ENSG00000153094 ENSG00000172965 - + 2 2 111642493 111969088 downstream downstream BCL2L11 AC068491.4 111594962 111903370 + - 0 111722219 111818109 - - N - - Y HCC1954 2 2 2 5 1 N 478 29.196 N - LINE 0 1 1 5 0.628473838073511 0.87843502367093 0.87843502367093 0.628473838073511 2 - - 38317 Y Y 3.37444731835856 3.34359427943881 3.34359427943881 33 0.0689716840536512 0.170033059661185 Y 0.991833084947839 0.991833084947839 N N 7326 3524 ENSG00000165525 ENSG00000165516 + + 14 14 49389289 49319606 intron coding SDCCAG1 KLHDC2 49320282 49304537 - + 0 49322047 49319061 - + N 0.398941957870044 - N HCC1954 20 3.52631578947368 1 5 1 N - - Y SINE - 0.811475409836066 0 0.811475409836066 19 0.871293275511003 0.921285512630487 0.921285512630487 0.871293275511003 1 0 - 18428 Y Y 3.11757305363188 3.83233862388491 3.11757305363188 272 0 0.320704669009623 Y 0 0.961182200152789 N N 0 0 ENSG00000223181 ENSG00000217260 + - 1 1 683579 653390 downstream upstream U6 RP11-206L10.1 683476 651474 - - 0 670010 662128 - + N - - N HCC1954 400 221.181818181818 120 11 4 N - - Y SINE DNA 1 1 1 11 0.499922371194838 0.449930134075354 0.499922371194838 0.449930134075354 3 - - 19221 Y Y 3.44143830342756 3.44871903508266 3.44143830342756 0 0 0.449921788640113 Y 0.984654631083202 0.994884877027734 N N 9207 15383 ENSG00000085998 ENSG00000117472 + + 1 1 46458564 46424217 intron coding POMGNT1 TSPAN1 46426941 46413346 - + 0 46434460 46423566 - + N 2.51066205727601 - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 66 1.38549914302569 1.54261760254407 1.54261760254407 1.38549914302569 1 0 - 34023 N Y 3.45720067037699 3.50848272165904 3.45720067037699 0 0 0.424664629817959 N 0.904317496229261 0.942590497737557 N N 1287 4199 ENSG00000212635 ENSG00000059769 - - X 9 42218751 113472347 utr3p intron Z93403.1 DNAJC25-GNG10 42029377 113433453 + + 0 42218415 113444958 - - Y - 0.17089648315775 N HCC1954 23 21.3333333333333 21 6 1 N 13 24.6597 N Other - 1 0 1 6 0.721316564152552 0.871293275511003 0.871293275511003 0.721316564152552 4 - 0 41470 Y Y 3.32320511986986 3.43784458057793 3.32320511986986 359 0 0.00998708400087145 Y 0.862453174526943 0.994268882271956 N N 4 45 ENSG00000184090 ENSG00000214789 + + 8 8 129029462 128893866 downstream intron TMEM75 AC084123.9 129029046 128875961 - + 0 128972018 128876163 - + N - 3.73024630541872 N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.185185185185185 0.185185185185185 45 1.3069399132665 1.34979040222606 1.34979040222606 1.3069399132665 1 - 0 48310 N N 3.5774559507845 3.38912318237562 3.38912318237562 1 0 0.847268217331432 N 0 0 N N 6369 0 ENSG00000154124 ENSG00000217946 - + 5 X 14752842 97532574 upstream intron FAM105B RP11-390F10.1 14717783 97531164 + + 0 14705544 97532107 - + Y - 1 N HCC1954 12 8.16666666666667 6 18 1 N - - N - - 0 0 0 18 0.478497126715059 0.278528178237124 0.478497126715059 0.278528178237124 3 - 0 9660 N Y 3.0897446761083 3.50785087947327 3.0897446761083 0 0 0.451732164107862 N 0 0.857569296375267 Y N 1649619 5929 ENSG00000141736 ENSG00000141564 - + 17 17 35138441 76554768 intron intron ERBB2 AC127496.5-2 35104766 76133220 + + 0 35125059 76176694 - + N 0.991162890469566 1.02373537503182 N HCC1954 9 7.5 6 4 1 N 414 20.7326 N - SINE 0 1 1 4 0.435646637755502 0.278528178237124 0.435646637755502 0.278528178237124 2 0 0 2908 N Y 3.41103992525442 3.74913061111987 3.41103992525442 0 0 0.184898294661302 N 0.908161708619375 0.881922196796339 N N 84 73 ENSG00000214650 ENSG00000109743 - - 11 4 66059237 15343508 coding upstream AP002748.4-1 BST1 66040318 15313739 + + 0 66042023 15292001 - - Y - - N HCC1954 35 29.8 23 5 1 N - - N SINE - 1 0 1 5 0.307095170876829 1.04269523134923 1.04269523134923 0.307095170876829 3 - - 22372 N Y 3.59102838701478 3.58909022855099 3.58909022855099 2 0 0.560078915004867 N 0 0.838269666841095 N N 1107 50281 ENSG00000169499 ENSG00000135862 - - 8 1 38950585 181381350 utr3p intron PLEKHA2 LAMC1 38877910 181259218 + + 0 38947332 181366100 - - Y - 1.28372031756573 N HCC1954 25 24.25 22 4 1 N - - N SINE - 1 0 1 4 0.307095170876829 0.407079645115797 0.407079645115797 0.307095170876829 2 - 0 27670 N N 3.71145150129163 3.70210463009675 3.70210463009675 10 0 0.40743079869153 N 0.560939214395436 0.496686416502085 N N 3 18920 ENSG00000166501 ENSG00000082781 - - 16 3 24139063 126088834 intron coding PRKCB ITGB5 23754823 125964488 + - 0.0469168312486284 23887866 126075067 - + Y 0.937931034482759 6.83877072634111 N HCC1954 20 17.4 13 5 1 N 371 27.7939 N SINE - 1 0 1 5 0.292811674556976 0.442788385915428 0.442788385915428 0.292811674556976 1 0 0 9516 Y Y 2.7459636226299 3.0244491082185 2.7459636226299 345 0 0.642588866465569 Y 0 0.955353666450357 N N 1312 5490 ENSG00000120093 ENSG00000173917 + - 17 17 44006809 43977392 utr3p upstream HOXB3 HOXB2 43981232 43975020 - - 0 43982253 43977956 - + N 0.860804819163446 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 5 0.328520415356608 0.707033067832699 0.707033067832699 0.328520415356608 3 0 - 3088 N Y 3.34152813989903 3.34359427943881 3.34152813989903 267 0.723262588431128 0.0139558684205745 N 0.833957553058677 0.833957553058677 N N 6223 12007 ENSG00000154127 ENSG00000160633 - + 11 19 122190390 5619488 upstream coding UBASH3B SAFB 122031640 5574164 + + 0 121994886 5618168 - + Y - - N HCC1954 1 1 1 0 1 N - - N - LINE 0 0.241666666666667 0.241666666666667 21 0.385654400636018 0.857009779191151 0.857009779191151 0.385654400636018 2 - - 46518 N N 3.13743300454072 3.40488554932505 3.13743300454072 0 0 0.0747615196928102 N 0 0 N N 0 642 ENSG00000182225 ENSG00000100154 + + 19 22 5527949 27405853 downstream intron AC011533.6 TTC28 5527671 26704004 - - 0 5518557 27280603 - - Y - 1.25405929375459 N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.414221393275723 0.271386430077198 0.414221393275723 0.271386430077198 2 - 0 29265 Y N 3.61464054707278 3.23034293992665 3.23034293992665 0 0 0.0924877917408471 Y 0.293478260869565 0.293478260869565 N N 4614 0 ENSG00000112237 ENSG00000207017 + + 6 6 100123411 100080802 intron downstream CCNC Y_RNA 100096985 100080694 - + 0.293478260869565 100108308 100086275 - + N 3.32238370756033 - N HCC1954 1 1 1 0 1 N - - Y LTR - 0.180327868852459 0 0.180327868852459 5 0.435646637755502 0.607048593593732 0.607048593593732 0.435646637755502 2 0 - 4483 Y Y 3.42100929106525 3.6533527266709 3.42100929106525 269 0 0.634342134717772 Y 0.992509153925706 0.985018307851413 N N 32979 386 ENSG00000106105 ENSG00000196295 - - 7 7 30640168 30570758 upstream upstream GARS AC005154.1 30600706 30566129 + - 0 30591471 30575130 - + N - - N HCC1954 4 1.6 1 1 4 N - - Y SINE Simple_repeat,LTR 1 0.949579831932773 1 5 0.749883556792257 0.707033067832699 0.749883556792257 0.707033067832699 4 - - 40338 N N 3.60273302279816 3.23527702852946 3.23527702852946 0 0 0.395727647379547 N 0 0.267525741414391 N N 60677 24 ENSG00000125740 ENSG00000196645 - + 19 15 50670254 21123747 upstream downstream FOSB AC100756.4-2 50663093 21121113 + - 0.267525741414391 50646611 21061586 - - Y - - N HCC1954 2 1.83333333333333 1 5 2 N 346 10.2249 N - - 0 0 0 6 0.435646637755502 0.592765097273879 0.592765097273879 0.435646637755502 2 - - 13678 Y Y 2.80253481394078 3.32207876414413 2.80253481394078 333 0.00300300300300282 0.0229337772797715 Y 0 0 N N 51 14981 ENSG00000182057 ENSG00000100207 - - 22 22 41000811 40941389 intron utr5p Z83851.17 TCF20 40995703 40885963 + - 0 40996291 40941293 - + N 3.07360415790882 90.2271956765243 N HCC1954 1 1 1 0 2 N - - Y Low_complexity,Low_complexity Simple_repeat,Simple_repeat 0.45578231292517 0.184357541899441 0.45578231292517 74 1.04983697950916 1.2783729206268 1.2783729206268 1.04983697950916 1 0 0 20223 N Y 3.59425138750382 3.74234439300473 3.59425138750382 247 0.725254781516125 0.0100841447580668 N 0.725254781516125 0.725254781516125 N N 0 8013 ENSG00000217794 ENSG00000143367 + + 16 1 29555243 149822683 intron intron AC009086.6-5 TUFT1 29537496 149779405 - + 0.69091162920564 29543335 149796726 - + Y 1 1.06832450817703 N HCC1954 14 9.3 6 10 1 N - - N - - 0 0 0 10 0.257102933757345 0.357087407996313 0.357087407996313 0.257102933757345 2 0 0 31537 N N 3.54975555433691 3.27461170274354 3.27461170274354 0 0 0.92893294596587 N 0 0 Y Y 614 7845 ENSG00000185614 ENSG00000004534 - + 3 3 49817465 50089685 coding utr5p C3orf54 RBM6 49815691 49952481 + + 0 49816618 49952662 - + N 0.466829233307036 - N HCC1954 1 1 1 0 2 N 568 9.12122 N Simple_repeat - 0.129807692307692 0 0.129807692307692 47 1.48548361726466 1.09268746846872 1.48548361726466 1.09268746846872 4 0 - 31344 Y Y 3.77104735399867 2.93226494661916 2.93226494661916 169 0 0.062191780100794 Y 0 0.984938138784293 N N 4941 457 ENSG00000182606 ENSG00000168038 - - 3 3 42242385 41978664 upstream upstream TRAK1 ULK4 42107750 41263097 + - 0 42103059 42030601 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE - 0.521739130434783 0 0.521739130434783 5 0.492780623034912 0.385654400636018 0.492780623034912 0.385654400636018 2 - - 19725 N Y 3.36976709257655 3.4722913423473 3.36976709257655 0 0 0.0444345886973425 N 0 0 N N 438 413 ENSG00000140660 ENSG00000179743 - + 16 1 12054642 16047229 utr3p utr3p RUNDC2A AL450998.19 11978103 16033561 + - 0 12053639 16033887 - - Y - - N HCC1954 26 24 22 4 1 N 459 23.7285 N SINE - 1 0 1 4 0.271386430077198 0.449930134075354 0.449930134075354 0.271386430077198 1 - - 2734 N N 2.02025662724323 1.65745028976499 1.65745028976499 67 0 0.181256043488579 N 0 0 N N 2366 17 ENSG00000176485 ENSG00000165061 + - 11 8 63138417 40874500 downstream intron PLA2G16 ZMAT4 63098825 40507270 - - 0.542864821284601 63095857 40769251 - + Y - 1.20544829232941 N HCC1954 2 1.4 1 2 1 N - - N Low_complexity Low_complexity 1 1 1 5 0.642757334393363 0.28566992639705 0.642757334393363 0.28566992639705 3 - 0 10857 N Y 3.22167408707565 3.49528100778935 3.22167408707565 0 0 0.230518369116396 N 0.884687016016781 0.993216883295105 N N 6267 0 ENSG00000125450 ENSG00000220911 - - 17 6 70743449 29712099 upstream intron NUP85 SUMO2P 70713192 29711816 + - 0 70690071 29712077 - + Y - 1 N HCC1954 8 4.46341463414634 1 37 1 N - - N - - 0 0 0 41 1.4426331283051 1.07126222398894 1.4426331283051 1.07126222398894 1 - 0 21761 N Y 2.91397707318275 3.63825270713077 2.91397707318275 0 0 0.102975627768174 N 0 0.588607594936709 N N 1284 498 ENSG00000123415 ENSG00000168243 - + 12 1 52869024 233880677 coding intron SMUG1 GNG4 52861519 233777610 - - 0.588607594936709 52863881 233832143 + - Y - 4.02243328599918 N HCC1954 6 1.5 1 1 1 N - - N - SINE 0 1 1 10 0.685607823352921 0.299953422716903 0.685607823352921 0.299953422716903 2 - 0 24388 N Y 3.0066299492991 3.61513506061274 3.0066299492991 0 0 0.946988210567797 N 0.898604882909816 0.953911310413553 N N 0 2527 ENSG00000206696 ENSG00000186001 + + 18 3 45272097 199082851 upstream intron SNORD58 LRCH3 45272032 199002542 - + 0.953911310413553 45272104 199062236 - + Y - 1.31517858497148 N HCC1954 6 2.39805825242718 1 102 2 N - - N - - 0 0 0 103 0.799875793911741 0.585623349113953 0.799875793911741 0.585623349113953 4 - 0 25352 N Y 3.37336081542618 1.45754247590989 1.45754247590989 0 0.0125000000000006 0.0779901285395233 N 0 0.0125000000000006 N N 218 1974 ENSG00000088386 ENSG00000172113 + - 13 3 98202909 48317852 utr3p upstream SLC15A1 NME6 98134057 48310595 - - 0.0125000000000006 98171205 48323408 - + Y - - N HCC1954 32 30.2 27 5 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.442788385915428 0.442788385915428 0.314236919036755 3 - - 47133 Y Y 3.3828009725769 3.45872825368684 3.3828009725769 196 0 0.0127244706495391 Y 0 0.980492196878752 N N 171 0 ENSG00000142512 ENSG00000105370 + - 19 19 56613263 56583009 downstream upstream SIGLEC10 LIM2 56605088 56574976 - - 0 56598634 56589703 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.657040830713216 0.507064119354764 0.657040830713216 0.507064119354764 1 - - 11065 N N 1.67870909903897 3.60000453584907 1.67870909903897 0 0 0.225264510215720 N 0 0 N N 37845 46217 ENSG00000204463 ENSG00000131746 - + 6 17 31728461 35911380 utr5p utr3p BAT3 TNS4 31714784 35885606 - - 0 31728105 35885937 + - Y - - N HCC1954 36 35.25 34 4 1 N - - N Simple_repeat Simple_repeat 0.974358974358974 0.147058823529412 0.974358974358974 4 0.278528178237124 0.621332089913584 0.621332089913584 0.278528178237124 2 - - 34724 Y Y 3.48081283043499 3.1767676787548 3.1767676787548 0 0 0.857809702502994 Y 0.482147588765236 0.97068759936407 N N 630 1646 ENSG00000136895 ENSG00000136828 - + 9 9 129195647 129025264 coding downstream GARNL3 RALGPS1 129045207 128716874 + + 0 129045277 129026889 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 1.07840397214886 0.742741808632331 1.07840397214886 0.742741808632331 2 - - 35179 N N 3.41059884487695 3.60419783086915 3.41059884487695 0 0.197231833910035 0.0496538383738201 N 0.197231833910035 0 N N 83 871 ENSG00000106536 ENSG00000084453 - + 7 12 39470915 21439638 utr5p utr5p POU6F2 SLCO1A2 38984123 21311651 + - 0 38984181 21439294 - - Y - - N HCC1954 23 23 23 4 1 N - - N - LINE 0 1 1 4 0.628473838073511 0.385654400636018 0.628473838073511 0.385654400636018 1 - - 32748 N N 3.4937534244795 2.5268617536873 2.5268617536873 0 0 0.132378270822939 N 0 0 N N 551733 0 ENSG00000204628 ENSG00000179170 + + 5 3 180603512 126949420 coding downstream GNB2L1 AF186996.5-3 180596536 126946642 - + 0 180597259 126958370 - + Y 0.543904135149075 - N HCC1954 22 8.09090909090909 1 13 2 N - - N - LINE 0 1 1 22 0.542772860154395 0.271386430077198 0.542772860154395 0.271386430077198 1 0 - 44366 N Y 3.02754831752817 3.57336771439491 3.02754831752817 0 0 0.170409822173291 N 0 0.915780396665708 N N 20 936 ENSG00000197612 ENSG00000151338 + - 10 14 51398687 37090214 upstream downstream AL442003.8-1 MIPOL1 51398379 36736907 - + 0 51399649 37105819 - - Y - - N HCC1954 20 17.5 5 6 1 N 549 23.4367 N Other SINE 1 1 1 6 0.435646637755502 0.435646637755502 0.435646637755502 0.435646637755502 3 - - 8004 N Y 3.47233119514066 3.37126417066287 3.37126417066287 3 0 0.118646660760074 N 0 0.891279940119761 N N 20739 0 ENSG00000143951 ENSG00000199529 - - 2 4 63669355 102864160 utr3p downstream C2orf86 U6 63202041 102864057 - + 0.875748502994012 63309485 102881799 + - Y - - N HCC1954 620 496 420 5 1 N - - N LINE LINE 1 1 1 5 0.442788385915428 0.328520415356608 0.442788385915428 0.328520415356608 4 - - 10396 N N 3.33996070379583 3.64549358599252 3.33996070379583 1 0.00374531835205982 0.363573811757965 N 0.00374531835205982 0 N N 18240 62029 ENSG00000062716 ENSG00000141367 + + 17 17 55273235 55129099 coding coding TMEM49 CLTC 55139811 55051832 + + 0 55270538 55115898 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 10 0.771308801272036 0.914143764470561 0.914143764470561 0.771308801272036 2 - - 46776 Y Y 3.36460593362372 3.55231620741665 3.36460593362372 337 0 0.00128679883611094 Y 0 0 N N 460 715 ENSG00000083807 ENSG00000083838 + + 19 19 63715244 63684403 intron downstream SLC27A5 ZNF446 63701516 63679607 - + 0 63702165 63686773 - + N 11.4657455911436 - N HCC1954 2 1.5 1 2 1 N - - Y - SINE 0 1 1 4 0.585623349113953 0.414221393275723 0.585623349113953 0.414221393275723 2 0 - 44063 N Y 3.32423818963975 3.39487633072086 3.32423818963975 283 0.857647652700656 0.00335696584975564 N 0.857647652700656 0.857647652700656 N N 9766 4441 ENSG00000154473 ENSG00000120254 + + 10 6 124914869 151464714 coding intron BUB3 MTHFD1L 124903860 151228384 + + 0.525492175668854 124913331 151332605 + + Y - 1.33727307282856 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 14 1.05697872766909 0.278528178237124 1.05697872766909 0.278528178237124 2 - 0 36962 N N 2.92404443115001 3.60632674564779 2.92404443115001 0 0 0.999747373323483 N 0 0.28298755186722 N N 3 12084 ENSG00000179242 ENSG00000177119 + + 20 12 59945671 44112391 intron coding CDH4 ANO6 59260965 43896170 + + 0.28298755186722 59575460 44047792 + + Y 0.929733246584255 3.7966873859614 N HCC1954 1 1 1 0 8 N - - N - - 0 0 0 4 0.785592297591888 0.578481600954027 0.785592297591888 0.578481600954027 2 0 0 1004 N Y 3.26824964015148 3.50000108636471 3.26824964015148 12 0 0.245443259287236 N 0.978493261728645 0.942648697943054 N N 8014 16018 ENSG00000149084 ENSG00000164916 - + 11 7 43834736 4777600 utr3p utr3p HSD17B12 FOXK1 43658719 4688456 + + 0 43834016 4774588 - + Y - - N HCC1954 105 67.7307692307692 35 26 1 N - - N - SINE 0 0.894409937888199 0.894409937888199 26 1.01412823870953 1.02126998686945 1.02126998686945 1.01412823870953 1 - - 13859 N Y 3.41423242051993 3.36617336972692 3.36617336972692 0 0 0.906845098968063 N 0.822737520128824 0.811658615136876 Y N 523 1381 ENSG00000100058 ENSG00000206062 - + 22 22 23957836 24187186 coding upstream CRYBB2 CRYBB2P1 23945612 24183283 + + 0 23953820 24179401 - + N - - N HCC1954 12 3.9375 1 22 3 Y - - N - SINE,SINE 0 1 1 32 1.06412047582901 0.621332089913584 1.06412047582901 0.621332089913584 4 - - 47747 Y N 3.59169073442408 3.31331159145566 3.31331159145566 0 0.00540540540540524 0.168833274585269 Y 0.154594594594595 0.00540540540540524 N N 32493 5600 ENSG00000176619 ENSG00000099800 + - 19 19 2407958 2378875 coding upstream LMNB2 TIMM13 2379165 2376630 - - 0.00540540540540524 2382547 2378917 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.735600060472404 0.592765097273879 0.735600060472404 0.592765097273879 2 - - 35149 N Y 3.73080759109069 3.39959640929622 3.39959640929622 35 0 0.533575467456327 N 0.757917728431016 0.806334182744813 N N 542 0 ENSG00000135482 ENSG00000157680 - - 12 7 54802545 137182149 upstream intron ZC3H10 DGKI 54798297 136724925 + - 0.806334182744813 54796830 136849135 - + Y - 1 N HCC1954 2 2 2 7 1 N - - N - - 0 0 0 7 0.485638874874985 0.378512652476092 0.485638874874985 0.378512652476092 4 - 0 9607 Y Y 3.7061623612628 3.51470859334435 3.51470859334435 0 0 0.586596191581493 Y 0 0.245199245199245 N N 14866 497 ENSG00000188554 ENSG00000198496 - + 17 17 38719232 38549760 upstream downstream AC109326.11 NBR2 38576772 38531135 + + 0.245199245199245 38564510 38554260 - + N - - N HCC1954 11 5 1 4 3 N - - Y SINE,Simple_repeat,SINE LTR 0.475336322869955 0.495049504950495 0.495049504950495 5 1.04269523134923 0.614190341753658 1.04269523134923 0.614190341753658 1 - - 38098 Y Y 3.23105146349406 3.23527702852946 3.23105146349406 254 0 0.81122573480593 Y 0 0.988808280987349 N N 0 10336 ENSG00000221236 ENSG00000133961 - - 14 14 72985644 72892230 downstream upstream AC005280.3 NUMB 72985548 72811671 + - 0 72994952 72903512 - + N - - N HCC1954 3 1.10526315789474 1 1 5 N - - Y - SINE 0 1 1 19 0.692749571512847 0.728458312312478 0.728458312312478 0.692749571512847 3 - - 7538 N Y 3.5310219591538 3.31588453542141 3.31588453542141 0 0 0.608941334609547 Y 0.99469442032132 0.98938884064264 N N 7661 1759 ENSG00000168883 ENSG00000168890 - - 2 2 85729917 85683332 coding upstream USP39 TMEM150 85696726 85679182 + - 0 85699854 85683715 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 87 1.40692438750547 1.49976711358451 1.49976711358451 1.40692438750547 4 - - 14050 Y Y 3.07717480442437 3.54080991072615 3.07717480442437 3 0 0.285971013301193 Y 0 0.990411777488049 N N 9629 1473 ENSG00000133422 ENSG00000184792 + + 22 22 29694187 29633811 utr3p downstream MORC2 OSBP2 29652600 29420063 - + 0 29652767 29637394 - + N - - N HCC1954 2 1.08333333333333 1 1 1 N - - Y - LINE,SINE 0 0.890756302521008 0.890756302521008 12 1.56404284702385 0.849868031031224 1.56404284702385 0.849868031031224 3 - - 16359 N Y 3.41679307359967 3.38503494598603 3.38503494598603 0 0 0.223981981299364 N 0.763739085772984 0.74686330618534 N N 49089 9161 ENSG00000117450 ENSG00000163161 - - 1 2 45760196 127768222 utr5p upstream PRDX1 ERCC3 45749295 127731336 - - 0 45760088 127768808 + + Y - - N HCC1954 6 2.09090909090909 1 4 1 N - - N - SINE 0 1 1 11 0.749883556792257 0.307095170876829 0.749883556792257 0.307095170876829 2 - - 42297 Y Y 3.52936639476796 3.4561676006071 3.4561676006071 213 0 0.660461539002707 Y 0 0.976016743028452 N N 2010 0 ENSG00000138735 ENSG00000209291 + - 4 4 120769429 120574710 downstream upstream PDE5A AC093752.2-3 120635000 120574608 - - 0 120629246 120602489 - + N - - N HCC1954 5 3.42857142857143 2 7 4 N - - Y - - 0 0 0 7 0.549914608314322 0.535631111994469 0.549914608314322 0.535631111994469 3 - - 13784 Y Y 3.62936984425232 3.32639761513537 3.32639761513537 287 0.00348432055749137 0.0100946309718681 Y 0.00348432055749137 0.992507400906447 N N 4291 30294 ENSG00000075240 ENSG00000075275 - - 22 22 45454352 45311731 intron upstream DIP CELSR1 45394963 45134397 + - 0 45401311 45350887 - + N 0.0152716918810117 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.635615586233437 0.528489363834543 0.635615586233437 0.528489363834543 1 0 - 10322 Y Y 3.23896403733493 3.20281953111478 3.20281953111478 0 0.00328947368420984 0.998150074834553 Y 0.00328947368420984 0 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 coding downstream C17orf37 ERBB2 35138937 35104766 - + 0 35139381 35138553 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.707033067832699 0.557056356474248 0.707033067832699 0.557056356474248 2 - - 11941 N N 3.45447218342791 3.57592836747465 3.45447218342791 0 0 0.721558008641199 N 0.0649497894395852 0 N N 33033 10 ENSG00000158470 ENSG00000184650 + + 20 17 47763745 8190088 utr3p upstream B4GALT5 ODF4 47682889 8183913 - + 0 47684684 8179441 - + Y 0.71199463258562 - N HCC1954 1 1 1 0 1 N - - N SINE SINE 0.339285714285714 1 1 5 0.39993789695587 0.278528178237124 0.39993789695587 0.278528178237124 3 0 - 16597 N N 3.63296356710195 3.44719145177281 3.44719145177281 0 0 0.39691108612079 N 0 0 N N 1843 82714 ENSG00000142794 ENSG00000108518 - + 1 17 21684085 4792570 intron coding NBPF3 PFN1 21639217 4789697 + - 0 21658853 4790729 - - Y 1.81942490660726 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 0.271386430077198 0.407079645115797 0.407079645115797 0.271386430077198 2 0 - 16607 N N 3.61513506061274 3.46448140203209 3.46448140203209 0 0 0.658897983904625 N 0 0 N N 3610 33310 ENSG00000198802 ENSG00000077549 + + 17 1 59794509 19684594 intron intron PECAM1 CAPZB 59752964 19537857 - - 0 59753663 19651895 - - Y 0.0207347635602216 5.35175425239081 N HCC1954 2 1.2 1 1 1 N - - N SINE SINE 0.121212121212121 1 1 5 0.471355378555133 0.314236919036755 0.471355378555133 0.314236919036755 2 0 0 33198 N N 2.91783662205815 3.14484171727181 2.91783662205815 9 0 0.999984364692416 N 0 0.0152458705145243 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0152458705145243 8407 14090 - + N 0.984947018030751 - N HCC1954 3 1.63636363636364 1 5 10 N 189 4.09957 N - - 0 0 0 11 1.14982145374813 1.22838068350732 1.22838068350732 1.14982145374813 1 0 - 37453 N N 2.52079822138568 3.50744965188915 2.52079822138568 12 0 0.0430211361355832 N 0 0 N N 122511 169845 ENSG00000187514 ENSG00000080824 - + 2 14 232286495 101675494 coding coding PTMA HSP90AA2 232280638 101617139 + - 0 232284881 101620830 - - Y - - N HCC1954 5 2.6 1 4 1 Y - - N Low_complexity Low_complexity,Low_complexity 0.337837837837838 0.313333333333333 0.337837837837838 5 0.807017542071667 0.828442786551446 0.828442786551446 0.807017542071667 1 - - 41358 N Y 3.60935140704395 3.56960615767593 3.56960615767593 237 0 0.0138750432976096 N 0 0.729957805907173 N N 15880 81 ENSG00000101266 ENSG00000152380 + - 20 5 472482 79873962 coding upstream CSNK2A1 FAM151B 407307 79819556 - + 0.729957805907173 407310 79819256 - - Y 0.0201105869836816 - N HCC1954 21 18.8 13 5 1 N - - N SINE - 1 0 1 5 0.278528178237124 0.349945659836387 0.349945659836387 0.278528178237124 1 0 - 23109 N N 3.34512186274866 3.47592491799029 3.34512186274866 0 0 0.0752945609278726 N 0.19619021134594 0.247497219132369 N N 5782 11775 ENSG00000123836 ENSG00000067082 + - 1 10 205320991 3817455 utr3p downstream PFKFB2 COPEB 205293243 3811260 + - 0.247497219132369 205315546 3759254 + + Y - - N HCC1954 3 2.25 2 4 1 N - - N - SINE 0 1 1 4 0.307095170876829 0.264244681917271 0.307095170876829 0.264244681917271 2 - - 7256 Y Y 3.49744043328497 3.58424216889964 3.49744043328497 256 0 0.00127700648582363 Y 0.981381425233645 0.981381425233645 N N 0 1714 ENSG00000221628 ENSG00000118263 + - 2 2 207842393 207738859 downstream upstream hsa-mir-1302-4 KLF7 207842244 207653774 - - 0 207808441 207759946 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR 1 1 1 6 0.728458312312478 0.978419497909897 0.978419497909897 0.728458312312478 1 - - 49115 Y N 3.47842908506506 3.20551049254209 3.20551049254209 0 0 0.217685188492205 N 0 0.0300486822225953 Y N 0 1302 ENSG00000196570 ENSG00000131187 + - 5 5 176760183 176769183 upstream intron PFN3 F12 176759770 176761747 - - 0.0300486822225953 176771463 176764293 - + N - 35.9936780098463 N HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 5 0.614190341753658 0.664182578873142 0.664182578873142 0.614190341753658 1 - 0 46908 Y Y 3.18445898556383 3.14846594534498 3.14846594534498 335 0 0.895728019938963 Y 0 0.986617249323851 N N 8 2309 ENSG00000131401 ENSG00000131398 + - 19 19 55539830 55524446 downstream coding NAPSB KCNC3 55528871 55507006 - - 0 55528258 55519151 - + N - 5.76520553235895 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 13 1.09982921662864 1.07840397214886 1.09982921662864 1.07840397214886 4 - 0 12376 N Y 3.07101108092519 3.52039024593366 3.07101108092519 1 0 0.354788696385133 N 0.806882753101241 0.878031212484994 N N 1649619 0 ENSG00000141736 ENSG00000221136 - - 17 4 35138441 176631253 coding upstream ERBB2 AC131094.3 35104766 176631147 + + 0 35125066 176503482 - - Y - - N HCC1954 25 21.1666666666667 5 6 1 N - - N - SINE 0 1 1 6 0.449930134075354 0.314236919036755 0.449930134075354 0.314236919036755 1 - - 9829 N Y 3.59528445727371 3.14272214456954 3.14272214456954 0 0 0.189283867801083 Y 0.989500537056928 0.984250805585392 N N 7432 0 ENSG00000178691 ENSG00000210238 - - 17 17 27352162 26053919 coding upstream SUZ12 AC005562.1 27288185 26053650 + - 0 27291418 26060955 - + N - - N HCC1954 4 2.125 1 7 1 N - - N - Simple_repeat 0 0.0103092783505155 0.0103092783505155 8 1.09268746846872 1.14982145374813 1.14982145374813 1.09268746846872 4 - - 35924 N N 3.58913008134434 3.54400240599166 3.54400240599166 3 0 0.0747838670706841 N 0 0 N N 208 975 ENSG00000086159 ENSG00000198487 - + 12 6 48657189 42218335 utr3p coding AQP6 AL512274.9 48652887 42183124 + - 0 48656401 42183238 - - Y - - N HCC1954 36 33 32 17 1 N - - N SINE - 1 0 1 17 0.278528178237124 0.799875793911741 0.799875793911741 0.278528178237124 2 - - 45836 N Y 3.18974812559266 3.62042420064156 3.18974812559266 0 0 0.733153396845954 N 0 0.883805668016194 N N 18437 0 ENSG00000163932 ENSG00000213290 - + 3 19 53201771 12532919 utr5p upstream PRKCD AC010422.7-1 53170263 12531373 + + 0 53174267 12528576 - + Y - - N HCC1954 3 2.8 2 5 1 N - - N - SINE 0 1 1 5 0.692749571512847 0.271386430077198 0.692749571512847 0.271386430077198 2 - - 5483 N N 3.5465630590714 3.53871326596283 3.53871326596283 9 0 0.250160977598339 N 0.515238416554206 0.593848403058929 N N 3641 250 ENSG00000142188 ENSG00000125618 + + 21 2 33774151 113752958 intron intron TMEM50B PAX8 33743321 113690045 - - 0.0173751686909583 33770432 113729440 - - Y 1.23158164287306 4.6738572162301 N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.321378667196682 0.321378667196682 0.278528178237124 0 0 0 13861 N Y 3.41423242051993 3.34934742778406 3.34934742778406 1 0 0.949853816605145 N 0.898364606644861 0.892012394560165 Y N 523 1381 ENSG00000100058 ENSG00000206062 - + 22 22 23957836 24187186 coding upstream CRYBB2 CRYBB2P1 23945612 24183283 + + 0 23953820 24174251 - + N - - N HCC1954 4 1.42105263157895 1 6 3 N - - N - - 0 0 0 19 0.749883556792257 0.942710757110266 0.942710757110266 0.749883556792257 4 - - 33523 N Y 3.5010341561346 3.29959295981186 3.29959295981186 421 0 0.00161689359365602 Y 0 0.990122527692199 N N 240508 275222 ENSG00000198899 ENSG00000198763 - + MT MT 9208 5512 coding coding MT-ATP6 MT-ND2 8528 4471 + + 0 8747 5422 - + N - - N HCC1954 4 2.77777777777778 1 8 2 N - - N - - 0 0 0 9 1.12125446110842 1.48548361726466 1.48548361726466 1.12125446110842 1 - - 3443 N Y 3.59425138750382 3.56232542602083 3.56232542602083 0 0 0.844851336186417 N 0 0.840526315789474 Y N 18589 9593 ENSG00000180530 ENSG00000205726 + + 21 21 15359192 34184448 downstream intron NRIP1 ITSN1 15255427 33936576 - + 0 15240749 34029381 - + N - 1.76309121152043 N HCC1954 20 6.64285714285714 1 6 2 N - - N SINE - 0.986842105263158 0 0.986842105263158 14 1.0069864905496 1.10697096478857 1.10697096478857 1.0069864905496 1 - 0 39778 N N 3.15997224203548 3.59169073442408 3.15997224203548 260 0.730452488687783 0.00729197842330653 N 0 0 N N 38799 899 ENSG00000187446 ENSG00000188312 + + 15 9 39361377 94417267 coding intron AC012652.1 CENPP 39310729 94128043 + + 0 39350048 94351665 + + Y - 2.24746964690453 N HCC1954 40 36.2 21 5 1 N - - N - SINE 0 1 1 5 0.521347615674617 0.299953422716903 0.521347615674617 0.299953422716903 3 - 0 18126 Y Y 3.78784279071799 3.61567361684267 3.61567361684267 451 0 0.00306904702288235 Y 0.542682926829268 0.994803215077605 N N 0 8 ENSG00000187980 ENSG00000158786 + + 1 1 20374274 20349466 downstream downstream PLA2G2C PLA2G2F 20363071 20338406 - + 0 20358712 20353669 - + N - - N HCC1954 15 3 1 65 1 N - - Y LTR LTR 1 1 1 134 1.42834963198525 1.46405837278488 1.46405837278488 1.42834963198525 1 - - 3131 N N 3.07892365476605 3.23999710710482 3.07892365476605 0 0 0.117913931107214 N 0 0.549051490514905 N N 1303 8913 ENSG00000197573 ENSG00000134909 - - 19 11 46148403 128567303 downstream intron CYP2B7P1 AP000751.4-1 46122010 128343052 + - 0 46162091 128516624 - + Y - 8.41376127142953 N HCC1954 40 24 20 5 1 N - - N LINE LINE 1 1 1 5 0.614190341753658 0.335662163516534 0.614190341753658 0.335662163516534 0 - 0 3765 N Y 3.64553343878587 3.67320333000992 3.64553343878587 229 0.889374090247453 0.0172164878059939 N 0.852498786996604 0.870936438622028 N N 36 153380 ENSG00000215557 ENSG00000185275 - + 21 Y 14632206 19614093 upstream utr3p ABCC13 CD24L4 14567991 19611898 + - 0.870936438622028 14552232 19612802 - - Y - - N HCC1954 1 1 1 0 1 N - - N SINE SINE 1 0.291139240506329 1 5 0.321378667196682 0.557056356474248 0.557056356474248 0.321378667196682 1 - - 35867 N Y 3.44615838200292 3.42464286670824 3.42464286670824 0 0 0.388581278727355 N 0 0.794369780432498 N N 3694 12 ENSG00000204520 ENSG00000205592 + + 6 12 31491995 39250827 utr5p downstream MICA MUC19 31475540 39222629 + + 0 31476226 39372659 + + Y - - N HCC1954 29 23.5714285714286 8 7 1 N - - N SINE - 1 0 1 7 0.364229156156239 0.764167053112109 0.764167053112109 0.364229156156239 1 - - 34721 Y Y 3.31063524818594 3.68680627146374 3.31063524818594 0 0 0.690385189363358 Y 0.537182286191747 0.993989380340152 N N 329 1173 ENSG00000218011 ENSG00000182150 - + 9 9 97774767 97770942 coding coding AL159167.23-1 C9orf102 97772706 97677721 + + 0 97772726 97768816 - + N - - N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 39 1.32836515774628 1.37835739486577 1.37835739486577 1.32836515774628 2 - - 36970 N N 2.88048419190053 3.50575423470996 2.88048419190053 10 0 0.0973425452054755 N 0 0 N N 871 19569 ENSG00000084453 ENSG00000088812 + + 12 20 21439638 3579760 utr3p coding SLCO1A2 ATRN 21311651 3399676 - + 0 21319335 3532863 - + Y - 2.05298576817199 N HCC1954 21 19.4117647058824 6 17 1 N 140 25.5595 N LINE,LINE - 1 0 1 17 0.378512652476092 0.956994253430118 0.956994253430118 0.378512652476092 3 - 0 41577 Y Y 3.56228557322748 3.64759957832565 3.56228557322748 0 0 0.966308534500642 Y 0 0 N N 0 0 ENSG00000222231 ENSG00000211422 + - 8 8 77340522 77211212 upstream upstream U2 AC021311.8 77340333 77211077 - - 0 77381128 77237804 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 1 0 1 9 0.521347615674617 0.449930134075354 0.521347615674617 0.449930134075354 4 - - 46817 Y Y 3.5319270478477 3.41216628098015 3.41216628098015 280 0 0.0406899458668586 Y 0.156868131868132 0 N N 6273 119 ENSG00000105677 ENSG00000105679 - + 19 19 40730268 40728061 coding intron TMEM147 GAPDHS 40728372 40716154 + + 0 40728681 40725841 - + N 0.834656489565276 0.291529812144202 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.771308801272036 0.857009779191151 0.857009779191151 0.771308801272036 3 0 0 46314 N Y 3.24735238667343 2.86800244849925 2.86800244849925 0 0.0215538847117795 0.178728524785801 N 0.965055495882564 0.982527747941282 N N 3570 6176 ENSG00000155352 ENSG00000197295 - + 2 19 114073079 21944 utr5p coding FAM39B AC008993.3-2 114058161 13115 + - 0.0215538847117795 114062747 21932 - - Y - 4.85685217683824 N HCC1954 6 3.55 1 13 1 N - - N - - 0 0 0 20 1.32122340958636 0.299953422716903 1.32122340958636 0.299953422716903 1 - 0 36290 N N 3.18445898556383 3.37126417066287 3.18445898556383 0 0 0.13243870099721 N 0 0 Y N 655 0 ENSG00000139133 ENSG00000213677 - - 12 12 34072501 41317210 downstream upstream ALG10 AC079600.19 34066483 41316885 + - 0 34100337 41638669 - + N - - N HCC1954 8 2.44444444444444 1 5 1 N 42 21.288 N - LTR 0 1 1 9 0.885576771830856 0.678466075192994 0.885576771830856 0.678466075192994 2 - - 794 Y Y 3.32374367609979 3.39128260787123 3.32374367609979 255 0.00392156862745097 0.210382163955929 Y 0.00392156862745097 0.980844645550528 N N 2663 642 ENSG00000137478 ENSG00000168010 + + 11 11 72530954 72218326 coding intron FCHSD2 ATG16L2 72225439 72203099 - + 0 72230275 72217679 - + N - 1.49598693867751 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.999844742389676 0.764167053112109 0.999844742389676 0.764167053112109 3 - 0 8794 N Y 3.43511609362884 3.50785087947327 3.43511609362884 6 0.010752688172043 0.130710957066209 N 0.102775693923481 0.792948237059265 N N 1693 317991 ENSG00000144134 ENSG00000171346 - + 2 17 114117439 36932191 utr3p intron RABL2A KRT15 114101286 36923523 + - 0.102775693923481 114116852 36924962 - - Y - 1.61822492111163 N HCC1954 36 32 29 4 1 N - - N SINE SINE 1 0.18 1 4 0.292811674556976 0.357087407996313 0.357087407996313 0.292811674556976 2 - 0 4853 Y Y 3.1986844216336 3.49744043328497 3.1986844216336 0 0.18236848574238 0.317106532211854 Y 0.18236848574238 0.995380612913799 N N 1279 1135 ENSG00000078399 ENSG00000153807 - + 7 7 27175794 27186405 coding utr3p HOXA9 HOXA10 27168583 27176736 - - 0 27171169 27177748 + - N - 1.50844928801702 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.685607823352921 0.671324327033068 0.685607823352921 0.671324327033068 1 - 0 13564 N N 2.61801975075847 2.35026774931265 2.35026774931265 0 0 0.0555552967417517 N 0.0728629329403095 0.61228813559322 N N 10901 0 ENSG00000130635 ENSG00000216847 + - 9 22 136876510 46438016 intron downstream COL5A1 RP11-191L9.5 136673473 46436903 + - 0.61228813559322 136746099 46430370 + + Y 0.535025920034587 - N HCC1954 1 1 1 0 1 N - - N Simple_repeat,Simple_repeat LINE 0.947368421052632 1 1 6 0.542772860154395 0.292811674556976 0.542772860154395 0.292811674556976 1 0 - 35012 N Y 3.43511609362884 3.29280674169672 3.29280674169672 0 0 0.549316966803863 N 0.993690541709254 0.993690541709254 N N 13649 111 ENSG00000148110 ENSG00000188152 + + 9 9 96263022 98744393 coding downstream HIATL1 FAM22G 96176654 98721960 + + 0 96240630 98745258 + + N - - Y HCC1954 4 4 4 5 2 N 261 23.4476 N - - 0 0 0 5 0.842726282871298 0.792734045751814 0.842726282871298 0.792734045751814 1 - - 40934 Y N 3.07051656738523 3.36344488277784 3.07051656738523 0 0 0.155224747753867 Y 0 0 N N 9033 0 ENSG00000166619 ENSG00000213979 + - 20 20 35589717 35507363 utr5p downstream BLCAP AL133293.28 35579233 35506549 - - 0 35589651 35488286 - + N 1.24321626789795 - N HCC1954 1 1 1 0 1 N - - Y Simple_repeat - 1 0 1 11 0.321378667196682 0.428504889595575 0.428504889595575 0.321378667196682 1 0 - 17322 Y Y 3.50744965188915 3.19872427442695 3.19872427442695 0 0.00767375012832361 0.9064126166965 Y 0.905990144748999 0.994777230263833 N N 10731 43044 ENSG00000160741 ENSG00000143570 - + 1 1 152197725 152206812 coding coding CRTC2 SLC39A1 152186775 152198210 - - 0 152197445 152199673 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 31 1.31408166142643 1.5783263433437 1.5783263433437 1.31408166142643 2 - - 48657 N N 2.47126085141401 3.41526549028982 2.47126085141401 8 0.413003095975232 0.0806399494929246 N 0.465413533834586 0.454931446262716 N N 179 850768 ENSG00000169252 ENSG00000075624 + - 5 7 148188381 5536758 downstream utr3p ADRB2 ACTB 148186349 5533313 + - 0.454931446262716 148215482 5533763 + + Y - 0.980591607573384 N HCC1954 4 3.25 1 3 1 N - - N DNA,Simple_repeat - 0.805555555555556 0 0.805555555555556 4 0.257102933757345 0.435646637755502 0.435646637755502 0.257102933757345 1 - 0 2430 N Y 3.353603498043 3.65016023140539 3.353603498043 235 0.018686401480111 0.0147693108414964 N 0.927844588344126 0.927844588344126 N N 3567 2923 ENSG00000177951 ENSG00000107362 - + 11 9 197428 73715968 coding utr3p BET1L FAM108B1 157784 73667188 - - 0 195611 73670473 + - Y - - N HCC1954 144 92.5 84 10 1 N - - N - SINE 0 1 1 10 0.707033067832699 0.28566992639705 0.707033067832699 0.28566992639705 3 - - 44820 N Y 3.53209488171704 3.3755202409218 3.3755202409218 246 0 0.119733720175223 Y 0.988143631436314 0.976287262872629 N N 82 82 ENSG00000214562 ENSG00000214562 - + 10 10 88984892 88984892 downstream upstream FAM22A FAM22A 88975185 88975185 + + 0 88995852 88958249 - + N - - N HCC1954 4 1.3 1 1 1 N - - N SINE SINE 1 1 1 10 0.45707188223528 0.449930134075354 0.45707188223528 0.449930134075354 4 - - 2943 N N 3.6800200533486 3.41103992525442 3.41103992525442 1 0 0.501323426641935 N 0 0 N N 38341 207 ENSG00000109475 ENSG00000186714 + - 4 11 109771086 32772763 coding intron RPL34 CCDC73 109761182 32580202 + - 0 109765775 32736716 + + Y - 3.64059092218427 N HCC1954 4 2.33333333333333 1 5 1 N - - N - - 0 0 0 6 0.421363141435649 0.257102933757345 0.421363141435649 0.257102933757345 1 - 0 49264 Y Y 3.47961192679575 2.72142344593906 2.72142344593906 108 0 0.0724633059583781 Y 0.98027659908848 0.99013829954424 N N 682 746 ENSG00000164181 ENSG00000049167 - + 5 5 60119016 60276648 utr5p downstream ELOVL7 ERCC8 60083376 60205415 - - 0 60119016 60175745 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.692749571512847 0.721316564152552 0.721316564152552 0.692749571512847 2 - - 6366 N N 2.66645438585154 2.59114959935755 2.59114959935755 0 0.281789260580353 0.182972730835701 N 0.281789260580353 0.190205340788586 N N 131026 29655 ENSG00000115053 ENSG00000136938 - + 2 9 232037449 99818046 coding coding NCL ANP32B 232027706 99785310 - + 0.190205340788586 232034670 99813449 + + Y - - N HCC1954 1 1 1 0 2 Y - - N Simple_repeat,Simple_repeat Low_complexity,Low_complexity 0.337209302325581 0.156565656565657 0.337209302325581 5 1.19267194270768 1.1426797055882 1.19267194270768 1.1426797055882 1 - - 47959 N N 3.53039946453785 3.38440310380026 3.38440310380026 6 0.0456911509543089 0.99999761580893 N 0.0456911509543089 0.0456911509543089 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0.0456911509543089 117944556 2617193 - + Y 1.05196738598717 - N HCC1954 2 1.42857142857143 1 3 12 N 282 1.61558 N - - 0 0 0 7 0.628473838073511 0.735600060472404 0.735600060472404 0.628473838073511 2 0 - 43238 N N 3.09608046627615 3.01979452572055 3.01979452572055 0 0 0.0665566516616394 N 0 0 N N 11845 166846 ENSG00000148735 ENSG00000142192 - + 10 21 115533178 26465003 downstream coding C10orf81 APP 115501203 26174733 + - 0 115536537 26316187 - - Y - - N HCC1954 3 2.4 2 5 1 N - - N Low_complexity Low_complexity 0.567567567567568 0.675 0.675 5 0.264244681917271 0.5713398527941 0.5713398527941 0.264244681917271 1 - - 40747 N N 3.48230056095149 3.37808089400154 3.37808089400154 34 0 0.257229335676226 N 0.922513524760716 0.147648772367873 N N 56 695 ENSG00000181092 ENSG00000149531 - + 3 20 188058944 28265815 downstream coding ADIPOQ FRG1B 188043157 28225518 + + 0.147648772367873 188073792 28246382 - + Y - 27.3202787919018 N HCC1954 40 35.5 22 4 1 N - - N Other - 1 0 1 4 0.642757334393363 0.521347615674617 0.642757334393363 0.521347615674617 2 - 0 10959 N Y 3.12328634918378 2.99930936485065 2.99930936485065 216 0 0.086852693473266 N 0.983945639187575 0.983945639187575 N N 4310 2906 ENSG00000183011 ENSG00000079819 - - 17 6 7701897 131426017 coding downstream LSMD1 EPB41L2 7700730 131202180 - - 0 7701426 131164595 + + Y - - N HCC1954 3 1.77777777777778 1 5 2 N - - N - Other 0 0.037037037037037 0.037037037037037 9 1.13553795742827 0.964136001590045 1.13553795742827 0.964136001590045 2 - - 34414 Y Y 3.35104284496326 3.51889316784735 3.35104284496326 323 0 0.81020732126565 Y 0 0.990321320147885 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5596667 5567513 - + N - - N HCC1954 20 7.07692307692308 1 9 7 N - - Y LTR LTR 1 1 1 13 0.799875793911741 0.714174815992626 0.799875793911741 0.714174815992626 1 - - 30163 N Y 3.40016547074969 3.41167176744019 3.40016547074969 1 0 0.459485327764622 N 0.00330033003300323 0.768209379077443 N N 0 31116 ENSG00000222476 ENSG00000112297 - + 9 6 9432367 107125028 intron utr3p SRP_euk_arch AIM1 9432060 107066423 + + 0.420523447693607 9432103 107123925 - + Y 1 2.19252640906946 N HCC1954 35 14.2 7 5 1 N - - N srpRNA SINE 1 0.986111111111111 1 5 0.45707188223528 0.51420586751469 0.51420586751469 0.45707188223528 2 0 0 33127 N Y 3.10140945909833 3.26766699832887 3.10140945909833 397 0 0.0100880359625642 Y 0 0.993880483998084 N N 59837 275222 ENSG00000198695 ENSG00000198763 + + MT MT 14674 5512 coding coding MT-ND6 MT-ND2 14150 4471 - + 0 14171 5421 - + N 0.348728222753458 1.18316631692041 N HCC1954 2 1.33333333333333 1 2 3 N - - N - - 0 0 0 6 0.614190341753658 1.21409718718746 1.21409718718746 0.614190341753658 1 0 0 18161 Y Y 3.71041843152174 2.81713097237113 2.81713097237113 320 0 0.00549659741786845 Y 0.0414663461538461 0.913731971153846 N N 1725 19 ENSG00000196369 ENSG00000203846 - + 1 1 142805834 142626072 upstream upstream SRGAP2P2 CR589924.4 142627547 142625689 + + 0.913731971153846 142627050 142625224 - + N - - N HCC1954 6 3.05263157894737 1 18 1 N - - Y - - 0 0 0 19 0.807017542071667 1.05697872766909 1.05697872766909 0.807017542071667 3 - - 31726 Y Y 3.09756396399333 3.54975555433691 3.09756396399333 32 0 0.999198212742074 Y 0.0331742698988358 0.992326779919832 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 utr5p upstream LPP AC022498.18 189413415 189379637 + + 0 189425889 189353847 - + N - - N HCC1954 1 1 1 0 7 N - - Y SINE SINE 0.0271317829457364 1 1 19 1.549759350704 0.928427260790413 1.549759350704 0.928427260790413 1 - - 10280 N N 2.92807923437712 3.58424216889964 2.92807923437712 0 0 0.104494861702174 N 0 0 N N 313916 20747 ENSG00000131748 ENSG00000073605 + - 17 17 35073248 35328429 intron utr5p STARD3 GSDMB 35046938 35314374 + - 0 35047054 35327101 + + N 1.09830374749134 3.1174035746532 Y HCC1954 1 1 1 0 1 N 313 17.1696 N - - 0 0 0 4 0.671324327033068 0.671324327033068 0.671324327033068 0.671324327033068 1 0 0 16439 N Y 3.64081336021051 3.684245618384 3.64081336021051 4 0.00411522633744843 0.670337239288171 N 0.00411522633744843 0 N N 30311 0 ENSG00000082898 ENSG00000220333 - - 2 1 61618922 162579726 utr5p upstream XPO1 RP11-541J2.1 61558488 162578866 - + 0 61617349 162437394 + - Y - - N HCC1954 11 7.5 2 4 1 N - - N - SINE 0 1 1 4 0.471355378555133 0.321378667196682 0.471355378555133 0.321378667196682 3 - - 37075 N N 3.13743300454072 3.46551447180198 3.13743300454072 0 0 0.0739536217469553 N 0 0 N N 0 1574 ENSG00000182225 ENSG00000178449 + + 19 12 5527949 48800501 downstream intron AC011533.6 C12orf62 5527671 48792167 - + 0 5518557 48795230 - + Y - 1.13412487608059 N HCC1954 23 22.25 21 4 1 N - - N - SINE 0 1 1 4 0.485638874874985 0.278528178237124 0.485638874874985 0.278528178237124 2 - 0 36933 N N 2.92395114519417 3.7061623612628 2.92395114519417 0 0 0.106039260360015 N 0 0 N N 3 12084 ENSG00000179242 ENSG00000177119 - + 20 12 59945671 44112391 intron coding CDH4 ANO6 59260965 43896170 + + 0 59589593 44058104 - + Y 0.929733246584255 - N HCC1954 1 1 1 0 1 N - - N LTR - 0.945054945054945 0 0.945054945054945 4 0.649899082553289 0.749883556792257 0.749883556792257 0.649899082553289 2 0 - 36418 Y Y 3.47911741325579 3.21063179870157 3.21063179870157 251 0 0.00737259333481688 Y 0.808764940239044 0.99203187250996 N N 139 0 ENSG00000118596 ENSG00000202471 - - 12 12 58461674 58266991 upstream upstream SLC16A7 U4 58369393 58266841 + - 0 58335201 58276285 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.442788385915428 0.521347615674617 0.521347615674617 0.442788385915428 1 - - 34344 Y Y 3.26356941436947 3.70144228268744 3.26356941436947 272 0 0.687385478680292 Y 0 0.979666866746699 N N 179 30778 ENSG00000196366 ENSG00000148396 - - 9 9 138500339 138491962 upstream utr5p C9orf163 SEC16A 138497768 138454370 + - 0 138497211 138491957 - + N - 59.679809178948 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.51420586751469 0.392796148795944 0.51420586751469 0.392796148795944 4 - 0 47645 N Y 3.67423639977982 3.48167806633553 3.48167806633553 5 0 0.194875573559884 N 0.943755929791271 0.943755929791271 N N 3702 779 ENSG00000167232 ENSG00000213096 - + 19 19 23370109 24104483 coding upstream ZNF91 ZNF254 23332341 24061816 - + 0 23349405 24024191 + + N 1.72878696391083 - Y HCC1954 5 2.83333333333333 2 6 1 Y - - N - Satellite 0 0.685714285714286 0.685714285714286 6 0.564198104634174 0.871293275511003 0.871293275511003 0.564198104634174 1 0 - 37458 N Y 3.37287988225536 3.44785379918211 3.37287988225536 20 0 0.0543645219733313 N 0 0.929499759321657 N N 3528 936 ENSG00000163093 ENSG00000151338 - - 2 14 170071410 37090214 utr3p downstream BBS5 MIPOL1 170044239 36736907 + + 0.153997111859888 170069800 37105946 - - Y - - N HCC1954 24 23.8888888888889 22 27 1 N - - N Other SINE 1 1 1 27 0.557056356474248 0.599906845433805 0.599906845433805 0.557056356474248 1 - - 23732 N N 3.2793317813189 3.45976132345673 3.2793317813189 0 0 0.223542978845248 N 0 0.138128137581391 N N 6135 43495 ENSG00000134744 ENSG00000105220 - + 1 19 52791331 39583076 utr3p downstream ZCCHC11 GPI 52661538 39547909 - + 0 52700710 39584382 + + Y - - N HCC1954 37 35.75 34 4 1 N - - N SINE SINE 1 1 1 4 0.314236919036755 0.34280391167646 0.34280391167646 0.314236919036755 3 - - 32494 N N 3.70040921291756 3.55809986098544 3.55809986098544 0 0 0.732573765163743 N 0 0 N N 64614 417 ENSG00000104341 ENSG00000172986 + + 8 3 98934002 73107077 utr3p upstream LAPTM4B GLT8D4 98856985 73020075 + + 0 98933699 73017375 + + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.585623349113953 0.242819437437493 0.585623349113953 0.242819437437493 1 - - 40362 N Y 3.24735238667343 2.86800244849925 2.86800244849925 0 0.0215538847117795 0.178567237910954 N 0.965055495882564 0.982527747941282 N N 4838 6176 ENSG00000185596 ENSG00000197295 - + 15 19 100334282 21944 coding coding FAM39B AC008993.3-2 100319118 13115 + - 0.0215538847117795 100330318 21932 - - Y - 4.85685217683824 N HCC1954 6 3.95833333333333 1 17 1 N - - N - - 0 0 0 24 1.4140661356654 0.299953422716903 1.4140661356654 0.299953422716903 1 - 0 38154 Y Y 3.55504469436573 3.5246463161926 3.5246463161926 198 0 0.0159301200637069 Y 0.980491186373539 0.960982372747079 N N 3478 0 ENSG00000182512 ENSG00000212530 - - 14 14 95080808 95069719 upstream downstream GLRX5 SCARNA13 95071076 95069445 + - 0.960982372747079 95070683 95069151 - + N - - N HCC1954 2 1.09090909090909 1 1 1 N - - Y - - 0 0 0 11 0.899860268150708 1.04269523134923 1.04269523134923 0.899860268150708 4 - - 44216 N Y 3.35975787397237 3.30232144676095 3.30232144676095 9 0.0415303297256482 0.0650753727615951 N 0.0415303297256482 0.845960231563051 N N 5301 0 ENSG00000107771 ENSG00000213113 - + 10 3 86268256 199332046 utr3p downstream KIAA1128 AC073135.3-1 86078322 199330983 + + 0.0928769192046313 86265264 199368867 - + Y - - N HCC1954 156 150.4 148 5 1 N - - N SINE - 1 0 1 5 0.28566992639705 0.321378667196682 0.321378667196682 0.28566992639705 2 - - 31376 Y Y 3.43465208531242 3.66592259835483 3.43465208531242 0 0 0.620689311260544 Y 0.973059876596854 0.993264969149214 N N 0 4815 ENSG00000214041 ENSG00000196220 - - 3 3 9365876 9266311 upstream intron AC026191.4-1 SRGAP3 9365127 8997278 + - 0 9342696 9141603 - + N - 0.74037240313532 N HCC1954 5 1.38461538461538 1 2 1 N - - Y LTR,LTR - 1 0 1 13 1.1426797055882 1.09268746846872 1.1426797055882 1.09268746846872 2 - 0 34076 N Y 3.38755574627241 3.51832410639388 3.38755574627241 2 0 0.0224504183582653 N 0.856093080220453 0.856093080220453 N N 916 3348 ENSG00000180815 ENSG00000165105 + - X 9 19443300 84867863 utr3p upstream MAP3K15 RASEF 19288095 84787144 - - 0.0214329454990813 19288436 84868068 - + Y - - N HCC1954 22 21.5 21 8 1 N - - N SINE - 1 0 1 8 0.307095170876829 0.621332089913584 0.621332089913584 0.307095170876829 1 - - 49099 Y Y 3.5816815158199 3.33680806132368 3.33680806132368 278 0 0.00519859855005489 Y 0 0 N N 17162 26 ENSG00000113161 ENSG00000145700 - - 5 5 74693681 74568459 upstream upstream HMGCR ANKRD31 74668855 74478817 + - 0 74666557 74607149 - + N - - N HCC1954 3 1.75 1 2 1 N - - Y LTR - 0.719101123595506 0 0.719101123595506 4 0.635615586233437 0.664182578873142 0.664182578873142 0.635615586233437 2 - - 40215 N N 2.94288307947016 3.09773603066199 2.94288307947016 0 0 0.655246464916975 N 0 0 N N 0 59828 ENSG00000200216 ENSG00000130702 + - 15 20 68272737 60375763 downstream intron U6 LAMA5 68272629 60317516 + - 0 68334176 60341400 + + Y - 1.31407360942352 N HCC1954 6 3.2 1 4 1 N 404 15.1049 N Simple_repeat - 0.95 0 0.95 5 0.428504889595575 0.842726282871298 0.842726282871298 0.428504889595575 2 - 0 5317 N Y 3.353603498043 3.56591914887046 3.353603498043 0 0 0.67769030141923 N 0.748271889400922 0.759216589861751 N N 17694 4653 ENSG00000153827 ENSG00000137364 - + 2 6 230494912 18263353 utr5p utr3p TRIP12 TPMT 230340174 18236526 - - 0 230453088 18238370 + - Y - - N HCC1954 22 21 20 4 1 N - - N - SINE 0 1 1 4 0.471355378555133 0.335662163516534 0.471355378555133 0.335662163516534 4 - - 33092 N Y 3.02448896101185 2.72548055699787 2.72548055699787 0 0 0.770597131171111 Y 0.106716417910448 0 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0 10856 5281 - + N 0.348862456747628 0.974309371977727 N HCC1954 6 2 1 1 4 N - - N - - 0 0 0 5 1.04983697950916 0.714174815992626 1.04983697950916 0.714174815992626 1 0 0 21685 N Y 3.46145674063593 3.54080991072615 3.46145674063593 1 0 0.171962058098139 N 0.903439153439153 0.903439153439153 N N 23977 16186 ENSG00000160691 ENSG00000106723 - + 1 9 153213476 90283443 coding utr5p SHC1 SPIN1 153201398 90193117 - + 0.0895691609977324 153209299 90221477 + + Y - - N HCC1954 22 21.25 21 4 2 N 477 22.2351 N - SINE 0 1 1 4 0.421363141435649 0.371370904316165 0.421363141435649 0.371370904316165 2 - - 29959 N N 3.54400240599166 3.49487978020523 3.49487978020523 0 0 0.0804500860595934 N 0 0 N N 975 0 ENSG00000198487 ENSG00000222864 + - 6 X 42218335 34984496 coding upstream AL512274.9 AL596268.5 42183124 34984369 - - 0 42183238 35090389 - + Y - - N HCC1954 24 19.125 6 8 1 N - - N - SINE 0 1 1 8 0.392796148795944 0.292811674556976 0.392796148795944 0.292811674556976 2 - - 28713 N Y 3.35000977519337 3.33098455496154 3.33098455496154 1 0 0.292321939140424 N 0 0.723479135243841 N N 13096 1303 ENSG00000166164 ENSG00000197573 - - 16 19 48960346 46148403 utr3p downstream BRD7 CYP2B7P1 48910442 46122010 - + 0.709653092006033 48940574 46162184 + - Y - - N HCC1954 62 34.5 21 6 1 N 593 26.9304 N LINE LINE 1 1 1 6 0.435646637755502 0.928427260790413 0.928427260790413 0.435646637755502 2 - - 26691 Y Y 3.49272035470961 3.00293359292381 3.00293359292381 346 0.00289017341040465 0.175161016100109 Y 0.438713011522413 0.986793247329939 N N 2486 2586 ENSG00000121281 ENSG00000121274 - + 16 16 48909547 48826722 utr5p downstream ADCY7 PAPD5 48857979 48745280 + + 0 48879324 48837615 - + N 0.0426598017370692 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.12258064516129 0.12258064516129 29 1.32122340958636 1.10697096478857 1.32122340958636 1.10697096478857 4 0 - 47555 N Y 3.17151839151932 3.31059539539258 3.17151839151932 0 0 0.549539813181443 Y 0.992724899695461 0.992724899695461 N Y 785 46239 ENSG00000167644 ENSG00000167642 - + 19 19 43487486 43474948 coding coding C19orf33 SPINT2 43486644 43447042 + + 0 43486855 43473055 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 1.07840397214886 0.928427260790413 1.07840397214886 0.928427260790413 4 - - 42554 Y N 3.36609132911919 3.2484388896058 3.2484388896058 8 0 0.633227398343375 Y 0.30875 0.30875 N N 1004 3530 ENSG00000007062 ENSG00000169762 - + 4 4 15694766 15837259 utr5p downstream PROM1 TAPT1 15574385 15771226 - - 0.30875 15686750 15736517 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.764167053112109 0.557056356474248 0.764167053112109 0.557056356474248 2 - - 24555 N N 3.26932256271472 2.28617672677823 2.28617672677823 1 0 0.134140240237956 N 0 0 N N 1992 14651 ENSG00000003436 ENSG00000134440 - - 2 18 188127464 53440175 intron upstream TFPI NARS 188037202 53418894 - - 0 188120677 53452141 + + Y 11.2383441972674 - N HCC1954 24 21.25 20 4 1 N - - N - Other 0 1 1 4 0.28566992639705 0.449930134075354 0.449930134075354 0.28566992639705 1 0 - 37580 N N 3.57592836747465 3.50525037360018 3.50525037360018 0 0 0.144563158275390 N 0.227777777777777 0.227777777777777 N N 8199 0 ENSG00000170043 ENSG00000165379 - + 17 14 7775988 41443498 utr5p downstream TRAPPC1 LRFN5 7774392 41146523 - + 0.227777777777777 7775875 41466730 + + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 13 0.835584534711372 0.264244681917271 0.835584534711372 0.264244681917271 1 - - 34760 Y Y 3.33375289470397 3.04729227420005 3.04729227420005 0 0.265957446808511 0.134252099075635 Y 0.297872340425532 0.840425531914894 N N 3463 188 ENSG00000160408 ENSG00000136840 - + 9 9 129701753 129719126 coding downstream ST6GALNAC6 ST6GALNAC4 129687421 129709987 - - 0 129698399 129706736 + - N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 5 0.592765097273879 0.707033067832699 0.707033067832699 0.592765097273879 1 - - 47934 N N 3.53871326596283 3.7297745213208 3.53871326596283 0 0 0.999958844390614 N 0 0 N N 0 86504 ENSG00000182152 ENSG00000104408 + + 5 8 117142614 109330135 downstream coding AC114322.2 EIF3E 117142420 109283149 - - 0 116899106 109296012 - - Y - - N HCC1954 2 1.21739130434783 1 15 7 N 241 0.00319582 N - - 0 0 0 69 1.19981369086761 1.20695543902754 1.20695543902754 1.19981369086761 4 - - 47367 Y Y 3.17151839151932 3.39015625214551 3.17151839151932 0 0.00289855072463752 0.994269450051947 Y 0.849275362318841 0.976811594202899 N N 4159 60677 ENSG00000012061 ENSG00000125740 - - 19 19 50619017 50670254 utr5p upstream ERCC1 FOSB 50604712 50663093 - + 0 50618479 50644271 + - N - - N HCC1954 1 1 1 0 4 N - - Y - SINE 0 1 1 19 1.42834963198525 0.599906845433805 1.42834963198525 0.599906845433805 4 - - 44728 Y Y 3.41489476792923 3.56658149627977 3.41489476792923 332 0 0.0103298076330304 Y 0 0 N N 1446 4873 ENSG00000152455 ENSG00000187522 - + 10 10 14986308 14953744 upstream coding SUV39H2 HSPA14 14960868 14920231 + + 0 14960438 14949886 - + N - 2.60472358967776 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 1.27123117246687 1.15696320190805 1.27123117246687 1.15696320190805 1 - 0 18478 Y Y 3.62295434849776 3.19975734419684 3.19975734419684 168 0 0.00355111984103273 Y 0.955820105820106 0.933730158730159 N N 319 0 ENSG00000162390 ENSG00000218563 - + 1 1 54873005 54776019 intron downstream ACOT11 RP5-866L20.3 54786489 54775057 + + 0 54822913 54780592 - + N 0.146066253777476 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.607048593593732 0.749883556792257 0.749883556792257 0.607048593593732 1 0 - 31150 Y Y 3.63296356710195 3.52833332499807 3.52833332499807 267 0 0.0776730093131857 Y 0.893258426966292 0.988139825218477 N N 0 2527 ENSG00000199306 ENSG00000186001 - + 3 3 199105881 199082851 upstream downstream U6 LRCH3 199105775 199002542 + + 0 199094807 199087041 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 42 1.37835739486577 0.692749571512847 1.37835739486577 0.692749571512847 2 - - 19613 N Y 3.41679307359967 3.52208566311286 3.41679307359967 1 0 0.110970799772556 N 0.86718954248366 0.86718954248366 N N 49089 1312 ENSG00000117450 ENSG00000101624 - - 1 18 45760196 12692703 utr5p intron PRDX1 CEP76 45749295 12662632 - - 0 45760088 12663863 + + Y - 0.2327650174634 N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.264244681917271 0.39993789695587 0.264244681917271 1 - 0 48806 Y Y 3.34785034969775 3.46128890676658 3.34785034969775 313 0.0378061767838127 0.133881870609869 Y 0.0378061767838127 0.98615548455804 N N 55216 1458 ENSG00000028310 ENSG00000188818 + - 5 5 945915 904101 downstream coding BRD9 ZDHHC11 916856 848722 - - 0 912716 903717 - + N - 3.56801771905363 N HCC1954 2 1.4 1 14 2 N - - Y LTR - 0.726666666666667 0 0.726666666666667 35 1.07126222398894 1.24266417982717 1.24266417982717 1.07126222398894 4 - 0 13742 Y Y 3.64553343878587 3.55504469436574 3.55504469436574 262 0 0.992222585420191 Y 0.470283533260632 0.992093784078517 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 upstream upstream AP000347.3 AP000347.4 22321400 22310865 - - 0 22332054 22312613 - + N - - N HCC1954 8 2.4 1 1 6 N - - Y - - 0 0 0 5 0.742741808632331 0.799875793911741 0.799875793911741 0.742741808632331 4 - - 38455 Y Y 3.28292550416853 3.65128658713112 3.28292550416853 118 0.00395256916996056 0.73431294752429 Y 0.683075817463169 0.988681279195113 N N 7970 10628 ENSG00000029364 ENSG00000100632 - - 14 14 68997021 68934774 coding upstream SLC39A9 ERH 68935162 68916601 + - 0 68935934 68934918 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 21 0.642757334393363 0.614190341753658 0.642757334393363 0.614190341753658 2 - - 24760 Y Y 3.62295434849776 3.60000453584907 3.60000453584907 253 0 0.0678751170210612 Y 0.988142292490119 0.976284584980237 N N 6908 5333 ENSG00000119541 ENSG00000119537 + - 18 18 59240732 59185486 downstream upstream VPS4B FVT1 59207407 59145951 - - 0 59199590 59186072 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 7 0.557056356474248 0.528489363834543 0.557056356474248 0.528489363834543 4 - - 38431 Y Y 3.54872248456702 3.41679307359967 3.41679307359967 326 0 0.0158146557557729 Y 0.993846095584337 0.993846095584337 N N 1060 1919 ENSG00000215256 ENSG00000157326 - - 14 14 23492716 23508326 coding intron AL136419.3-2 DHRS4 23479414 23492805 - + 0 23492623 23493798 + - N - 1.17446036476122 N HCC1954 2 1.7 1 7 1 N - - Y LTR - 0.432748538011696 0 0.432748538011696 10 1.19981369086761 1.04983697950916 1.19981369086761 1.04983697950916 2 - 0 26672 Y Y 3.61360747730288 3.74913061111987 3.61360747730288 244 0 0.0168447401894551 Y 0.448054513134505 0.976002370136283 N N 1518 0 ENSG00000175643 ENSG00000199668 - + 16 16 11353118 11316536 upstream upstream C16orf75 Y_RNA 11318137 11316425 + + 0 11317497 11314294 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.965811965811966 0 0.965811965811966 9 0.835584534711372 0.492780623034912 0.835584534711372 0.492780623034912 2 - - 27191 Y Y 3.34615493251855 3.23739660123173 3.23739660123173 0 0.439516129032258 0.260270092501285 Y 0.439516129032258 0 N N 1307 99 ENSG00000170100 ENSG00000182157 - - 16 16 87822471 87794030 utr5p upstream ZNF778 AC009113.8-3 87811612 87789935 + - 0 87811819 87796180 - + N - - N HCC1954 2 1.1 1 1 1 N - - Y - - 0 0 0 10 0.892718519990782 0.721316564152552 0.892718519990782 0.721316564152552 2 - - 16530 N N 3.08784637043786 3.28552601004162 3.08784637043786 2 0.00361010830324915 0.126513765445324 N 0.276431150077359 0.0273336771531718 N N 0 317991 ENSG00000220375 ENSG00000171346 - - 1 17 558984 36932191 intron coding RP5-857K21.14 KRT15 558778 36923523 + - 0.0273336771531718 558801 36928462 - + Y 1 15.2303329138735 N HCC1954 2 2 2 7 1 N - - N - Simple_repeat 0 0.645390070921986 0.645390070921986 7 0.45707188223528 0.907002016310634 0.907002016310634 0.45707188223528 2 0 0 24390 N Y 3.24893340314576 3.65384724021086 3.24893340314576 0 0 0.894928394690226 N 0.368869282439493 0.963935387567971 N N 0 2527 ENSG00000206696 ENSG00000186001 + + 18 3 45272097 199082851 upstream intron SNORD58 LRCH3 45272032 199002542 - + 0.963935387567971 45272639 199062232 - + Y - 1.31517858497148 N HCC1954 8 4.80952380952381 1 20 2 N - - N - - 0 0 0 21 0.728458312312478 0.942710757110266 0.942710757110266 0.728458312312478 3 - 0 19080 Y Y 3.51423587000429 3.68953475841283 3.51423587000429 271 0 0.84614917489485 Y 0 0 N N 17101 0 ENSG00000162407 ENSG00000219539 + - 1 1 56817845 56446716 downstream upstream PPAP2B RP4-710M16.1 56733023 56445827 - - 0 56613665 56570668 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 5 0.535631111994469 0.799875793911741 0.799875793911741 0.535631111994469 2 - - 46925 N Y 2.54888354970315 3.50844286886569 2.54888354970315 265 0 0.0164021852198419 Y 0.873895390494387 0.987389539049439 N N 4351 16224 ENSG00000105127 ENSG00000141867 + - 19 19 15351603 15252262 downstream intron AKAP8 BRD4 15325341 15209301 - - 0 15303648 15244945 - + N - 136.936834393603 N HCC1954 21 1.55555555555556 1 1 2 N - - N Low_complexity,Simple_repeat - 0.468354430379747 0 0.468354430379747 36 0.564198104634174 1.37835739486577 1.37835739486577 0.564198104634174 1 - 0 41536 Y Y 3.04267884229183 3.2493439782997 3.04267884229183 297 0 0.0116489030760006 Y 0.830360340998639 0.992931680874943 N N 0 278 ENSG00000188653 ENSG00000196922 - - 8 8 146191701 146174741 upstream upstream AF235103.4-2 ZNF252 146191064 146173476 + - 0 146190668 146174742 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 23 1.05697872766909 1.0069864905496 1.05697872766909 1.0069864905496 1 - - 36999 N N 3.54296933622177 3.13383928169109 3.13383928169109 0 0 0.946240095529148 N 0 0.0144676427271939 N N 2 20154 ENSG00000185610 ENSG00000168575 + + 12 8 43731149 42516225 intron intron DBX2 SLC20A2 43694806 42393173 - - 0.0144676427271939 43710507 42468436 - - Y 0.880880880880881 36.1317356738638 N HCC1954 1 1 1 0 4 N 141 0.300921 N - - 0 0 0 7 0.857009779191151 0.642757334393363 0.857009779191151 0.642757334393363 1 0 0 4823 N Y 3.74656995804013 2.68016419363033 2.68016419363033 0 0 0.240288880386742 Y 0 0 N N 310 4094 ENSG00000105991 ENSG00000105997 - + 7 7 27102150 27158458 coding intron HOXA1 HOXA3 27099141 27112334 - - 0 27101553 27119821 + - N - 48.60832586124 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.785592297591888 0.757025304952183 0.785592297591888 0.757025304952183 1 - 0 48912 Y Y 3.40951234194457 3.43101850966944 3.40951234194457 0 0 0.631627160049723 Y 0 0.99196546348483 N N 0 3135 ENSG00000211056 ENSG00000164300 + - 5 5 79571163 79534810 upstream upstream AC010260.7 SERINC5 79571064 79466607 - - 0 79587473 79536937 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.892561983471074 0.892561983471074 10 0.771308801272036 0.864151527351077 0.864151527351077 0.771308801272036 1 - - 24378 N N 3.40385247955516 3.4048456965317 3.40385247955516 0 0 0.638391302585293 N 0 0.671738517892364 N N 64 13271 ENSG00000166432 ENSG00000081923 + - X 18 101073656 53550037 coding upstream ZMAT1 ATP8B1 101023918 53464656 - - 0 101060142 53550059 - + Y - - N HCC1954 24 22 21 5 1 N - - N SINE - 1 0 1 5 0.349945659836387 0.414221393275723 0.414221393275723 0.349945659836387 4 - - 47194 Y Y 3.57489529770476 3.38383404234679 3.38383404234679 168 0.00313479623824464 0.175652423338132 Y 0.00313479623824464 0 N N 12432 21579 ENSG00000105373 ENSG00000024422 - + 19 19 52957851 52938202 upstream coding GLTSCR2 EHD2 52940620 52908502 + + 0 52939608 52931602 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.315068493150685 0 0.315068493150685 18 1.04269523134923 1.24980592798709 1.24980592798709 1.04269523134923 4 - - 46716 N N 3.17035218300025 3.46448140203209 3.17035218300025 0 0.0117113377609109 0.680078720569973 N 0.0117113377609109 0 N N 21579 439 ENSG00000024422 ENSG00000159917 - + 19 19 52938202 49505441 upstream coding EHD2 ZNF235 52908502 49482440 + - 0 52908269 49494803 - - N - - Y HCC1954 1 1 1 0 1 N 37 5.43387 N - - 0 0 0 9 0.871293275511003 0.87843502367093 0.87843502367093 0.871293275511003 1 - - 6793 N Y 3.26191384998362 3.1541351553042 3.1541351553042 185 0 0.00471288607722153 Y 0 0 N N 4786 4 ENSG00000135966 ENSG00000135973 + + 2 2 105312561 105226356 coding downstream TGFBRAP1 GPR45 105249974 105224632 - + 0 105252235 105233274 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.799875793911741 0.749883556792257 0.799875793911741 0.749883556792257 0 - - 39209 N N 3.59528445727371 3.55231620741665 3.55231620741665 28 0.330364776289541 0.232811383001308 N 0.330364776289541 0.330364776289541 N N 5 261771 ENSG00000159251 ENSG00000184009 + + 15 17 32875219 77094422 coding coding ACTC1 ACTG1 32867589 77091594 - - 0.330364776289541 32872914 77093641 - - Y 0.971666703485014 - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 5 0.271386430077198 0.585623349113953 0.585623349113953 0.271386430077198 2 0 - 31366 Y Y 3.12845685570642 2.97896005807504 2.97896005807504 305 0 0.00530957284874856 Y 0 0.991407574901074 N N 5073 19 ENSG00000161217 ENSG00000163959 + + 3 3 197498981 197444696 downstream downstream PCYT1A AC069257.28-2 197449652 197427780 - + 0 197448765 197446203 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.03555348318931 0.864151527351077 1.03555348318931 0.864151527351077 1 - - 33152 N Y 2.87060295437234 3.37717580530765 2.87060295437234 281 0 0.00643748424052026 Y 0 0.989934936554154 N N 339915 1291380 ENSG00000198727 ENSG00000198804 - + MT MT 15882 7446 coding coding MT-CYB MT-CO1 14748 5905 + + 0.124339480211366 14764 7296 - + N 0.343791605542793 1.65165080381395 N HCC1954 2 1.22222222222222 1 2 1 N - - N - - 0 0 0 9 0.5713398527941 1.3069399132665 1.3069399132665 0.5713398527941 2 0 0 44691 Y Y 3.62145727041145 3.4780843434859 3.4780843434859 321 0 0.193412045829966 Y 0 0 N N 828 4690 ENSG00000138347 ENSG00000148634 - - 10 10 69641464 69505109 intron upstream MYPN HERC4 69535918 69351663 + - 0 69551198 69517752 - + N 0.172312168438841 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 1.14982145374813 1.05697872766909 1.14982145374813 1.05697872766909 1 0 - 31620 Y Y 3.51001030496889 3.40914161958398 3.40914161958398 176 0 0.206427356823525 Y 0.985377673796791 0.985377673796791 N N 3882 5040 ENSG00000120756 ENSG00000175054 - - 3 3 143915191 143780358 utr5p upstream PLS1 ATR 143825034 143650770 + - 0 143825091 143798037 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.371370904316165 0.642757334393363 0.642757334393363 0.371370904316165 2 - - 34147 Y Y 3.60256518892881 3.69359248957888 3.60256518892881 276 0.143302180685358 0.0842214996536372 Y 0.972064201544088 0.981376134362725 N N 3243 394 ENSG00000107099 ENSG00000183784 - - 9 9 455255 205741 upstream intron DOCK8 C9orf66 263048 202824 + - 0 261625 205414 - + N - 10.2037697592133 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.771308801272036 0.964136001590045 0.964136001590045 0.771308801272036 1 - 0 188 Y Y 3.43465208531242 2.7810192986461 2.7810192986461 358 0 0.00569237160054259 Y 0 0.985547728928832 N N 0 3207 ENSG00000177236 ENSG00000177225 - - 11 11 770755 767487 downstream upstream AP006621.1 PDDC1 770117 757225 + - 0 773403 767640 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 18 1.12839620926835 0.899860268150708 1.12839620926835 0.899860268150708 2 - - 402 Y Y 2.84123764596909 3.47695798776018 2.84123764596909 0 0 0.99928685235559 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.991474199910924 1816335 1814664 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 20 1.12125446110842 1.16410495006798 1.16410495006798 1.12125446110842 1 - - 3152 N Y 2.98888957109253 3.26824964015148 2.98888957109253 5 0 0.212108136161026 N 0 0.894166516163988 N N 128 8014 ENSG00000167765 ENSG00000149084 - - 19 11 56789442 43834736 utr3p utr3p AC018755.3-2 HSD17B12 56786848 43658719 - + 0.241526699175245 56787088 43834016 + - Y - - N HCC1954 74 64.1666666666667 35 6 1 N - - N SINE - 1 0 1 6 0.599906845433805 0.814159290231593 0.814159290231593 0.599906845433805 1 - - 7005 Y Y 3.70040921291755 3.45720067037699 3.45720067037699 249 0 0.472217669723655 Y 0 0 N N 3237 633 ENSG00000003137 ENSG00000135636 + + 2 2 72228471 71767398 downstream downstream CYP26B1 DYSF 72209875 71534268 - + 0 72010425 71973487 - + N - - N HCC1954 1 1 1 0 3 N - - Y - SINE,DNA,DNA 0 0.576271186440678 0.576271186440678 16 0.657040830713216 0.842726282871298 0.842726282871298 0.657040830713216 1 - - 9346 Y Y 3.5529387020326 3.3184850412945 3.3184850412945 300 0.00333333333333319 0.998015490810087 N 0.0377011494252875 0.991408045977012 Y N 317991 1482 ENSG00000171346 ENSG00000171345 + - 17 17 36932191 36938167 upstream utr5p KRT15 KRT19 36923523 36933396 - - 0 36946875 36938106 - + N - 30.6982423681776 N HCC1954 2 1.1 1 1 8 N - - N - - 0 0 0 10 0.799875793911741 1.03555348318931 1.03555348318931 0.799875793911741 1 - 0 31339 Y Y 3.53974633573272 3.47592491799029 3.47592491799029 252 0 0.0171555189021650 Y 0.976836471022518 0.988418235511259 N N 4988 0 ENSG00000134077 ENSG00000214041 - + 3 3 9402412 9365876 upstream upstream THUMPD3 AC026191.4-1 9379736 9365127 + + 0 9379525 9347281 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 12 0.5713398527941 0.478497126715059 0.5713398527941 0.478497126715059 1 - - 47434 Y Y 3.40740634961144 3.4210491438586 3.40740634961144 0 0.0482851647390903 0.916744656580204 Y 0.25061823995204 0.99250618239952 N N 3678 521 ENSG00000198466 ENSG00000204517 - + 19 19 63068299 63045300 coding coding ZNF587 AC010522.3 63053081 63042237 + + 0 63053250 63044086 - + N - - N HCC1954 9 3.77777777777778 2 9 2 Y - - Y - - 0 0 0 9 1.09268746846872 1.12839620926835 1.12839620926835 1.09268746846872 2 - - 26655 Y Y 3.46551447180198 3.64553343878587 3.46551447180198 0 0 0.68963321701022 Y 0.945001631676275 0.986250407919069 N N 571 16734 ENSG00000135740 ENSG00000135723 - - 16 16 65863594 65838926 coding coding SLC9A5 FHOD1 65840356 65820795 + - 0 65843946 65838748 - + N 0.268306077169473 2.04694825396357 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.05697872766909 1.20695543902754 1.20695543902754 1.05697872766909 4 0 0 1726 N N 3.21023057111745 3.60273302279816 3.21023057111745 0 0 0.401819459287015 N 0 0 N N 9042 937 ENSG00000137692 ENSG00000100027 + + 11 22 102468079 20420071 coding utr3p DCUN1D5 YPEL1 102438032 20381828 - - 0 102442457 20384677 - - Y - - N HCC1954 37 25.75 22 4 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.335662163516534 0.39993789695587 0.335662163516534 3 - - 19236 N Y 3.5580693557619 2.93339130234489 2.93339130234489 0 0 0.350874540653479 Y 0.993650051617678 0.993650051617678 N N 134 197 ENSG00000203744 ENSG00000198929 - + 1 1 160620147 160604852 utr5p coding C1orf226 NOS1AP 160618274 160306205 + + 0 160618302 160603615 - + N 0.166324295981 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 13 1.12125446110842 1.14982145374813 1.14982145374813 1.12125446110842 0 0 - 37055 N N 3.56591914887046 3.65591337975064 3.56591914887046 0 0 0.195239022146255 N 0 0 N N 0 712661 ENSG00000214936 ENSG00000111640 + + 4 12 88348268 6517797 intron coding AC092658.2 GAPDH 88347259 6513918 + + 0 88347827 6516817 + + Y 1 0.91454183184415 N HCC1954 2 1.8 1 4 1 N - - N - - 0 0 0 5 0.542772860154395 0.585623349113953 0.585623349113953 0.542772860154395 2 0 0 30018 N Y 3.60103760561896 3.78784279071799 3.60103760561896 0 0 0.410418662222376 N 0.862105926860025 0.846784363177806 N N 891 0 ENSG00000183826 ENSG00000177418 + - 6 7 38673848 65659784 intron downstream BTBD9 AC006001.2-1 38250713 65659267 - - 0 38371679 65657260 - + Y 1.221326084665 - N HCC1954 36 16.3333333333333 7 6 1 N - - N SINE - 1 0 1 6 0.328520415356608 0.535631111994469 0.535631111994469 0.328520415356608 1 0 - 30462 Y Y 3.49272035470961 3.31742146630107 3.31742146630107 232 0 0.237319634007509 Y 0.243658819628647 0.990426061007958 N N 6 0 ENSG00000102128 ENSG00000208964 - + X X 102079884 101951770 upstream downstream RAB40AL AL590407.8-9 102078856 101951702 + + 0 102039159 102006737 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.535631111994469 0.507064119354764 0.535631111994469 0.507064119354764 1 - - 43828 N N 3.34934742778406 3.47911741325579 3.34934742778406 1 0 0.0890931167124829 N 0 0 N N 53981 5 ENSG00000138326 ENSG00000197046 + + 10 18 79470477 41676519 coding upstream RPS24 SIGLEC15 79463580 41659543 + + 0 79467055 41622537 + + Y 3.69287164811103 - N HCC1954 2 1.66666666666667 1 4 1 N - - N - - 0 0 0 6 0.385654400636018 0.271386430077198 0.385654400636018 0.271386430077198 1 0 - 41622 N Y 3.30380917727745 3.43681151080804 3.30380917727745 252 0 0.880172952397942 Y 0.12959387959388 0.991026741026741 N N 0 4 ENSG00000207110 ENSG00000184090 - - 8 8 129080722 129029462 upstream downstream U1 TMEM75 129080559 129029046 + - 0 129063769 129021101 - + N - - N HCC1954 1 1 1 0 5 N - - N - SINE 0 0.358974358974359 0.358974358974359 5 0.628473838073511 0.828442786551446 0.828442786551446 0.628473838073511 2 - - 9328 Y Y 3.5816815158199 3.06525793257994 3.06525793257994 492 0.0364451920381275 0.0174561250831378 Y 0 0.970503424246065 N N 3576 1877 ENSG00000108963 ENSG00000185924 - - 17 17 1893474 1787865 upstream coding DPH1 RTN4RL1 1880181 1786540 + - 0 1874889 1787845 - + N - 11.7660452222859 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 135 1.39264089118562 1.69259431390252 1.69259431390252 1.39264089118562 2 - 0 7058 Y Y 3.66848325143457 2.97316705693644 2.97316705693644 270 0 0.00318145229754252 Y 0.221077441077441 0.990942760942761 N N 30311 15137 ENSG00000082898 ENSG00000115464 + - 2 2 61618922 61551353 intron upstream XPO1 USP34 61558488 61268095 - - 0 61563265 61552017 - + N 0.744623795459671 - N HCC1954 1 1 1 0 1 N - - Y SINE Low_complexity 1 0.292207792207792 1 6 0.971277749749971 0.985561246069823 0.985561246069823 0.971277749749971 1 0 - 4428 N Y 3.09144009328749 3.64656650855576 3.09144009328749 238 0 0.0199078241980329 Y 0.253151260504202 0.986897390535161 N N 1745 82 ENSG00000176532 ENSG00000106069 - + 7 7 29573436 29520469 upstream downstream PRR15 CHN2 29569952 29200646 + + 0 29569791 29521461 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.414221393275723 0.39993789695587 0.414221393275723 0.39993789695587 1 - - 26313 N N 3.58424216889964 3.52039024593366 3.52039024593366 0 0 0.171010514636792 N 0 0 N N 45068 0 ENSG00000205336 ENSG00000188803 + + 16 17 56256445 11402921 upstream intron GPR56 AC007510.1 56220023 11085305 + + 0 56211650 11201132 + + Y - 1 N HCC1954 2 1.55555555555556 1 5 1 N - - N - SINE 0 1 1 9 0.449930134075354 0.278528178237124 0.449930134075354 0.278528178237124 3 - 0 3426 Y Y 3.49744043328497 3.18974812559266 3.18974812559266 243 0 0.093207137581152 Y 0.989056211278434 0.989056211278434 N N 1755 0 ENSG00000159231 ENSG00000214889 - + 21 21 36440728 36427200 coding downstream CBR3 AP000689.1-2 36429133 36426618 + + 0 36440426 36427244 - + N 1.16715326260321 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.585623349113953 0.871293275511003 0.871293275511003 0.585623349113953 2 0 - 18137 Y Y 3.49594335519865 3.33784113109356 3.33784113109356 364 0 0.0365628445435670 Y 0.993992453329803 0.993992453329803 N N 18522 3 ENSG00000179403 ENSG00000205116 - + 1 1 1366008 1353030 upstream downstream VWA1 AL391244.11-1 1360772 1351371 + + 0 1359420 1356196 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.142045454545455 0.142045454545455 26 1.4426331283051 1.25694767614702 1.4426331283051 1.25694767614702 1 - - 33081 N Y 2.87060295437234 3.49487978020523 2.87060295437234 407 0 0.149982634680461 Y 0 0.994607875688957 N N 339915 544065 ENSG00000198727 ENSG00000198744 - + MT MT 15882 9988 coding coding MT-CYB MT-CO3 14748 8367 + + 0.00245700245700242 14764 8863 - + N 0.343791605542793 0.576352891065352 N HCC1954 4 2 1 2 5 N - - N - - 0 0 0 4 0.871293275511003 0.649899082553289 0.871293275511003 0.649899082553289 2 0 0 45399 N N 3.54768941479713 3.56488607910057 3.54768941479713 13 0.192032368502957 0.0297345699626915 N 0.192032368502957 0.173669467787115 N N 7195 11413 ENSG00000150593 ENSG00000112877 - - 10 5 112649753 706664 utr3p coding PDCD4 CEP72 112621586 665405 + + 0.357298474945534 112649290 672182 - - Y - 0.868134916414089 N HCC1954 35 33.4 31 5 1 N 222 24.097 N SINE - 1 0 1 5 0.321378667196682 0.34280391167646 0.34280391167646 0.321378667196682 1 - 0 43076 N N 3.3227106063299 3.56016600052522 3.3227106063299 0 0 0.66507243612627 N 0 0 N N 3062 9848 ENSG00000145781 ENSG00000164134 - - 5 4 115656882 140531972 coding intron COMMD10 NARG1 115448622 140442126 + + 0 115451093 140443020 - - Y - 1.36681297140778 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 10 0.971277749749971 0.971277749749971 0.971277749749971 0.971277749749971 4 - 0 42194 N Y 3.37192651807217 3.51377186168787 3.37192651807217 289 0 0.0136808045690865 Y 0.944636678200692 0.993079584775086 N N 6685 6685 ENSG00000169020 ENSG00000169020 + - 4 4 658122 658122 upstream upstream ATP5I ATP5I 656228 656228 - - 0.993079584775086 659863 658473 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 20 0.928427260790413 0.871293275511003 0.928427260790413 0.871293275511003 1 - - 41371 N N 1.85456542840269 2.42680847320244 1.85456542840269 0 0.170489296636086 0.197936771298696 N 0.557594291539246 0 N N 1 5996 ENSG00000204746 ENSG00000187678 - - 20 5 20394222 141684750 coding utr3p AL121896.11 SPRY4 20387343 141670189 - - 0.170489296636086 20393803 141671703 + + Y - 1.17999248232857 N HCC1954 35 27.5 6 4 1 N - - N Simple_repeat,Simple_repeat - 0.71875 0 0.71875 4 0.45707188223528 0.39993789695587 0.45707188223528 0.39993789695587 1 - 0 5430 N N 3.47552369040616 3.66484967579158 3.47552369040616 1 0 0.134870540783965 N 0.925524564529619 0 N N 1992 11566 ENSG00000003436 ENSG00000130338 - + 2 6 188127464 158852842 utr5p upstream TFPI TULP4 188037202 158653680 - + 0 188127364 158650894 + + Y - - N HCC1954 21 12.5 2 4 1 N - - N - Other 0 1 1 4 0.678466075192994 0.642757334393363 0.678466075192994 0.642757334393363 2 - - 5052 N N 3.46232197653647 3.37808089400154 3.37808089400154 10 0.0436204411927724 0.968911535831443 Y 0.0436204411927724 0.180246092450948 N N 28646 3396 ENSG00000164880 ENSG00000188191 + - 7 7 1510772 733813 coding intron INTS1 PRKAR1B 1476439 555361 - - 0.180246092450948 1500978 731027 - + N - 0.636992906513447 N HCC1954 1 1 1 0 3 N 22 4.15045 N - LINE 0 1 1 12 1.01412823870953 0.821301038391519 1.01412823870953 0.821301038391519 4 - 0 36240 Y Y 3.13061628120204 3.59165088163073 3.13061628120204 208 0 0.0204807822098830 Y 0 0.989524291497976 N N 779 12958 ENSG00000050438 ENSG00000139629 - - 12 12 50177913 50071467 intron intron SLC4A8 GALNT6 50071399 50032100 + - 0 50071611 50062561 - + N 0.197701299225181 42.0285288627606 N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 6 0.264244681917271 0.51420586751469 0.51420586751469 0.264244681917271 1 0 0 27310 Y Y 3.51679652308403 3.4780843434859 3.4780843434859 208 0 0.277882677063138 Y 0.552952290977799 0.97420878601795 N N 69736 0 ENSG00000181019 ENSG00000210650 + - 16 16 68318034 68300079 coding downstream NQO1 AC092115.2-1 68300808 68299978 - - 0 68302479 68298611 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR,SINE 0 0.75 0.75 8 1.25694767614702 0.814159290231593 1.25694767614702 0.814159290231593 4 - - 3452 Y Y 3.6272104187567 3.25828027434064 3.25828027434064 342 0 0.00882556699839687 Y 0 0 N N 7736 0 ENSG00000154639 ENSG00000220521 - - 21 21 17887768 17795013 upstream intron CXADR AP000963.2 17807201 17794868 + - 0 17806523 17794992 - + N - 1 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.145539906103286 0 0.145539906103286 4 1.02841173502938 0.671324327033068 1.02841173502938 0.671324327033068 1 - 0 32166 N Y 3.09872082494259 3.57848902055439 3.09872082494259 1 0 0.335415208719855 N 0.90702154626109 0.893738910012674 N N 6576 1854 ENSG00000106635 ENSG00000221955 - + 7 3 72609960 126414303 coding utr3p BCL7B SLC12A8 72588622 126284170 - - 0 72609753 126285132 + - Y - - N HCC1954 38 36.75 35 4 1 N - - N - SINE 0 1 1 4 0.51420586751469 0.292811674556976 0.51420586751469 0.292811674556976 3 - - 31644 N Y 2.88274380859372 3.65488030998075 2.88274380859372 301 0 0.0237836666526944 N 0.96563180203918 0.98281590101959 N N 1131 2906 ENSG00000214116 ENSG00000214135 - + 3 3 197173943 196895854 coding downstream AC024937.21-2 AC069513.28-1 197171055 196874647 - + 0 197171356 196895915 + + N - - Y HCC1954 12 3.03076923076923 1 64 1 N - - N LINE - 0.648936170212766 0 0.648936170212766 65 1.34264865406614 0.907002016310634 1.34264865406614 0.907002016310634 2 - - 19214 Y Y 3.66761801553402 3.2216342342823 3.2216342342823 11 0 0.273624731435405 Y 0 0.942690626517727 N N 24618 9281 ENSG00000163386 ENSG00000213240 - + 1 1 144081660 144003011 intron utr3p NBPF8 NOTCH2NL 144001129 143920462 + + 0 144004467 143993403 - + N 0.0530065694654568 - N HCC1954 16 4.77777777777778 1 8 1 N - - Y - - 0 0 0 9 0.635615586233437 1.21409718718746 1.21409718718746 0.635615586233437 1 0 - 38666 N N 3.40016547074969 3.48912663185998 3.40016547074969 5 0 0.589185907272557 N 0 0.563395512300622 N N 0 16995 ENSG00000222639 ENSG00000121039 - + 14 8 49123344 74399345 intron utr3p SRP_euk_arch RDH10 49123048 74369891 + + 0 49123091 74398577 - + Y 1 - N HCC1954 49 15.8421052631579 7 19 1 N - - N srpRNA SINE 1 0.7 1 19 0.949852505270192 0.985561246069823 0.985561246069823 0.949852505270192 2 0 - 30245 Y Y 3.51207644450867 3.27088999881792 3.27088999881792 268 0 0.0996323318749057 Y 0 0 N N 0 7010 ENSG00000217748 ENSG00000213401 + - X X 151704649 151688896 upstream upstream U82671.12 MAGEA3 151703833 151685309 - - 0 151709936 151689148 - + N - - N HCC1954 2 2 2 16 3 N - - Y LINE Low_complexity 0.0144927536231884 0.344086021505376 0.344086021505376 16 0.492780623034912 0.664182578873142 0.664182578873142 0.492780623034912 3 - - 31386 Y Y 3.3184850412945 3.34040178417331 3.3184850412945 230 0 0.00854940530454795 Y 0.620703933747412 0.984195997239476 N N 1031 5028 ENSG00000175105 ENSG00000163320 - - 3 3 88276504 88190836 upstream upstream ZNF654 CGGBP1 88270952 88183798 + - 0.510075914423741 88244969 88218231 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.357087407996313 0.335662163516534 0.357087407996313 0.335662163516534 1 - - 47935 N N 3.39743698380061 3.7297745213208 3.39743698380061 0 0 0.999359796841163 N 0.0042372881355931 0 N N 0 86504 ENSG00000182152 ENSG00000104408 + + 5 8 117142614 109330135 downstream coding AC114322.2 EIF3E 117142420 109283149 - - 0 116900287 109296012 - - Y - - N HCC1954 2 1.125 1 1 7 N 241 0.00319582 N - - 0 0 0 8 0.807017542071667 1.09982921662864 1.09982921662864 0.807017542071667 4 - - 7286 Y Y 3.28239629550842 3.5074097990958 3.28239629550842 353 0 0.0632995437866454 N 0 0.991758949266031 Y N 3966 2842 ENSG00000175772 ENSG00000204588 - + 2 2 110111006 110111006 downstream downstream AC013268.5-1 AC013268.5-2 110103138 110108526 + + 0 110122493 110112196 - + N - - N HCC1954 16 7 4 4 2 N - - N LINE - 0.114035087719298 0 0.114035087719298 4 0.914143764470561 0.5713398527941 0.914143764470561 0.5713398527941 2 - - 33571 N Y 2.98996249365577 2.89674526228654 2.89674526228654 416 0.00863882211538469 0.00956241155315263 Y 0.00863882211538469 0.993765024038462 N N 247001 336285 ENSG00000198786 ENSG00000198868 - + MT MT 14149 12138 coding coding MT-ND5 MT-ND4 12338 10471 + + 0.993765024038462 13856 12119 - + N - - N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 4 0.821301038391519 0.414221393275723 0.821301038391519 0.414221393275723 4 - - 15547 N N 3.45976132345673 3.50529022639353 3.45976132345673 16 0 0.0465986319950009 N 0.548611111111111 0 N N 0 0 ENSG00000212456 ENSG00000194647 - + 1 7 146460937 119433391 intron intron U1 U1 146460770 119433224 + - 0 146460925 119433355 - - Y 1 1 N HCC1954 9 5.77777777777778 4 18 1 N - - N snRNA snRNA 0.175675675675676 1 1 18 0.528489363834543 0.28566992639705 0.528489363834543 0.28566992639705 2 0 0 33203 Y Y 3.0824639444532 3.37871273618731 3.0824639444532 540 0 0.9723526973729 Y 0.0783382999858095 0.889094650205761 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.889094650205761 14169 12955 - + N 0.320201474398206 - N HCC1954 2 1.1 1 2 10 N - - Y - - 0 0 0 20 1.52833410622422 1.19267194270768 1.52833410622422 1.19267194270768 2 0 - 30328 Y Y 3.22280044280138 3.39168383545536 3.22280044280138 252 0 0.094567475021699 Y 0 0 N N 4921 315 ENSG00000065923 ENSG00000147119 + + X X 46503551 46342781 utr3p downstream SLC9A7 CHST7 46351081 46318136 - + 0 46351287 46346649 - + N 0.22311124015967 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 0.864151527351077 0.978419497909897 0.978419497909897 0.864151527351077 4 0 - 31843 Y Y 3.37911396377143 3.48167806633553 3.37911396377143 362 0 0.0143599478975529 Y 0.754014732965009 0.980055248618784 N N 3381 7315 ENSG00000131368 ENSG00000177463 + + 3 3 15081820 15065784 utr3p utr3p MRPS25 NR2C2 15065024 14964095 - + 0 15066219 15063816 - + N - 2.04723677807305 N HCC1954 23 3 1 1 2 N - - Y SINE - 0.596153846153846 0 0.596153846153846 11 1.34264865406614 1.02126998686945 1.34264865406614 1.02126998686945 4 - 0 10534 N Y 3.07101108092519 3.70360170818306 3.07101108092519 2 0 0.308946645480109 N 0.830622710622711 0.810695970695971 N N 1649619 3 ENSG00000141736 ENSG00000056487 - - 17 22 35138441 43784473 coding upstream ERBB2 PHF21B 35104766 43655706 + - 0 35125066 43814454 - + Y - - N HCC1954 25 23.6666666666667 22 9 1 N 513 19.3357 N - SINE 0 1 1 9 0.735600060472404 0.357087407996313 0.735600060472404 0.357087407996313 1 - - 36348 N Y 3.36873402280666 3.17613583656903 3.17613583656903 264 0 0.003610889496241 Y 0.6307144723093 0.991411964472309 N N 18351 164905 ENSG00000167552 ENSG00000123416 + - 12 12 47869128 47811571 intron utr5p TUBA1A TUBA1B 47864847 47807836 - - 0 47868342 47811396 - + N 7.93119115404807 1.09188164308025 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.692749571512847 0.828442786551446 0.828442786551446 0.692749571512847 1 0 0 29953 N N 3.51832410639388 2.78061807106198 2.78061807106198 258 0.619661733615222 0.00272865632109698 N 0.746441155743481 0.257434813248767 N N 78560 0 ENSG00000112493 ENSG00000217035 + + 6 X 33390114 44379422 utr3p downstream TAPBP CHTF8P 33375449 44377882 - + 0.311768851303735 33376421 44385736 - + Y - - N HCC1954 28 6.2 1 7 1 N 184 25.9721 N SINE SINE 1 0.65625 1 10 0.557056356474248 0.22853594111764 0.557056356474248 0.22853594111764 2 - - 1720 N N 3.35823029066252 3.71873223294673 3.35823029066252 0 0 0.90039389858745 N 0.865969899665552 0 N N 12635 4030 ENSG00000109919 ENSG00000185214 + - 11 22 47620640 19180122 coding upstream MTCH2 KLHL22 47595444 19125806 - - 0 47612855 19185125 - + Y - - N HCC1954 1 1 1 0 3 N 341 20.4969 N - LTR,SINE 0 0.633663366336634 0.633663366336634 13 0.664182578873142 0.721316564152552 0.721316564152552 0.664182578873142 2 - - 31718 Y Y 3.6052936758779 3.45513453083721 3.45513453083721 0 0 0.93088327255627 Y 0.993264161994812 0.993264161994812 N N 3914 90 ENSG00000085276 ENSG00000206115 - + 3 3 170347054 170582016 utr5p coding EVI1 MDS1 170283981 170581663 - - 0 170345479 170581670 + - N - 0.213225734140327 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 61 1.2783729206268 1.09982921662864 1.2783729206268 1.09982921662864 3 - 0 41136 N Y 3.38383404234679 3.39909254818645 3.38383404234679 0 0 0.801300833034208 Y 0.992333419089272 0.984666838178544 N Y 289 2529 ENSG00000204070 ENSG00000198641 - + 20 20 43472664 43431263 coding coding DBNDD2 SYS1 43468085 43423991 + + 0 43470514 43427740 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 15 1.17838844638783 0.921285512630487 1.17838844638783 0.921285512630487 4 - - 13007 N N 2.88045368667699 3.12747721909902 2.88045368667699 0 0.243511759935118 0.0541591892856249 N 0.317315490673155 0 N N 48166 551733 ENSG00000168610 ENSG00000204628 + + 17 5 37794039 180603512 intron utr3p STAT3 GNB2L1 37718869 180596536 - - 0 37782089 180596544 - - Y 1.70205993449814 - N HCC1954 20 14.8421052631579 4 19 1 N - - N SINE,SINE - 0.864864864864865 0 0.864864864864865 19 0.264244681917271 0.607048593593732 0.607048593593732 0.264244681917271 2 0 - 36306 Y Y 3.25103939547889 3.31592438821476 3.25103939547889 324 0 0.107872722358907 Y 0.993124733929332 0.986249467858663 N N 0 847 ENSG00000215030 ENSG00000111671 - - 12 12 6863922 6852713 upstream upstream RPL13P5 SPSB2 6863421 6850365 + - 0 6863129 6853206 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 1.07840397214886 0.621332089913584 1.07840397214886 0.621332089913584 4 - - 44659 Y Y 3.47336426491055 3.56591914887046 3.47336426491055 309 0 0.0113735114393303 Y 0.878897861658047 0.990684450896773 N N 2263 1060 ENSG00000155640 ENSG00000196233 - + 10 10 98735572 98708680 upstream coding C10orf12 LCOR 98731031 98582029 + + 0 98730539 98701942 - + N - 3.71246858266856 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 39 1.47834186910473 0.799875793911741 1.47834186910473 0.799875793911741 1 - 0 24733 Y Y 3.52361324642271 3.45612774781375 3.45612774781375 253 0 0.0161416151080761 Y 0.0225702781574378 0.990691145506261 N N 0 13271 ENSG00000202159 ENSG00000081923 - - 18 18 53573730 53550037 downstream upstream U6 ATP8B1 53573624 53464656 + - 0 53580056 53550060 - + N - - N HCC1954 21 12.1 1 15 1 N - - Y SINE - 1 0 1 20 0.864151527351077 1.04269523134923 1.04269523134923 0.864151527351077 1 - - 44141 N N 3.36720643949681 3.3306536853943 3.3306536853943 0 0 0.0292804378760113 N 0.637468914064659 0.38369715390992 N N 30872 125 ENSG00000058262 ENSG00000120555 - - 3 10 129273215 38728662 intron upstream SEC61A1 RP11-291L22.2 129253902 38711957 + - 0.38369715390992 129268312 38731005 - + Y 1.65832413471081 - N HCC1954 20 16 8 7 1 N 150 23.0054 N - SINE 0 1 1 7 0.428504889595575 0.328520415356608 0.428504889595575 0.328520415356608 1 0 - 599 Y Y 2.64405251990529 3.60207067538885 2.64405251990529 0 0 0.555227562074205 Y 0.0457108408099578 0.993882761800064 N N 152158 0 ENSG00000110321 ENSG00000222048 - + 11 11 10787158 10836196 utr5p intron EIF4G2 ZBED5 10775169 10830827 - - 0 10785502 10835983 + - N - 1 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 1.15696320190805 0.942710757110266 1.15696320190805 0.942710757110266 2 - 0 42373 Y Y 3.73552766966605 3.51786009807746 3.51786009807746 284 0 0.0483304824943894 Y 0 0 N N 0 873 ENSG00000207944 ENSG00000174130 - - 4 4 38546143 38507555 upstream intron hsa-mir-574 TLR6 38546048 38504618 + - 0 38535704 38507553 - + N - 9.80946544092611 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 1.07126222398894 0.87843502367093 1.07126222398894 0.87843502367093 4 - 0 587 N Y 3.60000453584907 3.17932833183454 3.17932833183454 0 0 0.93224931807127 Y 0.989174087654968 0.989174087654968 N N 9074 0 ENSG00000166444 ENSG00000202276 - + 11 11 8817478 8855641 coding downstream ST5 Y_RNA 8671478 8855540 - - 0 8728801 8849077 + - N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 16 0.928427260790413 1.26408942430695 1.26408942430695 0.928427260790413 2 - - 44670 N N 3.05063126892605 3.36079094374226 3.05063126892605 0 0 0.250715077863664 Y 0.386452353616533 0 N N 2 0 ENSG00000188279 ENSG00000215065 + + 10 10 48877823 46676017 downstream intron FAM25B AL391137.11-1 48873392 46511545 - + 0 48869722 46559999 - + N - 1 N HCC1954 2 1.9 1 9 1 N - - N - LINE 0 0.979591836734694 0.979591836734694 10 1.09268746846872 1.04983697950916 1.09268746846872 1.04983697950916 1 - 0 34295 Y Y 3.26936241550807 3.2656754067026 3.2656754067026 0 0 0.846153194586878 Y 0 0.973055372445616 N N 7771 4429 ENSG00000165304 ENSG00000137075 - - 9 9 36667678 36391195 upstream upstream MELK RNF38 36562873 36326401 + - 0 36477180 36414661 - + N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.40952380952381 0 0.40952380952381 4 0.685607823352921 0.407079645115797 0.685607823352921 0.407079645115797 3 - - 13237 N N 3.51935717616377 3.03429984052315 3.03429984052315 0 0.349366512404218 0.542102759576129 N 0.349366512404218 0 N N 551733 9 ENSG00000204628 ENSG00000173838 + - 5 17 180603512 58239437 utr3p intron GNB2L1 MARCH10 180596536 58132408 - - 0 180596558 58214298 - + Y - 1.1612992573529 N HCC1954 22 17.375 3 8 1 N 139 21.3509 N - Simple_repeat 0 0.684210526315789 0.684210526315789 8 0.628473838073511 0.271386430077198 0.628473838073511 0.271386430077198 2 - 0 13646 Y Y 3.43511609362884 3.62192127872787 3.43511609362884 220 0.00454545454545452 0.0293062927861991 N 0.0148078725398312 0.0148078725398312 Y N 145 30 ENSG00000130487 ENSG00000217442 - - 22 22 49335409 49348200 upstream downstream KLHDC7B C22orf41 49333328 49336407 + - 0.989737582005623 49330141 49328631 - + N - - N HCC1954 19 12.2857142857143 1 6 2 N - - N - SINE 0 1 1 7 0.828442786551446 0.785592297591888 0.828442786551446 0.785592297591888 2 - - 45140 N N 3.09087103183403 3.25270389999991 3.09087103183403 0 0 0.069328976379602 N 0 0 N N 3891 5546 ENSG00000166295 ENSG00000148719 + - 10 10 73665622 73784875 intron downstream C10orf104 DNAJB12 73645812 73762594 + - 0 73645953 73735949 + + N 0.744979490524871 - Y HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.378512652476092 0.34280391167646 0.378512652476092 0.34280391167646 1 0 - 3835 N Y 3.41952156054875 3.34355442664546 3.34355442664546 0 0 0.432556577801121 N 0 0 N N 0 101048 ENSG00000207080 ENSG00000127954 + + 8 7 102044447 87774145 upstream utr3p Y_RNA STEAP4 102044339 87743687 - - 0.49031007751938 102072303 87745004 - - Y - - N HCC1954 126 50 1 3 1 N - - N SINE SINE 0.945945945945946 1 1 4 0.264244681917271 0.414221393275723 0.414221393275723 0.264244681917271 2 - - 8241 N N 3.35253057547976 3.62824348852659 3.35253057547976 108 0 0.0272142995855652 N 0.559484777517564 0.575800156128025 N N 10665 8 ENSG00000115233 ENSG00000151388 - - 2 5 161976474 33928054 upstream intron PSMD14 ADAMTS12 161872795 33563043 + - 0.641061670569867 161844627 33745637 - + Y - 1.02260113791449 N HCC1954 3 1.4 1 1 1 N - - N LINE LINE 0.576470588235294 1 1 5 0.542772860154395 0.299953422716903 0.542772860154395 0.299953422716903 1 - 0 2682 N N 3.40951234194457 3.38505706622857 3.38505706622857 0 0 0.0875265854191198 N 0 0 N N 2256 28 ENSG00000080839 ENSG00000184478 + + 20 11 35157824 5926100 intron upstream RBL1 OR56A3 35059592 5925153 - + 0 35130403 5906700 - + Y 1.16472826067811 - N HCC1954 3 2.6 1 4 1 N - - N SINE,Other LTR 0.829787234042553 1 1 5 0.542772860154395 0.564198104634174 0.564198104634174 0.542772860154395 1 0 - 34447 Y Y 3.77001428422878 3.47332441211719 3.47332441211719 253 0 0.0585413810784025 Y 0.988551178955977 0.988551178955977 N N 2696 0 ENSG00000198642 ENSG00000220319 + + 9 9 21325379 21311826 downstream downstream KLHL9 RP11-380P16.7 21319670 21311299 - + 0 21319331 21314321 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 8 0.614190341753658 0.985561246069823 0.985561246069823 0.614190341753658 1 - - 36584 Y Y 3.52680574168822 3.45976132345673 3.45976132345673 76 0 0.98524420143972 Y 0.991405043746783 0.991405043746783 N Y 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6313671 6328154 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 19 0.93556900895034 1.27123117246687 1.27123117246687 0.93556900895034 4 - - 49464 Y Y 3.32679884271949 3.53465553479678 3.32679884271949 0 0 0.600246873447551 Y 0 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883896 140857919 - + N - 0.193141372768201 N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 8 1.12839620926835 0.721316564152552 1.12839620926835 0.721316564152552 2 - 0 11373 N N 3.56079784271098 3.69677563727457 3.56079784271098 6 0 0.222293444048222 N 0 0 N N 2406 20747 ENSG00000153767 ENSG00000073605 - + 3 17 121984606 35328429 utr3p coding GTF2E1 GSDMB 121944248 35314374 + - 0 121983293 35314644 - - Y - - N HCC1954 34 31.8 24 5 1 N - - N SINE - 1 0 1 5 0.414221393275723 0.864151527351077 0.864151527351077 0.414221393275723 3 - - 41373 N N 3.33208798274832 3.58589773328548 3.33208798274832 0 0 0.0749659153711284 N 0 0 N N 9739 551733 ENSG00000149639 ENSG00000204628 - - 20 5 34925503 180603512 intron coding C20orf117 GNB2L1 34839259 180596536 - - 0 34851977 180598764 + + Y 1.17652779598279 0.84633074048019 N HCC1954 40 22.75 20 8 1 N 601 21.6473 N SINE - 1 0 1 8 0.371370904316165 0.657040830713216 0.657040830713216 0.371370904316165 2 0 0 47659 Y Y 3.38552945952599 3.44615838200292 3.38552945952599 0 0 0.783577840419232 Y 0 0.993399196612746 N Y 7761 1457 ENSG00000129455 ENSG00000169035 + - 19 19 56196770 56179106 coding intron KLK8 KLK7 56191076 56171541 - - 0 56196166 56176982 - + N - 37.0552029096617 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 104 1.12839620926835 1.05697872766909 1.12839620926835 1.05697872766909 4 - 0 22061 N Y 3.25256697878875 3.72551845106187 3.25256697878875 1 0 0.0714602030774415 N 0 0 N N 49089 95 ENSG00000117450 ENSG00000214770 - + 1 14 45760196 63875070 coding utr3p PRDX1 AL161756.6 45749295 63872306 - - 0 45757275 63872343 + - Y - - N HCC1954 30 19.1428571428571 6 7 1 N 552 21.8839 N - SINE 0 1 1 7 0.671324327033068 0.271386430077198 0.671324327033068 0.271386430077198 2 - - 34215 Y Y 3.13424050927521 3.63146648901564 3.13424050927521 440 0 0.00721738717935261 Y 0 0 N N 179 30778 ENSG00000196366 ENSG00000148396 - - 9 9 138500339 138491962 utr5p utr5p C9orf163 SEC16A 138497768 138454370 + - 0 138497803 138491962 - + N 0.319085286777889 196.010469436001 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 0.442788385915428 0.564198104634174 0.564198104634174 0.442788385915428 2 0 0 7343 N Y 3.6727393216935 3.27551679143744 3.27551679143744 0 0 0.222459372664098 N 0.94975132910307 0.983250443034357 N N 3 4147 ENSG00000152086 ENSG00000173272 + + 2 2 130672510 131966775 upstream coding TUBA3E FAM128A 130665790 131958003 - - 0 130676369 131958261 - - N - - Y HCC1954 4 3.3 1 29 1 N 437 8.36528 N - - 0 0 0 30 0.914143764470561 1.02126998686945 1.02126998686945 0.914143764470561 2 - - 21796 N Y 3.72551845106187 3.27717235582328 3.27717235582328 4 0 0.840731796812144 N 0 0.901827989211867 N N 2447 12 ENSG00000069812 ENSG00000205592 + + 1 12 6407317 39250827 utr3p downstream HES2 MUC19 6395065 39222629 - + 0 6395252 39372661 - + Y - - N HCC1954 24 20.9 2 10 1 N - - N SINE - 1 0 1 10 0.39993789695587 0.721316564152552 0.721316564152552 0.39993789695587 4 - - 203 Y Y 3.35356364524965 3.11551626166191 3.11551626166191 193 0 0.00354533053149542 Y 0.439091610627274 0.978833645684048 N N 3831 6785 ENSG00000165490 ENSG00000137509 - - 11 11 82323345 82289205 upstream upstream C11orf82 PRCP 82303402 82213058 + - 0 82302652 82290513 - + N - - N HCC1954 2 1.33333333333333 1 3 1 N - - Y SINE - 1 0 1 9 0.671324327033068 0.699891319672773 0.699891319672773 0.671324327033068 0 - - 31522 N Y 3.63552422018169 3.7297745213208 3.63552422018169 260 0 0.0165617663114028 Y 0 0.987701804368471 N N 6170 2648 ENSG00000114857 ENSG00000093183 - - 3 3 42665236 42598432 coding intron NKTR SEC22C 42617151 42564479 + - 0 42617532 42585618 - + N 0.275499820875675 1.17152681033766 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.557056356474248 0.471355378555133 0.557056356474248 0.471355378555133 1 0 0 24804 N Y 3.24637275006602 3.30016202126533 3.24637275006602 119 0.0531905744754042 0.0244731174255997 Y 0.619324045407637 0.990239078087375 N N 2212 1884 ENSG00000141759 ENSG00000101546 - - 18 18 75849520 75907373 coding upstream TXNL4A C18orf22 75833857 75895346 - + 0 75849229 75894841 + - N - - N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.121951219512195 0.121951219512195 7 0.714174815992626 0.585623349113953 0.714174815992626 0.585623349113953 1 - - 40528 N N 3.2948728812365 3.46295381872224 3.2948728812365 3 0 0.305534570680217 N 0.00421940928270059 0.00421940928270059 N N 17 10115 ENSG00000205273 ENSG00000133401 + - 15 5 80782278 32146794 upstream intron AC011295.3-2 PDZD2 80780956 31834788 - + 0.00421940928270059 80838240 31858533 - - Y - 0.0375567036741245 N HCC1954 8 5.6 4 5 1 N - - N - - 0 0 0 5 0.307095170876829 0.307095170876829 0.307095170876829 0.307095170876829 1 - 0 22531 N N 3.25256697878875 3.49847350305486 3.25256697878875 0 0 0.074841002268135 N 0 0 N N 49089 0 ENSG00000117450 ENSG00000222341 - - 1 8 45760196 33693128 coding downstream PRDX1 SRP_euk_arch 45749295 33692844 - + 0 45757275 33753790 + - Y - - N HCC1954 6 3.83333333333333 3 6 1 N - - N - SINE 0 1 1 6 0.485638874874985 0.257102933757345 0.485638874874985 0.257102933757345 2 - - 9358 N N 2.79418115972244 3.52936639476796 2.79418115972244 0 0 0.800068405279474 Y 0 0 N N 3927 0 ENSG00000176155 ENSG00000211264 + + 17 17 77763978 67836854 coding downstream CCDC57 AC005243.1 77652635 67836654 - + 0 77752836 67936045 - + N 0.775277139098501 - N HCC1954 1 1 1 0 4 N 449 0.607786 N - - 0 0 0 16 0.907002016310634 0.499922371194838 0.907002016310634 0.499922371194838 1 0 - 37298 N Y 3.50848272165904 3.49272035470961 3.49272035470961 0 0 0.0686457753087536 N 0.00337837837837807 0.848996723996724 N N 2963 2 ENSG00000133983 ENSG00000166157 + - 14 21 69896147 10012775 coding intron COX16 TPTE 69680762 9928081 - - 0 69879130 9946724 - + Y - 0.889955214331414 N HCC1954 20 17.5 14 4 1 N - - N - SINE,SINE 0 1 1 4 0.378512652476092 0.328520415356608 0.378512652476092 0.328520415356608 1 - 0 12255 N N 3.4780843434859 3.40591861909494 3.40591861909494 3 0 0.430479420829636 N 0.00423728813559321 0.308029301924734 N N 277 7529 ENSG00000205325 ENSG00000185900 - + 17 8 14624245 43097480 downstream downstream AC005863.1 AC113191.13-2 14611625 43067818 - + 0.00423728813559321 14586471 43098565 + + Y - - N HCC1954 22 10.8333333333333 3 6 1 N 285 23.9891 N SINE LINE,SINE 1 0.734939759036145 1 6 0.271386430077198 0.592765097273879 0.592765097273879 0.271386430077198 2 - - 34205 Y Y 3.31216283149579 3.26360926716282 3.26360926716282 273 0 0.0168495473383736 Y 0 0 N N 0 12388 ENSG00000200026 ENSG00000107338 - - 9 9 38137558 38059249 upstream upstream U8 SHB 38137425 37578417 + - 0 38117621 38086729 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.671324327033068 0.671324327033068 0.671324327033068 0.671324327033068 1 - - 21694 N Y 3.62464976567696 3.47080361183081 3.47080361183081 280 0.00357142857142845 0.0140350459103873 N 0.933571428571428 0.933571428571428 N N 18434 23977 ENSG00000136868 ENSG00000160691 - - 9 1 115068495 153213476 utr3p coding SLC31A1 SHC1 115023638 153201398 + - 0 115063144 153209298 - + Y - - N HCC1954 39 27.3076923076923 13 13 1 N 576 22.9821 N SINE - 1 0 1 13 0.578481600954027 0.964136001590045 0.964136001590045 0.578481600954027 1 - - 36264 N Y 3.37023110089298 3.01035165322472 3.01035165322472 267 0 0.021912517005064 Y 0 0 N N 278 0 ENSG00000198353 ENSG00000207924 - + 12 12 52736081 52671898 intron downstream HOXC4 hsa-mir-196a-2 52696909 52671789 + + 0 52733209 52675065 - + N 0.314022379653777 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.685607823352921 0.764167053112109 0.764167053112109 0.685607823352921 2 0 - 10875 N N 3.4780843434859 3.47911741325579 3.4780843434859 0 0 0.0481046624473298 N 0 0 N N 1877 975 ENSG00000185924 ENSG00000198487 + + 17 6 1787865 42218335 upstream coding RTN4RL1 AL512274.9 1786540 42183124 - - 0 1805754 42183205 - - Y - - N HCC1954 21 5 1 1 1 N 565 21.1777 N SINE - 1 0 1 5 0.264244681917271 0.478497126715059 0.478497126715059 0.264244681917271 1 - - 37678 N N 3.55401162459584 3.09555125761603 3.09555125761603 0 0 0.319531413097504 N 0.026848380390554 0 N N 15994 5921 ENSG00000119707 ENSG00000185721 + + 14 22 72657740 30160171 utr5p intron RBM25 DRG1 72595021 30125539 + + 0 72595166 30132706 + + Y 0.461464424625388 0.960883417566166 N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.614190341753658 0.314236919036755 0.614190341753658 0.314236919036755 4 0 0 2170 N Y 3.39128260787123 3.69784855983781 3.39128260787123 2 0 0.116802097200377 N 0.892736745326387 0.923383389518848 N N 12271 6524 ENSG00000177479 ENSG00000110395 - + 3 11 48997971 118684066 intron intron ARIH2 CBL 48931285 118582200 + + 0 48939897 118600651 - + Y 0.963247002497696 0.46951043953841 N HCC1954 23 3.77777777777778 1 4 1 N - - N Simple_repeat SINE,DNA 0.148387096774194 0.818181818181818 0.818181818181818 9 1.0069864905496 0.392796148795944 1.0069864905496 0.392796148795944 1 0 0 656 Y Y 3.26104861408308 3.30062602958175 3.26104861408308 0 0 0.992214522725232 Y 0.789450264206916 0.944266246407713 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 coding coding C11orf66 C11orf79 61005168 60954173 + + 0 61006845 60970008 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.814159290231593 0.657040830713216 0.814159290231593 0.657040830713216 3 - - 32992 N N 3.54313717009112 2.78995559468704 2.78995559468704 22 0 0.999918260377654 N 0 0.0437894412805909 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0437894412805909 8995 14082 - + N 0.569970266867756 2.00629659345316 N HCC1954 2 2 2 4 10 N 189 4.09957 N - - 0 0 0 4 0.728458312312478 0.642757334393363 0.728458312312478 0.642757334393363 1 0 0 46251 N Y 3.49164743214637 3.48743121468078 3.48743121468078 16 0.0471112368290786 0.271800097792084 N 0 0.765957145887844 N N 1862 609 ENSG00000204794 ENSG00000105750 - + 9 19 68199726 20925341 utr3p upstream PGM5P2 ZNF85 68131062 20897922 - + 0 68131574 20783575 + + Y - - N HCC1954 420 131.25 21 4 1 N 457 24.0916 N LINE LINE 1 1 1 4 0.321378667196682 0.385654400636018 0.385654400636018 0.321378667196682 2 - - 38262 Y Y 3.15057193767811 3.44871903508266 3.15057193767811 0 0 0.675898804527236 Y 0.986351002580901 0.986351002580901 N N 8350 4025 ENSG00000179364 ENSG00000185024 - - 14 14 104935529 104838374 intron coding PACS2 BRF1 104852126 104746670 + - 0 104852701 104823755 - + N 0.328314398751677 2.24733009298986 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.928427260790413 0.51420586751469 0.928427260790413 0.51420586751469 1 0 0 42351 Y Y 3.17142510556349 3.4446613039166 3.17142510556349 239 0 0.0742811117429768 Y 0.98994125353958 0.98994125353958 N N 7896 12251 ENSG00000134852 ENSG00000134851 + + 4 4 56107754 55987095 intron coding CLOCK TMEM165 55993417 55956877 - + 0 56013162 55985566 - + N 1.38384862198753 3.37703197651863 N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 6 0.721316564152552 0.628473838073511 0.721316564152552 0.628473838073511 1 0 0 48778 N Y 3.61207989399303 3.58743466416515 3.58743466416515 21 0.176192725555031 0.0411300330810621 N 0.776885529837821 0.845536136041568 N N 5515 153380 ENSG00000152620 ENSG00000185275 + + 5 Y 36278015 19614093 utr3p utr3p C5orf33 CD24L4 36228451 19611898 - - 0 36229218 19612795 - - Y - - N HCC1954 37 28.2 22 5 1 N 491 29.193 N SINE SINE 1 0.549450549450549 1 5 0.307095170876829 0.649899082553289 0.649899082553289 0.307095170876829 1 - - 23995 N N 3.51935717616377 2.97047842278071 2.97047842278071 0 0.262913385826772 0.554990866895944 N 0.38244094488189 0 N N 551733 5789 ENSG00000204628 ENSG00000187147 + + 5 1 180603512 44889983 utr3p intron GNB2L1 RNF220 180596536 44643453 - + 0 180596558 44696606 - + Y - 0.0113887214605194 N HCC1954 21 12.5 1 5 1 N - - N - SINE 0 0.261904761904762 0.261904761904762 6 0.5713398527941 0.299953422716903 0.5713398527941 0.299953422716903 2 - 0 45007 Y N 3.54400240599166 3.448886868952 3.448886868952 0 0 0.232266416044927 N 0.0380823031184498 0 Y N 2456 2746 ENSG00000171813 ENSG00000068383 - + 10 10 134081357 134446974 utr3p coding PWWP2B INPP5A 134060662 134201343 + + 0 134080566 134201664 - + N - - N HCC1954 1 1 1 0 2 N 205 11.6558 N - Low_complexity,Low_complexity 0 0.475609756097561 0.475609756097561 64 1.81400403262127 1.53547585438415 1.81400403262127 1.53547585438415 1 - - 3468 Y Y 3.28552601004162 3.17295268887334 3.17295268887334 248 0 0.0239329621957003 Y 0.604905358571048 0.991768861636897 N N 1755 0 ENSG00000159231 ENSG00000214889 - + 21 21 36440728 36427200 intron downstream CBR3 AP000689.1-2 36429133 36426618 + + 0 36431261 36427241 - + N 0.860938276065875 - N HCC1954 1 1 1 0 2 N - - Y DNA,DNA,SINE - 0.515873015873016 0 0.515873015873016 5 0.899860268150708 0.507064119354764 0.899860268150708 0.507064119354764 1 0 - 37145 N N 3.37232774565629 3.37076030955309 3.37076030955309 1 0 0.548704419968918 N 0 0 N N 12314 0 ENSG00000011105 ENSG00000222956 - - 12 5 3265990 68810848 intron downstream TSPAN9 SRP_euk_arch 3056818 68810578 + - 0 3191156 68801666 - + Y 0.623152350133906 - N HCC1954 8 5.46153846153846 4 13 1 N - - N - - 0 0 0 13 0.421363141435649 0.271386430077198 0.421363141435649 0.271386430077198 1 0 - 42114 N N 3.53296011761759 3.30062602958175 3.30062602958175 0 0 0.0930446791797405 N 0 0.0201749871332992 N N 446 26328 ENSG00000111837 ENSG00000205403 + + 6 4 10946714 110942783 upstream coding MAK CFI 10870942 110881297 - - 0.0201749871332992 10956066 110883156 - - Y - - N HCC1954 21 17.6666666666667 6 6 1 N - - N SINE - 1 0 1 6 0.507064119354764 0.857009779191151 0.857009779191151 0.507064119354764 2 - - 44050 N Y 3.38486711211668 3.64656650855576 3.38486711211668 255 0.3359477124183 0.0906642367568744 N 0.907770515613653 0.981554103122731 N N 0 0 ENSG00000217094 ENSG00000214975 - + 10 6 32517745 25085188 intron intron AL445071.15 AL160400.20-1 32517254 25084626 - + 0.981554103122731 32517531 25084912 + + Y 1 1 N HCC1954 13 6.58823529411765 5 17 1 N - - N - - 0 0 0 17 0.328520415356608 0.34280391167646 0.34280391167646 0.328520415356608 3 0 0 36408 Y Y 1.92192809488736 3.28247084342192 1.92192809488736 0 0 0.31035864411034 Y 0.0158730158730159 0.0158730158730159 N N 1725 53 ENSG00000119242 ENSG00000197653 + + 12 12 123023317 122986218 coding intron CCDC92 DNAH10 122986936 122812995 - + 0.0158730158730159 122993954 122974757 - + N 2.94039499458325 0.494541329832128 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.564198104634174 0.649899082553289 0.649899082553289 0.564198104634174 2 0 0 36528 Y Y 3.49953707804829 3.12907935032238 3.12907935032238 144 0 0.0336969736042277 Y 0 0.983449074074074 N N 1864 1303 ENSG00000075188 ENSG00000185480 - - 12 12 101036491 101119401 coding upstream NUP37 C12orf48 100992105 101038086 - + 0.983449074074074 101036401 101037988 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 78 1.19981369086761 0.707033067832699 1.19981369086761 0.707033067832699 2 - - 6560 N N 3.66385645881505 3.09001826628863 3.09001826628863 0 0.0108695652173911 0.0754937452365522 N 0.0108695652173911 0.0108695652173911 N N 33206 17330 ENSG00000163466 ENSG00000123983 - - 2 2 218827324 223516360 coding intron ARPC2 ACSL3 218790119 223433976 + + 0 218798899 223439743 - - N - 0.7515633223348 Y HCC1954 1 1 1 0 1 N - - N Low_complexity Simple_repeat 0.145454545454545 1 1 4 0.392796148795944 0.264244681917271 0.392796148795944 0.264244681917271 2 - 0 12953 N Y 3.07101108092519 3.70463477795295 3.07101108092519 0 0 0.143573107125849 N 0 0.800578034682081 N N 1649619 3107 ENSG00000141736 ENSG00000178996 - - 17 5 35138441 53875478 coding downstream ERBB2 SNX18 35104766 53849350 + + 0.800578034682081 35125066 53962295 - - Y 0.990793461175642 - N HCC1954 25 19.1111111111111 3 9 1 N - - N - SINE 0 1 1 9 0.464213630395207 0.378512652476092 0.464213630395207 0.378512652476092 1 0 - 47614 Y Y 3.42576922243396 3.7297745213208 3.42576922243396 0 0 0.415950038398534 Y 0.989515290201789 0.979030580403578 N N 205 37 ENSG00000012124 ENSG00000105695 - + 19 19 40530098 40496547 utr5p coding CD22 MAG 40511919 40474868 + + 0 40511932 40494760 - + N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 5 0.735600060472404 1.10697096478857 1.10697096478857 0.735600060472404 4 - - 16421 N N 3.29908909870209 3.81657625693547 3.29908909870209 0 0 0.0677358816367659 N 0 0.626637554585153 N N 411 2833 ENSG00000183023 ENSG00000133019 - - 2 1 40691697 238139338 coding utr5p SLC8A1 CHRM3 40192790 237858996 - + 0 40509134 237859403 + - Y - - N HCC1954 23 22.425 22 40 1 N - - N - LINE 0 1 1 40 0.978419497909897 0.392796148795944 0.978419497909897 0.392796148795944 1 - - 1412 N Y 3.43056384892283 3.52361324642271 3.43056384892283 6 0 0.90140418947716 N 0 0.0765589782118707 N N 3601 9042 ENSG00000182963 ENSG00000137692 - + 17 11 40263133 102468079 utr3p coding GJC1 DCUN1D5 40231342 102438032 - - 0.0765589782118707 40234175 102458687 + - Y - 0.765494554141182 N HCC1954 39 37 34 5 1 N - - N SINE - 1 0 1 5 0.378512652476092 0.364229156156239 0.378512652476092 0.364229156156239 4 - 0 11545 N Y 3.22167408707565 3.49528100778935 3.22167408707565 331 0 0.00372711910841306 N 0.870621065012338 0.992389474412491 N N 6267 0 ENSG00000125450 ENSG00000188612 - - 17 X 70743449 114859974 upstream intron NUP85 AC005000.2 70713192 114858916 + - 0.992389474412491 70690071 114859783 - + Y - 1 N HCC1954 8 4.83783783783784 3 37 1 N - - N - - 0 0 0 37 1.35693215038599 0.956994253430118 1.35693215038599 0.956994253430118 1 - 0 19596 N Y 3.77001428422878 3.24893340314576 3.24893340314576 0 0 0.64663604341094 N 0.509402287618547 0.911802658448278 N N 4626 0 ENSG00000133059 ENSG00000206696 + + 1 18 203447322 45272097 intron upstream DSTYK SNORD58 203378255 45272032 - - 0.911802658448278 203437933 45272639 - - Y 2.4630539786761 - N HCC1954 9 6.36585365853659 6 41 1 N 433 20.0375 N - - 0 0 0 41 0.371370904316165 1.06412047582901 1.06412047582901 0.371370904316165 3 0 - 48871 N N 3.59681204058356 3.59169073442408 3.59169073442408 0 0 0.998713896296583 N 0 0.10337216952102 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 coding downstream TICAM2 AC034236.1 114942238 115326170 - + 0.10337216952102 114989197 115391486 - + N 0.297159064262796 - N HCC1954 1 1 1 0 5 N - - N - Low_complexity,LTR 0 0.993288590604027 0.993288590604027 38 1.38549914302569 0.835584534711372 1.38549914302569 0.835584534711372 4 0 - 19718 N N 3.3519080808638 2.78130147148845 2.78130147148845 0 0.343283582089552 0.0516358880004681 N 0.343283582089552 0.343283582089552 N N 2050 2962 ENSG00000203705 ENSG00000103489 - + 1 16 211056590 17472239 utr3p upstream TATDN3 XYLT1 211031808 17103682 + - 0.343283582089552 211055638 17484740 - - Y - - N HCC1954 23 22.75 22 4 1 N - - N SINE LINE,LTR 1 0.34375 1 4 0.385654400636018 0.45707188223528 0.45707188223528 0.385654400636018 2 - - 38085 N N 3.80194024571177 3.52208566311286 3.52208566311286 0 0 0.985291263020472 Y 0.0822510822510826 0 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 utr5p downstream SIPA1L1 SNORD56 71065795 70934807 + + 0 71065799 70950670 - + N 0.0140231535012627 - N HCC1954 1 1 1 0 6 N - - N - - 0 0 0 6 0.378512652476092 0.34280391167646 0.378512652476092 0.34280391167646 1 0 - 19101 Y Y 3.6533527266709 3.46340847946885 3.46340847946885 377 0 0.00199916454783444 Y 0 0.990410120383595 N N 21819 0 ENSG00000143162 ENSG00000218805 + + 1 1 165789684 165756447 coding downstream CREG1 RP3-455J7.1 165776877 165755397 - + 0 165782015 165766281 - + N 1.16144942645359 - N HCC1954 1 1 1 0 1 N - - Y - LTR,LTR 0 0.270588235294118 0.270588235294118 4 0.999844742389676 0.607048593593732 0.999844742389676 0.607048593593732 3 0 - 20001 N Y 3.61360747730288 3.25935319690388 3.25935319690388 0 0 0.0417032193170136 N 0.0475449381371098 0 N N 8936 45068 ENSG00000143106 ENSG00000205336 + + 1 16 109770589 56256445 intron upstream PSMA5 GPR56 109745997 56220023 - + 0 109752913 56211247 - + Y 0.389903507436213 - N HCC1954 21 10.4615384615385 6 26 1 N - - N SINE - 1 0 1 26 0.307095170876829 0.492780623034912 0.492780623034912 0.307095170876829 1 0 - 1521 N N 2.97670734662359 3.01654588194744 2.97670734662359 0 0.0038022813688211 0.203381013976212 N 0 0.359587180879957 N N 143275 11059 ENSG00000167996 ENSG00000160551 + - 11 17 61491708 24895628 utr5p upstream FTHL16 TAOK1 61488335 24742069 - + 0 61491479 24741984 - - Y 0.953813485966137 - N HCC1954 10 5.75 4 4 1 N 525 24.8419 N - Low_complexity 0 1 1 4 0.264244681917271 0.292811674556976 0.292811674556976 0.264244681917271 2 0 - 20590 N Y 3.53465553479678 3.588962247475 3.53465553479678 4 0 0.647029416835159 N 0 0.978472891789661 N N 0 8888 ENSG00000201692 ENSG00000112159 + + 1 6 172100669 90586163 upstream intron snosnR60_Z15 MDN1 172100588 90409952 - - 0.978472891789661 172100877 90487992 - - Y - 1.96227421382155 N HCC1954 3 2 1 2 2 N - - N - SINE 0 0.433962264150943 0.433962264150943 4 0.721316564152552 0.899860268150708 0.899860268150708 0.721316564152552 3 - 0 48208 N Y 3.60103760561896 3.44615838200292 3.44615838200292 273 0 0.000692219680421546 N 0 0.570808678500986 N N 232 902 ENSG00000205464 ENSG00000173214 - - 5 6 81649981 111696952 utr5p utr3p ATP6AP1L KIAA1919 81611037 111687175 + + 0 81636616 111695605 - - Y - - N HCC1954 814 791 770 4 1 N - - N SINE SINE 1 1 1 4 0.28566992639705 0.307095170876829 0.307095170876829 0.28566992639705 2 - - 49136 N N 3.56232542602083 3.31229081257178 3.31229081257178 0 0 0.262811826776081 N 0 0 N N 6627 1458 ENSG00000113269 ENSG00000188818 + + 5 5 179431719 904101 intron coding RNF130 ZDHHC11 179315111 848722 - - 0 179367697 893651 - - N 1.40481845160553 - Y HCC1954 2 1.64285714285714 1 18 2 N 48 1.73211 N LINE - 1 0 1 28 0.921285512630487 1.0069864905496 1.0069864905496 0.921285512630487 2 0 - 5420 N N 3.40591861909494 2.95058796664834 2.95058796664834 29 0.240338983050847 0.284988499756515 N 0.527322033898305 0.257220338983051 N N 78560 5880 ENSG00000112493 ENSG00000065548 - - 6 2 33390114 187082330 utr3p upstream TAPBP ZC3H15 33375449 187059130 - + 0.257220338983051 33376420 186849211 + - Y - - N HCC1954 22 12.5 2 6 1 N - - N SINE SINE 1 0.583333333333333 1 6 0.478497126715059 0.257102933757345 0.478497126715059 0.257102933757345 2 - - 28701 N N 3.41273534243362 3.47233119514066 3.41273534243362 0 0 0.671246760644287 N 0.646274777853725 0.633173843700159 N N 1848 4096 ENSG00000198131 ENSG00000103121 - - 19 16 63466822 79597997 utr3p coding ZNF544 C16orf61 63431882 79567206 + - 0 63466514 79567577 - + Y - - N HCC1954 26 24.1666666666667 21 6 1 N - - N SINE - 1 0 1 6 0.299953422716903 0.564198104634174 0.564198104634174 0.299953422716903 4 - - 39216 N Y 3.07101108092519 3.66848325143457 3.07101108092519 0 0.00370370370370365 0.438348005160022 N 0.659801264679313 0.902800361336947 N N 1649619 11814 ENSG00000141736 ENSG00000170776 - - 17 15 35138441 84093590 coding intron ERBB2 AKAP13 35104766 83724875 + + 0 35125066 84047952 - - Y - 1.00981829488738 N HCC1954 22 20.1904761904762 20 21 1 N - - N - SINE 0 1 1 21 0.757025304952183 0.34280391167646 0.757025304952183 0.34280391167646 1 - 0 26701 Y Y 3.68527868815389 3.51782959285392 3.51782959285392 240 0 0.132790342336279 Y 0.851090342679128 0.972079439252337 N N 5 24977 ENSG00000048462 ENSG00000103342 - - 16 16 11969426 11917313 upstream upstream TNFRSF17 GSPT1 11966465 11874040 + - 0 11957497 11939021 - + N - - N HCC1954 17 3.8 1 3 2 N - - Y SINE - 0.927710843373494 0 0.927710843373494 10 0.592765097273879 0.914143764470561 0.914143764470561 0.592765097273879 3 - - 121 Y Y 2.96787791690762 3.58064844605001 2.96787791690762 247 0 0.0355114547964239 Y 0 0.791890748685721 N N 0 0 ENSG00000222225 ENSG00000209356 + - 11 11 143102 143101 upstream downstream U6 AC069287.7-1 142999 142999 - - 0.21215783431023 149457 138672 - + N - - N HCC1954 189 141.75 126 4 2 N - - Y - SINE 0 1 1 4 0.349945659836387 0.307095170876829 0.349945659836387 0.307095170876829 1 - - 33434 N Y 2.96319769112561 3.3241983368464 2.96319769112561 410 0 0.96142632838808 Y 0 0.994749679075738 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8593 5184 - + N - - N HCC1954 4 2.6 2 5 9 N - - N - - 0 0 0 5 0.749883556792257 1.0069864905496 1.0069864905496 0.749883556792257 1 - - 44806 Y N 3.5816815158199 3.7527243339695 3.5816815158199 0 0 0.197069346875312 Y 0.151273885350318 0 N N 137 82 ENSG00000184923 ENSG00000214562 - + 10 10 89117109 88984892 upstream downstream FAM22D FAM22A 89107405 88975185 + + 0 89080700 89038237 - + N - - N HCC1954 16 9 4 5 2 N - - Y - SINE 0 0.0818181818181818 0.0818181818181818 5 0.785592297591888 0.642757334393363 0.785592297591888 0.642757334393363 1 - - 9345 Y Y 3.39640391403072 3.29912895149544 3.29912895149544 288 0 0.999343050946365 N 0 0.992027777777778 Y N 317991 1482 ENSG00000171346 ENSG00000171345 + - 17 17 36932191 36938167 upstream utr5p KRT15 KRT19 36923523 36933396 - - 0 36946593 36938109 - + N - 31.5276649710027 N HCC1954 2 1.29411764705882 1 5 8 N - - N - - 0 0 0 17 0.964136001590045 1.02126998686945 1.02126998686945 0.964136001590045 2 - 0 49130 Y Y 3.28126993978269 3.65384724021086 3.28126993978269 300 0 0.773378214487909 Y 0.0299111111111112 0.973422222222222 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 utr3p utr3p TPPP CEP72 712978 665405 - + 0 715930 706463 - + N 0.673077310270093 - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 8 0.449930134075354 0.364229156156239 0.449930134075354 0.364229156156239 2 0 - 10332 Y Y 3.41216628098015 3.6769648867289 3.41216628098015 341 0 0.999996554823775 Y 0 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p upstream ORMDL3 GSDMB 35330822 35314374 - - 0 35331922 35329477 - + N - - N HCC1954 20 2.35714285714286 1 1 14 N - - Y - SINE 0 0.524691358024691 0.524691358024691 14 1.14982145374813 1.15696320190805 1.15696320190805 1.14982145374813 2 - - 28371 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.0780310507579784 N 0 0 N N 6309 45068 ENSG00000153310 ENSG00000205336 - + 8 16 131097879 56256445 intron upstream FAM49B GPR56 130922900 56220023 - + 0 131031222 56211646 + + Y 2.47303263252138 - N HCC1954 24 22.25 20 8 1 N - - N SINE,SINE - 1 0 1 8 0.349945659836387 0.442788385915428 0.442788385915428 0.349945659836387 1 0 - 24349 N Y 2.8004058936687 3.40591861909494 2.8004058936687 0 0 0.0435669127777121 N 0 0 N N 3968 0 ENSG00000124496 ENSG00000221621 - - 6 18 42527767 28360183 utr3p downstream TRERF1 AC009835.14 42300647 28360103 - + 0.292582417582418 42302800 28361903 + - Y - - N HCC1954 1 1 1 0 1 N - - N DNA SINE 1 1 1 11 0.464213630395207 0.292811674556976 0.464213630395207 0.292811674556976 1 - - 25628 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.072158494621684 N 0 0 N N 0 45068 ENSG00000146910 ENSG00000205336 + + 7 16 155019318 56256445 intron upstream CNPY1 GPR56 154959662 56220023 - + 0 155005995 56211646 - + Y 1 - N HCC1954 24 19.8 5 10 1 N - - N SINE - 1 0 1 10 0.385654400636018 0.542772860154395 0.542772860154395 0.385654400636018 1 0 - 48573 N N 3.6523103093312 3.63655728995158 3.63655728995158 31 0 0.0959908398652837 N 0 0 N N 27 850768 ENSG00000184188 ENSG00000075624 - + 5 7 79631912 5536758 coding coding AC026410.5-4 ACTB 79631253 5533313 - - 0 79631652 5534240 + - Y - - N HCC1954 4 2 1 2 1 Y - - N - - 0 0 0 4 0.707033067832699 0.907002016310634 0.907002016310634 0.707033067832699 2 - - 9554 Y Y 3.45976132345673 3.40169305405954 3.40169305405954 296 0 0.0249682570214597 Y 0 0 N N 313916 37605 ENSG00000131748 ENSG00000131771 - + 17 17 35073248 35046404 upstream intron STARD3 PPP1R1B 35046938 35036705 + + 0.992274250995181 35046771 35044806 - + N - 0.501048040752562 N HCC1954 20 7.11538461538461 1 12 2 N - - Y - SINE 0 0.631205673758865 0.631205673758865 26 0.949852505270192 1.0069864905496 1.0069864905496 0.949852505270192 1 - 0 41088 N N 3.4210491438586 3.63655728995158 3.4210491438586 0 0 0.888697360740907 N 0 0 Y Y 8726 19569 ENSG00000215305 ENSG00000088812 - + 20 20 2795378 3579760 coding coding VPS16 ATRN 2769373 3399676 + + 0 2788365 3513527 - + N - 1.74818121966506 N HCC1954 1 1 1 0 1 Y 374 3.23405 N - - 0 0 0 17 1.56404284702385 1.34264865406614 1.56404284702385 1.34264865406614 4 - 0 42451 Y Y 3.61257440753299 3.64826192573496 3.61257440753299 0 0 0.532664470338737 Y 0.747525340513145 0.993526290782388 N N 122 942 ENSG00000212760 ENSG00000155275 - + 4 4 8534090 8529181 downstream coding AC105345.3-1 C4orf23 8530206 8493450 + + 0 8545891 8523825 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 6 0.778450549431962 0.699891319672773 0.778450549431962 0.699891319672773 3 - - 36958 N N 3.37655331069169 3.78105657260285 3.37655331069169 0 0 0.999934552881768 N 0 0 N N 3 12084 ENSG00000179242 ENSG00000177119 + + 20 12 59945671 44112391 intron coding CDH4 ANO6 59260965 43896170 + + 0 59589772 44047841 + + Y 0.929733246584255 3.80876768576458 N HCC1954 1 1 1 0 8 N - - N LTR - 0.359756097560976 0 0.359756097560976 43 1.17124669822791 0.792734045751814 1.17124669822791 0.792734045751814 1 0 0 47942 N N 3.6052936758779 3.32333310094585 3.32333310094585 0 0.0512289862455424 0.0269749708493818 N 0.0512289862455424 0 N N 0 9183 ENSG00000222706 ENSG00000172172 - + 5 8 113617369 121526828 upstream coding 7SK MRPL13 113617109 121477264 + - 0 113585066 121495492 - - Y - - N HCC1954 1 1 1 0 1 N - - N LINE - 1 0 1 5 0.657040830713216 0.714174815992626 0.714174815992626 0.657040830713216 0 - - 13775 Y Y 3.57952209032428 3.34512186274866 3.34512186274866 322 0 0.00262124534403785 Y 0.978637976929903 0.992879325643301 N N 7 4485 ENSG00000161149 ENSG00000184436 + - 22 22 19698576 19686404 coding upstream AC002472.8-1 THAP7 19693395 19684063 - - 0 19693636 19687115 - + N 1.70339916133718 - N HCC1954 22 5.2 1 1 1 N - - Y - SINE 0 1 1 5 0.849868031031224 0.899860268150708 0.899860268150708 0.849868031031224 1 0 - 38237 Y Y 3.55657227767559 3.5010341561346 3.5010341561346 0 0.266361556064073 0.806002599828305 Y 0.266361556064073 0.986899313501144 N N 51898 4802 ENSG00000100644 ENSG00000027075 - + 14 14 61284729 61087443 upstream intron HIF1A PRKCH 61231992 60858186 + + 0 61187434 61067067 - + N - 1.41446770605714 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.428504889595575 1.02126998686945 1.02126998686945 0.428504889595575 1 - 0 15510 N Y 3.51782959285392 3.78208964237274 3.51782959285392 4 0 0.158766939316931 N 0 0.892990023377564 N N 0 2833 ENSG00000213483 ENSG00000133019 - + 7 1 93312560 238139338 upstream utr5p AC002076.2 CHRM3 93312037 237858996 + + 0.0533732837246057 93274514 237859446 - + Y - - N HCC1954 440 87.8888888888889 21 9 1 N - - N LINE LINE 1 1 1 9 1.17124669822791 0.678466075192994 1.17124669822791 0.678466075192994 3 - - 18694 N Y 3.41273534243362 3.06346518960165 3.06346518960165 15 0 0.157065090862316 Y 0.88561872909699 0.88561872909699 N N 0 0 ENSG00000220261 ENSG00000219021 + + 1 1 222242479 222204741 downstream downstream RP11-504P24.2 RP11-504P24.1 222237079 222201925 - + 0.123076923076923 222225903 222216980 - + N - - N HCC1954 238 190.125 2 8 3 N - - N LTR,SINE SINE 0.869565217391304 1 1 8 0.657040830713216 0.471355378555133 0.657040830713216 0.471355378555133 1 - - 4639 Y Y 3.41319935075004 3.58593758607883 3.41319935075004 0 0 0.101558022351316 Y 0 0 N N 3077 935 ENSG00000075790 ENSG00000105865 - + 7 7 107058401 107006204 utr5p coding BCAP29 DUS4L 107007946 106991661 + + 0 107008446 107004241 - + N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 8 0.885576771830856 1.17838844638783 1.17838844638783 0.885576771830856 1 - - 7912 N Y 3.17464810605253 3.52511032450902 3.17464810605253 114 0 0.0286181130743977 N 0.290083887306109 0.86170465337132 N N 10665 0 ENSG00000115233 ENSG00000221415 + + 2 4 161976474 48895063 upstream downstream PSMD14 AC118282.4-1 161872795 48894981 + + 0.880144032921811 161846879 48990005 + + Y - - N HCC1954 30 11.8333333333333 3 12 1 N 182 17.3857 N Satellite Satellite 1 0.302469135802469 1 12 0.549914608314322 1.14982145374813 1.14982145374813 0.549914608314322 2 - - 30559 Y N 3.25099954268554 3.38759559906577 3.25099954268554 0 0.00421940928270015 0.288020136353565 Y 0.00421940928270015 0.00421940928270015 N N 3574 3149 ENSG00000196459 ENSG00000123595 + + X X 13662648 13637681 downstream coding TRAPPC2 RAB9A 13640282 13617262 - + 0 13639739 13636851 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.670886075949367 0.670886075949367 4 0.671324327033068 0.564198104634174 0.671324327033068 0.564198104634174 2 - - 30806 N Y 3.66695566812472 3.13593592645441 3.13593592645441 0 0 0.286589557246081 N 0 0.823192436040045 N N 0 4873 ENSG00000218564 ENSG00000130021 + - Y X 16077348 7076189 upstream intron AC006998.1 HDHD1A 15969936 6976961 - - 0 16099168 7075762 - + Y - 0.638327297478365 N HCC1954 2 1.8 1 4 2 N - - N SINE DNA 0.0384615384615385 0.518518518518518 0.518518518518518 5 0.371370904316165 0.578481600954027 0.578481600954027 0.371370904316165 1 - 0 7757 N Y 3.71890006681607 3.62295434849776 3.62295434849776 255 0 0.0538078204276577 N 0 0.991835422693668 N N 0 27 ENSG00000155052 ENSG00000164749 + + 2 8 125389382 76641600 intron upstream CNTNAP5 HNF4G 124499334 76482732 + + 0.118225650916104 125073214 76388526 + + Y 1 - N HCC1954 23 22 20 4 1 N - - N LINE LTR 1 1 1 4 0.792734045751814 0.785592297591888 0.792734045751814 0.785592297591888 1 0 - 43655 N Y 3.12804628055249 3.50165665075055 3.12804628055249 1 0 0.250433970131510 N 0.845458368376787 0.948486122792262 N N 1649619 0 ENSG00000141736 ENSG00000218306 - - 17 10 35138441 43340671 coding downstream ERBB2 RP11-517P14.7 35104766 43338710 + + 0 35122227 43341576 - - Y - - N HCC1954 20 3.90909090909091 1 6 1 N - - N - SINE 0 1 1 11 0.885576771830856 0.349945659836387 0.885576771830856 0.349945659836387 2 - - 11201 N Y 3.12804628055249 3.47336426491055 3.12804628055249 0 0 0.382208656683935 N 0 0.868341170168442 N N 1649619 0 ENSG00000141736 ENSG00000206531 - - 17 3 35138441 114047487 intron upstream ERBB2 CD200R1L 35104766 114017246 + - 0 35125062 114084015 - + Y 0.991162890469566 - N HCC1954 4 2.875 1 6 1 N - - N - SINE 0 1 1 8 0.521347615674617 0.278528178237124 0.521347615674617 0.278528178237124 2 0 - 47537 Y Y 3.5701752191294 3.58849823915857 3.5701752191294 123 0 0.168181857643509 Y 0.0271307207454097 0.993919567004659 N N 2469 421 ENSG00000142252 ENSG00000170684 - - 19 19 50286622 50271528 utr5p coding GEMIN7 ZNF296 50274370 50266599 + - 0 50274475 50270918 - + N - 1.55631184293978 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 1.19981369086761 0.771308801272036 1.19981369086761 0.771308801272036 1 - 0 21546 N Y 3.5319270478477 3.05228683331189 3.05228683331189 20 0 0.203962802553357 N 0 0.870411431387041 N N 262 0 ENSG00000185842 ENSG00000220431 + + 1 9 223652370 42267232 utr3p downstream AC092811.2 RP11-216M21.4 223495119 42266761 + + 0.376355013550136 223651601 42281349 + + Y - - N HCC1954 144 126 108 4 1 N 507 23.5055 N SINE - 1 0 1 4 0.742741808632331 0.528489363834543 0.742741808632331 0.528489363834543 1 - - 45447 N N 3.51935717616377 3.20600500608205 3.20600500608205 0 0.344173441734417 0.612130988638956 N 0.368463314262773 0 N N 551733 9780 ENSG00000204628 ENSG00000151893 + - 5 10 180603512 120504748 utr3p downstream GNB2L1 C10orf46 180596536 120430484 - - 0 180596558 120421743 - + Y - - N HCC1954 21 13.7142857142857 3 21 1 N - - N - Low_complexity 0 0.411764705882353 0.411764705882353 21 0.93556900895034 0.364229156156239 0.93556900895034 0.364229156156239 2 - - 20298 N N 3.47336426491055 3.44040523365767 3.44040523365767 0 0 0.699711264567228 N 0.212835807092986 0 N N 16390 0 ENSG00000140950 ENSG00000208366 - + 16 1 83095794 169717771 utr5p upstream KIAA1609 AL049762.20-1 83068608 169717670 - + 0 83095708 169717257 + + Y - - N HCC1954 2 1.09090909090909 1 1 2 N - - N - SINE 0 0.846153846153846 0.846153846153846 11 0.557056356474248 0.278528178237124 0.557056356474248 0.278528178237124 3 - - 24689 Y Y 3.21808036422602 3.28292550416853 3.21808036422602 189 0 0.0666441571680185 Y 0 0 N N 7222 4519 ENSG00000101639 ENSG00000085415 - + 18 18 13115052 12977533 upstream coding CEP192 SEH1L 12998499 12937983 + + 0 12989475 12974160 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.778450549431962 0.621332089913584 0.778450549431962 0.621332089913584 2 - - 38211 N Y 3.64759957832565 3.43937216388778 3.43937216388778 178 0 0.084212109590997 Y 0 0.983961580282711 N N 2024 2004 ENSG00000129538 ENSG00000181784 + + 14 14 20340876 20238597 downstream downstream RNASE1 RNASE4 20339355 20222212 - + 0 20337909 20249756 - + N - - N HCC1954 1 1 1 0 2 N - - N LTR LTR 1 1 1 5 0.464213630395207 0.407079645115797 0.464213630395207 0.407079645115797 3 - - 4532 N Y 3.51273879191798 3.01397588129789 3.01397588129789 300 0 0.0105300094964937 Y 0.0579452054794521 0.979520547945205 N N 93 93 ENSG00000105982 ENSG00000105982 - + 7 7 156162585 156162585 downstream coding RNF32 RNF32 156117523 156117523 + + 0 156164438 156162085 - + N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 4 0.664182578873142 0.564198104634174 0.664182578873142 0.564198104634174 2 - - 27429 N Y 3.42886843174363 2.50591529984609 2.50591529984609 1 0 0.0972258370425375 N 0 0.870663650075415 N N 10303 23962 ENSG00000090857 ENSG00000103035 + + 16 16 68752706 72897685 coding coding PDPR PSMD7 68705030 72888182 + + 0 68744829 72897070 + + N - 3.57675053862192 Y HCC1954 2 1.75 1 3 1 N - - N - - 0 0 0 4 0.699891319672773 0.699891319672773 0.699891319672773 0.699891319672773 1 - 0 9529 Y Y 3.46720988898117 3.59169073442408 3.46720988898117 297 0 0.00578598613598391 Y 0 0 N N 245 14289 ENSG00000180638 ENSG00000072210 + + 17 17 19560635 19521501 intron intron SLC47A2 ALDH3A2 19522220 19492641 - + 0 19529181 19515862 - + N 1.57166893159904 3.17241001623974 N HCC1954 2 1.11111111111111 1 1 1 N - - Y Other - 1 0 1 9 1.09268746846872 0.964136001590045 1.09268746846872 0.964136001590045 1 0 0 4346 Y Y 3.63552422018169 3.55128313764676 3.55128313764676 237 0 0.617115651749258 Y 0 0.985356167783569 N N 0 0 ENSG00000219142 ENSG00000217741 + + 7 7 17039627 16944706 downstream upstream AC098592.8 AC098592.7 17039238 16944374 - + 0 17018596 16922535 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LTR 0 1 1 6 0.521347615674617 0.449930134075354 0.521347615674617 0.449930134075354 1 - - 47947 N N 3.56658149627977 3.5816815158199 3.56658149627977 0 0 0.457511211227319 N 0 0 N N 3661 551733 ENSG00000170873 ENSG00000204628 + - 8 5 125809911 180603512 upstream upstream MTSS1 GNB2L1 125632212 180596536 - - 0 125931165 180606989 - + Y - - N HCC1954 9 1.53333333333333 1 1 2 N 590 3.33799 N SINE,SINE - 0.410714285714286 0 0.410714285714286 15 1.19981369086761 1.1141127129485 1.19981369086761 1.1141127129485 1 - - 7170 Y Y 3.68783934123363 3.30956232562269 3.30956232562269 334 0 0.00421268746224623 N 0.918483787142696 0.9937295220879 Y N 6570 46 ENSG00000115977 ENSG00000220011 + - 2 2 69724353 69724713 upstream upstream AAK1 AC092431.7-2 69542036 69723955 - - 0 69733632 69725539 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 22 1.19981369086761 1.17838844638783 1.19981369086761 1.17838844638783 1 - - 25490 N N 3.53618311810663 3.00869608883888 3.00869608883888 0 0 0.149964962803875 N 0 0.35012247397428 N N 0 3556 ENSG00000176882 ENSG00000146054 + - 13 5 49092785 180564783 downstream downstream AL135901.23-1 TRIM7 49092451 180553531 + - 0.35012247397428 49094519 180551901 + + Y - - N HCC1954 19 10.625 8 16 1 N 488 16.5929 N SINE - 1 0 1 16 0.299953422716903 0.742741808632331 0.742741808632331 0.299953422716903 3 - - 26715 N Y 3.28655907981151 3.39384326095097 3.28655907981151 372 0 0.0302269488734935 Y 0.994333455522972 0.988666911045943 N N 738 2132 ENSG00000213918 ENSG00000188827 - - 16 16 3648096 3601586 upstream upstream DNASE1 BTBD12 3632940 3571187 + - 0 3630717 3602008 - + N - - N HCC1954 1 1 1 0 1 N - - N - LINE,LINE 0 0.378787878787879 0.378787878787879 10 1.27123117246687 1.18553019454776 1.27123117246687 1.18553019454776 4 - - 45438 N Y 3.00762316627563 3.44359772892318 3.00762316627563 0 0 0.0260303829526451 N 0.668571428571429 0.857959183673469 N N 3891 2 ENSG00000166295 ENSG00000204754 + - 10 5 73665622 174355340 intron upstream C10orf104 AC008413.7 73645812 174278691 + - 0 73645904 174414751 + + Y 0.744979490524871 - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.371370904316165 0.34280391167646 0.371370904316165 0.34280391167646 1 0 - 31880 Y Y 3.61936062564813 3.45144752203174 3.45144752203174 0 0 0.221641162074894 Y 0.992932173234871 0.978796519704614 N N 24661 3531 ENSG00000184432 ENSG00000175110 + + 3 3 140591158 140558575 coding coding COPB2 MRPS22 140559125 140545551 - + 0 140559734 140557301 - + N - 1.85019429892335 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.1141127129485 1.0069864905496 1.1141127129485 1.0069864905496 2 - 0 4308 Y Y 3.6533527266709 3.59681204058356 3.59681204058356 346 0 0.043773897862748 Y 0.986340961279594 0.986340961279594 N N 0 0 ENSG00000212024 ENSG00000197743 + - 7 7 29686970 29647868 upstream upstream AC007276.3-3 AC007276.3-1 29686874 29647515 - - 0.665353551350067 29690914 29657480 - + N - - N HCC1954 2 1.34615384615385 1 9 1 N - - Y Low_complexity - 0.232227488151659 0 0.232227488151659 26 1.49262536542459 1.09268746846872 1.49262536542459 1.09268746846872 4 - - 49038 N N 3.23424395875957 3.20865378744443 3.20865378744443 0 0 0.0719113578603472 N 0 0 Y N 6 38037 ENSG00000169862 ENSG00000131446 + - 5 5 11957110 180175147 intron upstream CTNND2 MGAT1 11024978 180150147 - - 0 11290692 180191503 - + N 1.05609263480405 - N HCC1954 21 20.4444444444444 20 9 1 N - - N SINE - 1 0 1 9 0.321378667196682 0.471355378555133 0.471355378555133 0.321378667196682 2 0 - 38322 Y Y 3.40385247955516 3.20335106704647 3.20335106704647 137 0 0.212981928159739 Y 0.993844072382885 0.98768814476577 N N 7603 2206 ENSG00000176153 ENSG00000197195 + + 14 14 64479197 64471666 upstream coding GPX2 CHURC1 64475959 64450893 - + 0 64479770 64460597 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 1.14982145374813 1.39978263934555 1.39978263934555 1.14982145374813 4 - - 17261 N Y 3.14887652049892 1.61433083515927 1.61433083515927 192 0.644717261904762 0.00245079549671456 N 0.786830357142857 0.644717261904762 N N 17278 124 ENSG00000100106 ENSG00000196482 - - 22 1 36502509 215377720 utr3p intron TRIOBP ESRRG 36422957 214743211 + - 0.644717261904762 36499942 215282437 - + Y - 2.18623553339424 N HCC1954 17 12.75 1 3 1 N - - N - Simple_repeat 0 0.64 0.64 4 0.714174815992626 0.357087407996313 0.714174815992626 0.357087407996313 1 - 0 396 Y Y 3.24103017687471 3.39743698380061 3.24103017687471 286 0 0.107157940982621 Y 0 0.992091242091242 N N 745 9059 ENSG00000149485 ENSG00000168496 + + 11 11 61340886 61321284 intron utr5p FADS1 FEN1 61323679 61316726 - + 0 61333686 61317075 - + N 0.800607890108977 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 20 0.956994253430118 0.928427260790413 0.956994253430118 0.928427260790413 1 0 - 19880 N Y 3.48809356209009 3.65488030998075 3.48809356209009 13 0 0.050272441165667 N 0 0 N N 45068 3473 ENSG00000205336 ENSG00000077157 + + 16 1 56256445 200824320 upstream intron GPR56 PPP1R12B 56220023 200584459 + + 0 56211646 200740060 + + Y - 0.920288551310406 N HCC1954 21 21 21 7 1 N - - N - SINE 0 1 1 7 0.428504889595575 0.271386430077198 0.428504889595575 0.271386430077198 1 - 0 482 Y Y 3.02125661295299 3.69784855983781 3.02125661295299 0 0 0.756695445986371 Y 0 0.991027171750063 N N 110 3156 ENSG00000172638 ENSG00000172732 + + 11 11 65396852 65390485 intron coding EFEMP2 MUS81 65390488 65384801 - + 0.991027171750063 65391302 65389939 - + N 1.14169515600924 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.578481600954027 0.678466075192994 0.678466075192994 0.578481600954027 2 0 - 48000 N N 3.7297745213208 3.53871326596283 3.53871326596283 0 0 0.999938538885085 N 0 0.00374531835205993 N N 86504 0 ENSG00000104408 ENSG00000182152 + + 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0.00374531835205993 109296012 116899106 - - Y 0.543515163097469 - N HCC1954 2 1.25 1 13 7 N 241 0.00319582 N - - 0 0 0 52 0.835584534711372 1.12125446110842 1.12125446110842 0.835584534711372 4 0 - 499 Y Y 2.82085783396995 3.53039946453785 2.82085783396995 287 0.00348432055749126 0.703482885837366 Y 0.990133508124332 0.990133508124332 N Y 1594 103869 ENSG00000188082 ENSG00000117984 - + 11 11 1728397 1741798 coding intron AC068580.3 CTSD 1710216 1730561 - - 0 1725925 1731609 + - N - 0.630362770003188 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 39 1.05697872766909 0.749883556792257 1.05697872766909 0.749883556792257 4 - 0 32352 N N 2.6718368118362 1.73452992143947 1.73452992143947 0 0.279377301640442 0.0675263310537791 N 0.862738533645799 0.279377301640442 N N 11502 767 ENSG00000159921 ENSG00000161267 - + 9 3 36248450 198784591 utr3p utr3p GNE BDH1 36204430 198721051 - - 0.279377301640442 36206342 198721921 + - Y - - N HCC1954 37 34.9 30 10 1 N - - N LINE Simple_repeat 0.355371900826446 0.984848484848485 0.984848484848485 10 0.864151527351077 0.471355378555133 0.864151527351077 0.471355378555133 1 - - 48552 N N 3.44615838200292 3.42424163912411 3.42424163912411 0 0 0.900156692041496 N 0.624672505427053 0 N N 27 850768 ENSG00000184188 ENSG00000075624 + + 5 7 79631912 5536758 downstream utr3p AC026410.5-4 ACTB 79631253 5533313 - - 0 79630870 5533539 - - Y - - N HCC1954 11 2.66666666666667 1 1 3 N - - N - - 0 0 0 6 0.292811674556976 0.864151527351077 0.864151527351077 0.292811674556976 2 - - 4713 Y Y 3.46704205511183 3.45720067037699 3.45720067037699 3 0 0.231181712087242 Y 0 0.962398921832884 N N 1030 30823 ENSG00000164776 ENSG00000106153 - + 7 7 56128121 56141685 coding utr3p PHKG1 CHCHD2 56115471 56136762 - - 0 56124072 56136981 + - N - - N HCC1954 4 1.6 1 1 1 Y - - Y - - 0 0 0 5 0.778450549431962 1.1141127129485 1.1141127129485 0.778450549431962 1 - - 14242 N Y 3.57592836747465 3.43937216388778 3.43937216388778 0 0 0.109342795210855 N 0.225531914893617 0.800851063829787 N N 156 9710 ENSG00000215400 ENSG00000122203 - + 22 5 36734810 175721415 intron utr3p AL031587.3 KIAA1191 36715598 175705674 + - 0 36717279 175707041 - - Y - - N HCC1954 78 52.6 36 5 1 N - - N SINE,SINE - 1 0 1 5 0.499922371194838 0.807017542071667 0.807017542071667 0.499922371194838 1 - - 17440 Y Y 3.47336426491055 3.6035982586987 3.47336426491055 0 0 0.242208143445807 Y 0 0.993730223836869 N N 7703 19965 ENSG00000163159 ENSG00000143398 - - 1 1 149429290 149488629 coding upstream VPS72 PIP5K1A 149415562 149437652 - + 0 149425049 149434022 + - N - - N HCC1954 21 6.70588235294118 1 9 1 N - - Y - SINE 0 1 1 17 1.02841173502938 1.06412047582901 1.06412047582901 1.02841173502938 1 - - 33225 N N 3.49744043328497 3.24631931690354 3.24631931690354 5 0 0.999101254761455 N 0 0 Y N 544065 336285 ENSG00000198744 ENSG00000198868 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10471 + + 0 8550 11115 - + N 0.665018403102692 - N HCC1954 6 3.11111111111111 1 7 7 N 189 4.09957 N - - 0 0 0 9 1.07126222398894 1.34979040222606 1.34979040222606 1.07126222398894 2 0 - 6783 Y Y 3.21232721588077 3.57336771439491 3.21232721588077 118 0.00403225806451601 0.354249658978563 Y 0.595046082949309 0.978110599078341 N N 11631 0 ENSG00000163166 ENSG00000202429 + + 2 2 128000932 127946391 coding upstream IWS1 U4 127954860 127946280 - + 0 127960599 127944431 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.564198104634174 0.549914608314322 0.564198104634174 0.549914608314322 4 - - 3856 N Y 3.7825841559127 2.79422101251579 2.79422101251579 0 0 0.0618373215296495 N 0 0.841838766569949 N N 4749 0 ENSG00000156162 ENSG00000203446 + - 8 7 95873238 65814279 intron downstream DPY19L4 AC027644.9 95801327 65814003 + - 0 95818864 65784753 + + Y 0.877593494385355 - N HCC1954 23 12.25 6 8 1 N - - N SINE - 1 0 1 8 0.271386430077198 0.614190341753658 0.614190341753658 0.271386430077198 1 0 - 14981 N Y 3.29756151539224 3.48639814491089 3.29756151539224 13 0.262027985432241 0.0514754992841301 N 0.367452558941921 0.915660341192256 N N 1186 0 ENSG00000137968 ENSG00000205485 - + 1 7 75849389 76018755 coding downstream SLC44A5 AC004980.5-1 75440404 76016614 - + 0.156603411922561 75538944 76034542 + + Y - - N HCC1954 20 20 20 5 1 N - - N - LINE 0 1 1 5 0.421363141435649 0.321378667196682 0.421363141435649 0.321378667196682 2 - - 35740 N N 3.65384724021086 3.31063524818594 3.31063524818594 1 0 0.398090253192559 N 0 0 N N 17333 712661 ENSG00000169180 ENSG00000111640 + + 16 12 28130691 6517797 upstream coding XPO6 GAPDH 28016817 6513918 - + 0 28158575 6517407 - + Y - - N HCC1954 2 1.25 1 1 2 N - - N - - 0 0 0 4 0.349945659836387 0.435646637755502 0.435646637755502 0.349945659836387 1 - - 47245 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 0 0 0.76334833249162 Y 0 0.993521594684385 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 132 1.5783263433437 1.1426797055882 1.5783263433437 1.1426797055882 4 - - 10482 N N 3.21551971114628 3.65384724021086 3.21551971114628 21 0 0.365382590398968 N 0 0.100862455197133 N N 9789 185 ENSG00000159842 ENSG00000198904 + + 17 22 1029881 37759190 intron utr5p ABR APOBEC3D 853510 37747276 - + 0.100862455197133 958921 37747347 - + Y 5.8974624016315 - N HCC1954 35 34.5 33 4 1 N - - N - SINE 0 1 1 4 0.314236919036755 0.299953422716903 0.314236919036755 0.299953422716903 1 0 - 45069 Y Y 3.6154267040907 3.39959640929622 3.39959640929622 2 0 0.533145911859087 Y 0.177753544165758 0.744820065430752 N N 13934 2859 ENSG00000067064 ENSG00000047056 - - 10 10 1085061 1168237 coding intron IDI1 WDR37 1075966 1085478 - + 0 1079266 1092247 + - N - 0.045224430150955 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.607048593593732 0.557056356474248 0.607048593593732 0.557056356474248 3 - 0 29604 Y Y 3.55128313764676 3.24996647291565 3.24996647291565 1 0 0.205594288647702 Y 0 0.88953488372093 N N 1828 6281 ENSG00000124596 ENSG00000001167 - - 6 6 41148294 41174713 coding utr3p C6orf130 NFYA 41142509 41148688 - + 0 41147319 41173474 + - N - 1.54950659182844 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.771308801272036 0.607048593593732 0.771308801272036 0.607048593593732 2 - 0 18507 Y N 2.77059950488798 3.36976709257655 2.77059950488798 0 0 0.653226553653953 Y 0.0736192332683561 0 N N 0 2873 ENSG00000216933 ENSG00000127124 - - 1 1 42279987 42156965 upstream intron RP1-21K4.1 HIVEP3 42278855 41744623 + - 0 42274093 42087350 - + N - 5.42060694906404 N HCC1954 1 1 1 0 3 N - - Y Low_complexity - 0.133333333333333 0 0.133333333333333 17 0.964136001590045 1.02126998686945 1.02126998686945 0.964136001590045 1 - 0 41582 N N 3.40847927217468 3.52208566311286 3.40847927217468 0 0 0.998553250919644 Y 0 0 N N 0 0 ENSG00000208525 ENSG00000222501 - - 8 8 130372654 129092039 downstream upstream AC103833.2-1 U4 130372411 129091912 + - 0 130395858 129102147 - + N - - N HCC1954 1 1 1 0 4 N 575 2.9574 N SINE LTR,LTR 0.179245283018868 1 1 5 0.757025304952183 1.09982921662864 1.09982921662864 0.757025304952183 4 - - 33485 N Y 3.31592438821476 3.63040291402221 3.31592438821476 435 0 0.00211882804715202 Y 0 0.977324973876698 N N 240508 275222 ENSG00000198899 ENSG00000198763 - + MT MT 9208 5512 coding coding MT-ATP6 MT-ND2 8528 4471 + + 0 8921 4570 - + N - 0.99080338139823 N HCC1954 4 2.5 2 4 2 Y - - N - - 0 0 0 4 0.421363141435649 0.271386430077198 0.421363141435649 0.271386430077198 2 - 0 22512 N Y 3.40847927217468 3.48271113610542 3.40847927217468 0 0 0.573576810692186 N 0 0.861673414304993 N N 14212 2926 ENSG00000085719 ENSG00000162419 - + 8 1 87642842 28918452 utr5p utr3p CPNE3 GMEB1 87566186 28867831 + + 0 87609877 28916428 - + Y - - N HCC1954 36 35.25 35 4 1 N - - N - SINE 0 1 1 4 0.592765097273879 0.28566992639705 0.592765097273879 0.28566992639705 1 - - 40870 N N 2.59078822456678 2.6718368118362 2.59078822456678 0 0.336206896551724 0.289890675448091 N 0.3984375 0.336206896551724 N N 2221 11502 ENSG00000088766 ENSG00000159921 - - 20 9 5968695 36248450 utr3p utr3p CRLS1 GNE 5934893 36204430 + - 0.336206896551724 5967932 36206342 - + Y - 0.659918255598569 N HCC1954 39 37.6 36 5 1 N - - N Simple_repeat LINE 0.977272727272727 0.507246376811594 0.977272727272727 5 0.314236919036755 0.492780623034912 0.492780623034912 0.314236919036755 1 - 0 22228 N N 3.62192127872787 3.76848670091893 3.62192127872787 8 0 0.709675807852385 N 0.277354863514033 0 N N 699 32260 ENSG00000188295 ENSG00000124098 - + 1 20 245334251 54377116 utr3p utr3p ZNF669 C20orf108 245328029 54367390 - + 0.121107266435986 245330184 54375843 + + Y - 0.993256465702668 N HCC1954 7 2.16666666666667 1 2 1 N - - N SINE,SINE DNA 0.682926829268293 0.496124031007752 0.682926829268293 6 0.292811674556976 0.757025304952183 0.757025304952183 0.292811674556976 3 - 0 38980 N N 3.40319013214585 3.78784279071799 3.40319013214585 0 0 0.287184453205434 N 0 0 N N 360 0 ENSG00000180953 ENSG00000177418 + - 15 7 78003132 65659784 coding downstream ST20 AC006001.2-1 77978240 65659267 - - 0 77978502 65657260 - + Y - - N HCC1954 26 20 4 4 1 N - - N SINE - 0.886363636363636 0 0.886363636363636 4 0.314236919036755 0.357087407996313 0.357087407996313 0.314236919036755 2 - - 19073 N Y 3.58064844605001 3.41592783769912 3.41592783769912 306 0 0.0124326729139452 Y 0.00326797385620903 0.991830065359477 N N 123 4500 ENSG00000143178 ENSG00000213064 - + 1 1 166550286 166479002 intron utr3p TBX19 SFT2D2 166516902 166461812 + + 0 166527021 166478930 - + N 0.297929692927609 2.84561146370245 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.664182578873142 0.835584534711372 0.835584534711372 0.664182578873142 1 0 0 42097 N N 3.48383749183115 2.8972397758265 2.8972397758265 51 0.485442176870748 0.250158262795259 N 0.634829931972789 0.502040816326531 N N 78560 1 ENSG00000112493 ENSG00000163116 + + 6 4 33390114 99283414 utr3p intron TAPBP C4orf37 33375449 98699050 - - 0.502040816326531 33376425 99124334 - - Y 0.848669951896309 0.907096774193548 N HCC1954 36 16.75 9 4 1 N - - N SINE LINE,SINE 1 0.921052631578947 1 4 0.314236919036755 0.271386430077198 0.314236919036755 0.271386430077198 2 0 0 19605 N Y 3.73808832274579 3.24893340314576 3.24893340314576 12 0.00317460317460327 0.936638755933931 N 0.971519274376417 0.971519274376417 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0.971519274376417 109336418 45272639 - - Y - - N HCC1954 9 5.27659574468085 4 47 2 N - - N - - 0 0 0 47 0.814159290231593 1.04269523134923 1.04269523134923 0.814159290231593 3 - - 45614 N Y 3.46145674063593 3.7297745213208 3.46145674063593 214 0.800796812749004 0.0193283556876915 N 0.909453096704093 0.909453096704093 N N 539 0 ENSG00000182141 ENSG00000198536 + - 19 X 21304052 92573954 utr5p downstream ZNF708 AL023280.1 21265803 92572406 - + 0 21303859 92635394 - - Y 0.934612776424441 - N HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.471355378555133 0.307095170876829 0.471355378555133 0.307095170876829 1 0 - 40995 Y Y 3.77208042376856 3.44871903508266 3.44871903508266 269 0 0.00358262533356035 Y 0.978802499406786 0.989401249703393 N N 1991 1329 ENSG00000125841 ENSG00000177732 - + 20 20 283512 258865 intron upstream NRSN2 SOX12 275668 254239 + + 0 276748 251213 - + N 0.214313825546372 - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.707317073170732 0.707317073170732 6 0.728458312312478 0.956994253430118 0.956994253430118 0.728458312312478 1 0 - 46984 Y Y 3.01551281217755 3.61936062564813 3.01551281217755 290 0 0.123597556609724 Y 0.00344827586206875 0 N N 675 793 ENSG00000179922 ENSG00000171443 + + 19 19 60827753 60806316 downstream downstream ZNF784 ZNF524 60823919 60803542 - + 0 60816833 60809956 - + N - - N HCC1954 1 1 1 0 4 N - - Y Simple_repeat - 0.426966292134831 0 0.426966292134831 5 0.635615586233437 0.642757334393363 0.642757334393363 0.635615586233437 1 - - 9743 Y Y 3.4064131326349 3.56079784271098 3.4064131326349 149 0.0543190249072601 0.54899231341422 Y 0 0 N N 3275 1042 ENSG00000181523 ENSG00000141527 + + 17 17 75808719 75797450 intron coding SGSH CARD14 75797685 75766869 - + 0 75804260 75795479 - + N 1.1906644222205 - N HCC1954 1 1 1 0 2 N - - Y LINE - 1 0 1 8 0.971277749749971 1.32122340958636 1.32122340958636 0.971277749749971 4 0 - 20455 N Y 3.25256697878875 3.49847350305486 3.25256697878875 0 0 0.0744497043520422 N 0 0 N N 49089 1 ENSG00000117450 ENSG00000203688 - - 1 6 45760196 167839819 coding upstream PRDX1 AL356123.21-2 45749295 167824221 - - 0 45757275 167845629 + + Y 3.11556065904221 - N HCC1954 15 5.88235294117647 2 17 1 N - - N - SINE 0 1 1 17 0.642757334393363 0.264244681917271 0.642757334393363 0.264244681917271 2 0 - 5212 N Y 3.70144228268744 3.33168675516419 3.33168675516419 0 0 0.137575709542722 N 0.846101179155572 0.855154050969951 N N 5744 0 ENSG00000155034 ENSG00000219468 - - 7 9 5523646 140250262 utr3p upstream FBXL18 RP11-885N19.5 5481955 140249980 - + 0 5486861 140241177 + - Y - - N HCC1954 185 141.666666666667 105 6 1 N - - N SINE - 1 0 1 6 0.278528178237124 0.385654400636018 0.385654400636018 0.278528178237124 2 - - 1729 N Y 3.70144228268744 3.33168675516419 3.33168675516419 13 0.0628285356695872 0.136763098188894 N 0.882853566958698 0.882853566958698 N N 0 3567 ENSG00000152214 ENSG00000177951 + - 18 11 38949655 197428 intron intron RIT2 BET1L 38577191 157784 - - 0 38727068 170406 - + Y 1 2.87394543524002 N HCC1954 100 87.2 84 5 1 N - - N SINE - 1 0 1 5 0.292811674556976 0.749883556792257 0.749883556792257 0.292811674556976 2 0 0 24980 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.735585481205612 N 0.249191400304414 0.959046803652968 N N 4312 3966 ENSG00000102531 ENSG00000175772 + + 13 2 48681915 110111006 intron upstream FNDC3A AC013268.5-1 48448049 110103138 + + 0 48627105 110102056 + + Y 0.880516123924578 - N HCC1954 60 40.3829787234043 18 47 1 N 585 24.1996 N LINE - 1 0 1 47 0.442788385915428 1.45691662462496 1.45691662462496 0.442788385915428 3 0 - 43673 N Y 3.08496250072116 3.1825606798934 3.08496250072116 0 0.391688770999116 0.0246037249045845 N 0.391688770999116 0.391688770999116 N N 111 15704 ENSG00000183688 ENSG00000181192 - + 17 10 295959 12205229 utr3p utr3p FAM101B DHTKD1 290008 12150940 - + 0.391688770999116 290871 12204339 + + Y - - N HCC1954 35 32 30 4 1 N 444 20.9338 N SINE SINE 1 0.0892857142857143 1 4 0.28566992639705 0.39993789695587 0.39993789695587 0.28566992639705 1 - - 42928 N Y 3.55231620741665 3.44975210485255 3.44975210485255 18 0 0.0184677891906979 N 0 0.949649954034368 N N 12076 970 ENSG00000148219 ENSG00000138675 - + 9 4 119217138 81431194 utr3p utr3p ASTN2 FGF5 118227328 81406766 - + 0.861537373594512 118415269 81431137 + + Y - - N HCC1954 651 567 462 11 1 N - - N LINE LINE 1 1 1 11 0.449930134075354 0.607048593593732 0.607048593593732 0.449930134075354 1 - - 35280 N N 3.41423242051993 2.86638673690676 2.86638673690676 16 0 0.0230820035093376 N 0.184705882352941 0.209411764705882 N N 4442 44188 ENSG00000139116 ENSG00000128641 + - 12 2 38123190 191998360 downstream intron KIF21A MYO1B 37973298 191818375 - + 0.209411764705882 37891193 191970595 - - Y - 2.06792545705933 N HCC1954 400 158.5 22 4 1 N - - N LINE Other,Other 1 1 1 4 0.578481600954027 0.557056356474248 0.578481600954027 0.557056356474248 1 - 0 46863 Y Y 3.13379942889774 3.55231620741665 3.13379942889774 303 0 0.0609684858897054 Y 0.902578227747587 0.992506017519045 N N 746 2845 ENSG00000126460 ENSG00000142546 - - 19 19 54785999 54775625 intron upstream PRRG2 NOSIP 54778280 54750782 + - 0 54778583 54776539 - + N 0.572121577489159 - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 28 1.03555348318931 1.04983697950916 1.04983697950916 1.03555348318931 2 0 - 33280 N Y 2.97696846644877 3.30488209984069 2.97696846644877 237 0 0.877868015199045 Y 0 0.9908643982503 N N 544065 151141 ENSG00000198744 ENSG00000198888 - + MT MT 9988 4264 coding coding MT-CO3 MT-ND1 8367 3308 + + 0 8395 4209 - + N 0.697389439671372 - N HCC1954 4 2.2 1 4 6 N - - N - - 0 0 0 5 0.928427260790413 0.757025304952183 0.928427260790413 0.757025304952183 1 0 - 37279 N N 3.12747721909902 2.91241015338352 2.91241015338352 0 0.277157578359811 0.0665706041831837 N 0.316230141691713 0 N N 551733 0 ENSG00000204628 ENSG00000215923 + - 5 12 180603512 16453532 utr3p upstream GNB2L1 AC007528.5 180596536 16453456 - - 0 180596544 16504815 - + Y - - N HCC1954 18 14.5 5 4 1 N - - N - Low_complexity 0 0.868421052631579 0.868421052631579 4 0.435646637755502 0.271386430077198 0.435646637755502 0.271386430077198 2 - - 9406 Y Y 3.53768019619294 3.52720696927234 3.52720696927234 321 0 0.112630849982340 Y 0 0.979655413567296 N N 0 12836 ENSG00000222777 ENSG00000167258 + + 17 17 34955984 34941095 upstream intron U6 CRKRS 34955883 34871265 - + 0 34956243 34936098 - + N - 2.62354953389778 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 5 0.371370904316165 0.649899082553289 0.649899082553289 0.371370904316165 1 - 0 39036 N Y 3.64809409186561 3.02420422244092 3.02420422244092 0 0 0.197281305730994 N 0 0 N N 17 537 ENSG00000205273 ENSG00000178385 + - 15 2 80782278 208598467 upstream upstream AC011295.3-2 PLEKHM3 80780956 208401288 - - 0 80838473 208604755 - + Y - - N HCC1954 5 4.25 4 4 1 N 186 23.326 N - - 0 0 0 4 0.442788385915428 0.278528178237124 0.442788385915428 0.278528178237124 2 - - 40731 N Y 3.24740581983591 3.65657572715995 3.24740581983591 32 0 0.849197908408025 N 0.581707317073171 0.541869918699187 N N 29024 0 ENSG00000124208 ENSG00000219462 - + 20 X 48203678 120973146 coding upstream UBE2V1 RP11-417D4.1 48131068 120972510 - - 0.521951219512195 48146617 120973156 + - Y - - N HCC1954 5 2.23529411764706 1 11 3 N - - N - - 0 0 0 17 0.792734045751814 0.364229156156239 0.792734045751814 0.364229156156239 2 - - 29651 N N 3.66848325143457 3.61460069427942 3.61460069427942 0 0 0.317679913221474 N 0 0 N N 18722 0 ENSG00000206503 ENSG00000217053 - + 6 6 30021640 29964024 coding intron HLA-A HCG4P7 30017016 29963050 + - 0 30018571 29963785 - - N - 1 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.814159290231593 0.392796148795944 0.814159290231593 0.392796148795944 1 - 0 42314 Y Y 3.79465951405667 3.0463658510973 3.0463658510973 342 0 0.00134227610232440 Y 0 0.984892787524367 N N 1034 2725 ENSG00000138646 ENSG00000138642 - + 4 4 89646334 89583271 upstream intron HERC5 HERC6 89597291 89518915 + + 0 89595436 89560797 - + N - 0.956245569266509 N HCC1954 2 1.5 1 2 1 N - - Y LTR LINE 1 1 1 4 0.578481600954027 0.421363141435649 0.578481600954027 0.421363141435649 2 - 0 47564 Y Y 3.12441270490951 3.37336081542618 3.12441270490951 0 0 0.0353295953984578 Y 0.862802641232575 0.942834433846906 N N 184 19 ENSG00000105613 ENSG00000132026 - - 19 19 12846765 12807230 coding intron MAST1 RTBDN 12810348 12797297 + - 0 12812292 12805803 - + N - 2.14420803782506 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.376237623762376 0.376237623762376 7 0.707033067832699 0.721316564152552 0.721316564152552 0.707033067832699 1 - 0 21155 N Y 3.353603498043 3.38486711211668 3.353603498043 205 0 0.0400516452976403 N 0.90829859795377 0.782209170140205 N N 667 3880 ENSG00000206530 ENSG00000137955 + + 3 1 114643030 76033688 intron intron WDR52 RABGGTB 114493094 76024474 - + 0.782209170140205 114562317 76028546 - + Y 1.41101489475111 1.56323085904127 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 18 0.628473838073511 1.23552243166724 1.23552243166724 0.628473838073511 2 0 0 33078 N Y 2.7261969576769 3.63399663687184 2.7261969576769 501 0 0.582343807310998 Y 0 0.995698258655103 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0.00629774932892846 13751 9080 - + N 1.05002130363144 0.584601331901127 N HCC1954 3 2.28571428571429 1 6 7 N - - N - - 0 0 0 7 1.27123117246687 1.10697096478857 1.27123117246687 1.10697096478857 3 0 0 13865 Y Y 3.18296190747752 3.48167806633553 3.18296190747752 372 0 0.0227316341050072 Y 0.994167767087971 0.994167767087971 N N 238 110 ENSG00000211643 ENSG00000198312 - + 22 22 21003581 20993088 coding downstream IGLV5-52 D87018.1-3 21003021 20991471 + + 0 21003256 20994768 - + N - - N HCC1954 14 3.85211267605634 1 70 2 N - - Y - - 0 0 0 142 1.49976711358451 1.25694767614702 1.49976711358451 1.25694767614702 1 - - 10624 N N 3.19496271770798 3.16254224268503 3.16254224268503 13 0.159573797364605 0.136743186906629 N 0.159573797364605 0.159573797364605 N N 92 12320 ENSG00000171791 ENSG00000108587 + + 18 17 59138341 25877957 downstream utr3p BCL2 GOSR1 58941559 25828552 - + 0.159573797364605 58874337 25875357 - + Y - - N HCC1954 160 62 24 4 1 N - - N SINE Other 0.447368421052632 1 1 4 0.271386430077198 0.328520415356608 0.328520415356608 0.271386430077198 1 - - 27988 N Y 2.84095081909183 3.47552369040616 2.84095081909183 1 0 0.0523810637364444 N 0.343674036346799 0.756221784928811 N N 17384 0 ENSG00000168802 ENSG00000217035 + - 16 X 67723985 44379422 utr5p upstream CHTF8 CHTF8P 67709414 44377882 - + 0.306169695566616 67723891 44377650 - - Y 0.58127594264248 - N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.213483146067416 0 0.213483146067416 4 0.607048593593732 0.271386430077198 0.607048593593732 0.271386430077198 1 0 - 14030 Y Y 3.37089344830228 3.59169073442408 3.37089344830228 0 0 0.919804093716138 Y 0.982088608706341 0.994029536235447 N N 8168 388 ENSG00000100099 ENSG00000128203 + + 22 22 25209820 25169557 coding downstream HPS4 ASPHD2 25177446 25155239 - + 0 25183827 25170662 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 33 1.17124669822791 1.2783729206268 1.2783729206268 1.17124669822791 3 - - 31458 Y Y 3.59784511035345 3.46973068926756 3.46973068926756 284 0 0.176665856772795 Y 0.374550494456098 0.978798321845969 N N 243 4516 ENSG00000197385 ENSG00000144645 - - 3 3 32007186 31998242 upstream upstream ZNF860 OSBPL10 32005624 31674407 + - 0 32005156 31998398 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR,LTR - 1 0 1 8 0.735600060472404 0.507064119354764 0.735600060472404 0.507064119354764 4 - - 34725 N Y 3.52720696927234 2.79313874238274 2.79313874238274 0 0 0.777258971521947 Y 0.631013417693902 0.988818588414967 N N 12832 1085 ENSG00000181090 ENSG00000203993 - - 9 9 139850397 139633086 coding upstream EHMT1 C9orf37 139711440 139629606 + - 0 139725302 139633320 - + N - - N HCC1954 1 1 1 0 4 N - - N - Simple_repeat 0 0.654761904761905 0.654761904761905 15 0.964136001590045 0.599906845433805 0.964136001590045 0.599906845433805 1 - - 16035 N N 3.09719324163274 2.96167010781576 2.96167010781576 0 0 0.641749725900478 N 0 0 N N 154774 0 ENSG00000122566 ENSG00000220375 - - 7 1 26206942 558984 coding intron HNRPA2B1 RP5-857K21.14 26196081 558778 - + 0 26202041 558828 + - Y - 1 N HCC1954 3 2 1 7 3 N - - N - - 0 0 0 8 0.814159290231593 0.657040830713216 0.814159290231593 0.657040830713216 2 - 0 6928 Y Y 3.57225493903832 3.29334529792665 3.29334529792665 359 0 0.0277543009579435 Y 0.87132716326714 0.993566358163357 N N 0 2365 ENSG00000201876 ENSG00000114956 + + 2 2 74048832 74039596 upstream coding 5S_rRNA DGUOK 74048741 74007461 - + 0 74061747 74038845 - + N - 0.533340522302343 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 102 1.45691662462496 1.17124669822791 1.45691662462496 1.17124669822791 1 - 0 31760 Y Y 3.36551102231762 3.41526549028982 3.36551102231762 8 0.00246305418719217 0.938847722353047 Y 0.00246305418719217 0.993804118348989 N N 6749 46 ENSG00000118855 ENSG00000214217 - + 3 3 160030198 159943998 coding downstream MFSD1 AC080013.17 160002606 159940900 + + 0 160004803 159944934 - + N - - N HCC1954 2 1.2 1 1 3 N - - Y - - 0 0 0 5 1.05697872766909 0.757025304952183 1.05697872766909 0.757025304952183 1 - - 10838 N N 3.41423242051993 3.26576869265844 3.26576869265844 47 0 0.531579469360485 N 0.394668611246151 0 N N 133 1041 ENSG00000217340 ENSG00000174111 + + 6 17 17990588 33809541 utr3p downstream AL023807.6-2 SOCS7 17986664 33761531 - + 0.394668611246151 17988310 33812366 - + Y - - N HCC1954 22 21.25 21 4 1 N - - N SINE SINE 1 0.377358490566038 1 4 0.271386430077198 0.378512652476092 0.378512652476092 0.271386430077198 2 - - 36314 Y Y 3.31162846516247 3.48656597878024 3.31162846516247 308 0 0.0125619020676687 Y 0.992561542934677 0.992561542934677 N N 3605 23783 ENSG00000170545 ENSG00000183283 + + 12 12 49950473 49923833 coding intron AC139768.14 DAZAP2 49925400 49918877 - + 0 49926113 49921168 - + N 1.46542399828567 2.20709441522532 N HCC1954 2 1.375 1 6 1 N - - Y - - 0 0 0 16 0.99270299422975 1.20695543902754 1.20695543902754 0.99270299422975 1 0 0 46763 Y N 3.42936294528359 2.82507405143554 2.82507405143554 0 0 0.990712857646809 Y 0 0.00793650793650791 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 coding upstream SLC44A2 AP1M2 10597229 10544347 + - 0.00793650793650791 10599599 10574178 - + N 0.455641572881242 - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 50 0.678466075192994 0.771308801272036 0.771308801272036 0.678466075192994 2 0 - 29201 Y Y 3.51576345331414 3.38693325165646 3.38693325165646 257 0 0.0212350709714181 Y 0 0.988932122784263 N N 9586 1168 ENSG00000112640 ENSG00000124587 - - 6 6 43088054 43054866 upstream upstream PPP2R5D PEX6 43060308 43039725 + - 0 43059869 43056558 - + N - - N HCC1954 1 1 1 0 1 N - - Y - DNA 0 0.402061855670103 0.402061855670103 10 0.857009779191151 0.692749571512847 0.857009779191151 0.692749571512847 1 - - 41442 N Y 3.59375687396386 3.61464054707278 3.59375687396386 253 0 0.949044495904604 Y 0.864942721243385 0.983117840155423 N N 0 4 ENSG00000207110 ENSG00000184090 - - 8 8 129080722 129029462 upstream downstream U1 TMEM75 129080559 129029046 + - 0 129065332 128972426 - + N - - N HCC1954 1 1 1 0 5 N - - N SINE - 1 0 1 4 0.678466075192994 0.542772860154395 0.678466075192994 0.542772860154395 4 - - 454 Y Y 3.60103760561896 2.98101685004501 2.98101685004501 404 0 0.000317332867832643 Y 0.173284280482843 0.986335277363353 N N 96 63956 ENSG00000149243 ENSG00000149273 + + 11 11 74818884 74794378 downstream utr3p KLHL35 RPS3P3 74811088 74788210 - + 0 74810296 74793555 - + N - - N HCC1954 2 1.14285714285714 1 1 1 N - - Y LINE - 0.632 0 0.632 7 0.685607823352921 0.835584534711372 0.835584534711372 0.685607823352921 1 - - 37443 N Y 3.37080016234644 3.29396779254261 3.29396779254261 0 0 0.113818531808245 N 0.761765184823319 0.826738316235141 N N 1490 110 ENSG00000206195 ENSG00000197927 - + 14 2 18995329 132241449 utr5p upstream AL589182.4-3 C2orf27 18961097 132196418 - + 0 18995313 132156571 + + Y - - N HCC1954 5 2.9 1 8 1 N - - N LINE,LINE - 0.666666666666667 0 0.666666666666667 10 0.621332089913584 0.699891319672773 0.699891319672773 0.621332089913584 2 - - 39127 N Y 3.56232542602083 3.22485723477134 3.22485723477134 57 0 0.0848571077177781 N 0.00806451612903225 0.917338709677419 N N 4 3153 ENSG00000103569 ENSG00000204104 + + 15 2 56265402 238974202 downstream intron AQP9 TRAF3IP1 56217700 238893821 + + 0.18991935483871 56339667 238923340 + + Y - 2.42654663575635 N HCC1954 378 46 20 20 1 N - - N LTR SINE 1 1 1 20 0.471355378555133 0.357087407996313 0.471355378555133 0.357087407996313 3 - 0 30564 Y Y 3.45400817511148 3.52936639476796 3.45400817511148 215 0 0.110317971602363 Y 0 0.97989194268264 N N 0 1934 ENSG00000200620 ENSG00000186312 - + X X 15644390 15631393 downstream coding SNORA7 CA5BP 15644252 15602976 + + 0 15649541 15616902 - + N - - N HCC1954 2 1.54545454545455 1 6 1 N - - Y LINE - 1 0 1 11 0.807017542071667 1.08554572030879 1.08554572030879 0.807017542071667 4 - - 11207 N N 3.55025006787687 3.47911741325579 3.47911741325579 0 0 0.665008105907796 N 0 0 N N 32611 5881 ENSG00000132142 ENSG00000132967 + + 17 3 32841015 22572731 intron coding ACACA AC104740.2 32516036 22398294 - + 0 32574986 22398821 - + Y 1.22139420269328 - N HCC1954 5 5 5 8 1 N 443 26.6582 N - - 0 0 0 8 0.321378667196682 0.349945659836387 0.349945659836387 0.321378667196682 1 0 - 24696 Y Y 3.45720067037699 3.55910242553179 3.45720067037699 176 0 0.00805162167013873 Y 0.836753731343284 0.985159430122117 N N 0 8692 ENSG00000206696 ENSG00000215472 + - 18 18 45272097 45271812 upstream coding SNORD58 AC100778.5 45272032 45269794 - - 0.985159430122117 45272802 45271276 - + N - 18.1370377992728 N HCC1954 8 5.50877192982456 5 57 1 N - - Y - - 0 0 0 57 0.542772860154395 0.549914608314322 0.549914608314322 0.542772860154395 2 - 0 39999 Y Y 3.17407904459906 3.56232542602083 3.17407904459906 0 0 0.388969666530557 Y 0.980277227722772 0.990138613861386 N N 4872 964 ENSG00000140320 ENSG00000128928 - + 15 15 38547718 38498355 upstream coding BAHD1 IVD 38520703 38484978 + + 0 38514909 38497621 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.771308801272036 0.564198104634174 0.771308801272036 0.564198104634174 1 - - 13721 Y Y 3.57063922744582 2.71719788090366 2.71719788090366 210 0 0.0939803552497125 Y 0 0.987402049427366 N N 26397 1 ENSG00000197077 ENSG00000206069 - - 22 22 23923415 23672662 coding upstream CTA-221G9.5 TMEM211 23753158 23661077 + - 0 23753974 23678716 - + N 0.0288832514760648 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 10 0.971277749749971 0.785592297591888 0.971277749749971 0.785592297591888 1 0 - 3324 N Y 3.03851605798873 3.41629856005971 3.03851605798873 229 0.884228699096171 0.00329576468938675 N 0.884228699096171 0.861074438915406 N N 21394 14048 ENSG00000113712 ENSG00000196611 + - 5 11 148911200 102174104 coding upstream CSNK1A1 MMP1 148855038 102165861 - - 0.51376053620392 148865240 102182891 - + Y - - N HCC1954 2 1.33333333333333 1 5 1 N - - N - - 0 0 0 15 0.899860268150708 0.39993789695587 0.899860268150708 0.39993789695587 2 - - 14231 N Y 3.54400240599166 3.43937216388778 3.43937216388778 0 0 0.175504732553908 N 0.178776901768591 0 N N 185 9710 ENSG00000198904 ENSG00000122203 - + 22 5 37759190 175721415 utr3p utr3p APOBEC3D KIAA1191 37747276 175705674 + - 0 37758773 175707041 - - Y - 0.53837359391661 N HCC1954 76 46.75 36 4 1 N - - N SINE - 1 0 1 4 0.328520415356608 0.807017542071667 0.807017542071667 0.328520415356608 1 - 0 47148 Y Y 3.48383749183115 3.64231043829683 3.48383749183115 229 0.272852166233256 0.241378006537185 Y 0.67558019724253 0.988813110249742 N N 521 2375 ENSG00000204517 ENSG00000178935 - - 19 19 63045300 63018093 upstream upstream AC010522.3 ZNF552 63042237 63010262 + - 0 63042202 63023728 - + N - - N HCC1954 2 1.5 1 2 3 N - - Y - LTR 0 1 1 4 0.685607823352921 0.378512652476092 0.685607823352921 0.378512652476092 1 - - 43089 N N 3.49168728493972 3.44206079804351 3.44206079804351 0 0 0.997337708767948 N 0 0 N N 9848 13 ENSG00000164134 ENSG00000152495 + + 4 5 140531972 110848645 coding intron NARG1 CAMK4 140442126 110587981 + + 0 140442434 110760181 + + Y 1.36446135228 1.00411712901805 N HCC1954 1 1 1 0 5 N 370 4.32528 N - - 0 0 0 7 0.742741808632331 0.792734045751814 0.792734045751814 0.742741808632331 2 0 0 42423 N N 3.4780843434859 3.65488030998075 3.4780843434859 13 0.0629664179104478 0.527591450705962 Y 0.0629664179104478 0 N N 110 12865 ENSG00000138685 ENSG00000172493 - + 4 4 124038840 88281215 upstream utr3p FGF2 AFF1 123967313 88147177 + + 0 123957737 88280483 - + N - - N HCC1954 2 1.28571428571429 1 6 1 N 554 4.00005 N LINE - 1 0 1 21 0.985561246069823 1.12125446110842 1.12125446110842 0.985561246069823 1 - - 31442 Y Y 3.74337746277462 3.34785034969775 3.34785034969775 279 0 0.124381362153563 Y 0.992619142439931 0.985238284879862 N N 4437 873 ENSG00000126062 ENSG00000114395 + + 3 3 50371943 50366477 intron coding TMEM115 CYB561D2 50367186 50363301 - + 0 50370553 50363995 - + N 0.954081059577037 0.656793950283327 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 0.914143764470561 0.835584534711372 0.914143764470561 0.835584534711372 4 0 0 33895 N N 3.28871850530713 2.67166897796686 2.67166897796686 0 0 0.999925444253932 N 0.046368054643373 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 9225 14364 - + N - 1.04243336632799 N HCC1954 4 2.5 2 4 10 N 189 4.09957 N - - 0 0 0 4 0.471355378555133 0.642757334393363 0.642757334393363 0.471355378555133 1 - 0 6121 N N 3.47548383761281 3.52680574168822 3.47548383761281 0 0 0.349369699667467 N 0.0430769230769232 0.0430769230769232 N N 154774 892 ENSG00000122566 ENSG00000185304 - + 7 2 26206942 87906586 coding intron HNRPA2B1 RGPD2 26196081 87836589 - - 0.0430769230769232 26202961 87905759 + - Y - 2.62981467744803 N HCC1954 3 2.5 2 4 1 N - - N - - 0 0 0 4 0.928427260790413 0.592765097273879 0.928427260790413 0.592765097273879 2 - 0 47049 Y Y 3.57336771439491 3.38230645903694 3.38230645903694 0 0 0.139482021436105 Y 0.17994287527769 0.956839098698826 N N 877 259 ENSG00000161277 ENSG00000105270 + - 19 19 41237504 41215635 intron intron THAP8 CLIP3 41217727 41197402 - - 0 41233676 41202121 - + N 4.68087923821004 2.14899069776909 N HCC1954 1 1 1 0 1 N - - Y LINE SINE 0.860215053763441 0.301075268817204 0.860215053763441 7 0.664182578873142 0.657040830713216 0.664182578873142 0.657040830713216 2 0 0 7563 Y Y 3.37655331069169 3.85272778345386 3.37655331069169 370 0 0.0323026022600672 Y 0.99445945945946 0.99445945945946 N N 2842 3966 ENSG00000204588 ENSG00000175772 - + 2 2 110111006 110111006 coding upstream AC013268.5-2 AC013268.5-1 110108526 110103138 + + 0 110108685 110102055 - + N - - N HCC1954 24 6.10062893081761 4 159 2 N - - Y - - 0 0 0 159 1.34979040222606 1.40692438750547 1.40692438750547 1.34979040222606 2 - - 211 Y Y 3.63296356710195 3.12229313220724 3.12229313220724 171 0 0.0074370823518568 Y 0 0 N N 3035 1575 ENSG00000110711 ENSG00000172663 - - 11 11 67015150 66993319 upstream intron AIP TMEM134 67007097 66988397 + - 0 67006884 66992274 - + N - 1.27692042165043 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.714174815992626 0.528489363834543 0.714174815992626 0.528489363834543 1 - 0 9624 Y Y 3.17403919180571 3.52039024593366 3.17403919180571 276 0 0.00794294131788864 Y 0 0.984671125975474 N N 79 12 ENSG00000171431 ENSG00000187242 + - 17 17 36295005 36276988 intron downstream KRT20 KRT12 36285721 36270956 - - 0 36291653 36260620 - + N 0.961160705768126 - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.641304347826087 0 0.641304347826087 5 0.657040830713216 0.292811674556976 0.657040830713216 0.292811674556976 2 0 - 31695 N N 3.31063524818594 3.55976477294109 3.31063524818594 0 0 0.502188566468807 N 0.741412213740458 0.741412213740458 Y N 12271 151 ENSG00000177479 ENSG00000214271 - + 3 3 48997971 143204805 utr5p coding ARIH2 AC128648.5 48931285 143179267 + + 0 48935242 143203662 - + N - - N HCC1954 34 23.35 20 40 1 Y - - N - SINE 0 1 1 40 1.02126998686945 0.428504889595575 1.02126998686945 0.428504889595575 2 - - 40962 Y Y 3.60422075331465 3.46910819465161 3.46910819465161 284 0 0.0669755693168694 Y 0 0 N N 6319 0 ENSG00000197818 ENSG00000217373 - - 20 20 47942179 47779786 upstream upstream SLC9A8 SNRPFP1 47862657 47779535 + - 0 47825240 47819477 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LTR 0 1 1 9 0.978419497909897 0.5713398527941 0.978419497909897 0.5713398527941 2 - - 29388 N N 3.58184934968924 3.43528392749819 3.43528392749819 0 0.649183006535948 0.486346639154788 N 0.852287581699346 0.372222222222222 Y N 0 18722 ENSG00000217053 ENSG00000206503 + + 6 6 29964024 30021640 intron coding HCG4P7 HLA-A 29963050 30017016 - + 0.372222222222222 29963926 30018727 - + N 1 - N HCC1954 1 1 1 0 1 N 202 15.264 N - - 0 0 0 5 0.785592297591888 0.971277749749971 0.971277749749971 0.785592297591888 2 0 - 48513 N N 3.55397177180249 3.20128492750669 3.20128492750669 0 0 0.0642954403686844 N 0 0 N N 551733 146 ENSG00000204628 ENSG00000136267 + - 5 7 180603512 14909359 coding intron GNB2L1 DGKB 180596536 14151199 - - 0 180597260 14163719 - + Y 0.546327604395875 3.78883321403006 N HCC1954 9 5.1 1 9 1 N - - N - - 0 0 0 10 0.51420586751469 0.264244681917271 0.51420586751469 0.264244681917271 1 0 0 33876 Y N 3.21804051143267 3.46720988898117 3.21804051143267 1 0 0.572492055116266 N 0 0 N N 59837 247001 ENSG00000198695 ENSG00000198786 - + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0 14442 12617 + + N - 0.801884270097248 Y HCC1954 3 1.5 1 1 2 N 316 3.86643 N - - 0 0 0 4 0.442788385915428 0.771308801272036 0.771308801272036 0.442788385915428 1 - 0 35756 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.0822910695801823 N 0 0 N N 2550 45068 ENSG00000139719 ENSG00000205336 + + 12 16 121317021 56256445 intron upstream VPS33A GPR56 121282049 56220023 - + 0 121293154 56211646 - + Y 0.774130427910603 - N HCC1954 24 20.8181818181818 20 11 1 N - - N SINE - 1 0 1 11 0.364229156156239 0.442788385915428 0.442788385915428 0.364229156156239 1 0 - 42244 Y Y 2.94694081063622 3.74913061111987 2.94694081063622 308 0 0.00828864409467045 Y 0.986530361530361 0.986530361530361 N N 95 7918 ENSG00000168993 ENSG00000185619 + + 4 4 809945 754428 downstream intron CPLX1 PCGF3 768746 689573 - + 0 765562 746629 - + N - 1.85241179406974 N HCC1954 1 1 1 0 3 N - - Y - LTR 0 0.934426229508197 0.934426229508197 9 0.449930134075354 0.871293275511003 0.871293275511003 0.449930134075354 1 - 0 47244 Y Y 3.44653009016999 3.30232144676095 3.30232144676095 0 0.292035398230089 0.314546294321024 Y 0.0654867256637167 0.971681415929204 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 16 0.735600060472404 0.478497126715059 0.735600060472404 0.478497126715059 4 - - 5510 N N 3.29908909870209 3.76426113588353 3.29908909870209 0 0 0.0716021100056123 N 0 0.361166517642204 N N 411 0 ENSG00000183023 ENSG00000207486 - - 2 X 40691697 72534198 coding downstream SLC8A1 U6 40192790 72534092 - - 0 40509134 72517592 + + Y - - N HCC1954 23 18.75 7 4 1 N - - N - LINE 0 0.977777777777778 0.977777777777778 4 0.557056356474248 0.321378667196682 0.557056356474248 0.321378667196682 1 - - 38399 N Y 3.06497660981571 3.53039946453785 3.06497660981571 0 0 0.920391376736026 Y 0.382758620689655 0.931417624521073 N N 2963 2822 ENSG00000133983 ENSG00000213463 - + 14 14 69896147 69953497 coding coding COX16 SYNJ2BP 69680762 69907901 - - 0 69865706 69953370 + - N - 0.810192324272395 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 7 0.478497126715059 0.621332089913584 0.621332089913584 0.478497126715059 4 - 0 17580 Y Y 3.57592836747465 3.39487633072086 3.39487633072086 0 0 0.123655383146508 Y 0.136165814383636 0 N N 616 18522 ENSG00000215915 ENSG00000179403 - + 1 1 1394342 1366008 coding downstream ATAD3C VWA1 1374932 1360772 + + 0 1375980 1368053 - + N - - N HCC1954 2 1.25 1 1 1 N - - Y - - 0 0 0 4 0.628473838073511 0.821301038391519 0.821301038391519 0.628473838073511 2 - - 46728 N Y 3.39231567764112 3.44785379918211 3.39231567764112 0 0 0.361942586824247 N 0.942095847848602 0.976838339139441 N N 1354 1285 ENSG00000130544 ENSG00000167785 - + 19 19 7038979 8794565 utr5p upstream ZNF557 ZNF558 7020471 8781382 + - 0.976838339139441 7026019 8795760 - - N 0.992808954244646 - Y HCC1954 2 2 2 15 1 N - - N - LTR 0 1 1 15 0.492780623034912 0.871293275511003 0.871293275511003 0.492780623034912 1 0 - 992 N N 3.52105259334297 3.08266569429255 3.08266569429255 0 0 0.114561385323607 N 0 0 N N 14402 2424 ENSG00000156689 ENSG00000135272 + + 11 7 58368833 114446501 intron utr3p GLYATL2 MDFIC 58358118 114349445 - + 0 58368480 114443802 - + Y 0.958134545874787 - N HCC1954 36 33.1666666666667 30 6 1 N 602 17.9251 N - SINE 0 1 1 6 0.51420586751469 0.335662163516534 0.51420586751469 0.335662163516534 3 0 - 45512 N N 2.98447330127442 3.47655676017605 2.98447330127442 0 0 0.047720455296869 N 0 0.2578125 N N 3968 6115 ENSG00000124496 ENSG00000197256 - + 6 19 42527767 11167496 utr3p utr3p TRERF1 KANK2 42300647 11135947 - - 0.208333333333333 42302800 11137344 + - Y - - N HCC1954 21 20.8 20 5 1 N - - N DNA SINE 1 1 1 5 0.349945659836387 0.299953422716903 0.349945659836387 0.299953422716903 1 - - 9783 Y Y 3.05063126892605 3.27551679143744 3.05063126892605 5 0 0.200971474826968 Y 0 0 N N 313916 37605 ENSG00000131748 ENSG00000131771 - + 17 17 35073248 35046404 utr5p utr3p STARD3 PPP1R1B 35046938 35036705 + + 0 35063299 35045682 - + N 0.813800919754611 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.11377245508982 0.11377245508982 13 0.956994253430118 1.19267194270768 1.19267194270768 0.956994253430118 1 0 - 9343 Y Y 3.25828027434064 3.29504071510585 3.25828027434064 287 0 0.642551721560769 Y 0.0468110892289049 0 N N 679 0 ENSG00000183308 ENSG00000201849 - - 17 17 59895221 59817128 upstream downstream C17orf60 Y_RNA 59875702 59817023 + - 0 59860910 59812663 - + N - - N HCC1954 1 1 1 0 3 N - - Y LTR,LTR LINE 1 1 1 6 0.857009779191151 0.949852505270192 0.949852505270192 0.857009779191151 4 - - 14933 N Y 3.61360747730288 3.41848849077886 3.41848849077886 0 0 0.0448970499124135 N 0 0 N N 49089 29178 ENSG00000117450 ENSG00000009954 - + 1 7 45760196 72574544 coding upstream PRDX1 BAZ1B 45749295 72492676 - - 0 45757256 72580052 + - Y - - N HCC1954 40 20.3684210526316 16 19 1 N - - N - SINE 0 1 1 19 0.956994253430118 0.328520415356608 0.956994253430118 0.328520415356608 1 - - 5418 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.107429000404181 N 0 0.92470436067997 N N 20739 9878 ENSG00000143951 ENSG00000123505 - + 2 6 63669355 111323609 utr3p downstream C2orf86 AMD1 63202041 111302680 - + 0.879526977087953 63309485 111335617 + + Y - - N HCC1954 620 543.333333333333 420 6 1 N 125 21.773 N LINE LINE 1 1 1 6 0.407079645115797 0.364229156156239 0.407079645115797 0.364229156156239 4 - - 37271 N N 3.12747721909902 3.21129414611088 3.12747721909902 0 0 0.129014665108542 N 0.0457131247460382 0 N N 551733 0 ENSG00000204628 ENSG00000199172 + + 5 12 180603512 94226420 utr3p upstream GNB2L1 hsa-mir-331 180596536 94226327 - + 0 180596544 94224006 - + Y - - N HCC1954 20 14.5 2 6 1 N - - N - SINE,Simple_repeat 0 0.54 0.54 6 1.13553795742827 0.357087407996313 1.13553795742827 0.357087407996313 3 - - 29939 N Y 3.41269548964026 3.66592259835483 3.41269548964026 263 0.943876184865849 0.00419624744709235 N 0.915814277298774 0.943876184865849 N N 0 10617 ENSG00000217238 ENSG00000112739 - + X 6 115766873 4010216 downstream utr3p RP11-232D9.1 PRPF4B 115766526 3966568 - + 0 115766235 4007534 + + Y - 12.1512233814384 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.699891319672773 0.778450549431962 0.778450549431962 0.699891319672773 1 - 0 10244 Y Y 3.59425138750382 3.14272214456954 3.14272214456954 0 0 0.0922244323977354 Y 0.930662321746881 0.994666332442068 N N 97 0 ENSG00000197522 ENSG00000210238 - - 17 17 26109477 26053919 utr3p upstream SUZ12P AC005562.1 26082850 26053650 + - 0 26083750 26060952 - + N - - N HCC1954 4 2.33333333333333 2 6 1 N - - Y - Simple_repeat 0 0.0103092783505155 0.0103092783505155 6 1.03555348318931 0.93556900895034 1.03555348318931 0.93556900895034 1 - - 2567 N N 3.47911741325579 3.35253057547976 3.35253057547976 0 0 0.400725366658884 N 0 0 N N 0 143275 ENSG00000197907 ENSG00000167996 + + 14 11 65550260 61491708 downstream coding AL391261.3 FTHL16 65549301 61488335 - - 0 65437638 61489126 - - Y - - N HCC1954 11 7.2 6 5 1 N - - N - - 0 0 0 5 0.249961185597419 0.364229156156239 0.364229156156239 0.249961185597419 2 - - 31342 Y Y 3.47336426491055 3.16719954052809 3.16719954052809 271 0 0.0268341120140762 Y 0 0 N N 279 4066 ENSG00000164088 ENSG00000221814 - - 3 3 52259653 52248223 upstream upstream PPM1M TWF2 52255226 52237670 + - 0 52253994 52248488 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.678466075192994 0.635615586233437 0.678466075192994 0.635615586233437 1 - - 29375 N Y 3.52720696927234 3.44512531223303 3.44512531223303 101 0.0477989663161649 0.288025668364976 Y 0.0477989663161649 0.987132418463732 N N 4547 7887 ENSG00000044090 ENSG00000124541 + + 6 6 43129632 43105312 coding coding CUL7 C6orf153 43113336 43097351 - + 0 43113986 43103193 - + N 0.726237900353995 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.87843502367093 0.907002016310634 0.907002016310634 0.87843502367093 4 0 - 26573 Y Y 2.80423023111998 3.3984700535705 2.80423023111998 153 0 0.00789113164329536 Y 0 0 N N 6566 89 ENSG00000167513 ENSG00000182376 - + 16 16 87403166 87339657 upstream upstream CDT1 AC138028.1-3 87397687 87336676 + + 0 87378877 87336333 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity - 0.104166666666667 0 0.104166666666667 28 0.685607823352921 0.699891319672773 0.699891319672773 0.685607823352921 1 - - 48139 N N 3.30587531681723 3.23846952379497 3.23846952379497 0 0 0.0532244999217502 N 0 0 N N 551733 194 ENSG00000204628 ENSG00000131016 + + 5 6 180603512 151719601 coding intron GNB2L1 AKAP12 180596536 151603202 - + 0 180597248 151668076 - + Y 0.533804592371237 0.307198186283771 N HCC1954 19 13.8571428571429 1 6 1 N - - N - Low_complexity 0 0.525 0.525 7 0.628473838073511 0.28566992639705 0.628473838073511 0.28566992639705 1 0 0 31290 Y Y 3.27551679143744 3.57167229721571 3.27551679143744 0 0 0.99991786309929 Y 0 0.980193022128897 N N 5747 20 ENSG00000145012 ENSG00000213132 - + 3 3 190080135 189380683 utr5p upstream LPP AC022498.18 189413415 189379637 + + 0 189606594 189353845 - + N 0.285844944168303 - N HCC1954 1 1 1 0 7 N - - Y - SINE 0 0.797752808988764 0.797752808988764 8 0.799875793911741 0.807017542071667 0.807017542071667 0.799875793911741 4 0 - 17445 Y Y 3.43681151080804 3.63655728995158 3.43681151080804 4 0 0.672732724934642 Y 0.991329625884732 0.991329625884732 N N 251 0 ENSG00000142583 ENSG00000212602 - - 1 1 9052257 9065525 coding downstream SLC2A5 SCARNA16 9019594 9065342 - + 0 9052152 9067663 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 1.03555348318931 0.771308801272036 1.03555348318931 0.771308801272036 2 - - 13493 N N 3.35719722089263 3.47911741325579 3.35719722089263 4 0.00894423558897228 0.113716260609115 N 0.00894423558897228 0 N N 0 238 ENSG00000219236 ENSG00000211643 + + 9 22 67024803 21003581 downstream coding RP11-236F9.4 IGLV5-52 67017595 21003021 - + 0 67017591 21003538 - + Y - - N HCC1954 11 10.5 9 4 1 N - - N - - 0 0 0 4 0.307095170876829 0.749883556792257 0.749883556792257 0.307095170876829 2 - - 31997 N Y 3.59784511035345 3.79040344379773 3.59784511035345 1 0 0.616624312823803 N 0.573089700996678 0.819748984865264 N N 109 4058 ENSG00000075213 ENSG00000134086 + - 7 3 83662153 10168744 intron coding SEMA3A VHL 83425601 10158319 - + 0.819748984865264 83555581 10166471 - - Y 0.700848403290697 0.895183558638116 N HCC1954 20 20 20 4 1 N 196 24.5382 N SINE - 1 0 1 4 0.314236919036755 0.442788385915428 0.442788385915428 0.314236919036755 3 0 0 26695 N Y 3.58271458558979 3.5016965035439 3.5016965035439 0 0 0.75119857636503 Y 0 0 N N 0 4 ENSG00000220991 ENSG00000153789 - - 16 16 83906889 83703615 downstream upstream AC092275.3 FAM92B 83906768 83689466 + - 0 83948570 83762914 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 7 1.06412047582901 0.892718519990782 1.06412047582901 0.892718519990782 4 - - 1778 N Y 3.61360747730288 3.36976709257655 3.36976709257655 11 0 0.0972998524718582 N 0 0.791335791264889 N N 3301 4015 ENSG00000070081 ENSG00000173141 - + 11 13 17309646 20651203 utr5p intron NUCB2 MRP63 17254860 20648372 + + 0 17260959 20650372 - + Y - - N HCC1954 38 35.2 32 5 1 N - - N - SINE 0 1 1 5 0.435646637755502 0.307095170876829 0.435646637755502 0.307095170876829 2 - - 24775 Y Y 3.46079439322662 3.56385300933068 3.46079439322662 312 0 0.764103749343747 Y 0.957583196944899 0.9858610656483 N N 10593 4475 ENSG00000134779 ENSG00000134775 + + 18 18 32663156 32614016 coding downstream C18orf10 FHOD3 32630033 32131700 - + 0 32632410 32614149 - + N 0.704189683606059 - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.821301038391519 0.821301038391519 0.821301038391519 0.821301038391519 4 0 - 18973 Y Y 3.48167806633553 3.19396434305824 3.19396434305824 418 0 0.0280276287966857 Y 0 0.994299384825701 N N 10984 0 ENSG00000136631 ENSG00000219469 - + 1 1 148384129 148293640 upstream downstream VPS45 RP11-458I7.1 148305966 148292470 + + 0 148305638 148299749 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LINE,SINE 0 0.677083333333333 0.677083333333333 6 0.914143764470561 0.678466075192994 0.914143764470561 0.678466075192994 1 - - 29620 N Y 3.70889084821189 3.29123930559352 3.29123930559352 0 0 0.91403249263508 Y 0.00297619047619047 0 N Y 6229 7560 ENSG00000064999 ENSG00000065060 - + 6 6 35193232 34953265 coding coding ANKS1A UHRF1BP1 34965016 34867772 + + 0 35193001 34935326 - + N - - N HCC1954 1 1 1 0 1 Y 220 1.03225 N - - 0 0 0 64 1.34979040222606 1.18553019454776 1.34979040222606 1.18553019454776 4 - - 45094 N Y 3.49594335519865 3.05063126892605 3.05063126892605 0 0 0.395902079521947 N 0.711164658634538 0.203212851405623 N N 491 2 ENSG00000215020 ENSG00000188279 - + 10 10 47899205 48877823 intron downstream AL591684.7-2 FAM25B 47875285 48873392 + - 0.203212851405623 47898732 48869722 - - N - - Y HCC1954 2 2 2 4 1 N - - N LINE - 1 0 1 4 0.507064119354764 0.385654400636018 0.507064119354764 0.385654400636018 1 - - 36965 N N 3.78105657260285 3.47762033516948 3.47762033516948 0 0 0.999937682893539 N 0 0 N N 12084 3 ENSG00000177119 ENSG00000179242 + + 12 20 44112391 59945671 coding intron ANO6 CDH4 43896170 59260965 + + 0 44047841 59575888 + + Y - 0.929733246584255 N HCC1954 1 1 1 0 8 N - - N - LTR 0 1 1 11 0.964136001590045 1.09982921662864 1.09982921662864 0.964136001590045 2 - 0 37415 N Y 3.38912318237562 3.3828009725769 3.3828009725769 41 0.141512160878722 0.0424494066275988 N 0.926415328075319 0.959119626708511 N N 110 1187 ENSG00000197927 ENSG00000215394 - + 2 14 132241449 18754290 utr5p utr5p C2orf27 AL589743.4-2 132196418 18720037 + + 0 132196461 18753692 - + Y 0.318615480015784 - N HCC1954 156 99.4 2 10 1 N - - N - LINE,SINE 0 0.743016759776536 0.743016759776536 10 0.757025304952183 1.18553019454776 1.18553019454776 0.757025304952183 1 0 - 21764 N Y 3.8333716936548 3.59425138750382 3.59425138750382 0 0 0.120737859561858 N 0 0 N N 6330 23800 ENSG00000143190 ENSG00000067182 - + 1 12 165663206 6321522 utr3p coding POU2F1 TNFRSF1A 165456744 6308185 + - 0 165656060 6310289 - - Y - - N HCC1954 23 21.8 21 5 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.578481600954027 0.578481600954027 0.314236919036755 2 - - 7177 Y N 3.14847529291479 2.57150888656861 2.57150888656861 0 0 0.251403978456212 Y 0 0.199571963616907 N N 0 14117 ENSG00000213729 ENSG00000068697 + - 2 2 20219305 20114926 downstream upstream AC098828.3 LAPTM4A 20218875 20095894 - - 0.199571963616907 20170050 20127653 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR SINE 1 0.0483870967741935 1 4 0.335662163516534 0.442788385915428 0.442788385915428 0.335662163516534 2 - - 42182 Y Y 3.50997045217554 3.17511211436896 3.17511211436896 0 0 0.805230240249251 Y 0 0.988281430219146 N N 3206 0 ENSG00000109756 ENSG00000206978 - - 4 4 160500747 160205000 upstream upstream RAPGEF2 Y_RNA 160408448 160204899 + - 0 160327245 160244834 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.0674846625766871 0.0674846625766871 15 0.5713398527941 1.1426797055882 1.1426797055882 0.5713398527941 1 - - 15631 N N 3.32060461399677 3.42424163912411 3.32060461399677 7 0.386552752191519 0.096854472789846 N 0.40666577670983 0.386552752191519 N N 19119 850768 ENSG00000092621 ENSG00000075624 - + 1 7 120088359 5536758 intron utr3p PHGDH ACTB 120056033 5533313 + - 0.386552752191519 120077438 5533539 - - Y 0.305677415439239 0.817090395442887 N HCC1954 2 1.25 1 1 1 N - - N SINE - 0.65 0 0.65 4 0.28566992639705 0.421363141435649 0.421363141435649 0.28566992639705 2 0 0 27150 Y Y 3.47336426491055 3.43937216388778 3.43937216388778 115 0 0.255960549156578 Y 0.308283582089552 0.992562189054726 N N 4369 211 ENSG00000140743 ENSG00000157341 - - 16 16 22293439 22385434 coding upstream CDR2 AC106788.3-1 22264758 22370389 - + 0 22293054 22348620 + - N - - N HCC1954 2 1.42857142857143 1 3 2 N - - Y - - 0 0 0 7 0.93556900895034 0.914143764470561 0.93556900895034 0.914143764470561 1 - - 41532 Y Y 3.62192127872787 3.51935717616377 3.51935717616377 303 0 0.0155283461051082 Y 0.993265542770493 0.986531085540987 N N 11 2437 ENSG00000177669 ENSG00000104660 + + 8 8 30109990 30085122 upstream coding MBOAT4 LEPROTL1 30109001 30072487 - + 0 30114330 30081544 - + N - 4.03885106564678 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.949852505270192 0.771308801272036 0.949852505270192 0.771308801272036 4 - 0 31147 Y Y 3.37291973504871 3.13118534265551 3.13118534265551 290 0 0.190604696614279 Y 0 0.984668435013263 N N 4941 457 ENSG00000182606 ENSG00000168038 - - 3 3 42242385 41978664 upstream upstream TRAK1 ULK4 42107750 41263097 + - 0 42050334 42030613 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE Low_complexity 1 0.214876033057851 1 4 0.814159290231593 0.814159290231593 0.814159290231593 0.814159290231593 4 - - 23623 N Y 3.60256518892881 3.40951234194457 3.40951234194457 2 0 0.390430763291090 N 0.891809908998989 0.891809908998989 N N 0 157 ENSG00000207623 ENSG00000105737 - - 1 19 207672210 47261797 upstream intron hsa-mir-205 GRIK5 207672101 47194317 + - 0.891809908998989 207669147 47232437 - + Y - 0.479961276711452 N HCC1954 9 5.2 1 4 1 N - - N SINE SINE 0.616541353383459 1 1 5 0.671324327033068 0.392796148795944 0.671324327033068 0.392796148795944 1 - 0 28122 N Y 3.09400074636723 3.59784511035345 3.09400074636723 1 0 0.165689403101403 N 0.885712381713981 0.885712381713981 N N 9663 0 ENSG00000172775 ENSG00000217145 - - 16 9 55777477 68792024 utr5p upstream AC009090.12 RP11-250H24.4 55743888 68790838 - + 0.885712381713981 55777235 68790297 + - Y - - N HCC1954 23 10.2 4 5 1 N - - N - SINE 0 1 1 5 0.542772860154395 0.292811674556976 0.542772860154395 0.292811674556976 1 - - 21725 N Y 3.57063922744582 3.61360747730288 3.57063922744582 0 0 0.340422677777682 N 0 0.963952584531675 N N 1186 871 ENSG00000137968 ENSG00000084453 - + 1 12 75849389 21439638 coding utr5p SLC44A5 SLCO1A2 75440404 21311651 - - 0 75577903 21439556 + - Y - - N HCC1954 25 21.4285714285714 20 14 1 N - - N LINE,LINE LINE 0.320422535211268 1 1 14 1.05697872766909 0.471355378555133 1.05697872766909 0.471355378555133 4 - - 46189 N Y 3.50000108636471 3.05228683331189 3.05228683331189 21 0 0.464520850319034 N 0 0.464892049458646 N N 1814 0 ENSG00000178229 ENSG00000220431 + + 19 9 62533956 42267232 utr3p downstream ZNF543 RP11-216M21.4 62523689 42266761 + + 0.464892049458646 62532991 42281349 + + Y - - N HCC1954 152 110.5 92 8 1 N - - N SINE - 1 0 1 8 0.87843502367093 0.757025304952183 0.87843502367093 0.757025304952183 2 - - 34472 Y Y 3.45400817511148 3.42320856935422 3.42320856935422 241 0 0.244235648711193 Y 0 0.988934993084371 N N 0 271 ENSG00000218219 ENSG00000165181 - - 9 9 113605531 113597044 downstream upstream RP11-430K21.2 C9orf84 113605081 113488274 + - 0 113610983 113598475 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.51420586751469 0.364229156156239 0.51420586751469 0.364229156156239 1 - - 17947 Y Y 3.42576922243396 3.36295036923788 3.36295036923788 266 0 0.0395956321069127 Y 0.992277204639506 0.992277204639506 N Y 1168 8310 ENSG00000117151 ENSG00000174021 + - 1 1 84812735 84744831 coding coding CTBS GNG5 84792821 84736603 - - 0 84801528 84740241 - + N - 2.83685396533457 N HCC1954 2 1.71428571428571 1 5 1 Y - - Y - - 0 0 0 7 0.728458312312478 0.928427260790413 0.928427260790413 0.728458312312478 4 - 0 14825 N Y 3.40847927217468 3.3755202409218 3.3755202409218 112 0 0.235732170186525 N 0.869173213617658 0.969809203142537 N N 3567 34 ENSG00000177951 ENSG00000197049 - - 11 1 197428 712376 coding upstream BET1L AL669831.13-3 157784 711183 - + 0 159052 703802 + - Y - - N HCC1954 14 9.71428571428571 8 7 1 N - - N LINE - 0.233333333333333 0 0.233333333333333 7 0.678466075192994 0.578481600954027 0.678466075192994 0.578481600954027 4 - - 13746 Y Y 2.65497101709999 3.15000287622464 2.65497101709999 358 0 0.0682021016548688 Y 0.0228712834164448 0.986614675115294 N N 18160 0 ENSG00000100023 ENSG00000207751 - + 22 22 20382565 20337674 upstream downstream PPIL2 hsa-mir-130b 20350273 20337593 + + 0 20345126 20342751 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 18 0.956994253430118 1.27123117246687 1.27123117246687 0.956994253430118 4 - - 45757 N Y 3.32167753656001 3.24575025545007 3.24575025545007 345 0.946583850931677 0.00621671448402739 N 0.946583850931677 0.946583850931677 N N 6657 9146 ENSG00000163428 ENSG00000104960 + + 3 19 121550876 55055802 downstream utr3p LRRC58 PTOV1 121526266 55045950 - + 0.946583850931677 121509541 55055397 - + Y - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 21 0.492780623034912 1.19267194270768 1.19267194270768 0.492780623034912 2 - - 17922 Y Y 3.04380519801756 3.39227582484777 3.04380519801756 305 0 0.128592833339883 Y 0.259578454332553 0.98576112412178 N N 13170 33725 ENSG00000196187 ENSG00000143819 + + 1 1 224136671 224099884 utr3p intron TMEM63A EPHX1 224099863 224064459 - + 0 224100804 224095511 - + N - 0.913004889743209 N HCC1954 1 1 1 0 2 N - - Y - LINE 0 0.366459627329193 0.366459627329193 7 0.93556900895034 1.02841173502938 1.02841173502938 0.93556900895034 4 - 0 38128 Y Y 3.59528445727371 3.34528969661801 3.34528969661801 335 0 0.0343614013198277 Y 0.783863897296733 0.986055735309467 N N 24758 9089 ENSG00000100836 ENSG00000129473 - + 14 14 22865202 22850806 upstream coding PABPN1 BCL2L2 22859337 22845852 + + 0 22858784 22847248 - + N - 0.945184797176591 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 20 1.03555348318931 1.39264089118562 1.39264089118562 1.03555348318931 4 - 0 11675 N N 3.45976132345673 3.6026931700048 3.45976132345673 0 0 0.11037727527285 N 0 0 N N 1649619 1 ENSG00000141736 ENSG00000069535 + - 17 X 35138441 43626665 upstream intron ERBB2 MAOB 35104766 43510804 + - 0 35103106 43576716 + + Y - 1.03367633302152 N HCC1954 2 1.5 1 2 1 N - - N DNA DNA 1 1 1 4 0.364229156156239 0.292811674556976 0.364229156156239 0.292811674556976 1 - 0 30457 Y Y 3.27192306858781 3.58424216889964 3.27192306858781 8 0 0.87618595206816 Y 0.976859313838361 0.976859313838361 N N 9759 4873 ENSG00000101846 ENSG00000130021 - - X X 7282682 7076189 coding coding STS HDHD1A 7147472 6976961 + - 0 7181238 7076116 - + N 0.0111368048834967 0.505076995171717 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 10 0.87843502367093 0.685607823352921 0.87843502367093 0.685607823352921 1 0 0 47589 N Y 3.48593413659447 3.63552422018169 3.48593413659447 69 0.151446869070209 0.0479646004780344 Y 0.151446869070209 0 N N 43 39 ENSG00000204936 ENSG00000183668 - - 19 19 48559320 48465522 coding intron CD177 PSG9 48549665 48449275 + - 0 48549934 48463049 - + N - 0.475107145056224 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.714174815992626 0.314236919036755 0.714174815992626 0.314236919036755 2 - 0 37326 N Y 3.60256518892881 3.56591914887046 3.56591914887046 0 0.737838915470495 0.868343875961304 N 0 0.912612971823498 N N 355 1 ENSG00000106066 ENSG00000126785 - - 7 14 29201417 62828312 coding upstream CPVL RHOJ 29001772 62740898 - + 0 29098843 62709945 + - Y - - N HCC1954 20 11.5 2 4 1 N - - N - SINE 0 1 1 4 0.528489363834543 0.307095170876829 0.528489363834543 0.307095170876829 4 - - 31062 N N 3.53039946453785 3.56911164413597 3.53039946453785 0 0 0.115238367385769 N 0.855587392550143 0 N N 8096 100806 ENSG00000010404 ENSG00000163931 - - X 3 148394714 53265078 utr3p coding IDS TKT 148368206 53234715 - - 0 148368594 53249309 + + Y - - N HCC1954 35 32.6666666666667 29 6 1 N - - N SINE - 1 0 1 6 0.292811674556976 1.04269523134923 1.04269523134923 0.292811674556976 2 - - 8855 N N 3.23999710710482 3.46145674063593 3.23999710710482 0 0.00362318840579701 0.323778227029811 N 0.653434152488973 0.653434152488973 N N 1649619 4364 ENSG00000141736 ENSG00000057935 + + 17 2 35138441 42837591 coding intron ERBB2 MTA3 35104766 42575213 + + 0.653434152488973 35122225 42730051 + + Y - 1.63524967043954 N HCC1954 22 18.375 1 7 1 N - - N - SINE 0 1 1 8 0.642757334393363 0.314236919036755 0.642757334393363 0.314236919036755 3 - 0 34181 Y Y 3.74913061111987 3.53768019619294 3.53768019619294 264 0 0.0103385339717563 Y 0.073943661971831 0.98596884336321 N N 0 1 ENSG00000217319 ENSG00000137142 + - 9 9 38444067 38414444 upstream upstream RP11-403F21.1 IGFBPL1 38442786 38398991 - - 0 38446116 38427850 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.421363141435649 0.392796148795944 0.421363141435649 0.392796148795944 1 - - 1185 N Y 3.27721220861663 3.30232144676095 3.27721220861663 0 0 0.0431321070185393 N 0 0 N N 1516 8014 ENSG00000168395 ENSG00000149084 - + 2 11 242317560 43834736 utr3p utr3p ING5 HSD17B12 242290129 43658719 + + 0 242314963 43834174 - + Y - 1.70020549745316 N HCC1954 37 34.375 21 8 1 N - - N SINE - 1 0 1 8 0.428504889595575 0.614190341753658 0.614190341753658 0.428504889595575 1 - 0 4637 N Y 3.71041843152174 3.48081283043499 3.48081283043499 239 0.68465829846583 0.00595017321066371 N 0.883821478382148 0.900418410041841 N N 650 0 ENSG00000127957 ENSG00000201959 - + 7 7 74995330 76509001 coding upstream PMS2L3 Y_RNA 74975006 76508900 - + 0 74981944 76507303 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.328520415356608 0.385654400636018 0.385654400636018 0.328520415356608 1 - - 16013 N Y 3.22526780992528 3.54296933622177 3.22526780992528 1 0 0.198022882086014 N 0.930300429184549 0 N N 11670 220 ENSG00000117360 ENSG00000187391 - - 1 7 148592292 78920572 coding intron PRPF3 MAGI2 148560642 77484310 + - 0 148567549 78520366 - + Y - 3.6677205184951 N HCC1954 40 25 20 4 1 N - - N - SINE 0 1 1 4 0.607048593593732 0.364229156156239 0.607048593593732 0.364229156156239 1 - 0 39836 Y Y 3.34615493251855 3.49015970162987 3.34615493251855 137 0 0.143893603829425 Y 0.801459854014599 0.917274939172749 N N 1304 0 ENSG00000186073 ENSG00000210354 - - 15 15 34889724 34649513 upstream upstream C15orf41 AC103988.7 34770651 34649295 + - 0 34733589 34659418 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.45707188223528 0.657040830713216 0.657040830713216 0.45707188223528 2 - - 6983 Y Y 3.63978029044062 3.33676820853032 3.33676820853032 307 0 0.0205164527028274 Y 0 0 N N 0 0 ENSG00000198702 ENSG00000200890 - - 2 2 81664354 81576962 upstream downstream AC013262.7 5S_rRNA 81663500 81576849 + - 0 81629256 81562742 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 54 1.06412047582901 1.1426797055882 1.1426797055882 1.06412047582901 2 - - 27400 Y Y 3.66488952858494 3.49640736351508 3.49640736351508 0 0.00274725274725274 0.939669175938955 Y 0.993648071673549 0.993648071673549 N N 1864 6656 ENSG00000154102 ENSG00000131153 + - 16 16 84342190 84280089 coding upstream C16orf74 GINS2 84298624 84268782 - - 0 84301413 84281882 - + N - - N HCC1954 1 1 1 0 3 N - - Y Low_complexity,Low_complexity - 0.395939086294416 0 0.395939086294416 18 1.40692438750547 1.21409718718746 1.40692438750547 1.21409718718746 2 - - 31614 Y Y 3.50272957331379 3.57808779297027 3.50272957331379 120 0.00362318840579701 0.756905955284923 Y 0.0114686751112631 0 N Y 87 1714 ENSG00000004838 ENSG00000114388 - + 3 3 50359287 50363490 coding intron ZMYND10 TUSC4 50353550 50359923 - - 0 50356285 50363010 + - N - 2.28403474266119 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.692749571512847 0.642757334393363 0.692749571512847 0.642757334393363 4 - 0 24987 N N 3.588962247475 3.2222965816916 3.2222965816916 0 0 0.116419888827504 N 0 0 N N 32611 47278 ENSG00000132142 ENSG00000189403 + + 17 13 32841015 30089734 intron coding ACACA HMGB1 32516036 29930877 - - 0 32574977 29934686 - - Y 1.22139420269328 - N HCC1954 5 5 5 8 1 N - - N - - 0 0 0 8 0.321378667196682 0.349945659836387 0.349945659836387 0.321378667196682 2 0 - 33049 N Y 3.13999365762046 2.93868044237372 2.93868044237372 411 0.00878701938723336 0.992076731059837 Y 0 0.993646070637098 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 8502 5412 - + N 0.58925071454747 1.1781446307412 N HCC1954 6 2.2258064516129 1 26 9 Y - - N - - 0 0 0 31 1.16410495006798 1.62831858046319 1.62831858046319 1.16410495006798 1 0 0 480 Y Y 3.27511556385332 3.44938138249196 3.27511556385332 347 0 0.0026810497807388 Y 0 0.98391744910291 N N 1286 251 ENSG00000150787 ENSG00000197580 - + 11 11 111609903 111594853 upstream utr3p PTS BCO2 111602309 111551418 + + 0 111599792 111593832 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.716417910447761 0 0.716417910447761 4 0.478497126715059 0.764167053112109 0.764167053112109 0.478497126715059 1 - - 107 Y Y 2.93868044237372 3.41679307359967 2.93868044237372 300 0 0.00137030255216586 Y 0 0 N N 21538 16676 ENSG00000149782 ENSG00000173457 - - 11 11 63791970 63770989 intron upstream PLCB3 PPP1R14B 63775618 63768529 + - 0 63776505 63772600 - + N 0.222073629656267 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.420212765957447 0.420212765957447 13 0.692749571512847 0.964136001590045 0.964136001590045 0.692749571512847 1 0 - 2385 N N 3.47279520345708 3.27039548527796 3.27039548527796 2 0 0.125048791997778 N 0 0 N N 1990 3567 ENSG00000182504 ENSG00000177951 + - 3 11 102972095 197428 utr3p coding CEP97 BET1L 102926177 157784 + - 0 102971835 170403 + + Y - 2.88016436250957 N HCC1954 190 171 145 5 1 N 551 25.0238 N SINE - 1 0 1 5 0.314236919036755 0.671324327033068 0.671324327033068 0.314236919036755 1 - 0 87 Y Y 3.28655907981151 3.73336824417043 3.28655907981151 307 0 0.0864098795997721 Y 0.945383963232341 0.993172995404043 N N 63500 30347 ENSG00000085733 ENSG00000131626 - + 11 11 69960337 69908148 upstream intron CTTN PPFIA1 69922292 69794471 + + 0 69921851 69905030 - + N - 2.12903214360713 N HCC1954 1 1 1 0 3 N - - Y LINE - 0.293333333333333 0 0.293333333333333 8 0.87843502367093 0.807017542071667 0.87843502367093 0.807017542071667 1 - 0 4099 N Y 3.57233464462502 3.71890006681607 3.57233464462502 12 0 0.281323748016391 N 0.972333779562695 0.880113044771679 Y N 0 291 ENSG00000213483 ENSG00000184903 - - 7 7 93312560 110989583 upstream intron AC002076.2 IMMP2L 93312037 110090346 + - 0 93274448 110676835 - + N - 1.17578109055393 N HCC1954 21 20.25 20 4 1 N - - N LINE LINE 1 1 1 4 0.542772860154395 0.5713398527941 0.5713398527941 0.542772860154395 1 - 0 28561 N N 3.46448140203209 3.60426060610801 3.46448140203209 61 0 0.0213363794387147 N 0 0 N N 131 0 ENSG00000180015 ENSG00000209495 + - 4 16 189897680 3142681 downstream upstream AC093909.2 AC108134.3-1 189896500 3142610 + - 0 190195924 3151266 + + Y - - N HCC1954 23 21.25 20 4 1 N 155 26.8329 N SINE - 1 0 1 4 0.28566992639705 0.392796148795944 0.392796148795944 0.28566992639705 1 - - 36606 Y Y 3.75169126419961 3.58271458558979 3.58271458558979 0 0 0.855922066797154 Y 0.960762134580097 0.994394590654299 N N 35326 55227 ENSG00000111321 ENSG00000111319 - - 12 12 6370994 6354976 coding upstream LTBR SCNN1A 6363595 6326276 + - 0 6363881 6355020 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 23 1.27123117246687 1.38549914302569 1.38549914302569 1.27123117246687 1 - - 38101 Y Y 3.47592491799029 3.42001607408871 3.42001607408871 244 0 0.130292594213004 Y 0.0538934426229508 0.987551229508197 N N 312 0 ENSG00000139973 ENSG00000213572 - + 14 14 61638180 61402019 upstream downstream SYT16 AL137918.4 61532294 61401469 + + 0 61506602 61464242 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.735600060472404 0.535631111994469 0.735600060472404 0.535631111994469 1 - - 47705 Y Y 3.71976530271662 3.38383404234679 3.38383404234679 272 0 0.0861116709984924 Y 0 0 N Y 10624 560 ENSG00000074219 ENSG00000063127 + - 19 19 54557526 54520286 coding intron TEAD2 SLC6A16 54535669 54484709 - - 0 54537507 54489622 - + N - 1.90529781133842 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.21409718718746 1.08554572030879 1.21409718718746 1.08554572030879 4 - 0 21787 N N 3.60426060610801 3.57167229721571 3.57167229721571 11 0 0.0808319354886883 N 0 0 N N 3044 2251 ENSG00000139428 ENSG00000186275 + + 12 1 108495741 143541658 utr3p upstream MMAB NBPF8 108475908 143326471 - + 0.0337286216554435 108477395 143310137 - + Y - - N HCC1954 50 39.3333333333333 22 12 1 N 308 21.8527 N SINE - 1 0 1 12 0.335662163516534 0.628473838073511 0.628473838073511 0.335662163516534 2 - - 221 Y Y 3.61889661733171 3.63040291402221 3.61889661733171 326 0 0.00854974213220416 Y 0.627727731614507 0.993690300535839 N N 0 19435 ENSG00000213411 ENSG00000173933 - + 11 11 66186733 66170516 upstream intron AP001157.4-1 RBM4 66186447 66140673 + + 0 66181186 66164173 - + N - 0.846260104931129 N HCC1954 2 1.25 1 1 2 N - - Y SINE - 1 0 1 4 0.849868031031224 0.721316564152552 0.849868031031224 0.721316564152552 1 - 0 19608 N N 3.55401162459584 3.61464054707278 3.55401162459584 0 0 0.163301466205059 N 0 0.627300613496932 N N 2833 0 ENSG00000133019 ENSG00000215401 - - 1 18 238139338 1353874 utr5p upstream CHRM3 AP005119.2 237858996 1352441 + - 0 237859380 1504367 - + Y - - N HCC1954 24 22.2727272727273 21 33 1 N - - N LINE - 1 0 1 33 0.371370904316165 0.799875793911741 0.799875793911741 0.371370904316165 3 - - 43108 N Y 3.48639814491089 3.12023634023727 3.12023634023727 239 0 0.00434525382065987 N 0.608786610878661 0.270920502092051 N N 0 673 ENSG00000216027 ENSG00000164291 - + 4 5 61212351 94966562 downstream intron AC095061.3 ARSK 61212262 94916581 - + 0.608786610878661 60902269 94934115 + + Y - 1.1698877709274 N HCC1954 168 46 2 5 1 N - - N SINE,SINE SINE 0.842105263157895 1 1 5 0.271386430077198 0.28566992639705 0.28566992639705 0.271386430077198 1 - 0 12180 N N 3.49528100778935 3.48743121468078 3.48743121468078 0 0 0.0454782961595721 N 0 0 N N 7525 5189 ENSG00000173894 ENSG00000157110 - + 17 8 75375973 30549276 upstream utr3p CBX2 RBPMS 75366588 30361486 + + 0 75358159 30539158 - + Y - - N HCC1954 22 21.2 21 5 1 N - - N LTR SINE 1 1 1 5 0.51420586751469 0.264244681917271 0.51420586751469 0.264244681917271 1 - - 17190 N N 3.32320511986986 3.6491271616355 3.32320511986986 0 0 0.0840468247333823 N 0 0 N N 7600 1 ENSG00000157978 ENSG00000185666 + - 1 22 25767964 31784358 utr3p intron LDLRAP1 SYN3 25742663 31238539 + - 0 25767252 31387823 + + Y 1.88521840727865 1.03292181069959 N HCC1954 3 1.5 1 1 1 N - - N SINE SINE 0.502369668246445 1 1 4 0.692749571512847 0.271386430077198 0.692749571512847 0.271386430077198 2 0 0 30308 N Y 3.44252480635993 3.51832410639388 3.44252480635993 199 0 0.306328024891046 Y 0 0.984206748025843 N N 8617 441 ENSG00000221867 ENSG00000147402 - + X X 151621480 151576655 upstream upstream MAGEA6 GABRQ 151617901 151557293 + + 0 151617786 151555134 - + N - - N HCC1954 2 2 2 21 4 N - - N Low_complexity - 0.390804597701149 0 0.390804597701149 21 0.621332089913584 0.714174815992626 0.714174815992626 0.621332089913584 1 - - 49511 N Y 3.59681204058356 3.2965682984157 3.2965682984157 0 0 0.672441962533543 Y 0.0103085618977021 0 N N 1955 2781 ENSG00000205570 ENSG00000082196 + - 5 5 69590632 34160396 utr3p intron AC140134.2-2 AMACR 69470446 34023069 - - 0 69528463 34100579 - + N - 22.4681704598243 N HCC1954 16 3.5 1 1 1 N - - N - LTR 0 1 1 6 0.757025304952183 0.792734045751814 0.792734045751814 0.757025304952183 3 - 0 36280 Y Y 3.55128313764676 3.23949324599505 3.23949324599505 150 0.00666666666666671 0.0282160519982552 Y 0.721169590643275 0.982573099415205 N N 2438 1815 ENSG00000188026 ENSG00000184209 + + 12 12 122584457 122516894 downstream utr5p RILPL1 AC145423.8 122522316 122508604 - + 0 122521704 122508695 - + N - 1.03463553565445 N HCC1954 7 2.5625 1 8 2 N - - Y SINE - 1 0 1 16 1.07840397214886 0.785592297591888 1.07840397214886 0.785592297591888 2 - 0 44483 N N 3.57167229721571 3.24781639498985 3.24781639498985 20 0 0.674162501232833 N 0 0.0813710387323946 N N 0 0 ENSG00000217094 ENSG00000167910 + - 10 8 32517745 59575275 downstream upstream AL445071.15 CYP7A1 32517254 59565292 - - 0.159220950704225 32517090 59579361 - + Y - - N HCC1954 18 8.625 6 8 1 N - - N - - 0 0 0 8 0.535631111994469 0.257102933757345 0.535631111994469 0.257102933757345 3 - - 21150 N N 3.02495296932827 3.52105259334297 3.02495296932827 0 0 0.151212666664889 N 0.00416666666666654 0 N N 24661 0 ENSG00000184432 ENSG00000217333 + - 3 1 140591158 169680726 intron upstream COPB2 RP1-81F6.1 140559125 169680447 - - 0.563230994152047 140590298 169691434 - + Y 1.65728101654443 - N HCC1954 154 90.75 20 4 1 N 326 23.9149 N SINE SINE 1 0.923076923076923 1 4 0.278528178237124 0.278528178237124 0.278528178237124 0.278528178237124 1 0 - 41349 N Y 3.50811568808642 3.57336771439491 3.50811568808642 0 0.0666666666666669 0.53278443221362 N 0.0666666666666669 0.782222222222222 N N 2594 1261 ENSG00000101347 ENSG00000151882 + - 20 5 35013590 43448245 intron intron SAMHD1 CCL28 34954059 43417357 - - 0 34994047 43417915 - + Y 1.01687517518187 1.35131819114521 N HCC1954 2 1.33333333333333 1 2 1 N - - N SINE - 1 0 1 6 0.5713398527941 0.528489363834543 0.5713398527941 0.528489363834543 1 0 0 30557 Y Y 3.75016368088976 3.44719145177281 3.44719145177281 16 0.0837445175438596 0.0261433609014189 Y 0.960731907894737 0.960731907894737 N N 264 884 ENSG00000198908 ENSG00000158301 - + X X 101895124 101859316 upstream utr5p BHLHB9 GPRASP2 101862310 101853760 + + 0 101862201 101855821 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.978419497909897 0.842726282871298 0.978419497909897 0.842726282871298 1 - - 1530 N N 3.44615838200292 3.52258017665282 3.44615838200292 0 0 0.794050654052295 N 0 0 N N 5225 0 ENSG00000166689 ENSG00000213180 + + 11 17 16992535 62651616 intron intron PLEKHA7 AC007448.14-1 16765791 62651306 - + 0 16952995 62651459 - + Y 2.34916178524675 1 N HCC1954 4 4 4 5 1 N - - N - - 0 0 0 5 0.299953422716903 0.235677689277566 0.299953422716903 0.235677689277566 2 0 0 13753 N N 3.12332620197713 3.45087846057827 3.12332620197713 0 0.167034215450414 0.671727210118638 N 0 0.184208767709169 Y N 110 15693 ENSG00000100399 ENSG00000100412 + + 22 22 39966881 40254939 coding intron CHADL ACO2 39955485 40195075 - + 0.184208767709169 39963904 40245634 - + N 0.53626976377683 1.52500948243817 N HCC1954 20 7.85714285714286 1 5 1 N 88 8.33806 N - SINE 0 1 1 7 0.814159290231593 0.799875793911741 0.814159290231593 0.799875793911741 2 0 0 25190 Y Y 3.66695566812472 3.60632674564779 3.60632674564779 4 0.0231092436974791 0.260394289424132 Y 0.990231092436975 0.990231092436975 N N 0 4201 ENSG00000222132 ENSG00000133119 + + 13 13 33433277 33309642 upstream coding AL160394.19-1 RFC3 33433143 33290206 - + 0 33438223 33307353 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.0103092783505155 0 0.0103092783505155 4 0.692749571512847 0.607048593593732 0.692749571512847 0.607048593593732 1 - - 22541 N Y 3.46145674063593 3.53039946453785 3.46145674063593 221 0.0248407055129745 0.0993681361808931 N 0.674946901837658 0.756210176378243 N N 15774 0 ENSG00000197894 ENSG00000155816 - + 4 1 100240090 238711086 coding intron ADH5 FMN2 100211152 238321604 - + 0.756210176378243 100240081 238400101 + + Y - 1 N HCC1954 2 1.3 1 6 2 N - - N - - 0 0 0 20 0.757025304952183 0.371370904316165 0.757025304952183 0.371370904316165 2 - 0 2798 N N 3.56911164413597 3.67320333000993 3.56911164413597 50 0 0.105684426236560 N 0.72687335257939 0.534078072047194 N N 5225 9 ENSG00000166689 ENSG00000177400 - - 11 8 16992535 12588894 coding upstream PLEKHA7 OR7E8P 16765791 12586149 - - 0.00389105058365746 16992488 12599127 + + Y - - N HCC1954 17 11.7142857142857 10 7 1 N - - N - - 0 0 0 7 0.349945659836387 0.671324327033068 0.671324327033068 0.349945659836387 1 - - 734 Y Y 3.22481738197799 3.34040178417331 3.22481738197799 0 0.00268096514745297 0.107897842618978 Y 0.00268096514745297 0.988403267036598 N N 2195 19270 ENSG00000177030 ENSG00000177106 - - 11 11 685740 717726 coding intron DEAF1 EPS8L2 634225 696113 - + 0 684871 696628 + - N - 0.373273106138616 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.956994253430118 0.835584534711372 0.956994253430118 0.835584534711372 1 - 0 14976 N N 3.22912265260009 3.73080759109069 3.22912265260009 0 0 0.216251650651840 N 0.263802622498275 0 N N 32979 14042 ENSG00000106105 ENSG00000142627 - + 7 1 30640168 16355151 utr5p upstream GARS EPHA2 30600706 16323420 + - 0 30600854 16359881 - - Y - - N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 6 0.378512652476092 0.307095170876829 0.378512652476092 0.307095170876829 1 - - 10267 Y N 3.39065076568547 3.07208400348843 3.07208400348843 12 0 0.461889849074639 Y 0 0.475081081081081 N N 11759 1993 ENSG00000108468 ENSG00000002919 - - 17 17 43533806 43555104 utr5p utr5p CBX1 SNX11 43502414 43539919 - + 0 43533650 43540138 + - N - 0.517683105786877 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.51420586751469 0.442788385915428 0.51420586751469 0.442788385915428 2 - 0 36955 N N 3.76170048280379 3.75744441254485 3.75744441254485 0 0 0.999961191031682 N 0 0.00423728813559332 N N 3 12084 ENSG00000179242 ENSG00000177119 + + 20 12 59945671 44112391 intron intron CDH4 ANO6 59260965 43896170 + + 0.00423728813559332 59576101 44047844 + + Y 0.929733246584255 3.80916331694549 N HCC1954 1 1 1 0 8 N - - N LTR - 0.719512195121951 0 0.719512195121951 5 0.99270299422975 0.564198104634174 0.99270299422975 0.564198104634174 1 0 0 14339 N N 3.40528677690917 3.329991337985 3.329991337985 30 0 0.355252449863688 N 0.225333333333333 0 N N 1696 0 ENSG00000130772 ENSG00000207727 - + 1 11 28535062 64968604 utr3p upstream MED18 hsa-mir-612 28528136 64968505 + + 0.225333333333333 28534356 64964669 - + Y - - N HCC1954 24 22.5 21 4 1 N - - N SINE SINE 1 0.236842105263158 1 4 0.299953422716903 0.542772860154395 0.542772860154395 0.299953422716903 2 - - 3724 N Y 3.53888109983218 3.5690912893859 3.53888109983218 246 0.842747111681643 0.0033088719293336 N 0.816538296961917 0.764120667522464 N N 0 0 ENSG00000198618 ENSG00000174495 + - 21 7 19152671 28285855 intron downstream PPIAL3 AC005017.1 19151924 28285354 + - 0.868955926401369 19152528 28285282 + + Y 1 - N HCC1954 8 3.25 2 12 1 N - - N - - 0 0 0 12 0.364229156156239 0.28566992639705 0.364229156156239 0.28566992639705 1 0 - 6736 Y Y 3.39384326095097 3.4555052531978 3.39384326095097 290 0 0.0298717548704455 Y 0.0124262193227711 0 N N 4164 0 ENSG00000163162 ENSG00000212283 + - 2 2 101291584 101255943 coding upstream RNF149 SNORD89 101258985 101255830 - - 0 101264756 101255992 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.04269523134923 0.742741808632331 1.04269523134923 0.742741808632331 1 - - 25456 N Y 3.57800808738356 3.51104337473878 3.51104337473878 0 0 0.424935235191897 N 0 0 N N 17943 17 ENSG00000105141 ENSG00000132938 + + 19 13 15027900 28978083 downstream intron CASP14 KIAA0774 15024015 28496748 + + 0 15029502 28884855 + + Y - 0.843460900401652 N HCC1954 20 7.56410256410256 1 38 1 N - - N SINE SINE 0.12781954887218 1 1 39 0.949852505270192 0.307095170876829 0.949852505270192 0.307095170876829 3 - 0 31439 Y N 3.35719722089263 3.18359374966329 3.18359374966329 0 0 0.215821235979685 Y 0 0 N N 0 45 ENSG00000208337 ENSG00000114279 + - 3 3 193734595 193609532 downstream intron AC026671.18 FGF12 193734493 193342424 - - 0 193715204 193561172 - + N - 2.31338429506026 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.707033067832699 0.614190341753658 0.707033067832699 0.614190341753658 3 - 0 49125 Y Y 3.44508545943967 3.72874145155091 3.44508545943967 0 0 0.234779048987953 Y 0 0 N N 0 0 ENSG00000209151 ENSG00000201910 + + 5 5 103624426 103462638 downstream downstream AC016566.6-1 U1 103624131 103462474 - + 0 103622306 103467886 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE LINE,LTR 1 0.683760683760684 1 4 0.549914608314322 0.564198104634174 0.564198104634174 0.549914608314322 1 - - 2524 N Y 3.26824964015148 3.50000108636471 3.26824964015148 14 0 0.479577380191603 N 0.990855092919313 0.935985650435192 N N 8014 2 ENSG00000149084 ENSG00000139304 - - 11 12 43834736 79591175 utr3p upstream HSD17B12 PTPRQ 43658719 79587022 + + 0 43834016 79560549 - - Y - - N HCC1954 46 21.75 1 3 1 N - - N - SINE 0 0.858267716535433 0.858267716535433 4 0.785592297591888 0.614190341753658 0.785592297591888 0.614190341753658 2 - - 47869 N Y 3.24165267149066 3.6344911504118 3.24165267149066 0 0 0.070089121213593 N 0 0.598601598173516 N N 3144 4523 ENSG00000171017 ENSG00000068796 + + 19 5 7872906 61718998 intron intron LRRC8E KIF2A 7859390 61637746 + + 0 7859604 61696440 + + Y 0.640336470312899 1.389949672205 N HCC1954 21 17.25 8 4 1 N 66 26.014 N - SINE 0 1 1 4 0.414221393275723 0.307095170876829 0.414221393275723 0.307095170876829 1 0 0 38932 N N 3.02548217798839 3.5319270478477 3.02548217798839 0 0 0.529844707335287 N 0 0 N N 16724 1007 ENSG00000122565 ENSG00000128891 - + 7 15 26219501 38644544 utr5p coding CBX3 C15orf57 26207624 38632592 + - 0 26207911 38642266 - - Y - - N HCC1954 1 1 1 0 1 N 388 0.271984 N - - 0 0 0 11 0.999844742389676 1.1141127129485 1.1141127129485 0.999844742389676 1 - - 34729 N Y 3.44785379918211 3.54975555433691 3.44785379918211 6 0 0.647329863074524 Y 0.0311076020753441 0 N Y 12832 7086 ENSG00000181090 ENSG00000197070 - + 9 9 139850397 139629630 coding coding EHMT1 ARRDC1 139711440 139619917 + + 0 139725240 139629273 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.728458312312478 0.907002016310634 0.907002016310634 0.728458312312478 4 - - 40209 N Y 3.59681204058356 3.61360747730288 3.59681204058356 1 0 0.415351668515821 N 0.884514435695538 0.927821522309711 N N 3790 27074 ENSG00000124120 ENSG00000137804 - - 20 15 42556631 39460535 utr3p coding TTPAL NUSAP1 42537958 39412361 + + 0 42553009 39445077 - - Y - - N HCC1954 29 25 21 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.328520415356608 0.328520415356608 0.278528178237124 1 - - 16533 N N 3.30960217841605 3.27209090245715 3.27209090245715 0 0 0.231515962536837 N 0 0 N N 0 317991 ENSG00000212679 ENSG00000171346 - - 1 17 559619 36932191 intron utr5p RP5-857K21.10 KRT15 558939 36923523 + - 0 559279 36928613 - + Y 1 29.4391540783278 N HCC1954 2 2 2 4 2 N - - N - Simple_repeat 0 0.335365853658537 0.335365853658537 4 0.949852505270192 0.849868031031224 0.949852505270192 0.849868031031224 1 0 0 44851 Y Y 3.53824925764641 3.44296588673741 3.44296588673741 269 0 0.0366609158229723 Y 0 0 N N 4783 0 ENSG00000019995 ENSG00000217116 - + 10 10 126665995 126546885 utr5p downstream ZRANB1 RP11-464O2.5 126620682 126546069 + + 0 126621016 126573572 - + N 0.0150701140514321 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 4 0.5713398527941 0.578481600954027 0.578481600954027 0.5713398527941 4 0 - 47962 N N 3.2003798388128 3.56232542602083 3.2003798388128 7 0 0.962771308988284 N 0.13155818540434 0 N N 3661 551733 ENSG00000170873 ENSG00000204628 + - 8 5 125809911 180603512 upstream upstream MTSS1 GNB2L1 125632212 180596536 - - 0 125930698 180606992 - + Y - - N HCC1954 1 1 1 0 2 N 590 3.33799 N - - 0 0 0 6 0.499922371194838 1.14982145374813 1.14982145374813 0.499922371194838 4 - - 25380 N Y 3.58424216889964 3.37448717115191 3.37448717115191 4 0.0140536901455862 0.828830891141741 N 0.0140536901455862 0.853572330219642 N N 7662 4 ENSG00000139496 ENSG00000181552 - - 13 14 24814561 20308947 utr3p upstream NUPL1 FAM12B 24773666 20306426 + + 0 24812931 20301961 - - Y - - N HCC1954 32 31.2 30 5 1 N - - N SINE LTR 1 1 1 5 0.278528178237124 0.635615586233437 0.635615586233437 0.278528178237124 4 - - 3379 N N 3.35832357661836 3.684245618384 3.35832357661836 10 0 0.785131540244176 Y 0.229919053549191 0.0185242839352429 N Y 14800 109 ENSG00000142207 ENSG00000187172 + - 21 21 32687206 10120608 coding intron URB1 BAGE2 32605200 10042713 - - 0.0185242839352429 32666687 10080194 - + N - 6.3265306122449 N HCC1954 2 1.57142857142857 1 4 1 Y - - N - - 0 0 0 7 0.978419497909897 0.964136001590045 0.978419497909897 0.964136001590045 4 - 0 10893 N N 2.75042265718288 2.65299816351605 2.65299816351605 0 0 0.096560678009215 N 0 0 N N 2906 64784 ENSG00000079819 ENSG00000170004 + - 6 17 131426017 7756803 downstream intron EPB41L2 CHD3 131202180 7728849 - + 0 131164566 7729449 - - Y - 0.175919311919343 N HCC1954 3 3 3 5 1 N - - N - - 0 0 0 5 0.564198104634174 0.721316564152552 0.721316564152552 0.564198104634174 2 - 0 5359 N Y 3.47911741325579 3.4780843434859 3.4780843434859 0 0 0.0464038266084046 N 0 0 N N 975 7635 ENSG00000198487 ENSG00000151694 + - 6 2 42218335 9613368 coding intron AL512274.9 ADAM17 42183124 9546864 - - 0 42183205 9587442 - + Y - 1.16486998940165 N HCC1954 21 20.5 20 8 1 N - - N - SINE 0 1 1 8 0.435646637755502 0.271386430077198 0.435646637755502 0.271386430077198 1 - 0 43477 N N 3.34993006960666 3.66658494576413 3.34993006960666 6 0 0.75001105430305 N 0 0.463800904977375 N N 153 0 ENSG00000135976 ENSG00000182645 + - 2 10 95884852 118129530 downstream intron AC073995.6-1 C10orf96 95868247 118073930 - + 0 95847233 118125010 - - Y - 1 N HCC1954 18 8.4 5 5 1 N - - N LINE,LINE LINE 1 1 1 5 0.464213630395207 0.299953422716903 0.464213630395207 0.299953422716903 3 - 0 29259 N Y 3.52720696927234 3.21551971114628 3.21551971114628 230 0 0.0165969294921826 Y 0.988286445012788 0.988286445012788 N N 8644 6539 ENSG00000056972 ENSG00000009413 + - 6 6 112034014 111911125 intron upstream TRAF3IP2 REV3L 111986836 111726927 - - 0 112002515 111911559 - + N 0.6917726700321 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.785592297591888 0.678466075192994 0.785592297591888 0.678466075192994 3 0 - 17715 N N 3.61360747730288 3.38296880644625 3.38296880644625 2 0 0.0221583828109315 N 0.560135135135135 0.00675675675675669 N N 49089 47 ENSG00000117450 ENSG00000183780 - + 1 1 45760196 232526872 coding intron PRDX1 SLC35F3 45749295 232107447 - + 0.00675675675675669 45757256 232524506 + + N 3.16366837851847 1.16926786023461 Y HCC1954 21 11.5652173913043 1 22 1 N - - N - SINE 0 1 1 23 0.435646637755502 0.378512652476092 0.435646637755502 0.378512652476092 1 0 0 33133 N Y 3.76273355257368 3.43953999775712 3.43953999775712 308 0 0.0246047541431870 Y 0 0.992930828037211 N N 247001 171855 ENSG00000198786 ENSG00000198886 - + MT MT 14149 12138 coding coding MT-ND5 MT-ND4 12338 10761 + + 0.992930828037211 12492 11002 - + N 0.721575730659704 0.551133939008252 N HCC1954 2 1.25 1 1 2 N - - N - - 0 0 0 4 0.985561246069823 1.01412823870953 1.01412823870953 0.985561246069823 2 0 0 17008 N N 3.7061623612628 3.15885523387956 3.15885523387956 0 0 0.130594851239188 N 0 0 N N 64239 36874 ENSG00000132507 ENSG00000198830 - + 17 1 7156496 26675021 coding utr5p EIF5A HMGN2 7151090 26671533 + + 0 7151156 26671625 - + Y - 1.53893966301419 N HCC1954 12 5.75 3 4 1 N - - N - - 0 0 0 4 0.592765097273879 0.421363141435649 0.592765097273879 0.421363141435649 2 - 0 31513 Y Y 3.51679652308403 3.6763025393196 3.51679652308403 253 0 0.323524370984426 Y 0.986719367588933 0.986719367588933 N N 98 2709 ENSG00000186451 ENSG00000163947 - - 3 3 57084500 57044217 downstream upstream SPATA12 ARHGEF3 57069509 56736489 + - 0 57087614 57044243 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.742741808632331 0.45707188223528 0.742741808632331 0.45707188223528 1 - - 3448 Y Y 3.52936639476796 3.66745018166468 3.52936639476796 364 0 0.0491451922260425 Y 0 0.987534340659341 N N 9282 1755 ENSG00000142197 ENSG00000159231 - + 21 21 36588442 36440728 upstream intron DOPEY2 CBR3 36458703 36429133 + + 0 36450199 36436118 - + N - 0.977126875662321 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.585623349113953 0.34280391167646 0.585623349113953 0.34280391167646 3 - 0 40922 Y Y 3.50268972052044 3.52936639476796 3.50268972052044 261 0 0.209565798065181 Y 0.771520967345074 0.990860838693803 N N 52353 525 ENSG00000088832 ENSG00000125775 + - 20 20 1321753 1257838 downstream intron FKBP1A SDCBP2 1297623 1238619 - - 0 1279005 1254174 - + N - 1.57072633895818 N HCC1954 9 2.2 1 4 3 N - - Y SINE - 1 0 1 20 0.864151527351077 0.849868031031224 0.864151527351077 0.849868031031224 1 - 0 16923 N N 3.28183900123616 3.051253763542 3.051253763542 4 0 0.114361235542699 N 0 0.0187793427230046 N N 68946 443941 ENSG00000143549 ENSG00000172057 - + 1 17 152431233 35337380 coding utr3p TPM3 ORMDL3 152394404 35330822 - - 0.0187793427230046 152422178 35331416 + - Y - 2.02100576418071 N HCC1954 5 3 2 4 1 N - - N - - 0 0 0 4 0.835584534711372 0.521347615674617 0.835584534711372 0.521347615674617 2 - 0 47008 Y Y 3.45041445226185 3.31229081257178 3.31229081257178 315 0 0.475260288795285 Y 0.578266178266178 0.987220187220187 N N 1423 1848 ENSG00000083842 ENSG00000198131 - + 19 19 63499066 63466822 upstream downstream ZNF8 ZNF544 63482130 63431882 + + 0 63481701 63470203 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LINE 0 0.855345911949686 0.855345911949686 7 0.821301038391519 0.864151527351077 0.864151527351077 0.821301038391519 4 - - 44884 Y N 3.48337348351473 3.60000453584907 3.48337348351473 0 0 0.068271851514695 Y 0.130014074595355 0.0895496129486276 N N 2035 0 ENSG00000107938 ENSG00000175018 - - 10 10 127442702 127361665 upstream upstream C10orf137 C10orf122 127398074 127334459 + - 0.0895496129486276 127385656 127379074 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.564198104634174 0.51420586751469 0.564198104634174 0.51420586751469 1 - - 40493 N N 3.41489476792923 3.2059651532887 3.2059651532887 0 0 0.124333967308330 N 0 0.245667793744717 N N 49140 150941 ENSG00000115268 ENSG00000182718 + - 19 15 1391492 58477477 coding upstream RPS15P5 ANXA2 1389363 58426625 + - 0.245667793744717 1391421 58477616 + + Y - - N HCC1954 10 6 4 4 1 N - - N - - 0 0 0 4 0.442788385915428 0.307095170876829 0.442788385915428 0.307095170876829 2 - - 1911 N Y 3.52105259334297 3.48912663185998 3.48912663185998 0 0 0.101168280755977 N 0.817907361455749 0.817907361455749 N N 14402 76 ENSG00000156689 ENSG00000166676 - + 11 16 58368833 10820122 utr5p utr3p GLYATL2 FAM18A 58358118 10768034 - - 0 58368484 10769822 + - Y - - N HCC1954 40 37.25 35 8 1 N - - N - SINE 0 1 1 8 0.699891319672773 0.314236919036755 0.699891319672773 0.314236919036755 1 - - 5753 N N 3.64706102209572 3.12755176701253 3.12755176701253 25 0 0.0540033889283439 N 0 0 N N 1992 2911 ENSG00000003436 ENSG00000163608 - - 2 3 188127464 114221245 upstream upstream TFPI C3orf17 188037202 114203981 - - 0 188127494 114249002 + + Y - - N HCC1954 21 15.1666666666667 1 5 1 N - - N - Other 0 1 1 6 0.5713398527941 0.39993789695587 0.5713398527941 0.39993789695587 2 - - 30071 N N 3.63552422018169 3.5246463161926 3.5246463161926 0 0.0285254198297676 0.0494629823146213 N 0.0285254198297676 0.0285254198297676 N N 568998 0 ENSG00000156508 ENSG00000216897 + + 6 7 74288344 20589354 coding intron EEF1A1 AC007095.2 74282194 20588220 - + 0.0285254198297676 74284940 20588883 - + Y - 1 N HCC1954 10 7.8 6 5 1 N - - N - - 0 0 0 5 0.364229156156239 0.22853594111764 0.364229156156239 0.22853594111764 0 - 0 40184 Y Y 3.57592836747465 3.35872480420248 3.35872480420248 13 0.00289855072463774 0.287938879235049 Y 0.0405250205086137 0 N N 3182 381 ENSG00000140326 ENSG00000159433 + + 15 15 40816709 40800348 coding utr3p CDAN1 STARD9 40803054 40766990 - + 0 40804063 40800041 - + N - 0.932508147037737 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.849868031031224 0.985561246069823 0.985561246069823 0.849868031031224 2 - 0 49195 Y Y 3.68680627146374 3.5587317031712 3.5587317031712 48 0.154067441417413 0.260947116758408 N 0.979367498571156 0.951857496666032 Y N 1458 100 ENSG00000188818 ENSG00000206077 - + 5 5 904101 809253 coding downstream ZDHHC11 AC026740.6-1 848722 786905 - - 0 867909 785076 + - N - - N HCC1954 2 1.39393939393939 1 13 1 N 608 18.9697 N - LINE 0 0.582781456953642 0.582781456953642 33 1.3069399132665 0.978419497909897 1.3069399132665 0.978419497909897 1 - - 36654 Y Y 3.51104337473878 3.62767442707312 3.51104337473878 0 0 0.334675143963839 Y 0 0.962735123624749 N N 408 35616 ENSG00000134285 ENSG00000134287 - + 12 12 47605555 47637577 coding coding FKBP11 ARF3 47602019 47616259 - - 0 47605152 47619156 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 8 1.27123117246687 1.13553795742827 1.27123117246687 1.13553795742827 3 - - 37460 N Y 3.23999710710482 3.24471718568018 3.23999710710482 0 0.257054324894515 0.145511592584793 N 0.987407700421941 0.987407700421941 N N 7734 3528 ENSG00000129493 ENSG00000163093 - + 14 2 30959490 170071410 utr5p utr3p HEATR5A BBS5 30832103 170044239 - + 0 30959429 170069759 + + Y - 0.0778970786587006 N HCC1954 2 1.75 1 3 1 N 357 22.3823 N - Other 0 0.072463768115942 0.072463768115942 4 0.764167053112109 0.492780623034912 0.764167053112109 0.492780623034912 2 - 0 44444 N N 3.12804628055249 3.44143830342756 3.12804628055249 0 0 0.115759389354839 N 0 0 N N 0 4805 ENSG00000149617 ENSG00000156110 + + 20 10 51925503 76139066 downstream intron AC005220.1 ADK 51925198 75580971 - + 0 51897834 75773468 - + Y - 1.04498775162732 N HCC1954 20 20 20 7 1 N - - N SINE SINE 0.564516129032258 1 1 7 0.442788385915428 0.314236919036755 0.442788385915428 0.314236919036755 3 - 0 22925 N N 3.44296588673741 3.60781447616429 3.44296588673741 3 0 0.788881991310972 N 0.00423728813559321 0 N N 1480 14045 ENSG00000053900 ENSG00000117859 - + 4 1 25029217 52026729 downstream coding ANAPC4 OSBPL9 24987946 51815439 + + 0 25058240 51890301 - + Y - - N HCC1954 20 13.25 2 4 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.521347615674617 0.521347615674617 0.271386430077198 3 - - 32508 N Y 3.42680229220385 3.69255941980899 3.42680229220385 243 0.684231657131386 0.0127818096920116 N 0.708521529659741 0.708521529659741 N N 0 7129 ENSG00000201398 ENSG00000169299 + + 3 4 155207981 37540953 upstream upstream U8 PGM2 155207846 37504737 - + 0.805681019773161 155224425 37499488 - + Y - - N HCC1954 42 42 42 17 1 N 372 18.3286 N - - 0 0 0 17 0.271386430077198 0.357087407996313 0.357087407996313 0.271386430077198 1 - - 16078 N N 3.04959819915616 3.16576524317408 3.04959819915616 0 0 0.051925515790818 N 0 0 N N 53009 440 ENSG00000131236 ENSG00000135931 + + 1 2 40310908 231944490 utr3p intron CAP1 ARMC9 40278492 231771586 + + 0 40310490 231875603 + + Y - 3.00220127438947 N HCC1954 20 8.83333333333333 1 5 1 N - - N - DNA 0 1 1 6 0.678466075192994 0.378512652476092 0.678466075192994 0.378512652476092 1 - 0 10449 Y N 3.38552945952599 3.41423242051993 3.38552945952599 0 0.136666666666666 0.0843091673426257 Y 0.136666666666666 0.136666666666666 N N 37999 256 ENSG00000007202 ENSG00000167524 + - 17 17 23996300 23965338 utr3p coding KIAA0100 AC005726.6 23965586 23959109 - - 0.136666666666666 23966189 23964747 - + N - 2.66584243603689 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.742741808632331 0.707033067832699 0.742741808632331 0.707033067832699 1 - 0 31087 N N 3.59524460448036 3.2044774227722 3.2044774227722 0 0.219004975124378 0.0314814244484616 N 0.169154228855721 0 N N 5906 41507 ENSG00000169083 ENSG00000188846 - + X 3 66860844 40478862 utr5p coding AR RPL14 66680599 40473834 + + 0.219004975124378 66681690 40478437 - + Y - - N HCC1954 72 30.8 4 10 1 N - - N Simple_repeat - 0.906666666666667 0 0.906666666666667 10 0.535631111994469 0.707033067832699 0.707033067832699 0.535631111994469 1 - - 151 Y Y 3.59528445727371 3.66592259835483 3.59528445727371 298 0 0.0100083878853136 Y 0.99155386190422 0.99155386190422 N N 2208 0 ENSG00000173914 ENSG00000213411 + + 11 11 66201851 66186733 intron upstream RBM4B AP001157.4-1 66189048 66186447 - + 0 66189904 66181307 - + N 0.699848265632176 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 7 1.0069864905496 0.742741808632331 1.0069864905496 0.742741808632331 1 0 - 26145 N Y 3.57229479183167 3.12804628055249 3.12804628055249 0 0 0.242832051060414 N 0 0.886054421768707 N N 0 1649619 ENSG00000184543 ENSG00000141736 + - 16 17 72532924 35138441 downstream intron AC092128.3 ERBB2 72532592 35104766 - + 0 72223964 35125062 - - Y - 0.991162890469566 N HCC1954 22 21.7 21 10 1 N 427 24.0855 N SINE - 1 0 1 10 0.328520415356608 0.385654400636018 0.385654400636018 0.328520415356608 2 - 0 24715 N Y 3.06782793322949 3.45612774781375 3.06782793322949 265 0 0.284626346159291 Y 0.3677793904209 0.980841799709724 N N 0 13271 ENSG00000141650 ENSG00000081923 - - 18 18 53657194 53550037 upstream upstream AC022724.8-1 ATP8B1 53656706 53464656 + - 0 53621228 53550062 - + N - - N HCC1954 1 1 1 0 2 N - - N Low_complexity - 0.425287356321839 0 0.425287356321839 30 0.621332089913584 0.771308801272036 0.771308801272036 0.621332089913584 4 - - 38574 Y Y 3.66488952858494 3.15103594599453 3.15103594599453 149 0.0945896209054103 0.0951334891799088 Y 0.0945896209054103 0 N N 2538 46 ENSG00000100931 ENSG00000139908 + + 14 14 23753025 23747292 coding upstream CHMP4A TSSK4 23748627 23744802 - + 0 23749397 23742176 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR,LINE 0 0.961904761904762 0.961904761904762 4 0.978419497909897 0.699891319672773 0.978419497909897 0.699891319672773 1 - - 20683 N N 3.46547461900863 3.38912318237562 3.38912318237562 0 0 0.703791120144177 N 0 0 N N 0 0 ENSG00000219959 ENSG00000217946 + + 1 X 192426095 97532574 intron intron EEF1AL12 RP11-390F10.1 192424720 97531164 + + 0 192425603 97532107 + + Y 1 1 N HCC1954 10 8.03571428571429 2 28 1 N 110 26.7639 N - - 0 0 0 28 0.364229156156239 0.278528178237124 0.364229156156239 0.278528178237124 3 0 0 4562 N Y 3.22912265260009 3.38296880644625 3.22912265260009 0 0 0.688884223282598 Y 0 0.954676447471836 N N 497 887 ENSG00000135205 ENSG00000123965 - + 7 7 76762457 73960105 utr5p coding CCDC146 PMS2L5 76589870 73944358 + + 0 76634911 73955028 - + N 0.0761152372392261 - N HCC1954 28 14 2 4 1 Y - - N - LTR 0 1 1 4 0.735600060472404 0.849868031031224 0.849868031031224 0.735600060472404 4 0 - 44085 N Y 3.49847350305486 3.63296356710195 3.49847350305486 0 0.741097046413502 0.0625432622131665 N 0.761012658227848 0.770970464135021 N N 0 249 ENSG00000122145 ENSG00000150076 - + X 10 79173924 33211797 upstream intron TBX22 C10orf68 79156911 32896657 + + 0.770970464135021 79127717 33113488 - + Y - 13.7178929359707 N HCC1954 25 21.25 20 4 1 N - - N LINE LINE 1 1 1 4 0.39993789695587 0.257102933757345 0.39993789695587 0.257102933757345 0 - 0 7831 N N 3.28288565137518 3.25679254382414 3.25679254382414 91 0 0.0269543358756106 N 0 0 N N 122511 0 ENSG00000187514 ENSG00000100118 - + 2 22 232286495 25287054 coding intron PTMA HMGB1L10 232280638 25286492 + + 0.00227790432801811 232283248 25287027 - + Y - 1 N HCC1954 44 21.8333333333333 4 6 1 N - - N Low_complexity LINE 0.261780104712042 0.635071090047393 0.635071090047393 6 1.05697872766909 1.04269523134923 1.05697872766909 1.04269523134923 2 - 0 287 Y Y 3.59321831773393 3.51529944499772 3.51529944499772 382 0 0.00734207661707331 N 0 0.994428032408085 Y N 1788 346 ENSG00000184937 ENSG00000183242 + + 11 11 32413663 32419526 upstream utr5p WT1 WIT1 32365897 32413701 - + 0 32430142 32413967 - + N - 0.93880781496644 N HCC1954 1 1 1 0 1 N - - N LTR,LINE - 0.74468085106383 0 0.74468085106383 5 0.928427260790413 0.885576771830856 0.928427260790413 0.885576771830856 1 - 0 26588 N Y 2.75018741738008 3.40698219408837 2.75018741738008 329 0 0.0774798700165124 Y 0.817862988075754 0.980827682955343 N N 6566 27302 ENSG00000167513 ENSG00000103335 - - 16 16 87403166 87330317 upstream upstream CDT1 FAM38A 87397687 87302916 + - 0 87378810 87343388 - + N - - N HCC1954 1 1 1 0 2 N - - N Low_complexity,Low_complexity - 0.173684210526316 0 0.173684210526316 148 1.24980592798709 0.871293275511003 1.24980592798709 0.871293275511003 4 - - 29040 N N 3.37655331069169 3.32895826821511 3.32895826821511 0 0 0.280534331357355 N 0 0 N N 975 7904 ENSG00000198487 ENSG00000104763 + + 6 8 42218335 17986787 intron upstream AL512274.9 ASAH1 42183124 17958214 - - 0 42204322 17991808 - - Y 0.755947860259476 - N HCC1954 20 20 20 6 2 N - - N - SINE,SINE 0 1 1 6 0.607048593593732 0.271386430077198 0.607048593593732 0.271386430077198 2 0 - 8624 N Y 3.09872082494259 3.6491271616355 3.09872082494259 97 0 0.225118069067569 N 0.960179372197309 0 N N 6576 460 ENSG00000106635 ENSG00000167889 - + 7 17 72609960 72458060 coding intron BCL7B MGAT5B 72588622 72376133 - + 0 72609753 72398783 + + Y - 0.549111642677122 N HCC1954 21 20.1666666666667 20 6 1 N - - N - SINE 0 1 1 6 0.557056356474248 0.421363141435649 0.557056356474248 0.421363141435649 3 - 0 45472 N N 3.64127736852694 3.5010341561346 3.5010341561346 0 0 0.120050226208608 N 0 0 N N 343 40617 ENSG00000178729 ENSG00000130164 - + 6 19 48144384 11105490 utr3p utr3p C6orf138 LDLR 47953998 11061132 - + 0 47976616 11104135 + + Y - - N HCC1954 40 39.2 39 5 1 N 38 23.1358 N SINE SINE 1 0.0895522388059701 1 5 0.278528178237124 0.478497126715059 0.478497126715059 0.278528178237124 3 - - 36820 Y Y 3.58640159439526 3.74081680969488 3.58640159439526 268 0 0.0626859224128872 Y 0 0.989512961508248 N N 35616 9 ENSG00000134287 ENSG00000139537 + + 12 12 47637577 47611527 coding intron ARF3 CCDC65 47616259 47584187 - + 0 47619708 47611381 - + N - 1.39339675433688 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 1.14982145374813 0.899860268150708 1.14982145374813 0.899860268150708 1 - 0 45904 N N 3.57800808738356 3.22423474015539 3.22423474015539 0 0 0.401964047155650 N 0 0 N N 17943 6778 ENSG00000105141 ENSG00000106571 + - 19 7 15027900 42243137 downstream intron CASP14 GLI3 15024015 41967072 + - 0.00375939849624063 15029502 42113268 + + Y - 0.822529037067891 N HCC1954 20 16 2 9 1 N - - N - SINE 0 1 1 9 0.771308801272036 0.292811674556976 0.771308801272036 0.292811674556976 3 - 0 24280 N N 3.52105277889958 3.47705127371601 3.47705127371601 0 0.354221478115283 0.0294437650376495 N 0.300406601291557 0.354221478115283 N N 11413 1869 ENSG00000112877 ENSG00000173614 - + 5 1 706664 9968143 coding utr3p CEP72 NMNAT1 665405 9926073 + + 0.354221478115283 672182 9964153 - + Y 0.868134916414089 - N HCC1954 34 25.6363636363636 21 11 1 N - - N - SINE 0 1 1 11 0.842726282871298 0.649899082553289 0.842726282871298 0.649899082553289 1 0 - 515 Y Y 2.88466990414258 3.61356762450953 2.88466990414258 0 0 0.985087730948836 Y 0.936957215836526 0.994268837803321 N N 1594 103869 ENSG00000188082 ENSG00000117984 - + 11 11 1728397 1741798 utr5p coding AC068580.3 CTSD 1710216 1730561 - - 0 1726821 1731340 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 67 1.28551466878673 1.37835739486577 1.37835739486577 1.28551466878673 1 - - 24737 Y Y 3.61936062564813 3.52567938596249 3.52567938596249 0 0 0.99001625962639 Y 0.20558424172882 0.976286096768024 N N 0 962 ENSG00000206944 ENSG00000184828 + - 18 18 43950259 43821492 upstream utr5p U6 ZBTB7C 43950153 43807746 - - 0 43966303 43821492 - + N - 20.3518617021277 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 8 0.478497126715059 1.02841173502938 1.02841173502938 0.478497126715059 4 - 0 18086 N N 3.54552998930151 3.21547985835293 3.21547985835293 0 0 0.300708550762442 Y 0.0843538851351351 0.146431587837838 N N 0 9 ENSG00000217689 ENSG00000090104 - + 1 1 190952401 190815782 downstream upstream RP11-92K2.2 RGS1 190951936 190811480 + + 0.146431587837838 190975195 190802970 - + N - - N HCC1954 1 1 1 0 2 N - - N LINE,LTR - 0.833333333333333 0 0.833333333333333 18 0.642757334393363 0.557056356474248 0.642757334393363 0.557056356474248 2 - - 7199 Y Y 3.3755202409218 3.39487633072086 3.3755202409218 138 0 0.0439336006684018 Y 0.0734299516908212 0.917270531400966 N N 30 0 ENSG00000152154 ENSG00000211215 - - 2 2 39798605 39569088 upstream upstream TMEM178 AC007388.4 39746563 39568835 + - 0 39669103 39628833 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 5 0.614190341753658 0.521347615674617 0.614190341753658 0.521347615674617 1 - - 33845 N Y 3.1767676787548 3.57592836747465 3.1767676787548 533 0 0.00085039892013783 Y 0 0.996085788912188 N N 59837 339915 ENSG00000198695 ENSG00000198727 - - MT MT 14674 15882 coding coding MT-ND6 MT-CYB 14150 14748 - + 0.996085788912188 14441 15478 + - N - 1.0851396577011 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.585623349113953 0.857009779191151 0.857009779191151 0.585623349113953 2 - 0 40866 N N 3.36464578641707 3.25153390901886 3.25153390901886 0 0 0.0235891326804517 N 0.483453034783833 0.102192179505234 N N 20796 0 ENSG00000124209 ENSG00000219468 - + 20 9 56375966 140250262 utr3p upstream RAB22A RP11-885N19.5 56318177 140249980 + + 0.102192179505234 56374180 140231632 - + Y - - N HCC1954 152 143.2 132 10 1 N - - N SINE - 1 0 1 10 0.349945659836387 0.542772860154395 0.542772860154395 0.349945659836387 0 - - 2545 N N 3.6533527266709 3.48487056160104 3.48487056160104 3 0 0.060380246639182 N 0 0 N N 12635 0 ENSG00000109919 ENSG00000209671 - - 11 12 47620640 30350725 coding downstream MTCH2 AC078776.12 47595444 30350635 - - 0 47620515 30307201 + + Y - - N HCC1954 3 1.4 1 1 1 N - - N - LTR 0 1 1 5 0.385654400636018 0.335662163516534 0.385654400636018 0.335662163516534 1 - - 24675 Y Y 3.56911164413597 3.40422320191574 3.40422320191574 346 0 0.0366019066198247 Y 0.975680248131961 0.99392006203299 N N 12709 2050 ENSG00000141458 ENSG00000141452 + + 18 18 19420468 19365744 coding intron NPC1 C18orf8 19365463 19337460 - + 0 19366246 19356867 - + N - 1.12150491231806 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 17 1.22123893534739 1.34264865406614 1.34264865406614 1.22123893534739 2 - 0 27450 Y Y 3.67423639977982 3.41782614336956 3.41782614336956 0 0 0.243195576750064 Y 0.993125411816385 0.993125411816385 N N 4397 10288 ENSG00000125124 ENSG00000087263 + + 16 16 55111696 55068908 utr3p coding BBS2 OGFOD1 55075801 55042925 - + 0 55076176 55062029 - + N - 1.08419690114714 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.864151527351077 1.03555348318931 1.03555348318931 0.864151527351077 1 - 0 33071 N N 3.30232144676095 3.39483647792751 3.30232144676095 7 0.0181007175641604 0.1620190541867 N 0.0181007175641604 0 Y N 247001 0 ENSG00000198786 ENSG00000210194 - - MT MT 14149 14743 coding intron MT-ND5 AF347015.1-22 12338 14675 + - 0 12428 14717 - + N 0.895896249670896 1 N HCC1954 4 1.52173913043478 1 7 1 N 189 4.09957 N - - 0 0 0 23 1.12839620926835 1.4140661356654 1.4140661356654 1.12839620926835 3 0 0 39602 N N 3.68208619288838 3.62039369541802 3.62039369541802 10 0.00303951367781163 0.179777007918564 N 0 0.74342928660826 N N 1 4109 ENSG00000137872 ENSG00000112406 + + 15 6 45853709 139543639 downstream utr3p SEMA6D HECA 45797978 139497942 + + 0.17164312533524 45985752 139541535 + + Y - 1.74176068470226 N HCC1954 11 3.5 1 1 1 N - - N SINE SINE 1 0.367647058823529 1 4 0.257102933757345 0.485638874874985 0.485638874874985 0.257102933757345 2 - 0 3838 N N 3.57592836747465 3.59425138750382 3.57592836747465 0 0 0.094400563262087 N 0 0.00309597523219807 N N 850768 13100 ENSG00000075624 ENSG00000169398 - + 7 8 5536758 142080514 utr3p coding ACTB PTK2 5533313 141737683 - - 0.00309597523219807 5533709 141958764 + - Y - 1.23599964962024 N HCC1954 18 10.75 5 4 1 N - - N - Simple_repeat 0 0.655172413793103 0.655172413793103 4 0.749883556792257 0.414221393275723 0.749883556792257 0.414221393275723 2 - 0 31201 Y Y 3.37188666527882 3.3241983368464 3.3241983368464 206 0 0.033355127824539 Y 0.893377253814147 0.988153028201572 N N 0 8002 ENSG00000210957 ENSG00000172340 + - 3 3 67967650 67787728 downstream upstream AC113171.3 SUCLG2 67967527 67507835 - - 0 67879894 67803019 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LTR 0 0.383720930232558 0.383720930232558 4 0.828442786551446 0.614190341753658 0.828442786551446 0.614190341753658 1 - - 38722 N N 3.45872825368684 3.4780843434859 3.45872825368684 0 0 0.0665466351725479 N 0 0 N N 32369 2128 ENSG00000163682 ENSG00000129480 + + 4 14 39136939 30996431 intron upstream RPL9 C14orf126 39132154 30984996 - - 0 39134275 31001853 - - Y 0.629990005848997 - N HCC1954 8 5 4 9 1 N - - N - - 0 0 0 9 0.428504889595575 0.307095170876829 0.428504889595575 0.307095170876829 1 0 - 26584 N Y 3.45447218342791 3.55703628599201 3.45447218342791 349 0 0.00432045777494305 Y 0 0.987050199084583 N N 23840 6229 ENSG00000102898 ENSG00000102901 - - 16 16 66462727 66425300 intron upstream NUTF2 CENPT 66438331 66419565 + - 0 66439051 66426841 - + N 1.0809318228776 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 56 1.04269523134923 1.01412823870953 1.04269523134923 1.01412823870953 1 0 - 38494 Y Y 3.61104682422314 3.21439335542055 3.21439335542055 1 0 0.654117048041642 Y 0.989052931801023 0.989052931801023 N N 372 12363 ENSG00000213920 ENSG00000129559 - + 14 14 23755081 23771412 coding coding AL136295.3 NEDD8 23753002 23755897 - - 0 23754965 23756233 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 5 0.642757334393363 0.928427260790413 0.928427260790413 0.642757334393363 2 - - 16257 N Y 3.54872248456702 3.33528047801382 3.33528047801382 0 0 0.552093289876567 N 0.81514397440455 0.774064857605561 N N 6191 1391 ENSG00000169905 ENSG00000064933 - + 1 2 178113557 190450599 utr5p utr3p TOR1AIP2 PMS1 178080577 190357355 - + 0 178088569 190379511 + + Y - - N HCC1954 21 20.8235294117647 20 17 1 N - - N - SINE 0 1 1 17 0.549914608314322 0.34280391167646 0.549914608314322 0.34280391167646 4 - - 23266 N N 3.27039548527796 3.4048456965317 3.27039548527796 1 0 0.108354100002112 N 0.0737373737373737 0 N N 34438 3891 ENSG00000127481 ENSG00000166295 - + 1 10 19409333 73665622 utr3p utr5p UBR4 C10orf104 19273587 73645812 - + 0 19310915 73645843 + + Y - 1.00743724211426 N HCC1954 34 25.8604651162791 2 86 1 N - - N SINE - 1 0 1 86 0.51420586751469 0.842726282871298 0.842726282871298 0.51420586751469 3 - 0 25913 N N 3.54975555433691 3.25935319690388 3.25935319690388 0 0 0.039280057105167 N 0.126556331612511 0.0862435469177041 N N 5 45068 ENSG00000144152 ENSG00000205336 + + 2 16 112662262 56256445 intron upstream FBLN7 GPR56 112612433 56220023 + + 0.0862435469177041 112631358 56211247 + + Y 1.03793522193827 - N HCC1954 21 20.0833333333333 20 12 1 N - - N SINE - 1 0 1 12 0.314236919036755 0.414221393275723 0.414221393275723 0.314236919036755 1 0 - 30417 N Y 3.38809011260573 3.61464054707278 3.38809011260573 248 0 0.0704814088811954 Y 0 0.991559595407326 N N 0 2547 ENSG00000220300 ENSG00000184205 + + X X 53189820 53134446 downstream downstream RP11-258C19.3 TSPYL2 53188739 53128274 - + 0 53187758 53145518 - + N - - N HCC1954 5 4 1 6 1 N - - N - DNA 0 1 1 7 0.956994253430118 0.692749571512847 0.956994253430118 0.692749571512847 1 - - 7301 Y Y 3.46720988898117 3.74487454086093 3.46720988898117 323 0 0.0426096412758219 Y 0 0 N N 3237 633 ENSG00000003137 ENSG00000135636 + + 2 2 72228471 71767398 downstream downstream CYP26B1 DYSF 72209875 71534268 - + 0 72010293 71936297 - + N - - N HCC1954 1 1 1 0 3 N - - Y - LTR 0 0.25 0.25 4 0.471355378555133 0.51420586751469 0.51420586751469 0.471355378555133 2 - - 9515 N N 3.17415359251257 2.78367323768168 2.78367323768168 0 0 0.0392698217154974 N 0 0 Y N 443941 47 ENSG00000172057 ENSG00000121101 + - 17 17 35337380 54124415 downstream intron ORMDL3 TEX14 35330822 53989041 - - 0 35329707 54024713 - + N - 1.07120865276424 N HCC1954 22 14.25 7 4 1 N - - N SINE SINE 0.787234042553192 1 1 4 0.664182578873142 0.257102933757345 0.664182578873142 0.257102933757345 1 - 0 44699 Y Y 3.45293525254824 3.5701752191294 3.45293525254824 300 0 0.00304471152205965 Y 0.993078703703704 0.993078703703704 N N 408 0 ENSG00000165568 ENSG00000207124 - + 10 10 4880249 4547249 upstream downstream AKR1CL2 U6 4858402 4547144 + + 0 4710242 4691873 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.427631578947368 0 0.427631578947368 8 1.0069864905496 1.04269523134923 1.04269523134923 1.0069864905496 1 - - 36330 Y N 3.23160360009313 3.32895826821511 3.23160360009313 0 0 0.115713592517119 N 0.0024691358024691 0.0410476775117661 Y N 6477 11 ENSG00000151176 ENSG00000135094 - - 12 12 112311584 112326075 downstream downstream PLBD2 SDS 112280761 112314640 + - 0.0410476775117661 112311699 112313361 - + N - - N HCC1954 1 1 1 0 1 N 160 25.5355 N Simple_repeat Simple_repeat 1 0.410891089108911 1 4 0.378512652476092 0.971277749749971 0.971277749749971 0.378512652476092 2 - - 48826 Y Y 3.56761456604966 3.3844963897561 3.3844963897561 330 0 0.0600053107598792 Y 0.993690065209053 0.993690065209053 N N 2506 38037 ENSG00000214302 ENSG00000131446 + - 5 5 180210585 180175147 downstream upstream AC022413.4-2 MGAT1 180208398 180150147 - - 0 180193919 180191548 - + N - - N HCC1954 21 3.52631578947368 1 4 3 N - - Y SINE,LTR,LTR - 0.517241379310345 0 0.517241379310345 19 1.03555348318931 1.22838068350732 1.22838068350732 1.03555348318931 1 - - 25437 N Y 3.69784855983781 2.91397707318275 2.91397707318275 0 0.094246031746032 0.0286357521164726 N 0.505952380952381 0.505952380952381 N N 0 27 ENSG00000197585 ENSG00000164749 + + 13 8 51726881 76641600 coding upstream AL158066.12-1 HNF4G 51725879 76482732 - + 0.505952380952381 51726809 76388473 - + Y - - N HCC1954 25 24 23 5 1 N - - N LINE LTR 1 1 1 5 0.364229156156239 0.328520415356608 0.364229156156239 0.328520415356608 1 - - 14435 N Y 3.50529022639353 3.2720510496638 3.2720510496638 0 0.0935776201733649 0.0539335835888134 N 0.0724980299448384 0.894602048857368 N N 2101 12566 ENSG00000203847 ENSG00000173039 + - 1 11 142559798 65186959 utr3p upstream PPIAL4G RELA 142555943 65177649 - - 0.0935776201733649 142556843 65187086 - + Y - - N HCC1954 35 33.1666666666667 26 12 1 N - - N SINE Low_complexity 1 0.0121951219512195 1 12 0.34280391167646 0.585623349113953 0.585623349113953 0.34280391167646 1 - - 7729 N N 3.31063524818594 3.28702308812794 3.28702308812794 0 0 0.160319837289680 N 0 0.0327801827801828 N N 23693 0 ENSG00000152102 ENSG00000185942 - + 2 8 131567474 64008644 utr5p intron FAM168B NKAIN3 131521919 63324187 - + 0.0327801827801828 131567257 63429950 + + Y - 1 N HCC1954 20 20 20 5 1 N - - N - SINE 0 1 1 5 0.464213630395207 0.264244681917271 0.464213630395207 0.264244681917271 3 - 0 43634 N Y 3.12804628055249 3.52101274054962 3.12804628055249 0 0 0.250971536276985 N 0.823245137126978 0.871451008819621 N N 1649619 0 ENSG00000141736 ENSG00000216660 - - 17 10 35138441 46198900 coding intron ERBB2 GLUDP7 35104766 46192800 + + 0 35122227 46198022 - - Y - 1 N HCC1954 22 16.75 1 3 1 N - - N - SINE 0 1 1 4 1.12839620926835 0.364229156156239 1.12839620926835 0.364229156156239 2 - 0 30836 N N 3.64656650855576 3.33101506018507 3.33101506018507 0 0 0.0254068885826524 N 0 0 N N 1974 56 ENSG00000172113 ENSG00000198738 + + 3 6 48317852 86502505 upstream utr3p NME6 C6orf161 48310595 86501644 - - 0 48344790 86501810 - - Y - - N HCC1954 33 30.5 28 10 1 N - - N - SINE 0 1 1 10 0.635615586233437 0.314236919036755 0.635615586233437 0.314236919036755 0 - - 49515 N Y 3.50848272165904 3.36976709257655 3.36976709257655 0 0 0.540276228546318 N 0 0.985238862050456 N N 2667 1400 ENSG00000170085 ENSG00000027847 + + 5 5 175705594 176969929 coding downstream C5orf25 B4GALT7 175597971 176959778 + + 0 175655927 176978998 + + N - - Y HCC1954 2 2 2 5 1 N - - N - - 0 0 0 5 0.649899082553289 0.871293275511003 0.871293275511003 0.649899082553289 2 - - 6525 Y N 3.13210558685828 3.50529022639353 3.13210558685828 0 0 0.0550598748660176 Y 0.12 0.12 N N 919 7889 ENSG00000172878 ENSG00000128708 - + 2 2 172654009 172556845 coding downstream AC015976.3 HAT1 172572736 172487204 + + 0.12 172572945 172564570 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 5 0.792734045751814 0.528489363834543 0.792734045751814 0.528489363834543 1 - - 33030 Y Y 2.75344269337789 3.22804973003685 2.75344269337789 292 0 0.999787900617638 Y 0 0.985344480257856 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.985344480257856 14478 13077 - + N 1.37383625291785 0.838359532284252 N HCC1954 2 1.2 1 1 10 N - - Y - - 0 0 0 5 0.714174815992626 1.01412823870953 1.01412823870953 0.714174815992626 2 0 0 43082 N N 3.52105259334297 3.1750722615756 3.1750722615756 0 0 0.990054984536852 N 0 0.0439669421487603 N N 9848 13 ENSG00000164134 ENSG00000152495 + + 4 5 140531972 110848645 intron intron NARG1 CAMK4 140442126 110587981 + + 0.0439669421487603 140446356 110789313 + + Y 1.36681297140778 1.00411712901805 N HCC1954 11 1.43333333333333 1 4 5 N 370 4.32528 N SINE - 1 0 1 30 0.849868031031224 0.45707188223528 0.849868031031224 0.45707188223528 2 0 0 4427 Y Y 3.60785432895764 3.54296933622177 3.54296933622177 288 0 0.0180411988247707 Y 0 0 N N 0 0 ENSG00000219101 ENSG00000213783 + - 7 7 27335677 27275855 upstream upstream AC004996.1 AC004996.1 27334732 27275497 - - 0 27352857 27303724 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.578481600954027 0.599906845433805 0.599906845433805 0.578481600954027 1 - - 27363 Y Y 3.42680229220385 3.26356941436947 3.26356941436947 347 0.00288184438040329 0.0630686145965134 Y 0.00288184438040329 0 N N 1956 4782 ENSG00000102871 ENSG00000125149 + + 16 16 65751313 65739941 utr3p downstream TRADD C16orf70 65745594 65701416 - + 0 65745864 65742079 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 16 1.34264865406614 1.1426797055882 1.34264865406614 1.1426797055882 1 - - 33141 N Y 3.30335451653084 3.50575423470996 3.30335451653084 555 0.0355754250491092 0.000187929091313377 Y 0.0355754250491092 0.966226376752693 N N 171855 1291380 ENSG00000198886 ENSG00000198804 - + MT MT 12138 7446 coding coding MT-ND4 MT-CO1 10761 5905 + + 0.0393280498543658 11099 6723 - + N 0.670997103293199 0.990329008044393 N HCC1954 2 1.4 1 2 1 Y - - N - - 0 0 0 5 1.12839620926835 0.942710757110266 1.12839620926835 0.942710757110266 3 0 0 17394 N Y 3.17511211436895 3.27145906027139 3.17511211436895 24 0.380630630630631 0.284757234381704 Y 0.851351351351351 0.95045045045045 N Y 25182 16110 ENSG00000116539 ENSG00000163374 - + 1 1 153798948 153925415 utr5p utr5p ASH1L YY1AP1 153571677 153895858 - - 0 153758033 153925074 + - N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.578481600954027 0.28566992639705 0.578481600954027 0.28566992639705 4 - - 30157 N Y 3.35087501109391 3.37655331069169 3.35087501109391 0 0 0.160706448227047 N 0 0.889398572884811 N N 34750 975 ENSG00000197694 ENSG00000198487 - + 9 6 130435762 42218335 intron intron SPTAN1 AL512274.9 130354687 42183124 + - 0 130372570 42204322 - - Y 0.508550922398055 0.755947860259476 N HCC1954 21 16 1 3 1 N 77 21.7442 N SINE - 1 0 1 4 0.271386430077198 0.392796148795944 0.392796148795944 0.271386430077198 2 0 0 32979 N N 3.47911741325579 3.62977107183644 3.47911741325579 13 0 0.999963956625146 N 0 0.0292753159494481 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0292753159494481 8756 13623 - + N 0.560423695130388 1.01791686651533 N HCC1954 6 2.83333333333333 2 6 10 N 189 4.09957 N - - 0 0 0 6 1.0069864905496 1.24980592798709 1.24980592798709 1.0069864905496 2 0 0 42353 Y Y 3.46720988898117 3.28189243439864 3.28189243439864 241 0 0.107464991290433 Y 0 0.989405844442483 N N 3331 439 ENSG00000138785 ENSG00000138784 + + 4 4 106849714 106772285 downstream downstream INTS12 AC105391.1 106823233 106693226 - + 0 106799659 106797305 - + N - - N HCC1954 1 1 1 0 2 N - - Y - DNA 0 0.274509803921569 0.274509803921569 8 0.899860268150708 0.728458312312478 0.899860268150708 0.728458312312478 1 - - 30285 Y Y 3.30017560163446 3.39959640929622 3.30017560163446 213 0 0.046055646706713 Y 0 0 N N 0 0 ENSG00000213468 ENSG00000203953 + + X X 130757838 130608580 downstream downstream AL121572.14 AL109853.4 130757360 130608329 - + 0 130711016 130654340 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 5 0.585623349113953 0.707033067832699 0.707033067832699 0.585623349113953 1 - - 16318 N N 3.21075977977757 3.23686739257161 3.21075977977757 1 0 0.0616286248241846 N 0 0 N N 122511 0 ENSG00000187514 ENSG00000212874 - - 2 1 232286495 558681 coding intron PTMA RP5-857K21.7 232280638 558000 + + 0 232284867 558649 - - Y - 1 N HCC1954 10 6 4 5 1 N 67 23.6937 N Low_complexity - 0.189655172413793 0 0.189655172413793 5 1.10697096478857 0.449930134075354 1.10697096478857 0.449930134075354 1 - 0 41546 Y N 3.00294294049363 3.54036883034868 3.00294294049363 0 0 0.980843728934031 Y 0.223221919146684 0.339738631274681 N N 3297 2237 ENSG00000104613 ENSG00000147408 - - 8 8 19753864 19584374 upstream utr5p INTS10 CSGALNACT1 19719198 19305952 + - 0.339738631274681 19658975 19407919 - + N - 8.39161995734006 N HCC1954 1 1 1 0 5 N - - Y Low_complexity - 0.207100591715976 0 0.207100591715976 16 1.20695543902754 1.13553795742827 1.20695543902754 1.13553795742827 2 - 0 22272 N N 3.45823374014688 3.3755202409218 3.3755202409218 0 0 0.216868686235660 N 0 0 N N 0 27540 ENSG00000216692 ENSG00000070831 + + 20 1 32454163 22292024 intron coding CDC42P1 CDC42 32453616 22235157 - + 0 32453766 22285862 - + Y 1 - N HCC1954 2 1.25 1 1 1 N - - N - - 0 0 0 4 0.257102933757345 0.435646637755502 0.435646637755502 0.257102933757345 2 0 - 35333 N Y 3.18989809546429 3.06415450479316 3.06415450479316 0 0 0.153349821796816 N 0 0 N N 3871 122756 ENSG00000138032 ENSG00000135480 - + 2 12 44325029 50928976 utr3p coding PPM1B KRT7 44249504 50913221 + + 0 44315214 50915394 - + Y - 0.806718945953364 N HCC1954 6 4.8 1 4 1 N - - N SINE - 0.7 0 0.7 5 0.28566992639705 0.492780623034912 0.492780623034912 0.28566992639705 3 - 0 14905 N N 3.25256697878875 3.59574846559013 3.25256697878875 0 0 0.0446678749297547 N 0 0 N N 49089 23 ENSG00000117450 ENSG00000205622 - + 1 21 45760196 39232223 coding upstream PRDX1 AP001042.1 45749295 39171085 - - 0 45757275 39276465 + - Y - - N HCC1954 18 6.25 1 2 1 N - - N - SINE 0 1 1 4 0.485638874874985 0.299953422716903 0.485638874874985 0.299953422716903 1 - - 44344 N Y 3.59425138750382 3.00762316627563 3.00762316627563 0 0 0.0303204127597881 N 0.577322404371585 0.577322404371585 N N 3849 3891 ENSG00000197905 ENSG00000166295 + + 12 10 3020103 73665622 intron intron TEAD4 C10orf104 2938757 73645812 + + 0.577322404371585 2946362 73645904 + + Y 0.453883803625124 0.744979490524871 N HCC1954 32 16.2857142857143 6 7 1 N - - N SINE - 1 0 1 7 0.421363141435649 0.664182578873142 0.664182578873142 0.421363141435649 1 0 0 14098 N Y 3.64231043829683 3.20600500608205 3.20600500608205 12 0 0.160989560386064 N 0 0.245430495430496 N N 3006 18603 ENSG00000100342 ENSG00000099940 + + 22 22 34993523 19574109 utr3p downstream APOL1 SNAP29 34979070 19543292 + + 0 34992730 19575218 + + N - - Y HCC1954 33 31.75 31 8 1 N - - N SINE SINE,SINE 1 0.54 1 8 0.34280391167646 0.357087407996313 0.357087407996313 0.34280391167646 1 - - 9496 Y Y 2.90931513397047 3.1531555186968 2.90931513397047 255 0 0.179369396803386 Y 0 0 N N 676 73 ENSG00000108846 ENSG00000006283 - + 17 17 46124061 46059541 intron downstream ABCC3 CACNA1G 46067227 45993820 + + 0 46071207 46059702 - + N 0.0908664852100871 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 0.792734045751814 0.649899082553289 0.792734045751814 0.649899082553289 3 0 - 19147 Y Y 3.59272380419397 3.707857778442 3.59272380419397 21 0.0450621640697108 0.974435032385762 Y 0.0450621640697108 0.993878603615832 N N 1166 27007 ENSG00000154198 ENSG00000142973 + + 1 1 47138734 47057605 intron coding CYP4Z2P CYP4B1 47096493 47037257 - + 0 47107086 47055437 - + N 0.197481874237702 - N HCC1954 3 1.53846153846154 1 8 4 N - - Y LINE - 1 0 1 26 1.22838068350732 1.39264089118562 1.39264089118562 1.22838068350732 2 0 - 26079 N N 3.44615838200292 3.21808036422602 3.21808036422602 0 0 0.234571887514121 N 0.0060606060606061 0.0060606060606061 N N 8418 45068 ENSG00000074755 ENSG00000205336 + + 17 16 3993002 56256445 intron upstream ZZEF1 GPR56 3854489 56220023 - + 0.0060606060606061 3874328 56211249 - + Y 0.964575783316972 - N HCC1954 21 20.4 20 5 2 N - - N SINE - 1 0 1 5 0.392796148795944 0.899860268150708 0.899860268150708 0.392796148795944 2 0 - 18314 N Y 3.55401162459584 3.04376534522421 3.04376534522421 0 0 0.790067617802609 Y 0.943310014495494 0.967605722568854 N N 3863 2251 ENSG00000219481 ENSG00000186275 - + 1 1 146862781 143541658 upstream upstream NBPF15 NBPF8 146827614 143326471 + + 0.967605722568854 146824793 143305322 - + N - - N HCC1954 42 7.7 1 19 2 N 28 18.9047 N SINE,SINE - 1 0 1 20 0.871293275511003 0.907002016310634 0.907002016310634 0.871293275511003 4 - - 38290 N Y 3.37336081542618 3.52258017665282 3.37336081542618 142 0.0299014778325122 0.370513438250942 Y 0.91055829228243 0.98623973727422 N N 0 1187 ENSG00000214385 ENSG00000215394 + + 14 14 18790591 18754290 downstream utr5p AL589743.4-1 AL589743.4-2 18789543 18720037 - + 0 18788327 18726089 - + N - - N HCC1954 16 13.0666666666667 4 15 2 N - - N - LINE,LINE,LINE,SINE 0 0.411552346570397 0.411552346570397 15 0.985561246069823 1.64260207678304 1.64260207678304 0.985561246069823 3 - - 45822 N Y 3.43142908482337 3.68527868815389 3.43142908482337 0 0 0.167343199555661 N 0.88406495114903 0.899522957662493 N N 1027 12271 ENSG00000189164 ENSG00000177479 - + 19 3 42575806 48997971 utr3p utr5p ZNF527 ARIH2 42553899 48931285 + + 0 42572789 48935245 - + Y - - N HCC1954 36 32 29 5 1 N - - N SINE - 1 0 1 5 0.528489363834543 1.04983697950916 1.04983697950916 0.528489363834543 1 - - 21356 N Y 3.69681549006792 2.74156081238732 2.74156081238732 0 0 0.134067612546789 N 0 0.852652652652653 N N 0 1842 ENSG00000218802 ENSG00000164051 - - 1 3 27848708 48456533 intron upstream CCDC72 CCDC51 27848517 48448174 + - 0 27848671 48456788 - + Y 1 - N HCC1954 1 1 1 0 1 N 544 21.0839 N - - 0 0 0 18 0.392796148795944 1.18553019454776 1.18553019454776 0.392796148795944 2 0 - 35079 N Y 3.54296933622177 2.85592709035528 2.85592709035528 0 0 0.452396966291585 Y 0 0.948873348873349 N N 7291 7291 ENSG00000147996 ENSG00000147996 + - 9 9 169078 169078 utr3p downstream CBWD1 CBWD1 111039 111039 - - 0.993609168609169 111445 110015 - + N - - N HCC1954 42 18.6 4 10 1 Y - - N - - 0 0 0 10 1.2783729206268 0.999844742389676 1.2783729206268 0.999844742389676 2 - - 49345 Y Y 3.6344911504118 3.71976530271662 3.6344911504118 0 0 0.425516838848816 Y 0.55259513288927 0.99155839873376 N N 28384 0 ENSG00000145555 ENSG00000201436 - + 5 5 16936722 16995060 coding downstream MYO10 U6 16715019 16994952 - - 0 16930815 16969163 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.649899082553289 0.678466075192994 0.678466075192994 0.649899082553289 1 - - 38544 Y Y 3.52614339427891 2.73296024785309 2.73296024785309 3 0.00235849056603787 0.119560821207561 Y 0.98879054483782 0.99439527241891 N N 814 86 ENSG00000119640 ENSG00000119703 - - 14 14 74600489 74614551 utr5p upstream ACYP1 FAM164C 74589683 74606052 - + 0 74600410 74605667 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.771308801272036 1.02841173502938 1.02841173502938 0.771308801272036 3 - - 36687 Y Y 3.31270138772572 3.04015804200544 3.04015804200544 0 0 0.172312109197032 Y 0 0.992614507999123 N N 9765 37 ENSG00000139182 ENSG00000139194 - - 12 12 7202793 7172754 utr5p intron CLSTN3 RBP5 7174234 7167557 + - 0 7174439 7172360 - + N - 1.733779405179 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.835584534711372 0.842726282871298 0.842726282871298 0.835584534711372 1 - 0 49006 Y Y 3.60785432895764 3.44512531223303 3.44512531223303 208 0 0.0061491262592871 Y 0 0.987402629016553 N N 0 0 ENSG00000182383 ENSG00000212363 + - 5 5 74322218 74214361 downstream upstream AC116337.2 SNORA40 74321774 74214237 - - 0 74307231 74266876 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 7 0.835584534711372 0.742741808632331 0.835584534711372 0.742741808632331 1 - - 20517 N N 3.32792519844522 3.47382827322697 3.32792519844522 0 0.529226145755072 0.0720278058009751 N 0.674079639368896 0.529226145755072 N N 78560 106 ENSG00000112493 ENSG00000158825 + + 6 1 33390114 20817985 utr3p upstream TAPBP CDA 33375449 20788031 - + 0.529226145755072 33376417 20773457 - + Y 0.850566832247118 - N HCC1954 91 33.6666666666667 6 6 1 N - - N SINE SINE,Low_complexity 1 0.921052631578947 1 6 0.735600060472404 0.271386430077198 0.735600060472404 0.271386430077198 1 0 - 22530 N N 3.61360747730288 3.49744043328497 3.49744043328497 2 0 0.0518182145376201 N 0 0.155130540376442 N N 49089 25232 ENSG00000117450 ENSG00000156471 - - 1 8 45760196 97415950 coding intron PRDX1 PTDSS1 45749295 97343340 - + 0.155130540376442 45757256 97360449 + - Y - 0.893451229078755 N HCC1954 16 4.8 1 3 1 N - - N - SINE 0 1 1 5 0.785592297591888 0.392796148795944 0.785592297591888 0.392796148795944 1 - 0 30652 Y Y 3.29908909870209 3.57912086274016 3.29908909870209 342 0 0.0147322978566881 N 0 0.987690419464298 Y N 8659 3794 ENSG00000214717 ENSG00000169084 - + X X 2429008 2428975 utr5p upstream ZBED1 DHRSX 2414455 2147557 - - 0 2428860 2430802 + - N - - N HCC1954 1 1 1 0 1 N - - N - LTR 0 0.75 0.75 30 1.31408166142643 1.17124669822791 1.31408166142643 1.17124669822791 2 - - 40735 N Y 3.23061038311659 3.55037804895286 3.23061038311659 36 0.0232176360225143 0.792584171642119 N 0.597795497185741 0.540337711069419 N N 29024 0 ENSG00000124208 ENSG00000219462 - + 20 X 48203678 120973146 coding upstream UBE2V1 RP11-417D4.1 48131068 120972510 - - 0.540337711069419 48134198 120973154 + - Y - - N HCC1954 5 2.23529411764706 1 11 3 N - - N - - 0 0 0 17 0.792734045751814 0.364229156156239 0.792734045751814 0.364229156156239 2 - - 44027 N N 3.48639814491089 3.46551447180198 3.46551447180198 0 0 0.0468856907725701 N 0 0 N N 0 975 ENSG00000220646 ENSG00000198487 + + 10 6 51457129 42218335 downstream coding RP11-324H6.4 AL512274.9 51454901 42183124 - - 0 51451068 42185980 - - Y - - N HCC1954 9 6.4 5 5 1 N - - N SINE - 1 0 1 5 0.307095170876829 0.464213630395207 0.464213630395207 0.307095170876829 1 - - 34657 Y Y 3.33680806132368 3.18296190747752 3.18296190747752 9 0.0247115384615383 0.141151398855115 Y 0.0247115384615383 0.980096153846154 N N 7086 3488 ENSG00000197070 ENSG00000165724 - - 9 9 139629630 139604763 coding upstream ARRDC1 ZMYND19 139619917 139596352 + - 0 139620078 139605033 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 0.942710757110266 0.757025304952183 0.942710757110266 0.757025304952183 2 - - 48811 Y Y 3.41592783769912 3.52361324642271 3.41592783769912 298 0.0181208053691275 0.819073117189682 Y 0.911409395973154 0.992617449664429 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 utr3p downstream TPPP CEP72 712978 665405 - + 0 716530 708698 - + N 0.799740819289583 - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 123 1.21409718718746 1.02126998686945 1.21409718718746 1.02126998686945 1 0 - 28596 N N 3.17780074852469 3.57800808738356 3.17780074852469 0 0 0.388851561719958 N 0.00421940928270037 0 N N 6731 17943 ENSG00000186187 ENSG00000105141 - + 16 19 73702393 15027900 intron downstream ZNRF1 CASP14 73590416 15024015 + + 0.00421940928270037 73636992 15029502 - + Y 1.66200404346727 - N HCC1954 14 9.27027027027027 1 34 1 N - - N SINE SINE 1 0.201550387596899 1 37 0.28566992639705 0.914143764470561 0.914143764470561 0.28566992639705 3 0 - 30830 N N 3.48656597878024 3.24272559405391 3.24272559405391 12 0.0486308677098152 0.176224627777705 N 0.0486308677098152 0.206098862019915 N N 0 78560 ENSG00000222873 ENSG00000112493 - + 3 6 15755319 33390114 intron utr3p SRP_euk_arch TAPBP 15755026 33375449 + - 0.0486308677098152 15755056 33376318 - - Y 1 - N HCC1954 266 91.3846153846154 5 13 1 N - - N LTR SINE,SINE 1 0.531531531531532 1 13 0.735600060472404 0.821301038391519 0.821301038391519 0.735600060472404 2 0 - 1701 N Y 3.47911741325579 3.56079784271098 3.47911741325579 13 0 0.0227517759896476 N 0 0.892838196286472 N N 2 1529 ENSG00000196844 ENSG00000100344 - + 11 22 125153924 42674781 utr3p upstream PATE2 PNPLA3 125151268 42650952 - + 0 125151456 42647373 + + Y - - N HCC1954 480 424.928571428571 147 14 1 N - - N LINE SINE 1 1 1 14 0.45707188223528 0.335662163516534 0.45707188223528 0.335662163516534 1 - - 46640 N N 3.55657227767559 3.47336426491055 3.47336426491055 0 0.298517786561265 0.23537738102825 N 0.298517786561265 0.298517786561265 N N 0 42670 ENSG00000152467 ENSG00000128050 - + 19 4 63257811 57022291 upstream utr3p ZSCAN1 PAICS 63237212 56996672 + + 0.298517786561265 63224363 57021681 - + Y - 3.19483154861071 N HCC1954 1 1 1 0 1 N - - N SINE,SINE DNA 0.677966101694915 1 1 15 0.421363141435649 0.521347615674617 0.521347615674617 0.421363141435649 1 - 0 43193 N N 3.51849194026323 3.54872248456702 3.51849194026323 1 0 0.0460480945647251 N 0 0 N N 659 6632 ENSG00000204832 ENSG00000158636 - - 10 11 17492636 75940234 utr3p upstream AL158164.15 C11orf30 17481107 75833717 + + 0 17491680 75832962 - - Y - - N HCC1954 21 20.5714285714286 20 7 1 N - - N SINE - 1 0 1 7 0.328520415356608 0.528489363834543 0.528489363834543 0.328520415356608 1 - - 26729 Y Y 3.588962247475 3.39168383545536 3.39168383545536 0 0 0.148647874523408 Y 0.98453527523295 0.992267637616475 N N 0 0 ENSG00000199130 ENSG00000207639 - + 16 16 14310729 14305407 downstream upstream hsa-mir-365-1 hsa-mir-193b 14310643 14305325 + + 0 14327367 14303951 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.132420091324201 0.132420091324201 8 0.764167053112109 1.32122340958636 1.32122340958636 0.764167053112109 2 - - 24720 Y Y 3.38590018188657 3.29447165365238 3.29447165365238 0 0 0.784261971664227 Y 0.781383773021404 0.987854654056745 N N 0 0 ENSG00000200872 ENSG00000206944 + - 18 18 44255969 43950259 downstream upstream 5S_rRNA U6 44255856 43950153 - - 0 44118545 43966366 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.699891319672773 0.528489363834543 0.699891319672773 0.528489363834543 2 - - 47930 N N 3.79722016713641 3.42254622194492 3.42254622194492 0 0 0.335158842076371 N 0 0 N N 0 86504 ENSG00000182152 ENSG00000104408 + - 5 8 117142614 109330135 downstream intron AC114322.2 EIF3E 117142420 109283149 - - 0 116869227 109296202 - + Y - 0.565637670791068 N HCC1954 2 1.25 1 1 2 N - - N Unknown - 0.296296296296296 0 0.296296296296296 4 0.914143764470561 0.699891319672773 0.914143764470561 0.699891319672773 2 - 0 29629 Y Y 3.66166652809589 3.18784981992222 3.18784981992222 1 0 0.604877534376243 Y 0.11144166121259 0.993217111917653 N N 8180 5587 ENSG00000112419 ENSG00000001036 - - 6 6 144194014 143874556 coding upstream PHACTR2 FUCA2 143971010 143857935 + - 0 144074844 143900035 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.25 0.25 49 1.36407389854591 1.1141127129485 1.36407389854591 1.1141127129485 3 - - 20867 N Y 3.61360747730288 3.61616813038263 3.61360747730288 0 0 0.529381246220521 N 0.639013213981245 0.624573742540494 N N 33725 200 ENSG00000143819 ENSG00000144724 - + 1 3 224099884 62255613 utr5p intron EPHX1 PTPRG 224064459 61522283 + + 0 224083049 61653227 - + Y - 0.58278189905552 N HCC1954 21 16 2 4 1 N - - N - LTR 0 0.94 0.94 4 0.849868031031224 0.357087407996313 0.849868031031224 0.357087407996313 4 - 0 22898 N N 3.46192074895235 3.32320511986986 3.32320511986986 1 0.075800229381712 0.376640586841238 N 0.321290793452195 0.0902408507976226 N N 0 0 ENSG00000208700 ENSG00000217866 + + 4 1 156603336 555926 downstream intron AC097526.3-14 RP5-857K21.8 156603269 554883 - + 0.0902408507976226 156602919 555217 - + Y - 1 N HCC1954 4 4 4 4 1 N 510 22.0605 N - - 0 0 0 4 0.257102933757345 0.421363141435649 0.421363141435649 0.257102933757345 2 - 0 41679 Y N 3.72717401544771 3.17088654933356 3.17088654933356 0 0 0.730786425851497 N 0 0 N N 79632 19339 ENSG00000182197 ENSG00000177570 + + 8 8 119193119 119703365 coding utr3p EXT1 SAMD12 118875910 119270880 - - 0 119191505 119271701 - - N 0.296748039644633 - Y HCC1954 1 1 1 0 1 N 166 4.4797 N - - 0 0 0 41 1.23552243166724 1.12125446110842 1.23552243166724 1.12125446110842 4 0 - 2230 N Y 3.41423242051993 3.65384724021086 3.41423242051993 0 0 0.27697121761221 N 0.887789547200559 0.887789547200559 N N 6632 3297 ENSG00000158636 ENSG00000174840 - + 11 3 75940234 57522721 upstream utr3p C11orf30 PDE12 75833717 57517044 + + 0 75832968 57521384 - + Y - - N HCC1954 37 34.1304347826087 23 23 1 N - - N - SINE 0 1 1 23 0.87843502367093 0.328520415356608 0.87843502367093 0.328520415356608 1 - - 26774 N Y 3.44719145177281 3.30335451653084 3.30335451653084 277 0 0.0549422669374777 Y 0.84057761732852 0.986714801444043 N N 1173 0 ENSG00000140987 ENSG00000209508 + + 16 16 3391026 3357718 intron upstream ZNF434 AC025283.6-2 3372087 3357649 - + 0 3373999 3355182 - + N 0.769214379969652 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 0.764167053112109 0.499922371194838 0.764167053112109 0.499922371194838 1 0 - 33533 N N 3.11547640886856 3.54400240599166 3.11547640886856 43 0 0.812143884832828 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 12342 14901 - + N - 0.650764805140031 N HCC1954 3 1.625 1 3 4 Y 189 4.09957 N - - 0 0 0 8 1.31408166142643 1.02841173502938 1.31408166142643 1.02841173502938 2 - 0 4740 Y Y 3.93849644929864 2.51628589324104 2.51628589324104 0 0 0.999636256380947 Y 0.573856523832451 0.96783822821377 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 coding downstream CRCP ASL 65216341 65178207 + + 0 65230126 65202245 - + N - - N HCC1954 2 1.4 1 2 6 N - - Y - Low_complexity,Simple_repeat,Simple_repeat 0 0.162280701754386 0.162280701754386 5 0.87843502367093 0.985561246069823 0.985561246069823 0.87843502367093 3 - - 9490 Y Y 3.30694823938047 3.40631984667906 3.30694823938047 312 0.10924713584288 0.0213252752374673 Y 0.116316603018731 0.99293053282415 N N 256 0 ENSG00000167524 ENSG00000203459 + + 17 17 23965338 23958792 intron upstream AC005726.6 AC005726.1-3 23959109 23958639 - + 0.130455537370431 23962290 23956362 - + N 0.200669721275499 - N HCC1954 21 9.33333333333333 1 3 2 N - - Y - Other 0 1 1 6 0.885576771830856 1.02126998686945 1.02126998686945 0.885576771830856 1 0 - 28189 N N 3.65488030998075 3.28862521935129 3.28862521935129 1 0 0.238377160586986 N 0 0 N N 4898 45068 ENSG00000136816 ENSG00000205336 + + 9 16 131613381 56256445 utr3p coding TOR1B GPR56 131605253 56220023 + + 0 131611945 56242688 + + Y - - N HCC1954 24 21.8 21 5 1 N - - N SINE - 1 0 1 5 0.292811674556976 0.799875793911741 0.799875793911741 0.292811674556976 2 - - 19327 N Y 3.09508724929961 3.5816815158199 3.09508724929961 0 0 0.54341375698306 N 0.844080267558528 0.878729096989966 N N 3299 3863 ENSG00000179571 ENSG00000219481 + - 1 1 16812569 146862781 intron upstream NBPF1 NBPF15 16762999 146827614 - + 0.878729096989966 16812389 146823317 - - N 3.27037699766731 - Y HCC1954 4 2.125 1 6 1 N 337 8.20393 N - - 0 0 0 8 0.335662163516534 0.821301038391519 0.821301038391519 0.335662163516534 1 0 - 10043 N Y 3.68105312311849 3.71041843152174 3.68105312311849 0 0 0.84493453193872 Y 0 0.973460011597306 N N 18240 62029 ENSG00000062716 ENSG00000141367 - + 17 17 55273235 55129099 coding coding TMEM49 CLTC 55139811 55051832 + + 0 55249911 55115895 - + N - 2.98602884350597 N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 293 1.3069399132665 1.45691662462496 1.45691662462496 1.3069399132665 1 - 0 47921 N N 3.23164345288648 3.16935896602371 3.16935896602371 0 0.144739130434783 0.628185451056118 N 0.198869565217391 0 N N 465 3176 ENSG00000145723 ENSG00000172167 + + 5 8 102483741 121605056 coding intron GIN1 MTBP 102449603 121526847 - + 0 102468144 121551107 - + Y 0.211194027231612 1.0515570303585 N HCC1954 1 1 1 0 1 N 589 1.9477 N - DNA 0 1 1 7 0.528489363834543 1.02126998686945 1.02126998686945 0.528489363834543 4 0 0 20450 N Y 3.49847350305486 3.34256120966892 3.34256120966892 60 0 0.239362183627889 N 0.960652028159571 0.954094032852833 N N 0 8888 ENSG00000201692 ENSG00000112159 - - 1 6 172100669 90586163 downstream intron snosnR60_Z15 MDN1 172100588 90409952 - - 0.954094032852833 172100465 90487965 + + Y - 1.96227421382155 N HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.871293275511003 0.871293275511003 0.871293275511003 0.871293275511003 2 - 0 30058 N Y 3.47233119514066 3.47279520345708 3.47233119514066 205 0.662034054302807 0.0335453346527462 N 0.69958582604694 0.662034054302807 N N 9989 0 ENSG00000160916 ENSG00000185796 - + 7 6 98901744 109335769 coding intron ATP5J2 RP11-249L21.4 98893721 109335511 - - 0.887344684767602 98895650 109335654 + - Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.849868031031224 0.371370904316165 0.849868031031224 0.371370904316165 2 - 0 34488 Y Y 3.74231388778119 3.85425536676371 3.74231388778119 327 0 0.00299617431347443 Y 0.567759457667714 0.993028378349479 N N 0 4646 ENSG00000216363 ENSG00000197579 + - 9 9 32557124 32542601 intron utr5p RP11-205M20.7 TOPORS 32556151 32530545 - - 0 32556329 32542477 - + N 1 2.00114100649744 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.628473838073511 0.578481600954027 0.628473838073511 0.578481600954027 3 0 0 33083 N N 3.46704205511183 2.85847416306589 2.85847416306589 0 0 0.163019852342914 N 0 0 Y N 0 171855 ENSG00000210082 ENSG00000198886 - + MT MT 3230 12138 intron coding AF347015.1-4 MT-ND4 1673 10761 + + 0 3224 12055 - + N 1 3.14617460359579 N HCC1954 2 1.2 1 1 1 N 168 10.2917 N - - 0 0 0 5 0.956994253430118 0.707033067832699 0.956994253430118 0.707033067832699 3 0 0 18094 N Y 3.35781971550858 3.54296933622177 3.35781971550858 267 0 0.332835123742513 Y 0.840599250936329 0.990037453183521 N N 0 0 ENSG00000220261 ENSG00000219021 + + 1 1 222242479 222204741 downstream downstream RP11-504P24.2 RP11-504P24.1 222237079 222201925 - + 0 222225901 222219036 - + N - - N HCC1954 224 152.117647058824 13 17 3 N - - N LTR,SINE SINE,SINE 0.754716981132076 1 1 17 0.757025304952183 0.599906845433805 0.757025304952183 0.599906845433805 2 - - 33046 N Y 3.48337348351473 3.36344488277784 3.36344488277784 442 0.00717740677172718 0.534856209001996 Y 0.00226244343891391 0.995085036667187 N N 171855 544065 ENSG00000198886 ENSG00000198744 - + MT MT 12138 9988 coding coding MT-ND4 MT-CO3 10761 8367 + + 0 10973 8912 - + N 0.536334839507319 0.582654081629347 N HCC1954 3 2 1 4 7 Y - - N - - 0 0 0 5 0.928427260790413 1.2783729206268 1.2783729206268 0.928427260790413 1 0 0 9591 Y Y 3.45976132345673 3.34256120966892 3.34256120966892 342 0 0.0120718994794639 Y 0 0.884396982795152 N N 70 117 ENSG00000184361 ENSG00000184922 + + 17 17 40695262 40680464 intron downstream C17orf46 FMNL1 40687543 40655075 - + 0 40692732 40681345 - + N 5.45238095238095 - N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 7 0.549914608314322 0.45707188223528 0.549914608314322 0.45707188223528 1 0 - 3486 N Y 2.52164063634332 3.45976132345673 2.52164063634332 0 0 0.527971096671233 N 0 0 N N 24125 166846 ENSG00000157557 ENSG00000142192 - + 21 21 39118749 26465003 upstream coding ETS2 APP 39099101 26174733 + - 0 39054483 26347507 - - N - - Y HCC1954 1 1 1 0 3 N - - N LTR - 1 0 1 6 0.642757334393363 1.02126998686945 1.02126998686945 0.642757334393363 2 - - 34768 Y Y 3.66336194527509 3.66641711189479 3.66336194527509 326 0 0.149331031060854 Y 0 0.987052824476137 N N 17291 0 ENSG00000070159 ENSG00000213539 - + 9 9 111300407 111336541 utr5p upstream PTPN3 AL162733.9 111177800 111334974 - - 0 111265552 111340332 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 74 1.12839620926835 1.2783729206268 1.2783729206268 1.12839620926835 4 - - 19254 Y Y 3.1986844216336 3.00187001793039 3.00187001793039 0 0 0.915325410063698 Y 0 0 N N 497 14630 ENSG00000186364 ENSG00000131788 + + 1 1 144300792 144297903 upstream coding NUDT17 PIAS3 144297502 144287345 - + 0 144301003 144296193 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE,LINE - 0.1 0 0.1 6 1.07126222398894 0.921285512630487 1.07126222398894 0.921285512630487 4 - - 30403 Y Y 3.25952103077323 3.54400240599166 3.25952103077323 239 0 0.00168841936056940 Y 0.97600443615466 0.97600443615466 N N 4275 79891 ENSG00000073009 ENSG00000160211 - - X X 153448998 153428981 coding intron IKBKG G6PD 153423672 153412800 + - 0 153433449 153422789 - + N 0.45341359465937 2.91812294387529 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.792734045751814 0.928427260790413 0.928427260790413 0.792734045751814 1 0 0 36335 Y Y 3.37808089400154 3.08355044738558 3.08355044738558 245 0 0.00356433473002815 Y 0.966429717954597 0.966429717954597 N N 878 42060 ENSG00000111077 ENSG00000063046 - + 12 12 51744430 51722259 upstream utr3p TENC1 EIF4B 51727077 51686329 + + 0 51726011 51720315 - + N - 3.00605628785859 N HCC1954 4 3 1 6 2 N - - Y - - 0 0 0 7 0.657040830713216 0.857009779191151 0.857009779191151 0.657040830713216 0 - 0 14960 N N 3.00553409879691 2.60850504569425 2.60850504569425 0 0 0.614001266042583 N 0 0.140325271059216 N N 258 4094 ENSG00000157064 ENSG00000105997 - - 1 7 181654360 27158458 utr3p intron NMNAT2 HOXA3 181484001 27112334 - - 0.140325271059216 181485457 27120907 + + Y - 47.2073357888275 N HCC1954 34 25.5 7 4 1 N - - N Simple_repeat - 0.96 0 0.96 4 0.357087407996313 0.642757334393363 0.642757334393363 0.357087407996313 1 - 0 46736 N Y 3.27192306858781 3.64553343878587 3.27192306858781 1 0 0.257552854734277 N 0.870870870870871 0.852423852423852 N N 32027 74 ENSG00000064666 ENSG00000166359 - - 19 19 990060 38358545 coding intron CNN2 WDR88 977298 38314838 + + 0 988625 38344585 - - N 1.1204043270164 0.143878038688653 Y HCC1954 5 1.8 1 1 1 N - - N - SINE 0 1 1 5 0.478497126715059 0.328520415356608 0.478497126715059 0.328520415356608 1 0 0 27865 N N 3.55041790174621 3.2044774227722 3.2044774227722 0 0.273640358386121 0.0568993755961723 N 0.273640358386121 0 N N 11083 41507 ENSG00000205250 ENSG00000188846 - + 16 3 65790322 40478862 coding coding E2F4 RPL14 65783569 40473834 + + 0 65786374 40478437 - + Y - - N HCC1954 44 12.5 1 3 1 N - - N Simple_repeat - 0.464285714285714 0 0.464285714285714 4 0.799875793911741 0.649899082553289 0.799875793911741 0.649899082553289 2 - - 7210 Y Y 3.30591516961058 3.20760713730541 3.20760713730541 265 0 0.0108293322975687 Y 0.915414738341047 0.981203275186899 N N 10099 4443 ENSG00000136536 ENSG00000123636 - - 2 2 160333329 160181326 upstream upstream MARCH7 BAZ2B 160277246 159883736 + - 0 160235465 160181358 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 1 0 1 7 0.821301038391519 1.12839620926835 1.12839620926835 0.821301038391519 4 - - 24730 Y Y 3.31485146565152 3.33680806132367 3.31485146565152 337 0 0.326762587520701 Y 0.281641078570507 0.987614501354664 N N 7222 4519 ENSG00000101639 ENSG00000085415 - + 18 18 13115052 12977533 upstream downstream CEP192 SEH1L 12998499 12937983 + + 0 12989420 12981436 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 67 1.19267194270768 1.18553019454776 1.19267194270768 1.18553019454776 4 - - 692 N N 3.69784855983781 3.28552601004162 3.28552601004162 0 0 0.643798925932434 N 0 0 Y N 5365 138744 ENSG00000166670 ENSG00000152558 - + 11 11 102156569 101828985 coding coding MMP10 TMEM123 102146455 101772268 - - 0 102155511 101778082 + - N - - N HCC1954 2 1.8 1 4 2 Y - - N - - 0 0 0 5 0.664182578873142 0.714174815992626 0.714174815992626 0.664182578873142 3 - - 6487 N N 2.78796400306077 2.48311911155744 2.48311911155744 47 0.068704790112206 0.341951762090588 N 0 0.234023466423649 N N 131026 122511 ENSG00000115053 ENSG00000187514 - + 2 2 232037449 232286495 coding coding NCL PTMA 232027706 232280638 - + 0.234023466423649 232034658 232285406 + + N - - Y HCC1954 5 2.25 1 2 2 Y - - N Simple_repeat,Simple_repeat,Simple_repeat Low_complexity 0.29047619047619 0.261780104712042 0.29047619047619 4 0.864151527351077 0.807017542071667 0.864151527351077 0.807017542071667 1 - - 45085 Y Y 3.47705127371601 3.6052936758779 3.47705127371601 118 0.674628712871287 0.109587003878017 N 0.792945544554455 0.891542904290429 N Y 14643 15033 ENSG00000187134 ENSG00000151632 - + 10 10 5010445 5050207 coding intron AKR1C1 AKR1C2 4995566 5021966 + - 0 4998106 5050092 - - N - 203.701156408042 Y HCC1954 36 7.33333333333333 1 3 1 Y - - N - LTR 0 1 1 6 0.657040830713216 0.449930134075354 0.657040830713216 0.449930134075354 4 - 0 41953 N N 3.25575947405425 3.49847350305486 3.25575947405425 0 0 0.244181614962606 N 0.292839167238618 0.292839167238618 N N 159165 0 ENSG00000164754 ENSG00000219931 + + 8 X 117956182 99944702 intron intron RAD21 RP3-347M6.2 117927355 99942822 - + 0.292839167238618 117947894 99943086 - + Y 1.53888536802777 1 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.321378667196682 0.257102933757345 0.321378667196682 0.257102933757345 1 0 0 13842 Y Y 3.51525959220437 3.54872248456702 3.51525959220437 0 0 0.711098743080437 Y 0.990519284636932 0.981038569273863 N N 6442 4831 ENSG00000100359 ENSG00000100357 - + 22 22 39136239 39092697 utr5p coding SGSM3 ADSL 39096541 39072479 + + 0 39126646 39092448 - + N 1.26657317503895 - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.348314606741573 0 0.348314606741573 6 0.635615586233437 0.649899082553289 0.649899082553289 0.635615586233437 4 0 - 3769 N N 3.64553343878587 3.66641711189479 3.64553343878587 0 0 0.266690704893256 N 0 0 N N 17298 3825 ENSG00000182871 ENSG00000183762 - + 21 22 45758062 27893094 intron intron COL18A1 KREMEN1 45649480 27799066 + + 0 45682993 27865959 - + Y 0.138337720616552 1.69479266640959 N HCC1954 1 1 1 0 1 N 403 7.83342 N - SINE 0 0.0340909090909091 0.0340909090909091 4 0.542772860154395 0.628473838073511 0.628473838073511 0.542772860154395 1 0 0 43660 N Y 3.07101108092519 3.62824348852659 3.07101108092519 0 0 0.303645703350035 N 0.835540915395284 0.932281553398058 N N 1649619 1 ENSG00000141736 ENSG00000148482 - + 17 10 35138441 18372222 coding intron ERBB2 SLC39A12 35104766 18280827 + + 0 35125066 18346387 - + Y - 1.03321033210332 N HCC1954 25 22.7916666666667 20 24 1 N - - N - SINE 0 1 1 24 0.99270299422975 0.407079645115797 0.99270299422975 0.407079645115797 1 - 0 1174 N N 3.23121929736341 3.10081746970591 3.10081746970591 0 0 0.912050294740802 N 0 0 N N 3570 15620 ENSG00000155352 ENSG00000149218 - + 2 11 114073079 94505463 utr5p coding FAM39B ENDOD1 114058161 94462665 + + 0 114062748 94463039 - + Y - 0.667718519530781 N HCC1954 6 5 4 19 2 N 181 4.74815 N - Low_complexity 0 0.191616766467066 0.191616766467066 19 1.72830305470215 1.19267194270768 1.72830305470215 1.19267194270768 4 - 0 24369 N N 3.79465951405667 2.46549722334402 2.46549722334402 52 0 0.031658506495449 N 0 0 N N 559 0 ENSG00000102290 ENSG00000215401 - - X 18 91764885 1353874 intron upstream PCDH11X AP005119.2 90920960 1352441 + - 0.111842105263158 91398077 1504289 - + Y 7.46019800411919 - N HCC1954 23 21.3333333333333 20 6 1 N 579 23.2947 N LINE - 1 0 1 6 0.335662163516534 0.621332089913584 0.621332089913584 0.335662163516534 2 0 - 32954 N Y 2.76022891149302 3.41576000382978 2.76022891149302 330 0.00303030303030305 0.385238849025757 Y 0.0128045157456923 0.951128936423054 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0.951128936423054 8492 6702 - + N 0.619501286280727 - N HCC1954 4 2 1 3 5 Y - - N - - 0 0 0 5 0.99270299422975 0.707033067832699 0.99270299422975 0.707033067832699 2 0 - 38925 N Y 3.47911741325579 3.71873223294673 3.47911741325579 187 0 0.007602880030805 N 0.045671339788987 0.919352507587802 N N 9284 36 ENSG00000197535 ENSG00000214173 + - 15 7 50608539 127896489 intron coding MYO5A AC010655.7-2 50386770 127893850 - + 0.153201329671918 50539603 127893854 - - Y 3.85193244570078 0.139196272568433 N HCC1954 38 24.25 18 4 1 N - - N Other - 1 0 1 4 0.507064119354764 0.435646637755502 0.507064119354764 0.435646637755502 1 0 0 44070 N Y 3.57229479183167 3.62617734898681 3.57229479183167 1 0 0.397275527743325 N 0.759977409638554 0.747976280120482 N N 975 0 ENSG00000198487 ENSG00000178473 + + 6 10 42218335 5406169 coding upstream AL512274.9 UCN3 42183124 5396976 - + 0.747976280120482 42186005 5373054 - + Y - - N HCC1954 21 18.8888888888889 4 9 1 N - - N - SINE 0 1 1 9 0.51420586751469 0.271386430077198 0.51420586751469 0.271386430077198 2 - - 658 Y Y 3.3755202409218 3.48743121468078 3.3755202409218 0 0 0.701006006155084 Y 0.0423076923076923 0 N N 5561 22727 ENSG00000172890 ENSG00000172893 - - 11 11 70890227 70837125 coding upstream NADSYN1 DHCR7 70841865 70823105 + - 0 70843806 70837581 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.53 0.53 4 0.699891319672773 0.692749571512847 0.699891319672773 0.692749571512847 1 - - 19693 N N 3.78208964237274 3.31804396091703 3.31804396091703 7 0 0.0408053219862595 N 0 0 N N 2833 23303 ENSG00000133019 ENSG00000136149 - + 1 13 238139338 53913472 utr5p upstream CHRM3 RPL13AP20 237858996 53912798 + - 0 237859411 54053779 - - Y - - N HCC1954 23 22.0666666666667 21 15 1 N - - N LINE LTR 1 1 1 15 0.592765097273879 1.17124669822791 1.17124669822791 0.592765097273879 1 - - 274 Y Y 3.46335504630636 3.4780843434859 3.46335504630636 272 0 0.963345932186217 Y 0.991104254201681 0.982208508403361 N N 72 2985 ENSG00000162148 ENSG00000167985 - + 11 11 61014975 60970801 upstream coding C11orf66 C11orf79 61005168 60954173 + + 0 60996793 60962161 - + N - 1.96392479999331 N HCC1954 1 1 1 0 6 N - - Y LTR - 1 0 1 18 1.17124669822791 0.885576771830856 1.17124669822791 0.885576771830856 4 - 0 37119 N N 2.92395114519417 3.05952771217364 2.92395114519417 0 0 0.246584858692817 N 0.431331953071084 0 N N 671 4006 ENSG00000187650 ENSG00000196935 - - 19 12 5861864 62823751 utr3p downstream AC104532.2 SRGAP1 5855885 62524808 + + 0.0285254198297676 5861707 62824284 - - Y - - N HCC1954 24 15.2 2 5 1 N - - N SINE,Simple_repeat Simple_repeat,LINE 0.730769230769231 0.906832298136646 0.906832298136646 5 0.371370904316165 0.735600060472404 0.735600060472404 0.371370904316165 2 - - 3550 N N 3.46977054206092 3.50678730447985 3.46977054206092 0 0 0.705995757852573 N 0 0 Y N 64 3005 ENSG00000197934 ENSG00000159113 - + 21 21 26863442 33591390 intron coding AP001597.1 IL10RB 26700133 33560542 + + 0 26764943 33570772 - + N 2.77065656565657 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 8 0.914143764470561 0.885576771830856 0.914143764470561 0.885576771830856 2 0 - 38356 Y Y 3.17979234015096 3.79362644428678 3.17979234015096 143 0.00330033003300334 0.94665198317879 Y 0.957284299858557 0.985761433286186 N N 10336 0 ENSG00000133961 ENSG00000221236 - - 14 14 72892230 72985644 utr5p upstream NUMB AC005280.3 72811671 72985548 - + 0 72892227 72946398 + - N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 81 1.17838844638783 1.06412047582901 1.17838844638783 1.06412047582901 4 - - 18557 Y Y 3.67017866861376 3.37824872787089 3.37824872787089 285 0 0.031875055147108 Y 0 0 N N 0 0 ENSG00000217983 ENSG00000218209 + - 1 1 226389316 226369797 downstream upstream RP11-520H14.1 RP5-881P19.6 226389118 226369326 - - 0 226385382 226377177 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR LTR 1 1 1 6 0.749883556792257 0.699891319672773 0.749883556792257 0.699891319672773 1 - - 43787 N N 3.50529022639353 3.09087103183403 3.09087103183403 8 0 0.0608327788011226 N 0 0 N N 0 3891 ENSG00000133454 ENSG00000166295 + + 22 10 24757007 73665622 downstream intron MYO18B C10orf104 24468120 73645812 + + 0 24758709 73645953 + + Y - 0.744979490524871 N HCC1954 29 21.5 20 6 1 N - - N SINE - 1 0 1 6 0.478497126715059 0.385654400636018 0.478497126715059 0.385654400636018 1 - 0 48783 N N 3.21808036422602 3.50322408685375 3.21808036422602 0 0 0.0749532211067777 N 0 0 N N 0 2273 ENSG00000213731 ENSG00000177556 - + 5 5 90808593 151118405 downstream intron AC008923.9 ATOX1 90808096 151102577 + - 0 90989022 151105875 - - N - 0.204548633599566 Y HCC1954 20 11 5 7 1 N - - N LTR - 1 0 1 7 0.421363141435649 0.771308801272036 0.771308801272036 0.421363141435649 2 - 0 7407 Y Y 3.37758638046158 3.24847874239916 3.24847874239916 0 0 0.762272871086661 Y 0.99344075007879 0.986881500157579 N N 5277 307 ENSG00000169756 ENSG00000214184 - - 2 2 108670134 108517107 coding upstream LIMS1 AC012487.12-1 108571199 108492643 + - 0 108642493 108517482 - + N - - N HCC1954 3 2.16788321167883 1 80 1 N - - Y - Simple_repeat 0 0.158620689655172 0.158620689655172 137 1.17124669822791 1.03555348318931 1.17124669822791 1.03555348318931 4 - - 42439 Y Y 3.59272380419397 3.4446613039166 3.4446613039166 0 0 0.885390015678788 Y 0 0.994029797547762 N N 7896 12251 ENSG00000134852 ENSG00000134851 + + 4 4 56107754 55987095 intron coding CLOCK TMEM165 55993417 55956877 - + 0 56007052 55985566 - + N 0.972939304868663 - N HCC1954 20 3.22222222222222 1 2 2 N - - Y SINE - 1 0 1 9 0.971277749749971 1.13553795742827 1.13553795742827 0.971277749749971 1 0 - 47082 N Y 3.60426060610801 3.46145674063593 3.46145674063593 243 0 0.0144498303472228 Y 0 0 N N 17943 24 ENSG00000105141 ENSG00000105143 - - 19 19 15027900 14951505 upstream upstream CASP14 SLC1A6 15024015 14922007 + - 0 15021901 14966043 - + N - - N HCC1954 1 1 1 0 1 N - - N SINE LTR 1 1 1 6 0.742741808632331 0.728458312312478 0.742741808632331 0.728458312312478 1 - - 47024 Y Y 3.40744620240479 3.12279699331701 3.12279699331701 321 0 0.176690754234330 Y 0 0 N N 584 560 ENSG00000197813 ENSG00000063127 + - 19 19 54535371 54520286 utr3p coding AC011450.4 SLC6A16 54523236 54484709 - - 0 54526685 54489621 - + N 0.533034779335655 1.90527336395854 N HCC1954 1 1 1 0 4 N - - Y LTR - 0.882352941176471 0 0.882352941176471 12 1.21409718718746 1.0069864905496 1.21409718718746 1.0069864905496 1 0 0 44662 N Y 2.8753230329477 3.59425138750382 2.8753230329477 313 0 0.0219055652823492 Y 0.992025559105431 0.992025559105431 N N 253 6115 ENSG00000203780 ENSG00000089876 - - 10 10 127688151 127559874 upstream utr5p FANK1 DHX32 127575098 127514896 + - 0 127574779 127559632 - + N - 80.1885017132751 N HCC1954 1 1 1 0 2 N - - N Low_complexity LINE 0.05 0.406060606060606 0.406060606060606 97 0.999844742389676 1.17838844638783 1.17838844638783 0.999844742389676 1 - 0 24354 N Y 3.67849247003875 3.62398741826765 3.62398741826765 268 0.739437428243398 0.00163811049904750 N 0.739437428243398 0.708783008036739 N N 0 14314 ENSG00000214012 ENSG00000154845 + - 6 18 19722245 9604606 intron upstream AL022068.2 PPP4R1 19720964 9536789 + - 0.923363949483352 19721464 9669009 + + Y 1 - N HCC1954 13 8.36363636363636 7 11 1 N - - N - - 0 0 0 11 0.414221393275723 0.264244681917271 0.414221393275723 0.264244681917271 1 0 - 32973 N N 3.55976477294109 3.50000108636471 3.50000108636471 0 0 0.0428143916327131 N 0 0 N N 0 0 ENSG00000223073 ENSG00000210196 - + MT MT 931 16024 upstream upstream SSU_rRNA_5 AF347015.1-24 155 15956 + - 0 1 16500 - - N - - Y HCC1954 1 1 1 0 1 N 408 4.00284 N - - 0 0 0 39 1.09982921662864 0.999844742389676 1.09982921662864 0.999844742389676 0 - - 303 Y Y 3.55657227767558 3.11551626166191 3.11551626166191 110 0 0.0138969081029445 Y 0 0.00909090909090893 N N 144 0 ENSG00000152268 ENSG00000201856 - - 11 11 14246222 13885713 upstream downstream SPON1 5S_rRNA 13941028 13885595 + - 0.00909090909090893 13929398 13851779 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 4 0.478497126715059 0.464213630395207 0.478497126715059 0.464213630395207 1 - - 33102 N N 2.80150174417089 3.48374420587532 2.80150174417089 0 0 0.999920926755815 N 0 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8463 15843 - + N 0.736309003119746 2.51112346367471 N HCC1954 3 2 1 21 8 N - - N - - 0 0 0 33 1.19267194270768 1.39264089118562 1.39264089118562 1.19267194270768 2 0 0 6446 Y N 2.91034820374036 3.03276925944058 2.91034820374036 0 0.00340136054421747 0.107397348694247 Y 0.00340136054421747 0.00340136054421747 N N 1024 5258 ENSG00000144504 ENSG00000142327 - - 2 2 241149200 241166814 coding intron ANKMY1 RNPEPL1 241067512 241156777 - + 0.00340136054421747 241143135 241157233 + - N - 0.399714641283073 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.341176470588235 0.341176470588235 4 0.735600060472404 0.607048593593732 0.735600060472404 0.607048593593732 1 - 0 33546 N Y 3.5293265419746 3.07142165607912 3.07142165607912 341 0.143260562615401 0.490100423001548 Y 0.106332138590203 0.874443358314326 N N 247001 275222 ENSG00000198786 ENSG00000198763 - + MT MT 14149 5512 coding coding MT-ND5 MT-ND2 12338 4471 + + 0.047246660149886 13807 5405 - + N - 1.2004092036623 N HCC1954 2 1.5 1 2 5 N - - N - - 0 0 0 4 1.02841173502938 0.864151527351077 1.02841173502938 0.864151527351077 2 - 0 36361 Y Y 3.33577499155379 3.14890702572245 3.14890702572245 231 0 0.00526150427154726 Y 0 0.983124220412356 N N 18261 44572 ENSG00000139613 ENSG00000092841 + + 12 12 54869618 54841633 downstream coding SMARCC2 MYL6 54843034 54838367 - + 0 54842945 54840330 - + N - 2.96955786645344 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.735600060472404 0.814159290231593 0.814159290231593 0.735600060472404 1 - 0 16541 N N 2.96319769112561 3.60000453584907 2.96319769112561 0 0.231354983202687 0.0858044783730973 N 0.231354983202687 0.231354983202687 N N 0 443941 ENSG00000212679 ENSG00000172057 - - 1 17 559619 35337380 intron utr3p RP5-857K21.10 ORMDL3 558939 35330822 + - 0.231354983202687 559004 35331910 - + Y 1 2.84883238070779 N HCC1954 2 2 2 5 1 N 506 15.0412 N - - 0 0 0 5 0.692749571512847 0.814159290231593 0.814159290231593 0.692749571512847 2 0 0 28151 N Y 3.47336426491055 3.23999710710482 3.23999710710482 0 0 0.102798624718796 N 0.503086419753087 0.791616885702907 N N 16390 7183 ENSG00000140950 ENSG00000147853 - + 16 9 83095794 4732043 utr5p intron KIAA1609 AK3 83068608 4701158 - - 0 83089218 4710031 + - Y - 0.999983676681723 N HCC1954 20 14.6666666666667 2 6 1 N - - N - SINE 0 1 1 6 0.51420586751469 0.271386430077198 0.51420586751469 0.271386430077198 2 - 0 22291 N N 3.39487633072086 2.99376390316809 2.99376390316809 5 0 0.0893097401780941 N 0 0.0223889379229185 N N 316358 0 ENSG00000087460 ENSG00000220375 - - 20 1 56919644 558984 coding intron GNAS RP5-857K21.14 56861431 558778 + + 0.0223889379229185 56904114 558808 - - Y - 1 N HCC1954 3 2.5 2 4 1 N - - N - - 0 0 0 4 0.771308801272036 0.642757334393363 0.771308801272036 0.642757334393363 1 - 0 36945 N N 3.79143651356762 3.21808036422602 3.21808036422602 0 0 0.646687196902253 N 0 0.00406504065040647 N N 0 252 ENSG00000185834 ENSG00000151229 - + 20 12 53125086 38786158 downstream coding AL121593.10 SLC2A13 53124590 38435090 + - 0.00406504065040647 53465267 38708372 - - Y - - N HCC1954 1 1 1 0 1 N 307 14.0044 N - - 0 0 0 12 0.592765097273879 0.814159290231593 0.814159290231593 0.592765097273879 1 - - 45602 N Y 3.57800808738356 3.22423474015539 3.22423474015539 0 0 0.390022604049116 N 0 0 N N 17943 0 ENSG00000105141 ENSG00000159261 + - 19 21 15027900 36870737 downstream intron CASP14 CLDN14 15024015 36754789 + - 0 15029502 36801115 + + Y - 1 N HCC1954 20 18.6 1 24 1 N - - N - SINE 0 1 1 25 0.664182578873142 0.34280391167646 0.664182578873142 0.34280391167646 3 - 0 19479 Y Y 3.44825502676623 3.43039601505348 3.43039601505348 160 0.0380215932302306 0.315223487303392 N 0.0380215932302306 0.991333527866939 Y N 67 462 ENSG00000188015 ENSG00000196154 - + 1 1 151788358 151789236 utr5p upstream S100A3 S100A4 151786449 151782713 - - 0 151787590 151789640 + - N - - N HCC1954 1 1 1 0 1 N - - N SINE - 0.0105263157894737 0 0.0105263157894737 9 1.04983697950916 0.764167053112109 1.04983697950916 0.764167053112109 3 - - 33544 N Y 2.7261969576769 3.7297745213208 2.7261969576769 299 0 0.982260141919232 Y 0 0.991021121455904 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0 13751 8601 - + N - 0.64395298707698 N HCC1954 2 1.5 1 2 7 Y - - N - - 0 0 0 4 0.864151527351077 0.707033067832699 0.864151527351077 0.707033067832699 4 - 0 7284 Y Y 3.63193049733206 3.39487633072086 3.39487633072086 262 0 0.0350805168164932 Y 0 0.966231077759089 N N 30 0 ENSG00000152154 ENSG00000211215 - - 2 2 39798605 39569088 upstream upstream TMEM178 AC007388.4 39746563 39568835 + - 0 39679895 39628833 - + N - - N HCC1954 1 1 1 0 2 N - - Y DNA LTR 1 1 1 9 0.607048593593732 0.614190341753658 0.614190341753658 0.607048593593732 1 - - 21833 N N 3.41679307359967 3.36191729946799 3.36191729946799 0 0 0.829584837963573 N 0 0 N N 0 712661 ENSG00000219973 ENSG00000111640 + + 1 12 187369046 6517797 intron coding RP11-373J16.2 GAPDH 187368104 6513918 - + 0 187368233 6517307 - + Y 1 - N HCC1954 15 9 5 5 1 N - - N - - 0 0 0 5 0.292811674556976 0.307095170876829 0.307095170876829 0.292811674556976 2 0 - 17550 Y Y 3.51104337473878 3.63655728995158 3.51104337473878 0 0 0.238921348969565 Y 0 0 N N 7001 11958 ENSG00000160783 ENSG00000160785 - + 1 1 154479736 154449210 coding intron PMF1 SLC25A44 154449408 154430523 + + 0 154468795 154430716 - + N - 0.55057286325707 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.93556900895034 0.307095170876829 0.93556900895034 0.307095170876829 2 - 0 3029 N N 3.3446273492087 3.52824003904223 3.3446273492087 0 0 0.355919620111437 N 0.071814728229106 0 N N 290 14402 ENSG00000142405 ENSG00000156689 + + 19 11 59019460 58368833 utr3p coding NALP12 GLYATL2 58988669 58358118 - - 0 58988760 58363624 - - Y - - N HCC1954 38 35.6 34 5 1 N - - N SINE - 1 0 1 5 0.328520415356608 0.592765097273879 0.592765097273879 0.328520415356608 3 - - 33217 Y Y 3.45360694752736 3.52105259334297 3.45360694752736 418 0 0.998840067079714 Y 0 0.993953892996955 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.993953892996955 14455 13503 - + N 1.36431549640773 - N HCC1954 2 1.16666666666667 1 1 10 N - - Y - - 0 0 0 6 0.771308801272036 0.914143764470561 0.914143764470561 0.771308801272036 3 0 - 22147 N N 3.81145495077599 3.40215706237596 3.40215706237596 27 0.31075561606535 0.427001721168093 N 0.368192648059905 0.329901293396868 N N 0 4347 ENSG00000216979 ENSG00000140299 + - 1 15 119471437 57769025 intron upstream RP4-610L12.1 BNIP2 119470685 57738637 - - 0.329901293396868 119471002 57848302 - + Y 1 - N HCC1954 11 4.78571428571429 3 14 1 N - - N - - 0 0 0 14 0.271386430077198 0.471355378555133 0.471355378555133 0.271386430077198 2 0 - 36734 N N 3.27717235582328 3.72551845106187 3.27717235582328 0 0 0.871781257930481 N 0 0.715451895043732 N N 12 16989 ENSG00000205592 ENSG00000090615 + - 12 12 39250827 131915361 downstream intron MUC19 GOLGA3 39222629 131855568 + - 0 39372661 131908347 + + N - 2.00781861281297 Y HCC1954 23 12.95 7 20 1 N - - N - SINE 0 1 1 20 0.707033067832699 0.378512652476092 0.707033067832699 0.378512652476092 4 - 0 4135 Y Y 3.24165267149066 3.30591516961058 3.24165267149066 357 0 0.000966718830544777 Y 0 0.986704014939309 N N 142494 106 ENSG00000106211 ENSG00000177679 - + 7 7 75771548 75754539 upstream downstream HSPB1 AC005077.11 75769859 75669152 + + 0 75769668 75759329 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.414221393275723 0.421363141435649 0.421363141435649 0.414221393275723 1 - - 49270 Y Y 3.45872825368684 3.18611454994968 3.18611454994968 0 0 0.857992132596432 Y 0 0 N N 29911 12950 ENSG00000145494 ENSG00000171421 - - 5 5 1869161 1852946 coding upstream NDUFS6 MRPL36 1854509 1851499 + - 0 1854662 1853462 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE,LINE 0 0.620689655172414 0.620689655172414 19 1.12839620926835 1.3069399132665 1.3069399132665 1.12839620926835 2 - - 29600 Y Y 3.80144573217181 3.6329237143086 3.6329237143086 2 0 0.0780242323827398 Y 0 0.985963893325589 N N 599 0 ENSG00000047936 ENSG00000219703 - - 6 6 117853711 117860298 coding downstream ROS1 RP1-92C8.2 117716223 117859447 - + 0 117846348 117870337 + - N - - N HCC1954 4 1.125 1 1 1 N - - Y - LTR 0 1 1 24 1.1426797055882 0.849868031031224 1.1426797055882 0.849868031031224 1 - - 33231 N N 3.11232376639641 3.45140766923839 3.11232376639641 34 0 0.0429249420217918 N 0 0 Y N 0 336285 ENSG00000210156 ENSG00000198868 - + MT MT 8365 12138 intron coding AF347015.1-16 MT-ND4 8296 10471 + + 0 8302 11807 - + N 1 - N HCC1954 4 1.75 1 8 1 N 189 4.09957 N - - 0 0 0 16 1.08554572030879 1.15696320190805 1.15696320190805 1.08554572030879 1 0 - 19191 N N 3.41103992525442 3.60781447616429 3.41103992525442 26 0.109806798728295 0.980444748261015 N 0.183989565500937 0 Y N 10857 14045 ENSG00000085832 ENSG00000117859 + + 1 1 51757583 52026729 intron coding EPS15 OSBPL9 51592523 51815439 - + 0 51727088 51890301 - + N 1.45624971499884 - N HCC1954 1 1 1 0 4 N - - N LTR - 1 0 1 5 0.599906845433805 0.907002016310634 0.907002016310634 0.599906845433805 4 0 - 36208 Y Y 2.96319769112561 3.53106181194715 2.96319769112561 342 0 0.00690478664797656 Y 0 0.982809034079452 N N 779 12958 ENSG00000050438 ENSG00000139629 - - 12 12 50177913 50071467 intron intron SLC4A8 GALNT6 50071399 50032100 + - 0 50071679 50063784 - + N 0.197701299225181 42.0285288627606 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 113 0.585623349113953 0.999844742389676 0.999844742389676 0.585623349113953 2 0 0 17619 Y Y 3.58320909912975 3.76695911760908 3.58320909912975 327 0 0.143407722279179 Y 0 0.987459850364472 N N 2967 0 ENSG00000120656 ENSG00000209804 - - 1 1 28842172 28847832 utr5p upstream TAF12 U11 28802200 28847699 - + 0 28821264 28847304 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.635615586233437 0.835584534711372 0.835584534711372 0.635615586233437 4 - - 23390 N N 3.56129235625094 3.12379021029355 3.12379021029355 0 0 0.281448674779879 N 0.48218487394958 0.0838655462184874 N N 342 4806 ENSG00000219665 ENSG00000196352 - + 19 1 11999553 205600934 intron intron AC008770.7-4 CD55 11959471 205561488 + + 0.0838655462184874 11975216 205565029 - + Y 2.49241491142571 2.38556922946302 N HCC1954 2 1.4 1 2 1 N - - N SINE SINE 1 0.714285714285714 1 5 0.392796148795944 0.299953422716903 0.392796148795944 0.299953422716903 0 0 0 41460 Y Y 3.78105657260285 3.18825104750635 3.18825104750635 251 0 0.186923388936886 Y 0.912116240918678 0.980470275759706 N N 4035 0 ENSG00000008853 ENSG00000210402 - + 8 8 22933655 22891585 upstream downstream RHOBTB2 AC107959.8 22913059 22891335 + + 0 22905523 22901021 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.785592297591888 0.599906845433805 0.785592297591888 0.599906845433805 4 - - 21523 N Y 3.33528047801382 3.26191384998362 3.26191384998362 12 0 0.327951087031291 N 0.456876456876457 0.741369741369741 N N 8013 42144 ENSG00000143367 ENSG00000135046 + + 1 9 149822683 74975129 downstream utr5p TUFT1 ANXA1 149779405 74956601 + + 0.0430680430680431 149824714 74956659 + + Y - 2.25033719092328 N HCC1954 2 1.25 1 1 1 N - - N SINE - 1 0 1 4 0.264244681917271 0.307095170876829 0.307095170876829 0.264244681917271 2 - 0 25461 N N 3.44975210485255 3.58424216889964 3.44975210485255 0 0 0.047920032052202 N 0 0 N N 33105 0 ENSG00000105372 ENSG00000221198 + + 19 13 47067322 49835374 coding upstream RPS19P3 AL138696.16 47055828 49835285 + + 0 47065658 49745922 + + Y - - N HCC1954 26 20.1666666666667 15 6 1 N - - N - SINE 0 1 1 6 0.478497126715059 0.335662163516534 0.478497126715059 0.335662163516534 1 - - 33082 N Y 2.87060295437234 3.33358506083463 2.87060295437234 361 0 0.246168755196553 Y 0 0.986523920041926 N N 339915 544065 ENSG00000198727 ENSG00000198744 - + MT MT 15882 9988 coding coding MT-CYB MT-CO3 14748 8367 + + 0 14764 9693 - + N 0.343791605542793 1.46424083953864 N HCC1954 2 1.75 1 3 5 N - - N - - 0 0 0 4 0.635615586233437 0.742741808632331 0.742741808632331 0.635615586233437 2 0 0 47452 Y Y 3.66273010308932 3.64231043829683 3.64231043829683 0 0 0.709366469280732 Y 0.0662510276788162 0.987873389969855 N Y 521 2375 ENSG00000204517 ENSG00000178935 - - 19 19 63045300 63018093 utr5p upstream AC010522.3 ZNF552 63042237 63010262 + - 0 63044018 63016474 - + N - - N HCC1954 3 2.07692307692308 1 11 3 Y - - Y - LTR 0 1 1 13 0.857009779191151 0.499922371194838 0.857009779191151 0.499922371194838 2 - - 14849 N N 3.25256697878875 3.50272957331379 3.25256697878875 0 0 0.0742487182770789 N 0 0 N N 49089 3114 ENSG00000117450 ENSG00000149177 - - 1 11 45760196 48148969 coding upstream PRDX1 PTPRJ 45749295 47958686 - + 0 45757275 47900184 + - Y - - N HCC1954 21 11.6666666666667 1 8 1 N - - N - SINE 0 1 1 9 0.621332089913584 0.378512652476092 0.621332089913584 0.378512652476092 2 - - 46669 N Y 3.47233119514066 2.80359838893421 2.80359838893421 13 0 0.0293445055665366 N 0.781969447034354 0.781969447034354 N N 7083 73 ENSG00000167674 ENSG00000109743 - - 19 4 4453213 15343508 coding upstream AC011498.7-2 BST1 4423255 15313739 + + 0 4447950 15292049 - - Y - - N HCC1954 27 23.2222222222222 21 9 1 N - - N SINE - 1 0 1 9 0.335662163516534 0.778450549431962 0.778450549431962 0.335662163516534 2 - - 34298 Y Y 3.28193228719199 3.62295434849776 3.28193228719199 249 0 0.00875399442969071 Y 0.784003483814777 0.988000193545265 N N 0 54 ENSG00000172724 ENSG00000187186 + - 9 9 34681274 34656025 downstream intron CCL19 AL162231.20-1 34679564 34655027 - - 0 34668129 34655796 - + N - 0.325911069580874 N HCC1954 40 14 1 6 1 N - - Y LTR - 1 0 1 7 0.821301038391519 0.771308801272036 0.821301038391519 0.771308801272036 2 - 0 424 Y Y 3.62295434849776 3.42886843174363 3.42886843174363 0 0 0.678675198434471 Y 0.978012564249001 0.985341709499334 N N 14 2381 ENSG00000134940 ENSG00000149554 + + 11 11 125056152 125030847 intron utr3p ACRV1 CHEK1 125047440 125001547 - + 0 125051033 125030452 - + N 0.873893857656634 - N HCC1954 20 4.42857142857143 1 3 1 N - - Y SINE - 1 0 1 7 0.99270299422975 0.828442786551446 0.99270299422975 0.828442786551446 4 0 - 31333 Y Y 3.39640391403072 3.38230645903694 3.38230645903694 276 0 0.204126325731663 Y 0 0.990774288781535 N N 0 95 ENSG00000207650 ENSG00000215837 - + 3 3 196911548 196900773 upstream downstream hsa-mir-570 AC069513.28-2 196911452 196900191 + + 0 196911083 196901492 - + N - - N HCC1954 2 1.25 1 6 2 N - - Y LTR - 0.163398692810458 0 0.163398692810458 24 1.09268746846872 0.735600060472404 1.09268746846872 0.735600060472404 1 - - 8686 N N 3.58337693299909 3.46335504630636 3.46335504630636 0 0.191977297131462 0.343464909672868 N 0.210768522779567 0.210768522779567 N N 6235 0 ENSG00000213977 ENSG00000213860 - + 17 7 3518722 20009181 intron downstream TAX1BP3 AC005062.1 3512939 20008913 - + 0.210768522779567 3515743 20009374 + + Y 1.29700983722277 - N HCC1954 15 10 9 6 1 N - - N - - 0 0 0 6 0.264244681917271 0.478497126715059 0.478497126715059 0.264244681917271 1 0 - 26628 N Y 3.38020046670381 3.35257042827311 3.35257042827311 245 0 0.0282960460498663 Y 0 0 N N 11 9024 ENSG00000184697 ENSG00000127564 + - 16 16 3010073 2970506 downstream upstream CLDN6 PKMYT1 3004714 2962793 - - 0.973791621911923 2988810 2987090 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.93556900895034 0.385654400636018 0.93556900895034 0.385654400636018 2 - - 26704 Y Y 3.41584813211242 3.42424163912411 3.41584813211242 182 0 0.0163962431751047 Y 0 0 N N 13930 1567 ENSG00000205730 ENSG00000167186 - + 16 16 19040447 18998851 upstream downstream ITPRIPL2 COQ7 19032783 18986428 + + 0 19031795 19012250 - + N - - N HCC1954 2 1.25 1 1 1 N - - Y SINE LTR,LTR 0.847826086956522 1 1 4 0.871293275511003 0.93556900895034 0.93556900895034 0.871293275511003 3 - - 37882 N Y 3.24272559405391 3.47721910758536 3.24272559405391 1 0 0.318650799205063 N 0.135326125362165 0.859020563917744 N N 78560 0 ENSG00000112493 ENSG00000222136 + - 6 14 33390114 49390382 utr3p intron TAPBP SRP_euk_arch 33375449 49390086 - - 0 33376318 49390352 - + Y - 1 N HCC1954 266 86.5 7 12 1 N - - N SINE srpRNA,srpRNA 1 1 1 12 0.792734045751814 0.592765097273879 0.792734045751814 0.592765097273879 2 - 0 4985 Y Y 3.27861600074711 3.33680806132368 3.27861600074711 0 0 0.511016668651794 Y 0 0 N N 5744 32858 ENSG00000155034 ENSG00000182095 + - 7 7 5523646 5431571 coding intron FBXL18 TNRC18B 5481955 5312952 - - 0 5488075 5400755 - + N - 64.6389041340244 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 6 0.971277749749971 0.928427260790413 0.971277749749971 0.928427260790413 2 - 0 2402 N N 3.68783934123363 3.62568283544685 3.62568283544685 0 0 0.36306196400035 N 0.505608069005429 0.733788960233692 N N 3301 7118 ENSG00000070081 ENSG00000137145 - + 11 9 17309646 19364139 intron utr3p NUCB2 DENND4C 17254860 19280749 + + 0 17273446 19362689 - + Y 0.997231916409902 - N HCC1954 28 22.8333333333333 20 6 1 N - - N - SINE 0 1 1 6 0.614190341753658 0.328520415356608 0.614190341753658 0.328520415356608 1 0 - 48963 Y Y 3.55025006787687 3.39384326095097 3.39384326095097 300 0 0.00161078148424521 Y 0 0.987056277056277 N N 4559 7 ENSG00000051596 ENSG00000145920 + + 5 5 175328151 175243629 coding downstream THOC3 CPLX2 175319142 175156216 - + 0 175320704 175277701 - + N 0.611879347429833 - N HCC1954 40 12 2 7 1 N - - Y - SINE 0 1 1 7 0.799875793911741 1.07126222398894 1.07126222398894 0.799875793911741 1 0 - 10453 Y N 3.52614339427891 3.43784458057793 3.43784458057793 7 0.0121487299055099 0.448557038554009 Y 0.0121487299055099 0 N N 28240 9513 ENSG00000136450 ENSG00000136451 + - 17 17 53439706 53420614 coding upstream SFRS1 VEZF1 53433283 53403909 - - 0 53437946 53422177 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.821301038391519 0.714174815992626 0.821301038391519 0.714174815992626 2 - - 32955 N Y 2.99376390316809 3.26720299001245 2.99376390316809 320 0 0.727910125399914 Y 0 0.992979753521127 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0.992979753521127 8399 6408 - + N 0.806109216236245 - N HCC1954 2 1.44444444444444 1 4 5 Y - - N - - 0 0 0 9 1.07126222398894 1.31408166142643 1.31408166142643 1.07126222398894 4 0 - 22268 N Y 3.61616813038263 3.61360747730288 3.61360747730288 1 0 0.484882351740283 N 0.8419452887538 0.826139817629179 N N 21 33725 ENSG00000124116 ENSG00000143819 + - 20 1 43853954 224099884 downstream utr5p WFDC3 EPHX1 43822388 224064459 - + 0 43821757 224083049 - - Y - 0.14530690475875 N HCC1954 21 19 9 6 1 N - - N LTR - 1 0 1 6 0.39993789695587 0.414221393275723 0.414221393275723 0.39993789695587 4 - 0 34390 Y Y 3.44785379918211 3.46448140203209 3.44785379918211 382 0.00261780104712039 0.00157462774781669 Y 0.00261780104712039 0.989275460226313 N N 796 3850 ENSG00000171097 ENSG00000198917 + - 9 9 130684175 130631906 utr3p upstream CCBL1 C9orf114 130635213 130624167 - - 0 130635328 130632106 - + N 0.627084535152805 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 1.02126998686945 0.678466075192994 1.02126998686945 0.678466075192994 1 0 - 45136 N N 3.09087103183403 3.50951579142893 3.09087103183403 7 0 0.109932955584622 N 0 0 N N 3891 0 ENSG00000166295 ENSG00000174681 + - 10 10 73665622 94419480 intron upstream C10orf104 AL590080.25-1 73645812 94418509 + - 0 73645953 94421302 + + N 0.744979490524871 - Y HCC1954 34 19.25 10 4 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.378512652476092 0.39993789695587 0.378512652476092 1 0 - 9425 Y Y 3.41592783769912 3.49015970162987 3.41592783769912 253 0 0.0240237186136317 Y 0.9900395256917 0.980079051383399 N N 796 505 ENSG00000166582 ENSG00000108474 + + 17 17 16197537 16170286 utr3p downstream CENPV PIGL 16186574 16061234 - + 0 16186612 16170944 - + N 0.345690311475952 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 4 0.757025304952183 0.714174815992626 0.757025304952183 0.714174815992626 4 0 - 36407 Y Y 3.44359772892318 2.90616249149831 2.90616249149831 344 0 0.0012751170030314 Y 0 0 N N 5028 2783 ENSG00000180818 ENSG00000123388 - + 12 12 52670327 52656468 coding intron HOXC10 HOXC11 52665213 52653177 + + 0 52665531 52653994 - + N 0.58248014951777 1.17209593025809 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.857009779191151 0.828442786551446 0.857009779191151 0.828442786551446 1 0 0 3294 N N 3.48167806633553 3.65760879692984 3.48167806633553 0 0.00662251655629142 0.0934163146618114 N 0.0219052470708099 0.00662251655629142 N N 2718 188 ENSG00000168876 ENSG00000152503 + - 11 5 93872385 114544142 coding downstream ANKRD49 TRIM36 93866801 114488377 + - 0.00662251655629142 93871038 114467600 + + Y 1.1277863937651 - N HCC1954 19 4.6 1 1 1 N 290 2.9811 N - SINE 0 1 1 5 0.549914608314322 0.621332089913584 0.621332089913584 0.549914608314322 2 0 - 11971 N N 3.07101108092519 3.53615261288309 3.07101108092519 0 0 0.205438992528 N 0.606641036981594 0.790766509032763 N N 1649619 0 ENSG00000141736 ENSG00000218856 - + 17 20 35138441 4942370 coding upstream ERBB2 RP5-1116H23.1 35104766 4942166 + - 0 35125066 4945926 - - Y - - N HCC1954 20 17 2 6 1 N - - N - SINE 0 1 1 6 0.635615586233437 0.328520415356608 0.635615586233437 0.328520415356608 1 - - 25458 N Y 3.57800808738356 3.30484224704734 3.30484224704734 0 0 0.406025017690916 N 0 0 N N 17943 5979 ENSG00000105141 ENSG00000132953 + - 19 13 15027900 20374949 downstream intron CASP14 XPO4 15024015 20249469 + - 0 15029502 20331299 + + Y - 0.975678944604997 N HCC1954 20 16.9 1 9 1 N - - N - SINE 0 1 1 10 0.664182578873142 0.299953422716903 0.664182578873142 0.299953422716903 3 - 0 32725 N N 3.40847927217468 3.69209541149257 3.40847927217468 0 0 0.0473819605291999 N 0 0.015896103896104 N N 1139 10 ENSG00000132570 ENSG00000077092 - - 5 3 134326223 25614424 intron intron PCBD2 RARB 134268709 25190893 + + 0.015896103896104 134290493 25483922 - - Y 1.57189749691755 0.745489078822412 N HCC1954 3 2 1 3 1 N - - N - LTR 0 1 1 5 0.578481600954027 0.292811674556976 0.578481600954027 0.292811674556976 1 0 0 10260 Y Y 3.61038447681384 3.38912318237562 3.38912318237562 268 0 0.0153147905731210 Y 0.975501590408613 0.991833863469538 N N 2826 11533 ENSG00000170291 ENSG00000175826 - - 17 17 7103974 7095983 utr5p coding C17orf81 DULLARD 7096096 7087655 + - 0.991833863469538 7096467 7095259 - + N - 3.17643049496671 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.757025304952183 0.785592297591888 0.785592297591888 0.757025304952183 2 - 0 39544 N Y 3.44781394638876 3.52680574168821 3.44781394638876 245 0 0.0902024394609949 N 0.826796805678794 0.696894409937888 N N 8888 1 ENSG00000112159 ENSG00000166206 + - 6 15 90586163 24767329 intron intron MDN1 GABRB3 90409952 24339786 - - 0.913398402839397 90487731 24441765 - + Y 1.96227421382155 1.01325966850829 N HCC1954 2 1.57142857142857 1 4 1 N - - N - - 0 0 0 7 0.692749571512847 0.385654400636018 0.692749571512847 0.385654400636018 3 0 0 18561 Y Y 3.32679884271949 3.44871903508266 3.32679884271949 152 0 0.0311384293781148 Y 0 0.962512413108242 N N 500 528 ENSG00000164002 ENSG00000187815 - + 1 1 40754799 40734602 upstream intron DEM1 ZNF642 40747000 40715474 + + 0 40746890 40725617 - + N - 0.989775252934465 N HCC1954 9 3 1 1 2 N - - Y - DNA 0 1 1 4 0.499922371194838 0.642757334393363 0.642757334393363 0.499922371194838 0 - 0 8295 N N 3.6491271616355 3.56232542602083 3.56232542602083 0 0 0.610903854798924 N 0 0 N N 0 51 ENSG00000182152 ENSG00000115290 + - 5 2 117142614 165186606 downstream intron AC114322.2 GRB14 117142420 165057579 - - 0 116871211 165138552 - + Y - 1.67260042593817 N HCC1954 2 2 2 138 3 N - - N DNA - 0.703030303030303 0 0.703030303030303 138 1.17838844638783 0.478497126715059 1.17838844638783 0.478497126715059 2 - 0 31341 Y Y 3.88465374493685 3.26034641388042 3.26034641388042 273 0 0.118372331231635 Y 0 0 N N 279 4066 ENSG00000164088 ENSG00000221814 - - 3 3 52259653 52248223 upstream upstream PPM1M TWF2 52255226 52237670 + - 0 52254185 52248491 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.828442786551446 0.549914608314322 0.828442786551446 0.549914608314322 4 - - 17763 N N 3.55290903461324 3.55231620741665 3.55231620741665 0 0 0.256733687002753 N 0 0.00980392156862753 N N 49089 2080 ENSG00000117450 ENSG00000067208 - - 1 1 45760196 93030549 coding intron PRDX1 EVI5 45749295 92746841 - - 0 45754020 92875477 + + N 1.6278638153223 0.589774829039507 Y HCC1954 20 4.77777777777778 2 9 2 N - - N - SINE 0 1 1 9 0.385654400636018 0.257102933757345 0.385654400636018 0.257102933757345 2 0 0 9857 Y Y 3.66745018166468 3.34252135687557 3.34252135687557 14 0 0.689885835235484 Y 0.0115945356445872 0 N Y 4004 16540 ENSG00000167862 ENSG00000109089 - + 17 17 70528950 70513490 coding coding ICT1 CDR2L 70520371 70495322 + + 0 70524768 70509918 - + N - 0.782448514219587 N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 9 1.07126222398894 0.871293275511003 1.07126222398894 0.871293275511003 4 - 0 13457 N N 3.41998556886518 3.43461223251907 3.41998556886518 33 0.197048077270919 0.0463218867646551 N 0.197048077270919 0.197048077270919 N N 8740 194 ENSG00000169919 ENSG00000169325 + - 7 22 65084681 22389508 coding downstream GUSB AP000347.1 65063106 22386399 - - 0 65078525 22382048 - + Y - - N HCC1954 3 2 1 3 1 N - - N - LINE 0 0.453125 0.453125 4 0.271386430077198 0.45707188223528 0.45707188223528 0.271386430077198 2 - - 34581 Y Y 3.28449294027173 3.24103017687471 3.24103017687471 0 0 0.537211495083785 Y 0 0.9585027100271 N N 7898 1190 ENSG00000167112 ENSG00000175854 + + 9 9 130124518 130091088 intron coding TRUB2 C9orf119 130111224 130077541 - + 0 130117522 130088131 - + N 1.28491977167205 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.721316564152552 0.521347615674617 0.721316564152552 0.521347615674617 3 0 - 46752 Y Y 3.44040523365767 3.0463658510973 3.0463658510973 430 0 0.00952807623887642 Y 0.1282003912193 0.99533797000652 N N 45374 7369 ENSG00000160007 ENSG00000042753 - - 19 19 52199404 52046043 upstream upstream GRLF1 AP2S1 52113773 52033263 + - 0 52113586 52056307 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity,Simple_repeat 0 0.167420814479638 0.167420814479638 325 1.61403508414333 1.5783263433437 1.61403508414333 1.5783263433437 1 - - 41478 Y Y 3.42204236083514 3.40169305405954 3.40169305405954 338 0 0.0272777804783072 Y 0.262751062588549 0.992978581548462 N N 2163 46928 ENSG00000178685 ENSG00000178209 + - 8 8 145132623 145121531 downstream upstream PARP10 PLEC1 145123309 145061309 - - 0.992978581548462 145122862 145121534 - + N - - N HCC1954 1 1 1 0 1 N - - Y Low_complexity - 0.529411764705882 0 0.529411764705882 50 1.09268746846872 1.12839620926835 1.12839620926835 1.09268746846872 2 - - 33095 N Y 3.50529022639353 3.1825606798934 3.1825606798934 461 0 0.0402932353659006 Y 0 0.983182626922421 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0 10975 5449 - + N 0.53740631802697 1.53136739020212 N HCC1954 6 2.2 1 2 4 Y - - N - - 0 0 0 5 1.04269523134923 1.02841173502938 1.04269523134923 1.02841173502938 3 0 0 38042 N N 2.80103773585447 2.6718368118362 2.6718368118362 0 0.189904111098865 0.181738344839015 N 0.421360079356332 0.189904111098865 N N 73 11502 ENSG00000205533 ENSG00000159921 - - 14 9 89811638 36248450 intron utr3p AL161662.6 GNE 89807959 36204430 - - 0.189904111098865 89810903 36206342 + + Y - - N HCC1954 39 35.3076923076923 30 13 1 N - - N Simple_repeat LINE 0.945454545454545 0.303571428571429 0.945454545454545 13 0.392796148795944 0.799875793911741 0.799875793911741 0.392796148795944 1 - - 3462 N N 3.2378376816092 3.2305569499541 3.2305569499541 0 0 0.676814428554998 N 0 0 Y N 0 542 ENSG00000209722 ENSG00000160191 - + 21 21 17725836 43068688 upstream downstream AP000952.2 PDE9A 17725745 42946931 + + 0 17662757 43084678 - + N - - N HCC1954 1 1 1 0 2 N 55 7.82755 N - LTR 0 1 1 5 0.407079645115797 0.521347615674617 0.521347615674617 0.407079645115797 2 - - 11085 N Y 3.42680229220385 3.77680050234392 3.42680229220385 244 0.715456674473068 0.0110295864598287 N 0.739168618266979 0.715456674473068 N N 0 0 ENSG00000201398 ENSG00000214799 + + 3 17 155207981 21348978 upstream intron U8 AC138710.5-1 155207846 21348468 - + 0.810304449648712 155224425 21348587 - + Y - 1 N HCC1954 42 41.0344827586207 36 29 1 N - - N - - 0 0 0 29 0.271386430077198 0.442788385915428 0.442788385915428 0.271386430077198 1 - 0 21931 N N 3.61360747730288 3.44785379918211 3.44785379918211 0 0 0.0452416674806599 N 0 0 N N 49089 0 ENSG00000117450 ENSG00000204603 - + 1 12 45760196 130263428 coding downstream PRDX1 AC126564.7 45749295 130215509 - + 0 45757256 130287452 + + Y - - N HCC1954 40 19.6818181818182 5 22 1 N - - N - SINE 0 1 1 22 0.792734045751814 0.314236919036755 0.792734045751814 0.314236919036755 1 - - 34144 Y Y 3.22270715684554 3.707857778442 3.22270715684554 195 0 0.990178743070753 Y 0.0723492723492725 0.973111573111573 N N 22394 168 ENSG00000107036 ENSG00000197646 - + 9 9 5766555 5565421 upstream downstream KIAA1432 PDCD1LG2 5619120 5500579 + + 0 5611428 5567483 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 55 0.914143764470561 1.09982921662864 1.09982921662864 0.914143764470561 4 - - 42204 Y Y 3.74913061111987 3.48912663185998 3.48912663185998 369 0 0.232680583611218 Y 0.994133588394707 0.982400765184122 N N 73 5741 ENSG00000109743 ENSG00000118564 - - 4 4 15343508 15266111 upstream upstream BST1 FBXL5 15313739 15215252 + - 0 15292001 15278761 - + N - - N HCC1954 26 6.51162790697674 1 19 3 N - - Y - SINE 0 1 1 43 1.24980592798709 1.1426797055882 1.24980592798709 1.1426797055882 4 - - 47340 N N 3.79040344379773 3.35100299216991 3.35100299216991 11 0.0701058201058202 0.103054696959226 N 0 0.00308641975308643 Y N 8826 197 ENSG00000167747 ENSG00000197124 - + 19 19 55999786 20011277 utr5p upstream C19orf48 ZNF682 55992774 19976227 - - 0 55997677 20026180 + - N - - N HCC1954 21 15.75 12 4 1 N - - N - SINE 0 1 1 4 0.349945659836387 0.235677689277566 0.349945659836387 0.235677689277566 3 - - 12057 N Y 3.35872480420248 3.67849247003875 3.35872480420248 225 0.923418803418803 0.0682613039203297 N 0.923418803418803 0.923418803418803 N N 24464 9 ENSG00000101166 ENSG00000173838 - - 20 17 57051296 58239437 coding upstream SLMO2 MARCH10 57041596 58132408 - - 0.923418803418803 57043576 58272612 + + Y - - N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.0101010101010101 0 0.0101010101010101 7 0.707033067832699 0.45707188223528 0.707033067832699 0.45707188223528 3 - - 24516 N N 3.38230645903694 3.5246463161926 3.38230645903694 15 0 0.628365643303706 N 0.457917850684578 0 N N 250 1 ENSG00000125618 ENSG00000168738 + + 2 18 113752958 10861413 intron upstream PAX8 C18orf58 113690045 10784068 - - 0.0545078791010075 113729437 11233246 - - Y 4.6738572162301 - N HCC1954 7 2.5 1 1 1 N - - N - SINE 0 1 1 4 0.392796148795944 0.314236919036755 0.392796148795944 0.314236919036755 4 0 - 46605 N Y 3.74913061111987 3.48912663185998 3.48912663185998 0 0 0.215041767761412 N 0.897359821121431 0.882696938424493 N N 73 1070 ENSG00000109743 ENSG00000120784 - + 4 19 15343508 42838153 upstream utr3p BST1 ZFP30 15313739 42815229 + - 0 15292001 42816113 - - Y - - N HCC1954 33 22.5555555555556 3 9 1 N - - N - SINE 0 1 1 9 1.10697096478857 0.364229156156239 1.10697096478857 0.364229156156239 3 - - 17847 Y Y 3.56914214935951 3.43681151080804 3.43681151080804 136 0 0.851863483176786 Y 0.99013709063214 0.98027418126428 N Y 43044 10731 ENSG00000143570 ENSG00000160741 + - 1 1 152206812 152197725 coding coding SLC39A1 CRTC2 152198210 152186775 - - 0 152201320 152194266 - + N - 2.03639138127073 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 14 1.0069864905496 0.771308801272036 1.0069864905496 0.771308801272036 4 - 0 10208 N N 3.50744965188915 3.34884356667429 3.34884356667429 0 0 0.316174672923246 N 0.958607456140351 0 N N 1620 0 ENSG00000176681 ENSG00000213330 - - 17 17 41770918 41020078 coding upstream LRRC37A AC126544.5-1 41726926 41019020 + + 0 41755502 41017721 - - N - - Y HCC1954 4 3 2 4 2 N 461 16.1917 N - - 0 0 0 4 0.735600060472404 0.428504889595575 0.735600060472404 0.428504889595575 3 - - 48016 N N 3.27398920812759 3.36609366414022 3.27398920812759 0 0 0.995476525070911 N 0 0.00313479623824453 N N 0 10798 ENSG00000212451 ENSG00000113761 - - 8 5 127753081 176426349 downstream intron U11 ZNF346 127752949 176382303 + + 0.00313479623824453 128071976 176410357 - - Y - 1.34575632127257 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 9 1.15696320190805 1.17124669822791 1.17124669822791 1.15696320190805 1 - 0 46762 Y Y 3.59425138750382 2.84806371687758 2.84806371687758 158 0 0.95127587255395 Y 0 0.984227446252763 N N 53269 3636 ENSG00000129353 ENSG00000129354 - - 19 19 10616233 10558991 intron upstream SLC44A2 AP1M2 10597229 10544347 + - 0 10599389 10574185 - + N 0.318219361537369 - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.032258064516129 0.032258064516129 226 0.549914608314322 0.885576771830856 0.885576771830856 0.549914608314322 2 0 - 41864 N N 2.87064280716569 3.37126417066287 2.87064280716569 0 0 0.989275937974254 N 0 0 N N 29840 30 ENSG00000164830 ENSG00000212993 + + 8 8 107834093 128498621 utr5p upstream OXR1 POU5F1P1 107739270 128497039 + + 0 107739588 128160561 + + N 1.03064103887627 - Y HCC1954 1 1 1 0 4 N 607 3.86243 N - LINE,LINE 0 0.543624161073825 0.543624161073825 88 1.8497127734209 1.06412047582901 1.8497127734209 1.06412047582901 1 0 - 9767 Y Y 3.67167574670007 3.43312450200257 3.43312450200257 0 0 0.94979268331033 Y 0.305555555555556 0.94047619047619 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron coding C17orf76 C17orf45 16286053 16283081 - + 0 16314402 16285115 - + N 3.43189971253672 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 4 0.771308801272036 0.621332089913584 0.771308801272036 0.621332089913584 1 0 - 4237 Y Y 3.5816815158199 3.66848325143457 3.5816815158199 264 0 0.543477889863747 Y 0.697778345250255 0.966419816138917 N N 0 0 ENSG00000223022 ENSG00000209951 + - 7 7 86961 86960 downstream downstream U6 AC097646.2-1 86858 86858 - - 0 84841 75414 - + N - - N HCC1954 210 65 8 10 3 N - - Y - LTR,SINE 0 0.661290322580645 0.661290322580645 10 0.635615586233437 1.15696320190805 1.15696320190805 0.635615586233437 4 - - 27946 N Y 3.41376841220351 3.49164743214637 3.41376841220351 0 0 0.255041020598768 N 0.851932010135135 0.838471283783784 N N 0 45068 ENSG00000147117 ENSG00000205336 - + X 16 47158042 56256445 intron upstream ZNF157 GPR56 47114943 56220023 + + 0 47152785 56211297 - + Y 1 - N HCC1954 20 13.8125 7 48 1 N - - N SINE - 1 0 1 48 0.34280391167646 0.707033067832699 0.707033067832699 0.34280391167646 1 0 - 33844 N N 2.89104554710378 3.72721386824106 2.89104554710378 8 0 0.492912252731968 N 0 0.00809141184582685 Y N 59837 275222 ENSG00000198695 ENSG00000198763 - - MT MT 14674 5512 coding coding MT-ND6 MT-ND2 14150 4471 - + 0.00809141184582685 14665 5016 + - N - 0.970627199553403 N HCC1954 8 3 1 3 2 N 106 8.09281 N - - 0 0 0 5 1.26408942430695 0.914143764470561 1.26408942430695 0.914143764470561 3 - 0 894 N Y 3.47080361183081 3.62977107183644 3.47080361183081 3 0 0.553979297417975 N 0 0.718754325259516 N N 0 9180 ENSG00000199629 ENSG00000014138 - + 7 11 53401402 64821663 upstream coding U1 POLA2 53401245 64786006 + + 0 53338458 64820035 - + Y - - N HCC1954 17 13.5 12 4 1 N - - N SINE - 1 0 1 4 0.357087407996313 0.442788385915428 0.442788385915428 0.357087407996313 1 - - 4415 Y Y 3.54400240599166 3.24057974892742 3.24057974892742 351 0 0.82952196884016 Y 0 0.992329607714223 N N 6349 2784 ENSG00000126522 ENSG00000169910 - + 7 7 65256986 65195756 upstream downstream CRCP ASL 65216341 65178207 + + 0 65212710 65202608 - + N - - N HCC1954 1 1 1 0 6 N - - Y LTR Simple_repeat,Simple_repeat 1 0.274336283185841 1 6 0.714174815992626 0.807017542071667 0.807017542071667 0.714174815992626 1 - - 32140 N Y 3.31063524818594 3.40016547074969 3.31063524818594 9 0 0.27742663384218 N 0.925677733780079 0.925677733780079 N N 12271 312 ENSG00000177479 ENSG00000197343 - - 3 7 48997971 99012008 utr5p utr3p ARIH2 ZNF655 48931285 98993981 + + 0 48935242 99010978 - - Y - - N HCC1954 56 28.8333333333333 23 24 1 N - - N Simple_repeat SINE 0.0123456790123457 1 1 24 0.578481600954027 0.335662163516534 0.578481600954027 0.335662163516534 2 - - 3425 N N 3.1772964287526 2.81304999724539 2.81304999724539 0 0 0.0404270523167131 Y 0 0 N N 0 488 ENSG00000210058 ENSG00000160233 - + 21 21 44717207 44703158 downstream utr5p AP001065.1-1 LRRC3 44717141 44699821 + + 0 44720097 44699824 - + N - 0.0631744262627286 N HCC1954 1 1 1 0 1 N - - N LTR Low_complexity 0.784810126582278 0.183673469387755 0.784810126582278 5 0.564198104634174 0.699891319672773 0.699891319672773 0.564198104634174 0 - 0 18370 Y Y 3.73080759109069 3.74913061111987 3.73080759109069 230 0 0.00799460741446500 Y 0 0 N N 132 0 ENSG00000215866 ENSG00000198789 + + 1 1 113194788 113092620 downstream downstream AL603832.28-3 AL603832.28-2 113164319 113092240 - + 0 113141791 113106866 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE SINE 0.112745098039216 1 1 9 1.22123893534739 0.649899082553289 1.22123893534739 0.649899082553289 3 - - 20055 N Y 3.40744620240479 3.43681151080804 3.40744620240479 0 0.00295857988165671 0.0753375722129171 N 0 0 N N 2873 75177 ENSG00000127124 ENSG00000125107 + + 1 16 42156965 57221251 intron utr5p HIVEP3 CNOT1 41744623 57111359 - - 0 42064762 57190762 - - Y 5.42060694906404 - N HCC1954 20 20 20 4 1 N 362 29.4505 N SINE - 1 0 1 4 0.292811674556976 0.314236919036755 0.314236919036755 0.292811674556976 2 0 - 37680 N Y 3.42576922243396 3.42464286670824 3.42464286670824 3 0 0.502895674391648 N 0.993354700854701 0.993354700854701 N N 1187 0 ENSG00000215394 ENSG00000218784 + - 14 22 18754290 14504973 utr5p upstream AL589743.4-2 LA16c-60H5.5 18720037 14480517 + - 0 18750683 14504975 + + Y - - N HCC1954 156 26.5833333333333 4 24 1 N - - N SINE,LTR - 0.423529411764706 0 0.423529411764706 24 1.21409718718746 1.04269523134923 1.21409718718746 1.04269523134923 2 - - 13647 Y Y 3.56232542602083 3.22639416565101 3.22639416565101 237 0 0.042429080725167 Y 0 0.988554246083709 N N 2726 0 ENSG00000177663 ENSG00000215568 - - 22 22 15971387 15869112 upstream upstream IL17RA GAB4 15945849 15822826 + - 0 15908216 15898275 - + N - - N HCC1954 2 2 2 10 2 N - - Y - - 0 0 0 10 0.657040830713216 0.864151527351077 0.864151527351077 0.657040830713216 2 - - 12545 N Y 3.6491271616355 3.76426113588353 3.6491271616355 12 0 0.486450862530344 N 0 0.902602974828375 N N 12320 20782 ENSG00000108587 ENSG00000205246 - + 17 19 25877957 23802761 utr3p downstream GOSR1 RPSAP8 25828552 23801726 + + 0.123426773455378 25874139 23803140 - + Y - - N HCC1954 63 34.6 22 5 1 N - - N Other,Other LINE 1 0.985185185185185 1 5 0.492780623034912 0.964136001590045 0.964136001590045 0.492780623034912 1 - - 10404 N N 3.40744620240479 3.46807512488172 3.40744620240479 0 0 0.732159118299382 N 0.844980842911877 0 Y Y 8390 1572 ENSG00000120071 ENSG00000136447 + - 17 17 41625943 42012364 coding intron KIAA1267 ARL17P1 41463181 41949797 - - 0 41527743 42003551 - + N - 1.25107910283559 N HCC1954 4 2.1304347826087 2 46 1 N 498 1.79514 N - - 0 0 0 46 1.09268746846872 1.02126998686945 1.09268746846872 1.02126998686945 4 - 0 45213 N Y 3.4748918482204 3.76170048280379 3.4748918482204 171 0.00584795321637421 0.0137947100132476 N 0.00584795321637421 0.879496721601985 N N 20621 342 ENSG00000107929 ENSG00000219665 + + 10 19 967440 11999553 intron utr5p LARP5 AC008770.7-4 845484 11959471 - + 0 956929 11959623 - + Y 2.68469148233476 1.84547862540645 N HCC1954 3 1.4 1 1 1 N - - N SINE - 0.864864864864865 0 0.864864864864865 5 0.264244681917271 0.585623349113953 0.585623349113953 0.264244681917271 2 0 0 21751 N Y 3.51463709758841 3.38486711211668 3.38486711211668 239 0.00418410041841011 0.118846951799471 N 0.935456376878971 0.963117929645126 N Y 14626 810 ENSG00000006831 ENSG00000154309 - + 12 1 1768105 221245958 utr5p utr5p ADIPOR2 DISP1 1670508 221112236 + + 0 1733685 221112397 - + Y - - N HCC1954 21 21 21 5 1 N - - N - LINE 0 1 1 5 0.521347615674617 0.378512652476092 0.521347615674617 0.378512652476092 4 - - 801 Y Y 3.55231620741665 3.46873747229102 3.46873747229102 116 0 0.199784773999185 Y 0.0412477620162511 0 N N 4003 0 ENSG00000078902 ENSG00000203582 + + 11 11 1287428 1246781 coding upstream TOLLIP AC136297.6 1252178 1246550 - + 0 1263811 1244817 - + N - - N HCC1954 20 4.16666666666667 1 1 1 N - - Y - LTR,LTR 0 0.58 0.58 6 0.51420586751469 0.714174815992626 0.714174815992626 0.51420586751469 2 - - 30405 Y Y 3.58320909912975 3.51529944499772 3.51529944499772 0 0 0.916532625404065 Y 0 0 N N 0 12932 ENSG00000207122 ENSG00000165175 + + X X 38825482 38550725 downstream downstream U6 MID1IP1 38825377 38545651 - + 0 38763425 38615040 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 16 1.20695543902754 1.02126998686945 1.20695543902754 1.02126998686945 1 - - 22051 N Y 3.3463227663879 3.87361145656277 3.3463227663879 0 0 0.168151614256755 N 0.831289096038268 0.855390653747087 N N 1696 2963 ENSG00000130772 ENSG00000133983 - + 1 14 28535062 69896147 downstream coding MED18 COX16 28528136 69680762 + - 0 28542838 69895990 - - Y - - N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.371370904316165 0.371370904316165 0.321378667196682 1 - - 28150 N N 3.57592836747465 3.47336426491055 3.47336426491055 2 0 0.141078436649982 N 0.406750085120872 0.585844399046646 N N 1015 16390 ENSG00000165275 ENSG00000140950 - - 9 16 37768969 83095794 utr3p intron RG9MTD3 KIAA1609 37743802 83068608 + - 0 37767855 83089222 - + Y - 1.98970794067006 N HCC1954 21 20.25 20 4 1 N - - N SINE - 1 0 1 4 0.257102933757345 0.314236919036755 0.314236919036755 0.257102933757345 1 - 0 46105 N N 3.49015970162987 1.46400562653446 1.46400562653446 10 0 0.0262188173119258 N 0.00333333333333341 0 N N 1835 850768 ENSG00000072954 ENSG00000075624 - - 19 7 16660814 5536758 downstream utr3p TMEM38A ACTB 16632938 5533313 + - 0 16665387 5533818 - + Y - 0.967442227952496 N HCC1954 38 16.8 5 5 1 N - - N SINE - 1 0 1 5 0.407079645115797 0.892718519990782 0.892718519990782 0.407079645115797 1 - 0 42001 N Y 3.36295036923788 3.57076720852182 3.36295036923788 0 0 0.106259513675251 N 0 0 N N 8783 14115 ENSG00000147697 ENSG00000136877 + + 8 9 130868316 129616377 intron intron GSDMC FPGS 130829625 129604975 - + 0.798436308161709 130830247 129608270 - + Y 0.402462401829109 0.83858490337563 N HCC1954 20 13.5 9 4 1 N - - N SINE SINE 1 1 1 4 0.34280391167646 0.407079645115797 0.407079645115797 0.34280391167646 2 0 0 26678 Y Y 3.4561676006071 3.3712946758864 3.3712946758864 263 0 0.0803641183425767 Y 0 0.988679571379191 N N 422 7487 ENSG00000184730 ENSG00000188603 - - 16 16 28417783 28411124 coding intron AC138894.2-3 CLN3 28413504 28396101 + - 0 28413922 28410425 - + N 0.10541146701938 2.85492978163712 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 17 0.635615586233437 0.692749571512847 0.692749571512847 0.635615586233437 1 0 0 36210 Y Y 3.34098442599591 3.60273302279816 3.34098442599591 399 0 0.0204631415723157 Y 0.806546669704564 0.987909166856535 N N 0 584 ENSG00000179821 ENSG00000136052 + - 12 12 103895935 103846563 downstream upstream AC090051.8 SLC41A2 103894657 103722495 - - 0 103875996 103846602 - + N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity Low_complexity 0.121338912133891 0.0116959064327485 0.121338912133891 21 1.70687781022238 1.22123893534739 1.70687781022238 1.22123893534739 4 - - 42039 N N 3.46977054206092 3.15745144174909 3.15745144174909 2 0 0.755842027011318 N 0 0 N N 0 0 ENSG00000184565 ENSG00000206719 + + Y 8 19698690 115032403 intron downstream TTTY14 Y_RNA 19553973 115032291 - + 0 19611942 115195939 - + Y 1 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.921285512630487 0.28566992639705 0.921285512630487 0.28566992639705 3 0 - 24645 Y Y 3.85425536676371 3.45400817511148 3.45400817511148 0 0 0.982060261794964 Y 0.0105649872216136 0 N Y 4163 124 ENSG00000141644 ENSG00000172361 + - 18 18 46062142 46046863 coding coding MBD1 CCDC11 46049215 46007564 - - 0 46053045 46042587 - + N - 3.10451263537906 N HCC1954 1 1 1 0 3 Y - - Y - - 0 0 0 18 1.42120788382533 0.978419497909897 1.42120788382533 0.978419497909897 4 - 0 14053 Y Y 3.306978744604 3.24165267149067 3.24165267149067 0 0 0.281567195650357 Y 0 0.982197134172818 N N 9169 1395 ENSG00000218537 ENSG00000133460 + + 22 22 22571117 22561170 utr3p coding AP000350.4 SLC2A11 22566613 22521912 - + 0 22567074 22556184 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.707033067832699 0.749883556792257 0.749883556792257 0.707033067832699 1 - - 47943 N N 3.48656597878024 3.44615838200292 3.44615838200292 0 0 0.86749454266179 N 0 0 N N 0 51629 ENSG00000208525 ENSG00000165671 - + 8 5 130372654 176655369 downstream coding AC103833.2-1 NSD1 130372411 176493532 + + 0 130419871 176571802 - + Y - 1.41929569714202 N HCC1954 1 1 1 0 1 N 57 8.55269 N LINE - 0.148936170212766 0 0.148936170212766 286 1.34264865406614 1.40692438750547 1.40692438750547 1.34264865406614 4 - 0 36852 N N 3.38912318237562 3.31485146565152 3.31485146565152 0 0 0.049397867669938 N 0 0.215751989945538 N N 17124 3163 ENSG00000111641 ENSG00000151327 - + 12 14 6547741 34622340 coding coding NOP2 C14orf24 6536290 34583864 - + 0 6543640 34585579 + + Y - - N HCC1954 30 29.8888888888889 29 9 1 N - - N SINE - 1 0 1 9 0.307095170876829 0.821301038391519 0.821301038391519 0.307095170876829 1 - - 18131 Y N 3.17504933363665 3.71976530271662 3.17504933363665 0 0 0.873228363997273 Y 0 0 N N 17101 0 ENSG00000162407 ENSG00000219539 + - 1 1 56817845 56446716 downstream upstream PPAP2B RP4-710M16.1 56733023 56445827 - - 0 56613483 56487417 - + N - - N HCC1954 1 1 1 0 4 N - - Y - LINE 0 0.582089552238806 0.582089552238806 5 0.428504889595575 0.699891319672773 0.699891319672773 0.428504889595575 2 - - 36400 Y Y 3.63552422018169 3.19806192701765 3.19806192701765 215 0 0.0127309856542579 N 0.957644730331519 0.968233547748639 Y N 1240 120 ENSG00000139725 ENSG00000212694 + - 12 12 120715977 120718831 upstream downstream RHOF AC084018.28-3 120700045 120718106 - - 0 120722143 120717997 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.607048593593732 0.849868031031224 0.849868031031224 0.607048593593732 2 - - 37187 N Y 3.56488607910057 3.49640736351508 3.49640736351508 28 0 0.0353349780147897 N 0 0.178245192307692 N N 11413 3189 ENSG00000112877 ENSG00000135679 - + 5 12 706664 67520481 coding utr3p CEP72 MDM2 665405 67488247 + + 0.178245192307692 672182 67520464 - + Y 0.868134916414089 - N HCC1954 34 31.7142857142857 29 7 1 N 114 24.8792 N - SINE 0 1 1 7 0.485638874874985 0.328520415356608 0.485638874874985 0.328520415356608 1 0 - 46901 Y Y 3.16406982599488 3.52361324642271 3.16406982599488 322 0 0.537558971355779 Y 0 0.987381083418508 N N 4980 0 ENSG00000063169 ENSG00000223326 - + 19 19 52898291 52776388 upstream downstream GLTSCR1 SRP_euk_arch 52874031 52776092 + + 0 52865512 52804237 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity,Low_complexity 0 0.128834355828221 0.128834355828221 13 0.914143764470561 1.16410495006798 1.16410495006798 0.914143764470561 4 - - 44930 N Y 3.40740634961144 3.58593758607883 3.40740634961144 0 0 0.761899325979861 Y 0.987614283882079 0.950457135528317 N N 104 1257 ENSG00000178440 ENSG00000204152 - + 10 10 51403098 51057774 intron utr3p AL442003.8-2 TIMM23B 51401190 51041413 + + 0 51402778 51057769 - + N 0.211032739669664 - N HCC1954 18 3.075 2 80 1 N - - N - - 0 0 0 80 1.31408166142643 1.19981369086761 1.31408166142643 1.19981369086761 4 0 - 19588 N Y 3.73808832274579 3.24893340314576 3.24893340314576 2 0 0.884430418134587 N 0.449741147235452 0.975812797680679 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0.975812797680679 109336418 45272639 - - Y 0.959657026618176 - N HCC1954 8 5.23404255319149 3 94 2 N - - N - - 0 0 0 94 0.87843502367093 0.578481600954027 0.87843502367093 0.578481600954027 3 0 - 6365 N N 3.23631009829935 2.43948851429108 2.43948851429108 0 0 0.0835117931820243 N 0 0 N N 131026 45208 ENSG00000115053 ENSG00000119335 - + 2 9 232037449 130498488 coding coding NCL SET 232027706 130485996 - + 0 232033757 130496751 + + Y - - N HCC1954 4 2.33333333333333 1 5 1 Y 162 22.3748 N Simple_repeat Low_complexity 0.448453608247423 0.425531914893617 0.448453608247423 6 1.26408942430695 1.09268746846872 1.26408942430695 1.09268746846872 2 - - 48877 Y Y 3.22064101730576 3.59528445727371 3.22064101730576 255 0 0.0315086131218116 Y 0.969815805109923 0.989938601703308 N N 81 5638 ENSG00000152380 ENSG00000039319 - + 5 5 79873962 79811254 upstream downstream FAM151B ZFYVE16 79819556 79739594 + + 0.0341057635175283 79817043 79814743 - + N - - N HCC1954 20 4.91666666666667 1 10 2 N - - Y LINE SINE 1 1 1 36 0.778450549431962 1.08554572030879 1.08554572030879 0.778450549431962 2 - - 49147 Y Y 3.61360747730288 3.20227814448323 3.20227814448323 190 0.00208768267223369 0.0259430944377593 Y 0.358484938860722 0.995248036584154 N N 20017 10798 ENSG00000160867 ENSG00000113761 - + 5 5 176457749 176426349 upstream utr3p FGFR4 ZNF346 176446521 176382303 + + 0 176438988 176424302 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 0.392694063926941 0 0.392694063926941 56 1.49976711358451 1.80686228446134 1.80686228446134 1.49976711358451 1 - - 45872 N Y 3.6491271616355 3.47233119514066 3.47233119514066 237 0.662719477337689 0.00512021268872587 N 0.662719477337689 0.951817068191099 N N 539 879 ENSG00000182141 ENSG00000152926 - + 19 7 21304052 64088849 coding upstream ZNF708 ZNF117 21265803 64072265 - - 0.229073091057575 21285268 64104353 + - Y - - N HCC1954 3 2.4 2 5 1 N - - N - - 0 0 0 5 0.364229156156239 0.392796148795944 0.392796148795944 0.364229156156239 1 - - 698 Y Y 3.5587317031712 3.23887075137909 3.23887075137909 116 0 0.795416035875609 Y 0 0.987765018439865 N Y 3010 2469 ENSG00000149591 ENSG00000149577 - + 11 11 116580717 116573371 utr5p coding TAGLN SIDT2 116575250 116554669 + + 0 116578928 116571841 - + N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 18 1.19267194270768 1.38549914302569 1.38549914302569 1.19267194270768 4 - - 12769 N Y 3.12804628055249 3.59784511035345 3.12804628055249 0 0 0.272464893624796 N 0.852394519061186 0.852394519061186 N N 1649619 8 ENSG00000141736 ENSG00000080573 - + 17 19 35138441 9982147 coding intron ERBB2 COL5A3 35104766 9931237 + - 0 35122227 9964329 - - Y - 0.92955599235151 N HCC1954 21 3.41176470588235 1 31 1 N - - N - SINE 0 1 1 34 0.956994253430118 0.299953422716903 0.956994253430118 0.299953422716903 2 - 0 22437 N N 3.33680806132368 3.29976079368121 3.29976079368121 2 0 0.0455082219148856 N 0 0 N N 260 5438 ENSG00000143515 ENSG00000120992 + - 1 8 152590403 55177130 utr3p coding ATP8B2 LYPLA1 152564654 55121492 + - 0.01929012345679 152589442 55137408 + + Y - 0.949084759894262 N HCC1954 70 65.2 60 5 1 N - - N SINE - 1 0 1 5 0.335662163516534 0.292811674556976 0.335662163516534 0.292811674556976 1 - 0 3490 N N 3.61720120015252 3.47705127371601 3.47705127371601 0 0 0.64427707395745 N 0 0 N N 6 166846 ENSG00000157554 ENSG00000142192 + + 21 21 38955488 26465003 upstream coding ERG APP 38673819 26174733 - - 0 39019355 26384132 - - N - - Y HCC1954 1 1 1 0 1 N - - N LTR - 0.838983050847458 0 0.838983050847458 8 0.835584534711372 0.942710757110266 0.942710757110266 0.835584534711372 2 - - 48116 N N 3.54296933622177 3.61464054707278 3.54296933622177 0 0 0.999999827804636 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117943360 2596253 - + Y - - N HCC1954 2 1.17647058823529 1 9 12 N 282 1.61558 N - - 0 0 0 51 1.26408942430695 1.42120788382533 1.42120788382533 1.26408942430695 1 - - 1666 N N 2.65773935684243 3.07614173465448 2.65773935684243 0 0 0.523308311662766 N 0 0 N N 64239 143275 ENSG00000132507 ENSG00000167996 - + 17 11 7156496 61491708 utr5p utr5p EIF5A FTHL16 7151090 61488335 + - 0 7151710 61491520 - - Y - 1.12702492381431 N HCC1954 28 11.1666666666667 1 5 1 N - - N Simple_repeat - 0.176470588235294 0 0.176470588235294 6 0.607048593593732 0.471355378555133 0.607048593593732 0.471355378555133 1 - 0 22079 N Y 3.2496867133392 3.78208964237274 3.2496867133392 213 0.828395661324267 0.010097048162104 N 0.897037396794561 0.828395661324267 N N 18 0 ENSG00000214896 ENSG00000183298 - + 15 1 50965962 102026647 coding intron RPSAP55 AL359760.10 50963988 102024480 + - 0.897037396794561 50965192 102025251 - - Y - 1 N HCC1954 12 5.6 4 5 1 N - - N - LTR 0 0.239583333333333 0.239583333333333 5 0.278528178237124 0.535631111994469 0.535631111994469 0.278528178237124 1 - 0 20823 N N 3.25256697878875 3.64297278570613 3.25256697878875 0 0 0.0757355037898456 N 0 0 N N 49089 6663 ENSG00000117450 ENSG00000163848 - - 1 3 45760196 126576888 coding upstream PRDX1 ZNF148 45749295 126427205 - - 0 45757275 126589123 + + Y - - N HCC1954 5 3.2 1 4 1 N - - N - SINE 0 1 1 5 0.45707188223528 0.392796148795944 0.45707188223528 0.392796148795944 2 - - 40622 N N 3.65657572715995 3.39487633072086 3.39487633072086 1 0 0.405140075250306 N 0.00366300366300365 0.0183150183150182 N N 0 568998 ENSG00000220165 ENSG00000156508 + + 20 6 18712334 74288344 intron coding RP5-1068E13.4 EEF1A1 18711068 74282194 - - 0.0183150183150182 18711402 74284803 - - Y 1 - N HCC1954 3 3 3 7 1 N - - N - - 0 0 0 7 0.264244681917271 0.357087407996313 0.357087407996313 0.264244681917271 2 0 - 33197 N N 2.94806716636195 0.494089294346095 0.494089294346095 12 0.0195832287220689 0.9999471348208 N 0.0374089881998493 0 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding downstream MT-CO3 MT-ND5 8367 12338 + + 0 8497 14190 - + N 0.603627792848188 - N HCC1954 2 1.5 1 2 10 Y 189 4.09957 N - - 0 0 0 4 0.699891319672773 1.02841173502938 1.02841173502938 0.699891319672773 2 0 - 16327 N Y 2.98746875060096 3.31489131844487 2.98746875060096 0 0 0.164630069239556 N 0 0 N N 2134 50640 ENSG00000138439 ENSG00000175793 - + 2 1 203342725 27063534 utr3p downstream FAM117B SFN 203208454 27062240 + + 0.157386546507886 203339096 27063538 - + Y - - N HCC1954 33 32.8 32 5 1 N 302 23.5915 N Simple_repeat,Simple_repeat - 0.972222222222222 0 0.972222222222222 5 0.257102933757345 0.364229156156239 0.364229156156239 0.257102933757345 1 - - 27580 N N 3.25252712599539 3.76529420565342 3.25252712599539 4 0 0.306555650907595 N 0 0.00184501845018459 N N 111030 0 ENSG00000167526 ENSG00000213916 - + 16 6 88157349 28937791 utr5p intron RPL13 AL662890.3-1 88154591 28937172 + + 0.00184501845018459 88154591 28937392 - + Y - 1 N HCC1954 2 1.3 1 6 2 N - - N - - 0 0 0 20 0.892718519990782 0.28566992639705 0.892718519990782 0.28566992639705 2 - 0 30573 Y Y 3.41103992525442 3.30062602958175 3.30062602958175 0 0 0.24867268689356 Y 0.992152950059325 0.992152950059325 N N 0 466 ENSG00000215269 ENSG00000049769 - + X X 49082313 49031501 upstream coding GAGE13 PPP1R3F 49047069 49013261 + + 0 49042695 49025467 - + N - - N HCC1954 20 6 1 8 1 N - - Y LINE,LINE - 1 0 1 12 0.956994253430118 1.22838068350732 1.22838068350732 0.956994253430118 1 - - 15686 N N 3.36767044781324 2.80208438599349 2.80208438599349 0 0 0.240916420561678 N 0 0.0539915966386553 N N 11670 0 ENSG00000117360 ENSG00000208307 - - 1 7 148592292 145325416 utr5p downstream PRPF3 AC073308.4 148560642 145325354 + + 0.0539915966386553 148563999 145325420 - - Y 1.69663597412496 - N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.414221393275723 0.257102933757345 0.414221393275723 0.257102933757345 1 0 - 9400 Y Y 3.45400817511148 3.05844120924126 3.05844120924126 297 0 0.0161973458225650 Y 0 0.985762385762386 N N 888 1263 ENSG00000160602 ENSG00000160606 - - 17 17 24093911 24078077 coding coding NEK8 TLCD1 24079959 24075504 + - 0 24085220 24077219 - + N 0.305417572549763 6.3216459469069 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 19 0.964136001590045 0.949852505270192 0.964136001590045 0.949852505270192 2 0 0 47052 N N 2.97999312784493 3.61464054707278 2.97999312784493 124 0 0.00397171786159112 Y 0.878183361629881 0.356112054329372 N N 2089 38 ENSG00000160336 ENSG00000213799 - + 19 19 58653326 58576124 downstream coding ZNF761 AC010467.9-3 58649710 58565733 + + 0.269100169779287 58656054 58570895 - + N - 0.639918530162433 N HCC1954 35 12.5 4 6 1 N - - N SINE - 0.882352941176471 0 0.882352941176471 6 0.849868031031224 0.785592297591888 0.849868031031224 0.785592297591888 1 - 0 32864 N N 2.7465279996206 2.72029709021333 2.72029709021333 0 0.283972537878788 0.204996769426711 N 0.75094696969697 0 N N 767 5996 ENSG00000161267 ENSG00000187678 - + 3 5 198784591 141684750 utr3p utr3p BDH1 SPRY4 198721051 141670189 - - 0 198721884 141671688 + - Y - 1.14614386371356 N HCC1954 39 32.8571428571429 30 14 1 N 161 25.0602 N Simple_repeat - 0.960526315789474 0 0.960526315789474 14 0.542772860154395 0.978419497909897 0.978419497909897 0.542772860154395 1 - 0 9846 Y Y 3.43887765034782 2.72088488970913 2.72088488970913 0 0 0.998791943292933 Y 0 0 N N 170868 252027 ENSG00000141741 ENSG00000141738 - - 17 17 35140314 35157070 coding upstream C17orf37 GRB7 35138937 35147713 - + 0 35140070 35145144 + - N - - N HCC1954 15 2.36585365853659 1 12 5 N - - Y - LINE,SINE,SINE 0 0.958579881656805 0.958579881656805 41 1.19267194270768 1.20695543902754 1.20695543902754 1.19267194270768 4 - - 43669 N Y 3.29868787111796 3.4561676006071 3.29868787111796 0 0 0.631055038707683 N 0 0 N N 6583 252027 ENSG00000166348 ENSG00000141738 - - 10 17 75055414 35157070 utr3p utr5p USP54 GRB7 74927302 35147713 - + 0 74928302 35147802 + - Y - 0.577506270929208 N HCC1954 27 25.75 23 4 1 N 440 22.6139 N SINE - 1 0 1 4 0.321378667196682 0.714174815992626 0.714174815992626 0.321378667196682 1 - 0 7044 Y Y 3.3478104969044 3.0212659605228 3.0212659605228 231 0 0.193476389389099 Y 0.817865061767501 0.975715341569 N N 0 3567 ENSG00000211215 ENSG00000011566 + - 2 2 39569088 39517797 downstream upstream AC007388.4 MAP4K3 39568835 39329930 - - 0 39555172 39535010 - + N - - N HCC1954 20 2.65217391304348 1 2 2 N - - Y DNA,DNA,LINE,Simple_repeat - 0.427536231884058 0 0.427536231884058 23 0.985561246069823 0.621332089913584 0.985561246069823 0.621332089913584 4 - - 24669 Y Y 3.45400817511148 3.59681204058356 3.45400817511148 0 0 0.980526460968073 Y 0 0.985239253852393 N N 2590 4614 ENSG00000134508 ENSG00000134490 + + 18 18 19092614 19271923 utr3p coding CABLES1 C18orf45 18969725 19129975 + - 0 19091395 19143643 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.785592297591888 0.692749571512847 0.785592297591888 0.692749571512847 1 - - 40807 N N 3.25153390901886 3.57336771439491 3.25153390901886 32 0 0.0798425326028193 N 0.301359058366703 0.182441451280184 N N 0 0 ENSG00000209951 ENSG00000125997 + + 7 20 86960 31401738 upstream downstream AC097646.2-1 AL355392.7-1 86858 31399202 - + 0.182441451280184 126099 31402202 - + Y - - N HCC1954 116 89 80 4 1 N 144 28.7709 N - SINE 0 1 1 4 0.51420586751469 0.321378667196682 0.51420586751469 0.321378667196682 1 - - 49175 Y Y 3.16783138271386 3.32895826821511 3.16783138271386 1 0 0.310557950589261 Y 0 0.987387802071346 N N 23230 951 ENSG00000186468 ENSG00000152348 + + 5 5 81609995 81586524 utr3p coding RPS23 ATG10 81604899 81303630 - + 0 81607678 81510087 - + N 0.0186583526010866 - N HCC1954 2 1.90909090909091 1 10 1 N - - Y - - 0 0 0 11 0.985561246069823 0.835584534711372 0.985561246069823 0.835584534711372 3 0 - 17180 N N 3.4064131326349 3.61360747730288 3.4064131326349 20 0 0.29208188042126 N 0 0.070696535461636 N N 25182 12495 ENSG00000116539 ENSG00000100320 - - 1 22 153798948 34754419 utr3p intron ASH1L RBM9 153571677 34464730 - - 0.070696535461636 153573561 34739247 + + Y - 3.48440322463009 N HCC1954 1 1 1 0 1 N - - N - SINE,SINE 0 0.253846153846154 0.253846153846154 4 0.642757334393363 0.692749571512847 0.692749571512847 0.642757334393363 3 - 0 21617 N Y 3.33168675516419 3.755916829235 3.33168675516419 5 0 0.111445352532717 N 0.861699623352166 0.870919648462021 N N 0 145 ENSG00000219468 ENSG00000187010 - + 9 1 140250262 25529523 upstream utr3p RP11-885N19.5 RHD 140249980 25471568 + + 0 140241177 25528872 - + Y - - N HCC1954 190 185 180 4 1 N 479 24.3467 N - SINE 0 1 1 4 0.371370904316165 0.271386430077198 0.371370904316165 0.271386430077198 2 - - 8304 N N 2.72029709021333 2.96376675257908 2.72029709021333 0 0.218457701101642 0.331438356359616 N 0.374766160881314 0 N N 5996 0 ENSG00000187678 ENSG00000221372 + + 5 2 141684750 41677136 utr3p upstream SPRY4 AC010739.3 141670189 41677030 - + 0 141671688 41497661 - + Y 1.14614386371356 - N HCC1954 33 32 31 4 1 N - - N - LTR,Simple_repeat 0 0.921052631578947 0.921052631578947 4 0.535631111994469 0.271386430077198 0.535631111994469 0.271386430077198 1 0 - 22513 N N 3.32486295761736 3.11916341767403 3.11916341767403 0 0 0.154340883534232 N 0 0.342723004694836 N N 1971 26897 ENSG00000147586 ENSG00000065526 - - 8 1 81105061 16139537 coding intron MRPS28 SPEN 80993653 16046946 - + 0.342723004694836 81077889 16135529 + - Y - 1.09166176580314 N HCC1954 20 5.8 1 4 1 N 365 25.6399 N - SINE 0 1 1 5 0.649899082553289 0.371370904316165 0.649899082553289 0.371370904316165 3 - 0 49227 Y Y 3.0431827034016 3.32952732966858 3.0431827034016 0 0 0.773762754545761 Y 0.993957703927492 0.945619335347432 N N 12549 10798 ENSG00000087206 ENSG00000113761 - - 5 5 176366358 176426349 utr5p upstream UIMC1 ZNF346 176264612 176382303 - + 0 176365891 176382072 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 25 1.18553019454776 1.15696320190805 1.18553019454776 1.15696320190805 1 - - 27585 N N 3.47332441211719 3.29855989004197 3.29855989004197 0 0 0.0880680893505612 N 0.863616467390052 0 N N 1133 7047 ENSG00000183137 ENSG00000135709 - + 6 16 109591806 83685327 utr5p utr3p C6orf182 KIAA0513 109523049 83618911 + + 0 109573115 83683328 - + Y - - N HCC1954 46 33.3333333333333 22 6 1 N - - N - SINE 0 1 1 6 0.971277749749971 0.321378667196682 0.971277749749971 0.321378667196682 3 - - 39548 N Y 3.47332441211719 3.58064844605001 3.47332441211719 1 0 0.420077311492674 N 0.876808455340899 0.887074417395824 N N 1133 38799 ENSG00000183137 ENSG00000187446 - + 6 15 109591806 39361377 utr5p utr3p C6orf182 AC012652.1 109523049 39310729 + + 0 109573115 39360278 - + Y 0.225629479086086 - N HCC1954 52 40.8333333333333 20 6 1 N - - N - SINE 0 1 1 6 0.635615586233437 0.34280391167646 0.635615586233437 0.34280391167646 4 0 - 25241 N N 3.68680627146374 3.58424216889964 3.58424216889964 0 0 0.351468739158293 N 0 0 N N 1 45068 ENSG00000184226 ENSG00000205336 + + 13 16 66702578 56256445 intron upstream PCDH9 GPR56 65774970 56220023 - + 0 66411685 56211650 - + Y 0.985024958402662 - N HCC1954 3 1.6 1 2 1 N - - N SINE - 1 0 1 5 0.242819437437493 0.599906845433805 0.599906845433805 0.242819437437493 3 0 - 23805 N N 3.59375687396386 3.66385645881505 3.59375687396386 0 0 0.0906560438635746 N 0 0.230577667860302 N N 601 10091 ENSG00000183474 ENSG00000116685 - + 5 1 68924107 11909072 utr5p intron GTF2H2C KIAA2013 68891830 11782803 + - 0 68891986 11836563 - - Y - 0.0363361732839079 N HCC1954 10 5.25 2 4 1 N - - N - SINE 0 1 1 4 0.557056356474248 0.264244681917271 0.557056356474248 0.264244681917271 2 - 0 41952 N N 3.66592259835483 3.65960038855611 3.65960038855611 0 0 0.995627866950409 N 0 0 N N 86504 559 ENSG00000104408 ENSG00000102290 + + 8 X 109330135 91764885 coding upstream EIF3E PCDH11X 109283149 90920960 - + 0.0117079889807163 109309672 90854612 - + Y 0.593852950305209 - N HCC1954 2 1.61904761904762 1 13 3 N - - N - - 0 0 0 21 0.907002016310634 1.08554572030879 1.08554572030879 0.907002016310634 4 0 - 35071 N Y 3.46807512488172 3.29383981146661 3.29383981146661 0 0 0.766821923313598 Y 0 0.98523424086338 N N 50 0 ENSG00000107018 ENSG00000214195 + + 9 9 5329873 5301716 coding upstream RLN1 AL135786.17-1 5324969 5301445 - + 0 5329262 5298268 - + N - - N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.628473838073511 1.10697096478857 1.10697096478857 0.628473838073511 4 - - 24633 Y Y 3.68783934123363 3.2778440508024 3.2778440508024 222 0 0.0389297678878565 Y 0.988938938938939 0.988938938938939 N Y 3896 356 ENSG00000141646 ENSG00000141642 - + 18 18 46865413 46768488 utr5p coding SMAD4 ELAC1 46810611 46748385 + + 0 46827288 46754929 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.635615586233437 0.707033067832699 0.707033067832699 0.635615586233437 4 - - 41663 N N 3.48593413659447 3.42316871656087 3.42316871656087 0 0 0.980980332506497 Y 0 0 N N 8783 0 ENSG00000147697 ENSG00000221261 + + 8 8 130868316 129231616 coding downstream GSDMC hsa-mir-1208 130829625 129231544 - + 0 130844056 129244884 - + N 0.654578271661651 - N HCC1954 1 1 1 0 4 N 6 9.04195 N - - 0 0 0 4 0.635615586233437 0.735600060472404 0.735600060472404 0.635615586233437 2 0 - 42239 Y N 3.04587133755734 3.65760879692984 3.04587133755734 0 0 0.517832035573019 Y 0.550841514726508 0.262096774193548 N N 1 5644 ENSG00000189099 ENSG00000109686 - - 4 4 152432055 152367022 downstream utr5p AC104819.4 SH3D19 152417775 152260886 + - 0.262096774193548 152465858 152319991 - + N - 5.5126279476189 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 11 0.807017542071667 0.335662163516534 0.807017542071667 0.335662163516534 2 - 0 4181 Y N 3.16931911323035 3.65657572715995 3.16931911323035 0 0 0.221837928757788 Y 0 0.00312500000000004 N N 4592 22352 ENSG00000146828 ENSG00000196411 - - 7 7 100302567 100263079 upstream upstream SLC12A9 EPHB4 100288294 100238123 + - 0.00312500000000004 100288144 100273296 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 21 0.778450549431962 0.785592297591888 0.785592297591888 0.778450549431962 1 - - 20684 N N 3.25256697878875 3.41423242051993 3.25256697878875 0 0 0.0902544571649209 N 0 0.284280604133545 N N 49089 4191 ENSG00000117450 ENSG00000101849 - + 1 X 45760196 9647777 coding intron PRDX1 TBL1X 45749295 9391352 - + 0.284280604133545 45757275 9580841 + + Y 3.11556065904221 0.180743845129654 N HCC1954 7 4.9375 1 14 1 N - - N - SINE 0 1 1 16 0.642757334393363 0.264244681917271 0.642757334393363 0.264244681917271 2 0 0 9541 Y Y 3.59594680468302 3.60785432895764 3.59594680468302 293 0 0.0166377429057752 Y 0 0 N N 4044 504 ENSG00000074356 ENSG00000083457 + - 17 17 3696266 3651293 utr3p upstream C17orf85 ITGAE 3661571 3564672 - - 0 3662451 3652418 - + N 0.211540736202174 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.907002016310634 0.949852505270192 0.949852505270192 0.907002016310634 2 0 - 29368 N N 3.69632097652796 3.72551845106187 3.69632097652796 0 0 0.91669111902184 Y 0 0 N N 343 52571 ENSG00000178729 ENSG00000096433 + + 6 6 48144384 33772324 intron coding C6orf138 ITPR3 47953998 33697139 - + 0 48120072 33697445 - + N 5.08738813241339 - N HCC1954 1 1 1 0 4 N 104 11.3593 N - - 0 0 0 29 1.17124669822791 0.785592297591888 1.17124669822791 0.785592297591888 1 0 - 37689 N Y 3.3828009725769 3.42464286670824 3.3828009725769 1 0 0.146211941438210 N 0.983513456240729 0.991756728120365 N N 1490 0 ENSG00000206195 ENSG00000218784 + - 14 22 18995329 14504973 utr5p upstream AL589182.4-3 LA16c-60H5.5 18961097 14480517 - - 0 18964701 14504974 - + Y - - N HCC1954 152 63.6842105263158 6 19 1 N - - N SINE,LINE - 0.723684210526316 0 0.723684210526316 19 1.08554572030879 0.921285512630487 1.08554572030879 0.921285512630487 1 - - 40789 N Y 3.6272104187567 3.44781394638876 3.44781394638876 0 0 0.7572101331829 N 0.161875725900116 0.878532713898568 N N 6663 8 ENSG00000163848 ENSG00000183566 - + 3 20 126576888 31261921 utr5p intron ZNF148 AL121901.20 126427205 31245072 - + 0.878532713898568 126524843 31252223 + + Y - 0.836948915325402 N HCC1954 20 18.5 17 4 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.364229156156239 0.39993789695587 0.364229156156239 2 - 0 33194 N N 2.91783662205815 3.14484171727181 2.91783662205815 9 0 0.999983917617154 N 0 0.0353236439916091 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0353236439916091 8407 14090 - + N 0.984947018030751 - N HCC1954 4 1.46153846153846 1 4 10 N 189 4.09957 N - - 0 0 0 13 1.47120012094481 1.04269523134923 1.47120012094481 1.04269523134923 1 0 - 24473 N N 3.61530289448208 3.54296933622177 3.54296933622177 3 0.00540540540540524 0.147418947565124 N 0.0994886778670563 0 N N 2054 5144 ENSG00000154889 ENSG00000157778 + - 18 7 11898641 1577167 utr3p upstream MPPE1 PSMG3 11873470 1573498 - - 0.00540540540540524 11873904 1582050 - + Y - - N HCC1954 33 26.6666666666667 22 6 1 N - - N SINE SINE 1 0.101694915254237 1 6 0.357087407996313 0.421363141435649 0.421363141435649 0.357087407996313 3 - - 26384 N Y 3.51782959285392 3.38127338926705 3.38127338926705 1 0 0.100170744548316 N 0 0.588361431529134 N N 75177 4227 ENSG00000125107 ENSG00000154803 + - 16 17 57221251 17081227 utr5p intron CNOT1 FLCN 57111359 17056254 - - 0 57190783 17074675 - + Y - 0.515605680741462 N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.335662163516534 0.278528178237124 0.335662163516534 0.278528178237124 2 - 0 45039 N Y 3.20124507471334 3.50272957331379 3.20124507471334 13 0.052861472633268 0.213052773098477 Y 0.728486955488203 0.993685743150888 N N 8377 6478 ENSG00000171988 ENSG00000165476 - - 10 10 64895728 65054887 coding intron JMJD1C REEP3 64596987 64951179 - + 0 64810245 64951501 + - N - 0.509258675362506 N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.246835443037975 0.246835443037975 27 1.17124669822791 1.12839620926835 1.17124669822791 1.12839620926835 1 - 0 32999 N Y 3.34785034969775 3.34040178417331 3.34040178417331 503 0 0.00161615718494912 Y 0 0.996007952286282 N N 59837 151141 ENSG00000198695 ENSG00000198888 + + MT MT 14674 4264 utr3p coding MT-ND6 MT-ND1 14150 3308 - + 0 14150 4231 - + N 0.139669276630922 1.7871488758144 N HCC1954 2 2 2 4 2 N - - N - - 0 0 0 4 0.914143764470561 0.685607823352921 0.914143764470561 0.685607823352921 3 0 0 44712 N Y 3.50272957331379 3.20124507471334 3.20124507471334 0 0 0.303771863108496 Y 0.523411371237458 0.991334752204317 N N 6478 8377 ENSG00000165476 ENSG00000171988 - - 10 10 65054887 64895728 intron coding REEP3 JMJD1C 64951179 64596987 + - 0 64951501 64810245 - + N 0.509258675362506 5.15958024073579 N HCC1954 1 1 1 0 1 N - - N Simple_repeat - 0.229411764705882 0 0.229411764705882 29 1.21409718718746 0.892718519990782 1.21409718718746 0.892718519990782 1 0 0 40895 N N 3.44143830342756 3.26088078021373 3.26088078021373 13 0 0.0815644558284657 N 0.417713760343243 0.0959239963224026 N N 108 0 ENSG00000215420 ENSG00000219468 + + 20 9 61542083 140250262 utr3p upstream AL353658.33 RP11-885N19.5 61537798 140249980 - + 0.0959239963224026 61539664 140231634 - + Y - - N HCC1954 108 98.4 88 5 1 N - - N SINE - 1 0 1 5 0.299953422716903 0.371370904316165 0.371370904316165 0.299953422716903 1 - - 41699 N Y 3.62192127872787 2.98826707647657 2.98826707647657 24 0.0550077173726633 0.537207987899477 Y 0.0550077173726633 0 N Y 24621 24621 ENSG00000083307 ENSG00000083307 - + 8 8 102750995 102750995 downstream coding GRHL2 GRHL2 102574162 102574162 + + 0 102745858 102730903 - + N - - N HCC1954 1 1 1 0 1 Y - - N LINE - 0.535353535353535 0 0.535353535353535 5 0.707033067832699 0.671324327033068 0.707033067832699 0.671324327033068 4 - - 9436 Y Y 3.80194024571177 3.19293127328835 3.19293127328835 304 0 0.110476343346378 Y 0.99302999631947 0.99302999631947 N N 14866 497 ENSG00000188554 ENSG00000198496 - + 17 17 38719232 38549760 upstream downstream AC109326.11 NBR2 38576772 38531135 + + 0 38575670 38554327 - + N - - N HCC1954 2 1.11111111111111 1 1 3 N - - Y - LTR 0 0.628378378378378 0.628378378378378 9 1.04269523134923 1.04269523134923 1.04269523134923 1.04269523134923 1 - - 38261 Y Y 3.56591914887046 3.34256120966892 3.34256120966892 0 0 0.62417928958138 Y 0.649076976663184 0.988679902473006 N N 2249 0 ENSG00000032219 ENSG00000209824 - - 14 14 57910201 57828858 upstream upstream ARID4A AL132989.5-2 57834975 57828768 + - 0 57834427 57829610 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.385654400636018 0.578481600954027 0.578481600954027 0.385654400636018 1 - - 44051 N Y 3.20703807585194 3.59528445727371 3.20703807585194 0 0 0.165040144900041 N 0.857745629897529 0.857745629897529 N N 1260 0 ENSG00000156398 ENSG00000217874 + + 10 6 104488930 170791556 downstream downstream SFXN2 RP1-191N21.4 104464288 170790619 + + 0.359855334538879 104493891 170802347 + + Y - - N HCC1954 10 8.25 8 8 1 N 323 21.0938 N Low_complexity,Low_complexity - 1 0 1 8 0.607048593593732 0.485638874874985 0.607048593593732 0.485638874874985 1 - - 23158 N N 3.61464054707277 3.09087103183403 3.09087103183403 7 0 0.102665042009466 N 0 0 N N 0 3891 ENSG00000219067 ENSG00000166295 - + 1 10 198113309 73665622 upstream intron RP11-567B20.1 C10orf104 198112729 73645812 + + 0 198107811 73645953 - + Y - 0.744979490524871 N HCC1954 29 27.5 26 4 1 N - - N SINE - 1 0 1 4 0.335662163516534 0.34280391167646 0.34280391167646 0.335662163516534 1 - 0 9331 Y Y 3.22064101730576 3.33420755545058 3.22064101730576 252 0.0389167362851573 0.99999232426144 Y 0.0389167362851573 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p intron ORMDL3 GSDMB 35330822 35314374 - - 0 35331931 35327942 - + N 2.88860269062801 9.44764878355004 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 24 1.36407389854591 0.792734045751814 1.36407389854591 0.792734045751814 1 0 0 33148 N N 2.92867122376953 3.54400240599166 2.92867122376953 10 0 0.112348207128484 N 0.00429184549356232 0.00429184549356232 Y N 1291380 339915 ENSG00000198804 ENSG00000198727 - + MT MT 7446 15882 coding coding MT-CO1 MT-CYB 5905 14748 + + 0.00429184549356232 6402 15755 - + N 1.076191806669 2.70809483532521 N HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.699891319672773 0.814159290231593 0.814159290231593 0.699891319672773 2 0 0 11978 N Y 3.12804628055249 3.50165665075055 3.12804628055249 1 0 0.236340454523606 N 0.881862958134145 0.898739678400695 N N 1649619 2979 ENSG00000141736 ENSG00000131043 - + 17 20 35138441 34322254 coding intron ERBB2 C20orf4 35104766 34287795 + + 0 35122227 34321631 - + Y - 53.004775924069 N HCC1954 20 6 1 3 1 N - - N - SINE 0 1 1 5 0.778450549431962 0.335662163516534 0.778450549431962 0.335662163516534 2 - 0 2389 N Y 3.54296933622177 3.71976530271662 3.54296933622177 242 0 0.0105346555760729 N 0 0.459386068476977 N N 0 0 ENSG00000137634 ENSG00000220830 + + 11 9 113971694 11003096 intron downstream FAM55D RP11-109M17.1 113946524 11001748 - + 0 113961805 11036658 - + Y 1 - N HCC1954 180 19.3 3 40 1 N - - N LTR SINE 1 1 1 40 0.371370904316165 0.971277749749971 0.971277749749971 0.371370904316165 1 0 - 34443 Y Y 3.34643934467102 3.44615838200292 3.34643934467102 0 0 0.265884138183405 Y 0 0.905384375972612 N N 891 1892 ENSG00000187713 ENSG00000176058 + - 9 9 139219910 139215578 downstream upstream TMEM203 C9orf75 139219148 139205890 - - 0 139218490 139216187 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.721316564152552 0.607048593593732 0.721316564152552 0.607048593593732 2 - - 19308 N N 3.41319935075004 2.70434571087551 2.70434571087551 0 0 0.0300730632240488 N 0 0 N N 0 0 ENSG00000220674 ENSG00000208696 - + 1 1 146560480 147554054 upstream upstream RP11-289I10.2 AL356957.27-7 146559962 147553983 + - 0 146542685 147557783 - - N - - Y HCC1954 36 21.1666666666667 1 23 1 N 164 29.506 N - LTR 0 1 1 24 0.885576771830856 0.578481600954027 0.885576771830856 0.578481600954027 0 - - 3657 Y Y 3.29599923696223 3.41103992525442 3.29599923696223 256 0 0.00526236594114937 Y 0.0030487804878051 0 N N 21319 22838 ENSG00000184787 ENSG00000184900 - + 21 21 45046166 45062472 coding utr3p UBE2G2 SUMO3 45013384 45049960 - - 0 45032264 45051133 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.849868031031224 0.778450549431962 0.849868031031224 0.778450549431962 2 - - 41405 Y Y 3.36654409208751 2.99396679165933 2.99396679165933 307 0 0.0106351491131217 Y 0.739980172780059 0.991332672426002 N N 578 0 ENSG00000184489 ENSG00000204882 - - 8 8 142510802 142446547 upstream upstream PTP4A3 GPR20 142501189 142435767 + - 0 142500667 142471363 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 45 1.04269523134923 0.885576771830856 1.04269523134923 0.885576771830856 1 - - 5783 N Y 3.29081515007045 3.20856565916179 3.20856565916179 0 0 0.496845079929043 N 0 0 N N 3273 20739 ENSG00000163961 ENSG00000143951 + + 3 2 197714979 63669355 downstream coding RNF168 C2orf86 197683026 63202041 - - 0 197682027 63440538 - - Y - - N HCC1954 23 21.3333333333333 21 6 1 N - - N SINE SINE 0.241935483870968 1 1 6 0.442788385915428 0.34280391167646 0.442788385915428 0.34280391167646 2 - - 122 N N 3.36551102231762 3.5074097990958 3.36551102231762 0 0 0.843997633150875 Y 0.196828358208955 0 N Y 41815 5698 ENSG00000109861 ENSG00000162105 + - 11 11 87710586 70536020 coding intron CTSC SHANK2 87666421 69991609 - - 0 87707753 70344435 - + N 0.852418718773701 1.22280867813864 N HCC1954 1 1 1 0 1 N 239 6.28592 N - - 0 0 0 13 0.921285512630487 0.93556900895034 0.93556900895034 0.921285512630487 4 0 0 47538 Y Y 3.54975555433691 3.54400240599166 3.54400240599166 293 0 0.470641657185741 Y 0 0.982203803022916 N N 2469 421 ENSG00000142252 ENSG00000170684 - - 19 19 50286622 50271528 utr5p coding GEMIN7 ZNF296 50274370 50266599 + - 0 50285205 50270920 - + N - 1.56268899744127 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 12 0.835584534711372 1.01412823870953 1.01412823870953 0.835584534711372 4 - 0 14292 N Y 3.73808832274579 3.59272380419397 3.59272380419397 179 0 0.0213541625721536 N 0 0.974824977017184 N N 21 0 ENSG00000205561 ENSG00000220101 + - 5 22 70185264 22325521 coding intron AC139834.2 AP000347.3 70127358 22321400 + - 0.0307616151615868 70182394 22324747 + + Y - 1 N HCC1954 8 6.75 3 8 1 N - - N - - 0 0 0 8 0.735600060472404 0.664182578873142 0.735600060472404 0.664182578873142 2 - 0 11409 N N 1.57910687713873 2.90202505474556 1.57910687713873 0 0.253424657534246 0.168542433508618 N 0.406568317527221 0 N N 22745 31 ENSG00000166750 ENSG00000144868 + + 17 3 30618852 134597745 utr3p intron SLFN5 TMEM108 30594199 134239943 + + 0.253424657534246 30617311 134533615 + + Y 2.45104030592242 1.38542680019075 N HCC1954 3 2.5 2 4 1 N - - N - Simple_repeat 0 0.41025641025641 0.41025641025641 4 0.707033067832699 0.278528178237124 0.707033067832699 0.278528178237124 1 0 0 41924 N N 3.48593413659447 3.38080938095063 3.38080938095063 0 0 0.98679854938494 Y 0 0 N N 8783 0 ENSG00000147697 ENSG00000221261 + + 8 8 130868316 129231616 coding upstream GSDMC hsa-mir-1208 130829625 129231544 - + 0 130844056 129230801 - + N - - N HCC1954 1 1 1 0 4 N 6 9.04195 N - LINE 0 1 1 12 1.16410495006798 1.1141127129485 1.16410495006798 1.1141127129485 2 - - 363 Y Y 3.12759161980588 3.69784855983781 3.12759161980588 241 0.0167550816744577 0.864206758893219 Y 0.911760071432323 0.974788591837807 N N 1172 1543 ENSG00000174165 ENSG00000174483 + + 11 11 66070247 66057660 coding intron ZDHHC24 BBS1 66063311 66034666 - + 0 66067751 66051053 - + N 0.992414660450361 1.77735570313508 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 10 0.728458312312478 0.657040830713216 0.728458312312478 0.657040830713216 4 0 0 27831 N Y 3.16783138271386 3.37146250975575 3.16783138271386 0 0.0828007970865112 0.0605782032704041 N 0.883735312306741 0.987081701367415 N N 98 17540 ENSG00000221883 ENSG00000005339 - - 3 16 48931586 3870122 coding intron C3orf71 CREBBP 48930714 3715056 - - 0 48931405 3827595 + + Y - 1.11768218371656 N HCC1954 21 20.6 20 5 1 N - - N - SINE 0 1 1 5 0.742741808632331 0.278528178237124 0.742741808632331 0.278528178237124 3 - 0 34264 Y Y 3.29127915838687 3.24255776018456 3.24255776018456 197 0 0.0133718310350066 Y 0.988945290468133 0.988945290468133 N N 27635 10436 ENSG00000148358 ENSG00000187239 - - 9 9 131942264 131845267 upstream coding GPR107 FNBP1 131855526 131689287 + - 0 131855444 131797057 - + N - 1.54573808579314 N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 4 0.585623349113953 0.685607823352921 0.685607823352921 0.585623349113953 1 - 0 35168 N N 2.92701565938369 3.3012485241977 2.92701565938369 21 0 0.0493593461115881 N 0 0 N N 1673 4442 ENSG00000212774 ENSG00000139116 - + 7 12 23644794 38123190 coding downstream AC006026.2-1 KIF21A 23643291 37973298 - - 0 23644436 37890912 + - Y - - N HCC1954 240 58.5 21 6 1 N - - N Other LINE 1 1 1 6 0.421363141435649 0.299953422716903 0.421363141435649 0.299953422716903 2 - - 4573 N Y 3.28296535696188 3.72146071989581 3.28296535696188 0 0 0.934970248580486 N 0 0.972844827586207 Y N 0 13708 ENSG00000208312 ENSG00000050327 - + 7 7 143514559 143708657 upstream coding AC004889.1-2 ARHGEF5 143514455 143683366 + + 0 143511049 143705216 - + N - - N HCC1954 2 1.8 1 4 1 N - - N LINE,LINE - 1 0 1 5 0.478497126715059 0.507064119354764 0.507064119354764 0.478497126715059 4 - - 24613 N Y 3.81657625693547 3.07311707325832 3.07311707325832 0 0 0.0960207241184784 N 0 0.754589821055078 N N 46 0 ENSG00000145416 ENSG00000215401 - - 4 18 164994733 1353874 intron upstream MARCH1 AP005119.2 164667738 1352441 - - 0 164772883 1504575 + + Y 2.48299877099549 - N HCC1954 24 21.3333333333333 20 9 1 N - - N LINE - 1 0 1 9 0.39993789695587 0.699891319672773 0.699891319672773 0.39993789695587 2 0 - 5834 N Y 3.4780843434859 3.25512763186849 3.25512763186849 249 0.980470903220726 0.0109756519635436 N 0.980470903220726 0.980470903220726 N N 47769 0 ENSG00000170144 ENSG00000222549 - - 2 3 177796931 75314889 utr3p upstream HNRNPA3 SRP_euk_arch 177785668 75314597 + - 0 177795040 75347494 - + Y 23.6224295432973 - N HCC1954 2 1.71428571428571 1 5 1 N - - N - - 0 0 0 7 0.299953422716903 0.349945659836387 0.349945659836387 0.299953422716903 1 0 - 25806 N Y 3.35975787397237 3.30232144676095 3.30232144676095 11 0 0.0932544279401938 N 0 0.877712031558185 N N 864 0 ENSG00000048052 ENSG00000221151 + - 7 16 19003518 88689322 intron upstream HDAC9 AC133919.3-4 18501894 88689218 + - 0.0522682445759368 18575126 88700544 + + Y 0.0960319548532015 - N HCC1954 84 23.5 8 8 1 N - - N SINE - 1 0 1 8 0.328520415356608 0.657040830713216 0.657040830713216 0.328520415356608 2 0 - 34334 N N 3.59528445727371 3.28871850530713 3.28871850530713 0 0 0.74172975902748 Y 0 0 N N 11640 27825 ENSG00000137038 ENSG00000080503 + + 9 9 7789799 2183624 upstream coding C9orf123 SMARCA2 7786490 2005342 - + 0 7813335 2060469 - + N - 1.39425044219368 N HCC1954 1 1 1 0 1 N - - N LTR - 1 0 1 6 0.742741808632331 0.449930134075354 0.742741808632331 0.449930134075354 3 - 0 4876 Y Y 2.74715517869933 3.55657227767559 2.74715517869933 291 0 0.00627980333800537 Y 0 0 N N 498 4094 ENSG00000105996 ENSG00000105997 - + 7 7 27108919 27158458 coding intron HOXA2 HOXA3 27106499 27112334 - - 0 27108444 27119767 + - N - 48.60832586124 N HCC1954 1 1 1 0 1 N - - Y Low_complexity,Low_complexity - 0.358974358974359 0 0.358974358974359 4 0.635615586233437 0.99270299422975 0.99270299422975 0.635615586233437 1 - 0 34971 N Y 3.64127736852694 3.25463311832853 3.25463311832853 96 0 0.253590995338637 Y 0 0 N N 11291 3337 ENSG00000107223 ENSG00000054148 + + 9 9 138880559 138865308 coding coding EDF1 PHPT1 138876392 138862997 - + 0 138877180 138863813 - + N - 0.431946032616087 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 1.02841173502938 1.02841173502938 1.02841173502938 1.02841173502938 1 - 0 36789 Y Y 3.27870928670295 3.57489529770476 3.27870928670295 233 0 0.0040961841901086 Y 0.00429184549356232 0 N N 4047 45 ENSG00000111665 ENSG00000111664 + + 12 12 6830686 6826818 coding coding CDCA3 GNB3 6828262 6819636 - + 0 6828854 6826306 - + N - 0.374865891145802 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.857009779191151 1.02126998686945 1.02126998686945 0.857009779191151 1 - 0 4538 Y N 3.65488030998075 2.96953605618939 2.96953605618939 0 0 0.175654381974316 Y 0.912156862745098 0 N N 5674 93 ENSG00000105983 ENSG00000105982 + + 7 7 156378663 156162585 downstream coding LMBR1 RNF32 156166332 156117523 - + 0 156164532 156162079 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.921285512630487 0.564198104634174 0.921285512630487 0.564198104634174 3 - - 41545 Y N 3.6052936758779 3.55657227767559 3.55657227767559 0 0 0.98607110376356 Y 0.988808107512668 0 N N 3297 2237 ENSG00000104613 ENSG00000147408 - - 8 8 19753864 19584374 upstream utr5p INTS10 CSGALNACT1 19719198 19305952 + - 0 19659641 19407921 - + N - 8.40671697736019 N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 16 0.635615586233437 1.17124669822791 1.17124669822791 0.635615586233437 4 - 0 26713 N Y 3.40910176679063 3.588962247475 3.40910176679063 205 0 0.0053630676311921 Y 0 0 N N 9394 3260 ENSG00000183723 ENSG00000217555 + + 16 16 65288111 65161194 coding coding CMTM4 CKLF 65206155 65143967 - + 0 65213543 65157399 - + N 1.16268579170563 5.77260785130443 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.885576771830856 0.857009779191151 0.885576771830856 0.857009779191151 1 0 0 36186 N Y 3.75016368088976 2.625 2.625 0 0.452380952380953 0.0283804241858598 N 0.452380952380953 0.452380952380953 N N 157783 1213 ENSG00000205426 ENSG00000135443 + + 12 12 50971566 51047576 coding coding KRT81 KRT85 50965966 51040057 - - 0.452380952380953 50968074 51042984 - - N 5.90109455640002 24.1767540526299 Y HCC1954 4 2.2 1 4 1 N 597 24.9442 N - - 0 0 0 10 0.314236919036755 0.442788385915428 0.442788385915428 0.314236919036755 1 0 0 30921 N N 2.8046314587041 3.39487633072086 2.8046314587041 0 0 0.283745165579332 N 0 0 N N 9927 6539 ENSG00000114650 ENSG00000009413 - + 3 6 47492449 111911125 utr5p coding SCAP REV3L 47430188 111726927 - - 0 47492434 111736057 + - Y - - N HCC1954 31 26 21 5 2 N - - N - LINE 0 1 1 5 0.5713398527941 0.714174815992626 0.714174815992626 0.5713398527941 2 - - 31850 Y Y 3.51100352194543 3.57696143724454 3.51100352194543 141 0 0.815837773565763 Y 0.607365306758019 0.961694176269075 N N 41283 6846 ENSG00000047457 ENSG00000163755 + + 3 3 150422519 150373995 coding intron CP HPS3 150373220 150330061 - + 0 150378319 150366529 - + N - 1.33045161304183 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 24 0.978419497909897 0.814159290231593 0.978419497909897 0.814159290231593 3 - 0 40234 N N 3.23168330567983 3.16065309955075 3.16065309955075 0 0 0.514543143609314 N 0 0 N N 269689 27 ENSG00000067225 ENSG00000164749 + + 15 8 70310738 76641600 utr3p upstream PKM2 HNF4G 70278424 76482732 - + 0 70278826 76452058 - + Y 1.30096043776549 - N HCC1954 2 1.44444444444444 1 4 1 N - - N - - 0 0 0 9 0.471355378555133 0.607048593593732 0.607048593593732 0.471355378555133 2 0 - 14070 N Y 3.6052936758779 3.032709476481 3.032709476481 0 0 0.701458709403316 Y 0 0 N Y 10156 10156 ENSG00000100304 ENSG00000100304 + - 22 22 41913076 41913076 coding downstream TTLL12 TTLL12 41892572 41892572 - - 0 41894724 41894109 - + N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 7 0.87843502367093 0.807017542071667 0.87843502367093 0.807017542071667 4 - - 10066 N Y 3.39483647792751 3.4944157718888 3.39483647792751 309 0.00323624595469252 0.125436094192177 Y 0.9508637586034 0.992980536943343 N N 8390 0 ENSG00000120071 ENSG00000207064 - + 17 17 41625943 41648314 utr5p upstream KIAA1267 Y_RNA 41463181 41648213 - - 0 41625562 41656815 + - N - - N HCC1954 2 1.82051282051282 1 32 2 N - - N - - 0 0 0 39 1.24980592798709 1.07126222398894 1.24980592798709 1.07126222398894 2 - - 2535 N Y 3.56488607910057 3.26824964015148 3.26824964015148 3 0 0.143250451201120 N 0.937793427230047 0.888028169014084 N N 1 8014 ENSG00000205857 ENSG00000149084 - - 12 11 7817984 43834736 coding utr3p AC006517.46-2 HSD17B12 7809079 43658719 + + 0 7809151 43834016 - - Y - - N HCC1954 78 52.6 37 5 1 N - - N SINE - 1 0 1 5 0.392796148795944 0.557056356474248 0.557056356474248 0.392796148795944 2 - - 22338 N N 3.66592259835483 3.52833332499806 3.52833332499806 5 0 0.144575631050700 N 0 0 N N 50281 4891 ENSG00000135862 ENSG00000173281 - - 1 8 181381350 9045630 coding utr3p LAMC1 PPP1R3B 181259218 9031186 + - 0.0366438356164382 181366176 9034115 - + Y - - N HCC1954 31 28.25 27 4 1 N 35 25.8229 N - SINE 0 1 1 4 0.528489363834543 0.364229156156239 0.528489363834543 0.364229156156239 3 - - 13969 Y Y 3.37183323211633 2.99662073069491 2.99662073069491 354 0 0.087174563184129 Y 0 0 N N 19152 9629 ENSG00000182457 ENSG00000133422 - - 22 22 29702049 29694187 coding upstream TUG1 MORC2 29696663 29652600 + - 0 29697764 29695370 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE - 0.0397727272727273 0 0.0397727272727273 30 1.24980592798709 1.0069864905496 1.24980592798709 1.0069864905496 0 - - 9836 Y Y 3.58424216889964 3.51273879191798 3.51273879191798 389 0 0.564929757328864 Y 0 0 N N 252027 170868 ENSG00000141738 ENSG00000141741 - - 17 17 35157070 35140314 utr5p coding GRB7 C17orf37 35147713 35138937 + - 0 35152032 35140043 - + N - 1.90403885026224 N HCC1954 1 1 1 0 5 N - - Y - SINE 0 0.168316831683168 0.168316831683168 170 1.45691662462496 1.4426331283051 1.45691662462496 1.4426331283051 1 - 0 313 Y Y 3.4561676006071 3.59272380419397 3.4561676006071 296 0 0.0190372379175811 Y 0 0.986711711711712 N N 724 2039 ENSG00000149292 ENSG00000149294 - + 11 11 112759476 112654343 upstream downstream TTC12 NCAM1 112690461 112337302 + + 0 112690149 112660428 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 7 0.721316564152552 0.93556900895034 0.93556900895034 0.721316564152552 2 - - 32216 N Y 3.64759957832565 3.1352735790451 3.1352735790451 8 0 0.0491911476638558 N 0 0.921546052631579 N N 1076 0 ENSG00000133627 ENSG00000213113 + + 7 3 152183396 199332046 intron downstream ACTR3B AC073135.3-1 152087784 199330983 + + 0.00625000000000009 152101526 199368886 + + Y 0.453759467768371 - N HCC1954 88 83 80 4 1 N - - N SINE - 1 0 1 4 0.314236919036755 0.507064119354764 0.507064119354764 0.314236919036755 1 0 - 4322 Y Y 3.19081170058609 3.6272104187567 3.19081170058609 303 0 0.141706181871052 Y 0.764559133078662 0.984303942205244 N N 0 6389 ENSG00000210544 ENSG00000006451 - + 7 7 39774568 39714240 upstream downstream AC004987.2-1 RALA 39774466 39629687 + + 0 39769672 39740168 - + N - - N HCC1954 2 1.11111111111111 1 1 2 N - - Y LTR SINE,LTR,LTR 1 0.811188811188811 1 9 0.949852505270192 1.02126998686945 1.02126998686945 0.949852505270192 4 - - 49159 Y Y 3.64656650855576 3.54296933622177 3.54296933622177 11 0 0.535389059961361 Y 0 0.973777861022664 N N 388 6604 ENSG00000212643 ENSG00000153037 - + 5 5 112256690 112231502 utr5p coding ZRSR1 SRP19 112255212 112224892 + + 0 112255225 112228055 - + N 0.0478864044393667 - N HCC1954 6 3 1 3 1 Y - - Y - - 0 0 0 4 0.864151527351077 0.778450549431962 0.864151527351077 0.778450549431962 3 0 - 5712 N N 2.44890574350284 3.46232197653647 2.44890574350284 4 0 0.109397076255792 N 0 0.252906976744186 N N 122511 5881 ENSG00000187514 ENSG00000132967 - + 2 3 232286495 22572731 coding coding PTMA AC104740.2 232280638 22398294 + + 0.252906976744186 232284902 22398827 - + Y - - N HCC1954 44 18.1666666666667 4 6 1 N - - N Low_complexity Low_complexity 0.239234449760766 0.265151515151515 0.265151515151515 6 1.05697872766909 0.892718519990782 1.05697872766909 0.892718519990782 2 - - 33059 N Y 2.73215889136457 3.03652446636246 2.73215889136457 0 0 0.999871879419346 Y 0 0.253164556962026 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0 9092 5492 - + N 0.575761399678038 163.649702896659 N HCC1954 4 1.5 1 1 9 N - - N - - 0 0 0 6 0.521347615674617 0.999844742389676 0.999844742389676 0.521347615674617 2 0 0 18326 N Y 3.5816815158199 3.51529944499772 3.51529944499772 2 0 0.478090055126826 N 0.993352826510721 0.973411306042885 Y N 0 0 ENSG00000208696 ENSG00000213223 + + 1 1 147554054 147820286 downstream downstream AL356957.27-7 AL451058.16-1 147553983 147819627 - + 0 147551280 147843325 - + N - - N HCC1954 14 8.72727272727273 5 11 2 N 486 21.4198 N - - 0 0 0 11 1.1141127129485 1.34979040222606 1.34979040222606 1.1141127129485 1 - - 30541 Y Y 3.32167753656001 2.84284912476227 2.84284912476227 208 0 0.0167763626375436 Y 0.630815756823821 0.983948511166253 N N 217 4501 ENSG00000156500 ENSG00000156504 - - X X 133816282 133758830 upstream utr5p FAM122C FAM122B 133768890 133731262 + - 0 133765795 133758141 - + N - 0.552630502339831 N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 4 0.771308801272036 0.278528178237124 0.771308801272036 0.278528178237124 2 - 0 46889 Y Y 3.69167809238928 3.24255776018456 3.24255776018456 0 0 0.411923487853047 Y 0.244398124022928 0.973944762897342 N N 22 5830 ENSG00000174788 ENSG00000076924 + - 19 19 7604636 7600439 downstream upstream PCP2 XAB2 7602509 7590412 - - 0.973944762897342 7602180 7600725 - + N - - N HCC1954 2 1.28260869565217 1 13 2 N - - Y - - 0 0 0 46 0.785592297591888 0.471355378555133 0.785592297591888 0.471355378555133 2 - - 23774 N N 3.68577320169385 3.5010341561346 3.5010341561346 0 0 0.120344651829739 N 0 0 N N 1125 40617 ENSG00000132854 ENSG00000130164 + + 1 19 62557671 11105490 utr3p utr3p KANK4 LDLR 62474425 11061132 - + 0 62475107 11104135 - + Y - 2.27267372255859 N HCC1954 39 37.2 36 5 1 N - - N SINE SINE 1 0.262295081967213 1 5 0.257102933757345 0.435646637755502 0.435646637755502 0.257102933757345 3 - 0 38744 N N 3.69784855983781 3.08295845799316 3.08295845799316 7 0 0.142718829624962 N 0 0 N N 1054 2530 ENSG00000187621 ENSG00000138744 + + 14 4 95228718 77081190 utr5p utr3p TCL6 NAAA 95186588 77050833 + - 0 95200174 77055061 + - Y - - N HCC1954 36 26.3333333333333 22 6 1 N - - N SINE - 1 0 1 6 0.39993789695587 0.5713398527941 0.5713398527941 0.39993789695587 1 - - 41745 Y Y 3.24099032408136 3.29396779254261 3.24099032408136 1 0 0.998750144565352 Y 0.994396690820547 0.994396690820547 N N 9799 0 ENSG00000076554 ENSG00000222697 - - 8 8 81155565 81279688 coding upstream TPD52 SRP_euk_arch 81109662 81279396 - + 0 81139381 81246213 + - N - - N HCC1954 1 1 1 0 6 N - - Y - Low_complexity 0 0.104395604395604 0.104395604395604 1076 1.54261760254407 1.29979816510658 1.54261760254407 1.29979816510658 2 - - 3077 N N 3.38080938095063 3.48590363137093 3.38080938095063 0 0 0.0441554853600985 N 0 0 N N 36582 452 ENSG00000177600 ENSG00000152439 - + 11 19 802876 62716248 upstream utr3p RPLP2 ZNF773 799936 62703121 + + 0 799396 62711053 - + Y - - N HCC1954 35 26.4 23 5 1 N 428 23.3238 N - SINE 0 1 1 5 0.407079645115797 0.271386430077198 0.407079645115797 0.271386430077198 1 - - 30389 Y Y 3.35297165585723 3.47552369040616 3.35297165585723 228 0 0.271493498574662 Y 0 0 N N 0 0 ENSG00000213468 ENSG00000203953 + + X X 130757838 130608580 downstream downstream AL121572.14 AL109853.4 130757360 130608329 - + 0 130704805 130654345 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LTR 0 1 1 4 0.849868031031224 0.685607823352921 0.849868031031224 0.685607823352921 4 - - 3433 N Y 3.40488554932505 3.18974812559266 3.18974812559266 242 0 0.0204196594894556 Y 0.832470842666255 0.99069282459257 N N 9282 0 ENSG00000142197 ENSG00000214889 - + 21 21 36588442 36427200 upstream downstream DOPEY2 AP000689.1-2 36458703 36426618 + + 0 36450387 36427244 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 11 0.492780623034912 1.0069864905496 1.0069864905496 0.492780623034912 2 - - 39130 N N 3.43829924132454 3.55976477294109 3.43829924132454 0 0 0.421105249776734 N 0 0 N N 2399 45131 ENSG00000137834 ENSG00000155066 + + 15 2 64861377 95320781 downstream utr3p SMAD6 PROM2 64781688 95303928 + + 0 64897518 95320454 + + Y - 3.29675489361641 N HCC1954 1 1 1 0 1 N 582 23.813 N SINE SINE 0.8125 0.523809523809524 0.8125 4 0.22853594111764 0.449930134075354 0.449930134075354 0.22853594111764 1 - 0 47595 N N 3.43673180522133 3.24169252428402 3.24169252428402 0 0 0.150639079659627 N 0 0 N N 15928 7383 ENSG00000142453 ENSG00000064607 - + 19 19 10894448 19005368 coding coding CARM1 SFRS14 10843253 18962697 + - 0 10843593 18990928 - - N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.892718519990782 0.871293275511003 0.892718519990782 0.871293275511003 2 - - 37457 N N 3.52567938596249 3.38912318237562 3.38912318237562 0 0 0.299044671611404 N 0 0 N N 3528 2128 ENSG00000163093 ENSG00000129480 - + 2 14 170071410 30996431 utr3p intron BBS5 C14orf126 170044239 30984996 + - 0 170069761 30995889 - - Y - 2.31805637674966 N HCC1954 23 6.75 1 2 1 N - - N Other - 0.858695652173913 0 0.858695652173913 4 0.585623349113953 0.714174815992626 0.714174815992626 0.585623349113953 2 - 0 28998 N N 2.16780768912624 1.47661442613786 1.47661442613786 0 0 0.107400713829573 N 0 0.342358803986711 N N 25305 357 ENSG00000153113 ENSG00000140795 + - 5 16 96136143 45339722 utr5p upstream CAST MYLK3 96023533 45293695 + - 0.342358803986711 96023799 45357356 + + Y 0.0278427559323116 - N HCC1954 20 15.8333333333333 8 6 1 N - - N - Simple_repeat 0 1 1 6 0.771308801272036 0.371370904316165 0.771308801272036 0.371370904316165 1 0 - 10321 Y Y 3.26932256271472 2.89095226114794 2.89095226114794 0 0 0.990316982694778 Y 0.0337926509186351 0.989610673665792 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 utr3p coding C17orf37 ERBB2 35138937 35104766 - + 0 35139256 35133161 - + N - 1.1093441688433 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 6 1.02126998686945 0.949852505270192 1.02126998686945 0.949852505270192 1 - 0 32161 N N 3.40169305405954 3.1019133202081 3.1019133202081 10 0 0.202250263293347 N 0.184859749915512 0.196181142277797 N N 36 0 ENSG00000214173 ENSG00000209192 - - 7 3 127896489 117784367 coding downstream AC010655.7-2 AC078784.24 127893850 117784147 + - 0.241466711726935 127893881 117720790 - + Y - - N HCC1954 38 23 16 4 1 N - - N - Other 0 1 1 4 0.699891319672773 0.849868031031224 0.849868031031224 0.699891319672773 1 - - 20637 N N 3.38805025981237 3.31489131844487 3.31489131844487 18 0 0.0594415906830235 N 0 0 N N 194 50640 ENSG00000185760 ENSG00000175793 - + 6 1 73965295 27063534 utr3p downstream KCNQ5 SFN 73388241 27062240 + + 0 73963879 27063537 - + Y - - N HCC1954 33 32.8 32 5 1 N - - N Simple_repeat - 0.972222222222222 0 0.972222222222222 5 0.257102933757345 0.364229156156239 0.364229156156239 0.257102933757345 2 - - 39618 N N 3.39128260787123 3.59784511035345 3.39128260787123 0 0 0.327938056501366 N 0.855401350337585 0 N Y 12271 2 ENSG00000177479 ENSG00000206187 - + 3 15 48997971 23849360 intron utr3p ARIH2 AC100836.2 48931285 23698600 + + 0 48939899 23845482 - + Y 0.963247002497696 - N HCC1954 38 14.1428571428571 1 8 1 N - - N Simple_repeat SINE,SINE 0.257425742574257 0.791666666666667 0.791666666666667 14 0.721316564152552 0.34280391167646 0.721316564152552 0.34280391167646 4 0 - 29810 Y N 3.65913638023969 3.68577320169385 3.65913638023969 2 0.00485436893203883 0.346284449697809 N 0.00485436893203883 0 N N 3886 0 ENSG00000146416 ENSG00000217648 + + 6 6 143703134 143706213 coding intron AIG1 RP1-95L4.4 143423716 143705076 + + 0 143696262 143705460 + + N 2.16278357429827 1 Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.942710757110266 0.51420586751469 0.942710757110266 0.51420586751469 2 0 0 47963 N N 2.87895660859068 3.37465500502126 2.87895660859068 0 0 0.999999510354148 N 0 0.00427350427350437 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 intron downstream RAD21 IRX2 117927355 2798959 - - 0.00427350427350437 117944024 2620943 - + Y 1.0363918474073 - N HCC1954 1 1 1 0 12 N 282 1.61558 N - LINE 0 1 1 4 0.87843502367093 0.657040830713216 0.87843502367093 0.657040830713216 4 0 - 46352 N Y 3.25360004855864 3.64656650855576 3.25360004855864 0 0 0.46445671666615 N 0.362573646310671 0.928177312260357 N N 609 3966 ENSG00000105750 ENSG00000175772 - + 19 2 20925341 110111006 upstream upstream ZNF85 AC013268.5-1 20897922 110103138 + + 0 20830400 110102053 - + Y - - N HCC1954 60 41.4285714285714 20 28 1 N 502 23.3289 N LINE - 1 0 1 28 0.492780623034912 1.02126998686945 1.02126998686945 0.492780623034912 1 - - 32686 N Y 3.48908677906663 2.96595182135875 2.96595182135875 116 0 0.478675355544728 N 0.948913681738109 0.940399295361127 N N 2216 1157 ENSG00000185485 ENSG00000185986 + - 3 5 197201530 1646257 downstream downstream AC024937.21-3 AC091849.2 197174603 1625243 - - 0 197174568 1622113 - + Y - - N HCC1954 8 5.16666666666667 2 12 1 Y 309 4.62985 N - LINE 0 0.75 0.75 12 0.835584534711372 0.742741808632331 0.835584534711372 0.742741808632331 4 - - 21183 N N 1.32501121082418 3.6387167154472 1.32501121082418 0 0 0.0565081151415726 N 0 0.240265906932574 N N 9302 1376 ENSG00000145041 ENSG00000198161 + + 3 1 51492884 146422374 upstream utr3p VPRBP PPIAL4A 51408338 146418535 - - 0.240265906932574 51509022 146419459 - - Y - - N HCC1954 24 23.25 22 4 1 N 75 23.4292 N - SINE,SINE 0 1 1 4 0.614190341753658 0.299953422716903 0.614190341753658 0.299953422716903 2 - - 34668 N N 2.82826926204616 2.6718368118362 2.6718368118362 0 0.198380566801619 0.313147617285066 N 0.635627530364372 0.198380566801619 N N 17291 11502 ENSG00000070159 ENSG00000159921 - - 9 9 111300407 36248450 utr3p utr3p PTPN3 GNE 111177800 36204430 - - 0.198380566801619 111179515 36206342 + + N - 0.659918255598569 Y HCC1954 38 35.5 30 8 1 N 343 29.8189 N SINE,Simple_repeat LINE 0.966101694915254 0.666666666666667 0.966101694915254 8 0.421363141435649 0.757025304952183 0.757025304952183 0.421363141435649 1 - 0 47690 Y Y 3.32316526707651 3.29972094088785 3.29972094088785 293 0 0.069821755625896 Y 0.977520593292104 0.992506864430701 N N 4775 0 ENSG00000127527 ENSG00000219228 + - 19 19 16443762 16330138 coding downstream EPS15L1 AC020917.4-2 16333408 16329998 - - 0 16348934 16327663 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 17 1.43549138014518 1.13553795742827 1.43549138014518 1.13553795742827 1 - - 46431 N N 3.17614518413885 3.44975210485255 3.17614518413885 0 0 0.150359182966023 N 0 0 N N 24464 33105 ENSG00000101166 ENSG00000105372 + + 20 19 57051296 47067322 upstream coding SLMO2 RPS19P3 57041596 47055828 - + 0 57063459 47065658 - + Y - - N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.357087407996313 0.435646637755502 0.435646637755502 0.357087407996313 2 - - 18477 N Y 3.30950889246021 3.55976477294109 3.30950889246021 0 0 0.859242466337855 Y 0 0.974152061530702 N N 0 9 ENSG00000217689 ENSG00000090104 - + 1 1 190952401 190815782 downstream downstream RP11-92K2.2 RGS1 190951936 190811480 + + 0 190975144 190829410 - + N - - N HCC1954 1 1 1 0 2 N - - N LINE,LTR LTR 0.823008849557522 1 1 15 0.771308801272036 0.528489363834543 0.771308801272036 0.528489363834543 4 - - 15090 N N 3.66273010308932 3.67849247003875 3.66273010308932 0 0.302941176470588 0.848223570015754 N 0.302941176470588 0.302941176470588 N N 0 850768 ENSG00000217168 ENSG00000075624 - - 1 7 78013137 5536758 intron coding RP4-706L14.2 ACTB 78012138 5533313 - - 0.302941176470588 78012222 5533968 + + Y 1 1.03802969096984 N HCC1954 3 1.85714285714286 1 4 1 N - - N - Simple_repeat 0 0.383333333333333 0.383333333333333 7 0.299953422716903 0.428504889595575 0.428504889595575 0.299953422716903 4 0 0 24019 N Y 3.44359772892318 3.50678730447985 3.44359772892318 0 0 0.657021729596784 N 0.599901189839022 0.93486763555519 N N 2470 0 ENSG00000151883 ENSG00000207106 + - 5 1 50173926 143022733 coding downstream PARP8 U1 49998570 143022570 + - 0 49999714 143012895 + + Y - - N HCC1954 5 3.8 3 10 1 N 80 23.5165 N - - 0 0 0 10 0.478497126715059 0.728458312312478 0.728458312312478 0.478497126715059 2 - - 33534 Y N 2.96998390924075 3.25463311832853 2.96998390924075 11 0 0.997431808953974 N 0 0 Y N 247001 59837 ENSG00000198786 ENSG00000198695 - - MT MT 14149 14674 coding coding MT-ND5 MT-ND6 12338 14150 + - 0 12358 14319 - + N - 0.872800709132782 N HCC1954 2 1.61538461538462 1 8 7 N 189 4.09957 N - - 0 0 0 13 1.47834186910473 0.871293275511003 1.47834186910473 0.871293275511003 2 - 0 33825 Y N 3.10447397328784 2.97254456232049 2.97254456232049 14 0.0350702511339749 0.998531869557279 N 0.0838588339418077 0 Y N 59837 247001 ENSG00000198695 ENSG00000198786 - - MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0 14635 12394 + - N - 1.18981516772479 N HCC1954 4 2.21333333333333 1 48 7 N 189 4.09957 N - - 0 0 0 75 1.7140195583823 1.7140195583823 1.7140195583823 1.7140195583823 2 - 0 11163 N N 3.28825449699071 3.53717633508317 3.28825449699071 1 0 0.188667694762103 N 0.00367647058823517 0.00367647058823517 N N 1649619 0 ENSG00000141736 ENSG00000213178 - + 17 3 35138441 170684502 utr5p intron ERBB2 AC074033.18 35104766 170684153 + - 0.00367647058823517 35109798 170684166 - - Y 0.0359604946548298 1 N HCC1954 4 2.33333333333333 2 6 1 N - - N Simple_repeat - 0.306818181818182 0 0.306818181818182 6 0.628473838073511 0.814159290231593 0.814159290231593 0.628473838073511 1 0 0 33264 N N 3.10231454779222 2.96951990092433 2.96951990092433 0 0.162383399961926 0.999998032341621 N 0 0.162383399961926 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0.162383399961926 8790 12036 - + N 0.588140047520677 - N HCC1954 4 2.7 2 10 12 N 189 4.09957 N - - 0 0 0 10 1.34264865406614 1.47120012094481 1.47120012094481 1.34264865406614 1 0 - 21453 N Y 3.59169073442408 3.56911164413597 3.56911164413597 0 0 0.817361026384688 N 0.91285140562249 0.887951807228916 N N 2926 147 ENSG00000162419 ENSG00000179082 - + 1 9 28918452 131127005 utr3p downstream GMEB1 C9orf106 28867831 131123116 + + 0 28916474 131144143 - + Y - - N HCC1954 35 32.25 29 20 1 N - - N SINE - 1 0 1 20 0.314236919036755 0.714174815992626 0.714174815992626 0.314236919036755 4 - - 26768 Y Y 3.28126993978269 3.36038036858832 3.28126993978269 258 0 0.0462882014355794 Y 0 0.991106035437431 N N 1558 52 ENSG00000103202 ENSG00000103200 - + 16 16 402487 390754 upstream intron DECR2 NME4 391859 386726 + + 0.991106035437431 391653 390124 - + N - 0.727395785324335 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.901098901098901 0.901098901098901 4 0.642757334393363 0.649899082553289 0.649899082553289 0.642757334393363 1 - 0 17987 Y Y 3.39600268644659 3.21448664137639 3.21448664137639 337 0 0.00855958747544816 Y 0.591380065184609 0.991827601303692 N N 18306 3709 ENSG00000131795 ENSG00000152022 - + 1 1 144222801 144213026 upstream intron RBM8A LIX1L 144218990 144188516 + + 0 144218657 144205333 - + N - 0.736589869841989 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.928427260790413 0.714174815992626 0.928427260790413 0.714174815992626 1 - 0 4383 Y Y 3.21269793824135 3.55401162459584 3.21269793824135 182 0.0995693495693496 0.0595675489426356 Y 0.328036828036828 0.946242946242946 N N 36 2583 ENSG00000214173 ENSG00000135245 - + 7 7 127896489 127885707 upstream utr5p AC010655.7-2 C7orf68 127893850 127883120 + + 0 127890499 127883275 - + N - 0.51254171322986 N HCC1954 16 5 1 2 2 N - - Y Other - 1 0 1 4 0.471355378555133 0.51420586751469 0.51420586751469 0.471355378555133 3 - 0 49212 Y Y 3.43312450200257 3.660633458326 3.43312450200257 0 0 0.886577775657982 Y 0.982973282185881 0.982973282185881 N N 322 226 ENSG00000215068 ENSG00000177721 - - 5 5 43081249 43079029 intron intron AC025171.8 C5orf39 43077952 43075258 + - 0 43079331 43077733 - + N - 9.50550804087227 N HCC1954 3 1.22222222222222 1 1 2 N - - Y SINE - 0.815217391304348 0 0.815217391304348 9 0.657040830713216 0.871293275511003 0.871293275511003 0.657040830713216 4 - 0 48359 N N 3.59272380419397 3.34615493251855 3.34615493251855 0 0 0.211546112491481 N 0 0 N N 19352 0 ENSG00000170561 ENSG00000219931 - + 5 X 2804774 99944702 downstream intron IRX2 RP3-347M6.2 2798959 99942822 - + 0.00383141762452099 2608428 99943091 + + Y - 1 N HCC1954 2 2 2 14 1 N - - N LINE - 0.984126984126984 0 0.984126984126984 14 0.899860268150708 0.592765097273879 0.899860268150708 0.592765097273879 1 - 0 10307 N Y 3.41419256772658 3.55976477294109 3.41419256772658 0 0 0.134893748583793 N 0 0.820539092055485 N N 313916 391 ENSG00000131748 ENSG00000108984 + + 17 17 35073248 65050046 intron intron STARD3 MAP2K6 35046938 64922433 + + 0 35047017 64970656 + + N 1.09830374749134 1.22086264249097 Y HCC1954 8 6 1 3 1 N - - N - SINE,DNA 0 0.754385964912281 0.754385964912281 4 0.621332089913584 0.407079645115797 0.621332089913584 0.407079645115797 1 0 0 26736 N Y 3.52680574168821 3.57592836747465 3.52680574168821 132 0 0.866304944123182 Y 0 0.983993157380254 N N 69736 15881 ENSG00000181019 ENSG00000102908 + + 16 16 68318034 68296054 coding intron NQO1 NFAT5 68300808 68156498 - + 0 68302531 68278756 - + N 0.277797344221225 0.911369880019537 N HCC1954 8 1.88888888888889 1 2 5 N - - N - SINE 0 1 1 9 0.771308801272036 0.914143764470561 0.914143764470561 0.771308801272036 2 0 0 26792 Y Y 3.02279354383265 3.38912318237562 3.02279354383265 286 0 0.0277914323229131 Y 0.601398601398601 0.992027972027972 N N 106880 21 ENSG00000167978 ENSG00000205913 - - 16 16 2761412 2730806 upstream upstream SRRM2 AC092117.4-2 2742331 2727105 + - 0 2739548 2733722 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.842726282871298 0.778450549431962 0.842726282871298 0.778450549431962 1 - - 14131 N Y 3.7297745213208 3.62295434849776 3.62295434849776 0 0 0.612633814344316 N 0 0.86165791776028 N N 1269 27 ENSG00000184319 ENSG00000164749 + + 22 8 49584800 76641600 utr5p upstream AC002055.2 HNF4G 49542380 76482732 + + 0 49542614 76388526 + + Y - - N HCC1954 23 22.4285714285714 20 14 1 N - - N LINE LTR 1 1 1 14 0.528489363834543 0.771308801272036 0.771308801272036 0.528489363834543 1 - - 17678 Y Y 3.47332441211719 3.49528100778935 3.47332441211719 127 0 0.527787431979632 Y 0 0.988931460195828 N Y 266 95718 ENSG00000213085 ENSG00000158710 - + 1 1 158136579 158161908 coding utr5p CCDC19 TAGLN2 158108776 158154521 - - 0 158129719 158161864 + - N - 0.413517556985099 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.621332089913584 0.542772860154395 0.621332089913584 0.542772860154395 4 - 0 6566 Y Y 3.61720120015252 3.68783934123363 3.61720120015252 47 0 0.0756612935354019 Y 0 0.963936889556724 N N 10969 31210 ENSG00000138029 ENSG00000084754 - - 2 2 26366836 26321098 coding intron HADHB HADHA 26321120 26267009 + - 0 26330690 26319609 - + N - 1.86572745678636 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.44578313253012 0.44578313253012 4 0.699891319672773 0.592765097273879 0.699891319672773 0.592765097273879 1 - 0 42941 N N 3.6344911504118 3.56473517872551 3.56473517872551 0 0 0.113737586020500 N 0.104117492787831 0.0721216889588253 N N 2 7291 ENSG00000205097 ENSG00000147996 - - 4 9 191185406 169078 downstream upstream FRG2 CBWD1 191182516 111039 - - 0.136113296616837 191179660 182260 + + Y - - N HCC1954 15 11.25 5 4 1 N 209 21.0859 N - - 0 0 0 4 0.528489363834543 0.278528178237124 0.528489363834543 0.278528178237124 2 - - 44719 Y Y 3.28552601004162 3.45872825368684 3.28552601004162 250 0 0.0320725769249451 Y 0.741298701298701 0.987064935064935 N N 103 0 ENSG00000188199 ENSG00000218922 - - 10 10 81144443 81114745 downstream upstream FAM22B RP11-119F19.4 81133041 81114254 + - 0 81196032 81121817 - + N - - N HCC1954 8 8 8 5 1 N - - Y - LTR 0 0.857142857142857 0.857142857142857 5 0.442788385915428 0.449930134075354 0.449930134075354 0.442788385915428 1 - - 21088 N N 3.3755202409218 3.3593167935949 3.3593167935949 0 0 0.297042879556924 N 0 0 N N 0 2 ENSG00000183920 ENSG00000169903 + + 1 3 96686462 150716260 downstream intron EEF1AL9 TM4SF4 96685074 150674451 + + 0 96686577 150696637 + + Y - 0.834848228998655 N HCC1954 14 10.2 4 5 1 N - - N - - 0 0 0 5 0.778450549431962 0.257102933757345 0.778450549431962 0.257102933757345 1 - 0 36994 N N 3.30401686394014 3.44296588673741 3.30401686394014 0 0 0.996035980690118 N 0 0 N N 2 20154 ENSG00000185610 ENSG00000168575 + + 12 8 43731149 42516225 intron intron DBX2 SLC20A2 43694806 42393173 - - 0 43725608 42477706 - - Y 0.918684047175667 36.1317356738638 N HCC1954 1 1 1 0 4 N 141 0.300921 N - - 0 0 0 20 0.814159290231593 0.892718519990782 0.892718519990782 0.814159290231593 4 0 0 3236 N Y 3.59425138750382 3.26824964015148 3.26824964015148 48 0 0.127020108832923 N 0.968033960720131 0.833776595744681 N N 12188 8014 ENSG00000168724 ENSG00000149084 - - 5 11 34994825 43834736 utr3p utr3p DNAJA5 HSD17B12 34965455 43658719 + + 0.136916939443535 34991634 43834016 - - Y - 1.56799368003871 N HCC1954 105 53.8867924528302 23 106 1 N - - N SINE - 1 0 1 106 1.2783729206268 1.08554572030879 1.2783729206268 1.08554572030879 1 - 0 36051 N N 3.18296190747752 3.43034293992665 3.18296190747752 7 0 0.0369410036212550 N 0.152380952380953 0.152380952380953 N N 6923 160 ENSG00000179715 ENSG00000144642 - - 12 3 45916706 30021623 downstream intron FAM113B RBMS3 45759653 29297947 + + 0.152380952380953 45937560 29985290 - - Y - 2.93177916290199 N HCC1954 11 4.85714285714286 3 14 1 N - - N - LINE 0 1 1 14 0.378512652476092 0.314236919036755 0.378512652476092 0.314236919036755 1 - 0 15257 N Y 3.58271458558979 3.66273010308932 3.58271458558979 0 0 0.0965725457751755 N 0.00425531914893618 0.940552556367101 N N 27679 8048 ENSG00000188643 ENSG00000049541 + + 1 7 151852183 73306674 coding utr3p S100A16 RFC2 151845986 73283770 - - 0 151846771 73283995 - - Y - - N HCC1954 23 22.25 21 8 1 N - - N - SINE 0 1 1 8 0.871293275511003 0.378512652476092 0.871293275511003 0.378512652476092 1 - - 36392 Y Y 3.68783934123363 3.38127338926705 3.38127338926705 274 0 0.0491761240636515 Y 0.275381552753815 0.984903782349038 N N 112 2428 ENSG00000053702 ENSG00000111203 + + 12 12 2814451 2804367 upstream utr3p NRIP2 ITFG2 2804773 2792124 - + 0 2816222 2803777 - + N - 1.4754139454346 N HCC1954 2 1.11111111111111 1 1 2 N - - Y LTR - 1 0 1 9 0.757025304952183 0.771308801272036 0.771308801272036 0.757025304952183 3 - 0 35538 N N 3.37129074227971 3.57336771439491 3.37129074227971 0 0 0.324386225510462 N 0 0.00793650793650746 N N 3189 20747 ENSG00000135679 ENSG00000073605 - + 12 17 67520481 35328429 utr3p intron MDM2 GSDMB 67488247 35314374 + - 0.00793650793650746 67520451 35326376 - - Y - 1.3429789198597 N HCC1954 35 28.8 25 5 1 N 603 23.7938 N SINE SINE 1 1 1 5 0.385654400636018 0.39993789695587 0.39993789695587 0.385654400636018 2 - 0 43796 N N 3.47589441276675 3.21279122419719 3.21279122419719 10 0 0.0389884879994122 N 0.0035460992907802 0 N N 2413 3891 ENSG00000100228 ENSG00000166295 + + 22 10 21836531 73665622 utr3p intron RAB36 C10orf104 21817513 73645812 + + 0 21835316 73645955 + + Y - 0.744979490524871 N HCC1954 33 25.1428571428571 23 14 1 N - - N SINE - 1 0 1 14 0.621332089913584 0.521347615674617 0.621332089913584 0.521347615674617 1 - 0 19593 N Y 3.69359248957888 3.24893340314576 3.24893340314576 0 0 0.981932064122205 N 0.971344189016603 0.971344189016603 N N 2418 0 ENSG00000142892 ENSG00000206696 + + 1 18 77457720 45272097 intron upstream PIGK SNORD58 77327254 45272032 - - 0.971344189016603 77367378 45272639 - - Y 0.349582486358079 - N HCC1954 8 2.8578431372549 2 204 3 N - - N - - 0 0 0 204 1.12125446110842 1.40692438750547 1.40692438750547 1.12125446110842 3 0 - 36287 Y Y 3.15741158895574 3.28548615724827 3.15741158895574 261 0 0.153776084031069 Y 0 0 N N 1803 27079 ENSG00000139055 ENSG00000111341 + - 12 12 14982750 14930025 downstream upstream ERP27 MGP 14958241 14925119 - - 0 14954927 14930030 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.642757334393363 0.742741808632331 0.742741808632331 0.642757334393363 2 - - 44486 N N 3.44512531223303 3.00935843624818 3.00935843624818 0 0 0.155786058044107 N 0 0 N N 23228 0 ENSG00000120549 ENSG00000217620 - - 10 8 24876778 103888783 intron upstream KIAA1217 AP003356.2 24023681 103888246 + + 0 24820482 103838036 - - Y 0.573810988823245 - N HCC1954 20 16.962962962963 7 54 1 N 292 26.0556 N SINE - 1 0 1 54 0.28566992639705 0.735600060472404 0.735600060472404 0.28566992639705 2 0 - 48707 N Y 3.54292948342842 3.38855412092215 3.38855412092215 0 0 0.0837979707413701 N 0 0 N N 16 46607 ENSG00000130950 ENSG00000146063 + - 9 5 96130747 180595414 intron intron FAM22F TRIM41 96120299 180582912 - + 0 96129309 180590223 - - Y 1.46714172604909 0.918349107249301 N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.299953422716903 0.442788385915428 0.442788385915428 0.299953422716903 2 0 0 35132 N Y 3.58424216889964 3.58424216889964 3.58424216889964 0 0.236882716049383 0.840142777674195 N 0.834104938271605 0.817515432098765 N N 34637 0 ENSG00000197111 ENSG00000220595 + - 12 21 52159872 39465902 coding intron PCBP2 AF129408.11 52132161 39464926 + - 0.120756172839506 52147344 39465182 + + Y - 1 N HCC1954 1 1 1 0 2 N - - N SINE - 0.375 0 0.375 6 0.5713398527941 0.407079645115797 0.5713398527941 0.407079645115797 3 - 0 35185 N Y 3.39168383545536 2.72254980166479 2.72254980166479 0 0 0.110736173507231 N 0 0.688387784090909 N N 4592 740 ENSG00000151136 ENSG00000197008 + + 12 7 106577549 63931140 intron intron BTBD11 ZNF138 106236848 63892241 + + 0 106349633 63894904 + + Y 0.637043837455726 1.20870090574902 N HCC1954 22 21 20 4 1 N - - N SINE SINE 1 0.39622641509434 1 4 0.299953422716903 0.378512652476092 0.378512652476092 0.299953422716903 2 0 0 8006 N N 3.27192306858781 3.52936639476796 3.27192306858781 0 0 0.780072777633545 N 0 0 N Y 3699 8425 ENSG00000115947 ENSG00000109586 - + 2 4 148495606 174481692 coding coding ORC4L GALNT7 148408202 174326479 - + 0 148432905 174461844 + + Y - 2.31051772939774 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 69 1.18553019454776 0.914143764470561 1.18553019454776 0.914143764470561 4 - 0 10 Y Y 3.46248981040582 3.3975649648766 3.3975649648766 335 0 0.018482888301397 Y 0 0.983101441942828 N N 0 0 ENSG00000129586 ENSG00000222048 + - 11 11 10836165 10836196 upstream upstream AC069360.7 ZBED5 10830921 10830827 - - 0 10843193 10836384 - + N - - N HCC1954 1 1 1 0 3 N - - Y - DNA 0 0.0930232558139535 0.0930232558139535 184 0.564198104634174 0.614190341753658 0.614190341753658 0.564198104634174 1 - - 30236 Y N 3.11704384497176 3.56911164413597 3.11704384497176 0 0 0.0454515394509217 N 0 0 Y N 0 0 ENSG00000217445 ENSG00000208602 - - X X 133484686 133488116 upstream downstream AC004383.3 AC004383.1 133484398 133487977 + - 0 133482017 133475662 - + N - - N HCC1954 140 26.2 1 9 1 N - - N Simple_repeat SINE 1 1 1 10 0.671324327033068 0.592765097273879 0.671324327033068 0.592765097273879 1 - - 550 N Y 3.31216283149579 3.07317050642081 3.07317050642081 134 0 0.956916418965212 Y 0.935239491691105 0.99352394916911 N N 9074 0 ENSG00000166444 ENSG00000202276 - + 11 11 8817478 8855641 utr5p downstream ST5 Y_RNA 8671478 8855540 - - 0 8817475 8849079 + - N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 47 1.34264865406614 1.16410495006798 1.34264865406614 1.16410495006798 3 - - 39889 Y Y 3.45720067037699 3.28296535696188 3.28296535696188 333 0 0.00334576305882783 Y 0 0.9862483172828 N N 1113 2587 ENSG00000214445 ENSG00000214446 + - 15 15 88256923 88257163 utr3p downstream AC027176.22-1 C15orf38 88245111 88244836 - - 0 88245619 88242123 - + N 1.10642074215278 - N HCC1954 1 1 1 0 1 N - - Y SINE SINE 0.464646464646465 0.268518518518519 0.464646464646465 5 0.707033067832699 0.771308801272036 0.771308801272036 0.707033067832699 2 0 - 47512 Y Y 2.97316705693644 3.39384326095097 2.97316705693644 0 0 0.997818361821084 Y 0 0 N Y 6250 3492 ENSG00000105245 ENSG00000123815 - + 19 19 45888396 45914440 coding coding NUMBL ADCK4 45863650 45889274 - - 0 45884740 45890696 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 16 1.15696320190805 1.04983697950916 1.15696320190805 1.04983697950916 4 - - 26761 Y Y 3.35616415112274 3.17511211436896 3.17511211436896 249 0 0.0264454832783368 Y 0 0.952000774181062 N N 0 13000 ENSG00000159723 ENSG00000159720 + - 16 16 66075217 66072590 upstream upstream AGRP ATP6V0D1 66073978 66029418 - - 0 66075438 66072836 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.664182578873142 0.585623349113953 0.664182578873142 0.585623349113953 2 - - 5574 N N 3.32167753656001 3.63552422018169 3.32167753656001 0 0 0.238017763482756 N 0 0 N N 86 38670 ENSG00000183690 ENSG00000171848 + + X 2 44087867 10188996 intron utr3p EFHC2 RRM2 43892072 10179906 - + 0 44052946 10187321 - + Y 3.32113144758735 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.242819437437493 0.407079645115797 0.407079645115797 0.242819437437493 1 0 - 17867 Y Y 3.53039946453785 3.45041445226185 3.45041445226185 0 0 0.348483864260918 Y 0 0 N N 13757 568 ENSG00000135823 ENSG00000215828 + - 1 1 179258669 179212241 coding intron STX6 AL162431.17-1 179208801 179179798 - - 0 179220437 179186678 - + N - 0.0731551073274452 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 34 1.31408166142643 1.35693215038599 1.35693215038599 1.31408166142643 1 - 0 29202 Y Y 3.61257440753299 3.38656252929588 3.38656252929588 270 0 0.409199015400293 Y 0.00370370370370365 0.991104497354497 N N 0 0 ENSG00000221559 ENSG00000218208 - + 6 6 114132819 114009842 upstream downstream AL357519.19 RP11-367G18.2 114132752 114009396 + + 0 114082326 114055569 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.464213630395207 0.442788385915428 0.464213630395207 0.442788385915428 1 - - 33913 N N 3.35356364524965 3.36506059437033 3.35356364524965 2 0 0.219302630277561 N 0 0 N N 544065 247001 ENSG00000198744 ENSG00000198786 + + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0 8731 13997 + + N 0.550047422199827 1.4627104780477 Y HCC1954 3 1.8 1 3 2 N 316 3.86643 N - - 0 0 0 5 0.792734045751814 0.764167053112109 0.792734045751814 0.764167053112109 1 0 0 42360 Y Y 3.31535532676129 3.51104337473878 3.31535532676129 274 0 0.0593138825405838 Y 0.86161800486618 0.981549067315491 N N 12 1483 ENSG00000205129 ENSG00000109775 - - 4 4 186607816 186584062 upstream upstream C4orf47 UFSP2 186587538 186558437 + - 0 186587479 186584544 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.799875793911741 0.942710757110266 0.942710757110266 0.799875793911741 4 - - 16742 N Y 3.12804628055249 3.52101274054962 3.12804628055249 0 0 0.248622926125196 N 0.758533956162415 0.758533956162415 N N 1649619 9230 ENSG00000141736 ENSG00000133065 - - 17 1 35138441 204048821 coding upstream ERBB2 SLC41A1 35104766 204024847 + - 0 35122227 204051557 - + Y - - N HCC1954 23 21.6 20 5 1 N - - N - SINE 0 1 1 5 0.34280391167646 0.307095170876829 0.34280391167646 0.307095170876829 2 - - 25152 Y Y 3.63552422018169 3.62824348852659 3.62824348852659 291 0 0.00784195206934446 Y 0.98466825270949 0.992334126354745 N N 0 0 ENSG00000215571 ENSG00000218629 - + 13 13 20792941 20778512 downstream intron AL139380.6 RP11-101P17.8 20791295 20770398 + + 0 20802861 20773756 - + N - 1 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.942710757110266 0.971277749749971 0.971277749749971 0.942710757110266 1 - 0 17189 N Y 3.6314359837921 3.42680229220385 3.42680229220385 0 0.674005681818182 0.473742020751908 N 0.674005681818182 0.674005681818182 N N 15578 81 ENSG00000163362 ENSG00000133424 + - 1 22 199151486 32646410 utr3p intron C1orf106 LARGE 199127292 31998847 + - 0.674005681818182 199150339 32087080 + + Y 1.40491621275824 0.692052643815131 N HCC1954 2 1.8 1 4 1 N - - N SINE SINE 0.271604938271605 1 1 5 0.578481600954027 0.34280391167646 0.578481600954027 0.34280391167646 2 0 0 34659 Y Y 3.01183938374122 3.16613596553466 3.01183938374122 0 0 0.852259592484315 Y 0 0 N Y 1229 545 ENSG00000081386 ENSG00000196597 - + 9 9 98580159 98655175 utr5p coding ZNF510 ZNF782 98557968 98619094 - - 0 98578348 98629183 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.05697872766909 1.04983697950916 1.05697872766909 1.04983697950916 4 - - 45723 N Y 3.43142908482337 3.74487454086093 3.43142908482337 1 0 0.777616327813023 N 0.0532005153505327 0 N N 2135 100806 ENSG00000188039 ENSG00000163931 + + 19 3 16789756 53265078 utr3p coding NWD1 TKT 16703001 53234715 + - 0 16789107 53249307 + - Y - - N HCC1954 32 30.25 29 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.407079645115797 0.407079645115797 0.278528178237124 4 - - 42147 Y Y 3.3755202409218 3.30488209984069 3.30488209984069 300 0 0.00140394377970299 Y 0 0 N N 0 2861 ENSG00000145384 ENSG00000164096 + - 4 4 120462766 120445048 upstream intron FABP2 C4orf3 120457854 120439095 - - 0 120474933 120441704 - + N - 320.436681222707 N HCC1954 2 1.55555555555556 1 5 1 N - - Y - SINE 0 0.101382488479263 0.101382488479263 9 1.09268746846872 1.42834963198525 1.42834963198525 1.09268746846872 1 - 0 47042 Y Y 2.92551858129737 3.17151839151932 2.92551858129737 297 0 0.205922205746265 Y 0 0.988801876442326 N N 60677 4159 ENSG00000125740 ENSG00000012061 - - 19 19 50670254 50619017 upstream utr5p FOSB ERCC1 50663093 50604712 + - 0 50646461 50618479 - + N - 2.80588813503834 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 7 0.385654400636018 0.621332089913584 0.621332089913584 0.385654400636018 2 - 0 13687 Y Y 3.35616415112274 3.5246463161926 3.35616415112274 324 0 0.0395563242430316 Y 0 0 N N 19152 9629 ENSG00000182457 ENSG00000133422 - - 22 22 29702049 29694187 intron upstream TUG1 MORC2 29696663 29652600 + - 0 29697916 29695315 - + N 0.63802764549611 - N HCC1954 1 1 1 0 3 N - - Y LINE - 0.285714285714286 0 0.285714285714286 19 0.799875793911741 0.885576771830856 0.885576771830856 0.799875793911741 3 0 - 13675 Y N 3.33767777970086 3.47080361183081 3.33767777970086 0 0 0.181112087194381 Y 0.18547418967587 0.18547418967587 N N 4357 1260 ENSG00000100216 ENSG00000100211 - + 22 22 37410709 37399795 upstream downstream TOMM22 CBY1 37407900 37382604 + + 0.18547418967587 37407771 37402372 - + N - - N HCC1954 1 1 1 0 2 N - - Y DNA LINE,LINE 0.645454545454546 0.417808219178082 0.645454545454546 12 0.785592297591888 1.04269523134923 1.04269523134923 0.785592297591888 1 - - 43420 N N 3.52680574168821 3.09087103183403 3.09087103183403 0 0 0.116647413501258 N 0 0 N N 4 3891 ENSG00000213981 ENSG00000166295 - + 2 10 171260130 73665622 intron intron AC007277.2 C10orf104 171214273 73645812 - + 0 171247004 73645953 + + Y 0.672538860103627 0.744979490524871 N HCC1954 30 23.2 20 5 1 N - - N SINE - 1 0 1 5 0.378512652476092 0.364229156156239 0.378512652476092 0.364229156156239 1 0 0 42907 N N 3.61720120015252 3.67849247003875 3.61720120015252 0 0 0.997618045359556 N 0 0 N N 11640 21519 ENSG00000137038 ENSG00000164111 + + 9 4 7789799 122837585 upstream coding C9orf123 ANXA5 7786490 122808598 - - 0 7813337 122837186 - - Y - - N HCC1954 1 1 1 0 4 N - - N LTR,LTR - 1 0 1 20 1.02126998686945 1.08554572030879 1.08554572030879 1.02126998686945 4 - - 173 Y Y 3.52105259334297 3.05575257508553 3.05575257508553 261 0 0.0562198876182869 Y 0 0.990512680167853 N N 0 1020 ENSG00000200983 ENSG00000166436 - - 11 11 8662479 8649989 upstream upstream SNORA3 TRIM66 8662350 8590160 + - 0 8657754 8650553 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.735600060472404 0.749883556792257 0.749883556792257 0.735600060472404 1 - - 37779 N Y 3.68680627146374 3.48809356209009 3.48809356209009 0 0 0.0862605984313682 N 0 0 N N 428 45068 ENSG00000119699 ENSG00000205336 - + 14 16 75517242 56256445 intron upstream TGFB3 GPR56 75494195 56220023 - + 0 75511380 56211646 + + Y 1.04071996303 - N HCC1954 21 20.125 20 8 1 N - - N SINE - 1 0 1 8 0.371370904316165 0.442788385915428 0.442788385915428 0.371370904316165 1 0 - 19117 Y Y 3.31894904961092 3.54400240599166 3.31894904961092 255 0 0.0785727214064696 Y 0 0.978806841885691 N N 0 3449 ENSG00000180867 ENSG00000131791 - - 1 1 145117830 145110753 upstream upstream AL356378.17-1 PRKAB2 145116308 145093314 + - 0 145115299 145112889 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE - 1 0 1 5 0.628473838073511 0.621332089913584 0.628473838073511 0.621332089913584 2 - - 13540 N N 3.57489529770476 3.28548615724827 3.28548615724827 0 0 0.935108094037931 N 0 0 N N 640 2 ENSG00000178445 ENSG00000219036 - + 9 22 6635692 27610368 coding coding GLDC AL031596.7 6522469 27609890 - + 0 6555429 27610054 + + Y - 2.03614457831325 N HCC1954 2 1.5 1 10 1 N - - N - Low_complexity 0 0.0753424657534247 0.0753424657534247 20 1.10697096478857 1.04269523134923 1.10697096478857 1.04269523134923 4 - 0 11765 N Y 3.55703628599201 3.49065421516983 3.49065421516983 2 0 0.114689424996999 N 0 0.72851805728518 N N 10798 0 ENSG00000108448 ENSG00000213601 + + 17 9 15528338 99502842 utr3p downstream TRIM16 AL445531.10 15471999 99501258 - + 0.457036114570361 15472190 99525637 - + Y - - N HCC1954 25 23.5 21 4 1 N - - N SINE SINE,SINE 1 0.641025641025641 1 4 0.592765097273879 0.278528178237124 0.592765097273879 0.278528178237124 0 - - 38136 N Y 3.60888739872753 3.61936062564813 3.60888739872753 0 0 0.580758421500375 Y 0.0125923546418247 0 N N 231 1060 ENSG00000129535 ENSG00000215256 + - 14 14 23654063 23492716 utr5p intron NRL AL136419.3-2 23619156 23479414 - - 0 23653773 23480209 - + N 0.346463218653911 6.43477785625399 N HCC1954 1 1 1 0 1 N - - N - LTR 0 0.346938775510204 0.346938775510204 7 0.821301038391519 1.02841173502938 1.02841173502938 0.821301038391519 3 0 0 41134 Y Y 3.42783536197374 2.79101916968047 2.79101916968047 0 0 0.230438191081250 Y 0.756184729635646 0.992828962636343 N N 3725 0 ENSG00000174306 ENSG00000218353 - - 20 20 39362153 39393714 utr5p upstream ZHX3 RP3-450M14.1 39240502 39393177 - + 0 39331136 39379562 + - N - - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.790419161676647 0.790419161676647 13 0.892718519990782 1.12839620926835 1.12839620926835 0.892718519990782 1 - - 2026 N Y 3.26824964015148 3.58424216889964 3.26824964015148 3 0 0.34075849662442 N 0.97629179331307 0.92887537993921 N N 8014 0 ENSG00000149084 ENSG00000207131 - - 11 6 43834736 88592722 utr3p upstream HSD17B12 Y_RNA 43658719 88592610 + - 0 43834016 88595608 - + Y 1.56799368003871 - N HCC1954 68 33.75 1 3 1 N - - N - SINE 0 0.770642201834862 0.770642201834862 4 0.892718519990782 0.678466075192994 0.892718519990782 0.678466075192994 2 0 - 45948 N N 3.09918483325901 3.11022712163309 3.09918483325901 20 0.315364583333334 0.476177823120529 N 0.356857638888889 0 N N 12272 0 ENSG00000105355 ENSG00000211686 + - 19 7 4818676 38255698 utr3p intron M6PRBP1 TRG@ 4789346 38246150 - - 0 4789599 38248171 - + Y - 1 N HCC1954 18 11.5 1 3 1 N - - N SINE SINE 1 0.789473684210526 1 4 0.499922371194838 0.271386430077198 0.499922371194838 0.271386430077198 2 - 0 5272 N Y 3.74590761063082 3.4636794512778 3.4636794512778 0 0.336448598130841 0.505855840437189 N 0.336448598130841 0.336448598130841 N N 850768 9560 ENSG00000075624 ENSG00000107077 + + 7 9 5536758 7165647 coding intron ACTB JMJD2C 5533313 6747654 - + 0.336448598130841 5535384 6824766 - + Y - 0.724374047070759 N HCC1954 2 2 2 5 1 N - - N - - 0 0 0 5 0.678466075192994 0.271386430077198 0.678466075192994 0.271386430077198 3 - 0 38234 Y Y 3.39743698380061 3.39487633072086 3.39487633072086 237 0.0147013102376193 0.192304568196870 Y 0.958072396180324 0.979036198090162 N N 12878 1318 ENSG00000100804 ENSG00000100802 + - 14 14 22573949 22549186 coding upstream PSMB5 C14orf93 22564900 22525951 - - 0 22572417 22555684 - + N 0.688979930465747 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.649899082553289 0.621332089913584 0.649899082553289 0.621332089913584 4 0 - 40176 Y Y 3.56079784271098 3.31422897103557 3.31422897103557 0 0 0.531427758186291 Y 0.0159659896079357 0.993166430483388 N N 803 2124 ENSG00000169609 ENSG00000169612 + + 15 15 81471362 81450795 coding intron C15orf40 FAM103A1 81464398 81445975 - + 0 81468307 81448588 - + N - 3.86431756115535 N HCC1954 1 1 1 0 2 N - - Y - SINE 0 1 1 8 1.37121564670584 0.621332089913584 1.37121564670584 0.621332089913584 2 - 0 16183 N N 3.49061436237648 3.52783881145811 3.49061436237648 0 0 0.440975657336732 N 0.565896380711195 0.57866413421969 N N 10665 2402 ENSG00000115233 ENSG00000162636 - + 2 1 161976474 108989045 upstream intron PSMD14 FAM102B 161872795 108904234 + + 0.642502901762161 161844632 108954123 - + Y - 0.777287905031898 N HCC1954 1 1 1 0 1 N - - N LINE LINE 0.166666666666667 1 1 4 0.299953422716903 0.328520415356608 0.328520415356608 0.299953422716903 1 - 0 48024 N N 3.27192306858781 3.79722016713641 3.27192306858781 0 0 0.361557991012977 N 0 0 N N 86504 0 ENSG00000104408 ENSG00000182152 - + 8 5 109330135 117142614 coding downstream EIF3E AC114322.2 109283149 117142420 - - 0 109297881 116869229 + - Y - - N HCC1954 2 1.25 1 1 2 N 485 24.0701 N - Unknown 0 0.296296296296296 0.296296296296296 4 0.771308801272036 0.821301038391519 0.821301038391519 0.771308801272036 2 - - 9734 N Y 3.66848325143457 3.64549358599252 3.64549358599252 0 0.00323624595469274 0.986818699306015 Y 0.00323624595469274 0.990507011866235 N Y 18240 62029 ENSG00000062716 ENSG00000141367 - + 17 17 55273235 55129099 intron coding TMEM49 CLTC 55139811 55051832 + + 0 55270438 55115899 - + N 0.534889297752894 - N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 250 0.814159290231593 1.49976711358451 1.49976711358451 0.814159290231593 4 0 - 9360 Y Y 3.68577320169385 3.5580693557619 3.5580693557619 323 0 0.906317450740956 Y 0.0102679466334052 0.992828028598793 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 intron utr3p C17orf37 ERBB2 35138937 35104766 - + 0.992828028598793 35139768 35138232 - + N 1.35620378426741 2.37973796965433 N HCC1954 1 1 1 0 6 N - - Y SINE - 0.213836477987421 0 0.213836477987421 26 1.13553795742827 1.32122340958636 1.32122340958636 1.13553795742827 1 0 0 29312 Y Y 3.52039024593366 3.52105259334297 3.52039024593366 237 0 0.374882217222855 Y 0 0.976005286970667 N N 0 4158 ENSG00000208766 ENSG00000111885 - - 6 6 120625246 119712625 upstream upstream AL606830.4 MAN1A1 120625131 119540968 + - 0 120179907 120090888 - + N - - N HCC1954 2 1.4 1 2 2 N - - Y - LINE 0 1 1 5 0.564198104634174 0.685607823352921 0.685607823352921 0.564198104634174 4 - - 18408 N Y 3.61360747730288 3.56488607910057 3.56488607910057 301 0 0.110323421389080 Y 0.301598079394718 0.992724979993695 N N 0 0 ENSG00000220261 ENSG00000219021 + + 1 1 222242479 222204741 downstream downstream RP11-504P24.2 RP11-504P24.1 222237079 222201925 - + 0 222228312 222219039 - + N - - N HCC1954 240 195.833333333333 168 6 3 N - - N Simple_repeat SINE,SINE 0.134228187919463 1 1 6 0.592765097273879 0.585623349113953 0.592765097273879 0.585623349113953 2 - - 59 Y Y 2.27429484578767 3.63296356710195 2.27429484578767 272 0.00367647058823506 0.147385284181618 Y 0.977859477124183 0.988929738562092 N N 1289 3448 ENSG00000177595 ENSG00000177542 + - 11 11 795245 786221 downstream intron LRDD SLC25A22 789180 780478 - - 0 788218 785170 - + N - 14.9779932254324 N HCC1954 1 1 1 0 4 N - - Y Low_complexity - 0.349514563106796 0 0.349514563106796 88 0.735600060472404 0.985561246069823 0.985561246069823 0.735600060472404 1 - 0 4572 N Y 3.45972147066338 3.72146071989581 3.45972147066338 0 0 0.743842060639976 N 0.983261046354025 0.983261046354025 Y N 4071 13708 ENSG00000213214 ENSG00000050327 + + 7 7 143523669 143708657 downstream coding AC004889.1-3 ARHGEF5 143514610 143683366 - + 0 143509910 143705216 - + N - - N HCC1954 2 2 2 10 1 N - - N - - 0 0 0 10 0.635615586233437 0.378512652476092 0.635615586233437 0.378512652476092 4 - - 27062 Y Y 3.3014562108604 3.49318436302603 3.3014562108604 221 0 0.044230571997477 Y 0 0.983943949788352 N N 4999 5945 ENSG00000141013 ENSG00000003249 - - 16 16 88638880 88613438 coding upstream GAS8 DBNDD1 88616509 88598782 + - 0 88625220 88614115 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 6 0.885576771830856 0.607048593593732 0.885576771830856 0.607048593593732 2 - - 41725 N N 3.66016945000958 3.46977054206092 3.46977054206092 11 0.0213647959183672 0.962511558492638 Y 0.0213647959183672 0 N N 22 25232 ENSG00000164935 ENSG00000156471 - + 8 8 105438092 97415950 downstream coding TM7SF4 PTDSS1 105421228 97343340 + + 0 105446363 97391026 - + N - - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 14 0.828442786551446 0.871293275511003 0.871293275511003 0.828442786551446 4 - - 1256 N Y 3.25463311832853 3.55401162459584 3.25463311832853 0 0 0.644891062652256 N 0 0.971321911542931 N N 0 52 ENSG00000148935 ENSG00000214164 - + 11 2 22791113 110569923 intron downstream GAS2 AC112229.4-2 22646230 110569013 + - 0 22676704 110566591 - - Y 1 - N HCC1954 220 160 100 6 1 N - - N LINE - 1 0 1 6 0.749883556792257 0.914143764470561 0.914143764470561 0.749883556792257 4 0 - 41009 Y Y 3.46401739371567 3.58271458558979 3.46401739371567 283 0 0.00681703348817764 Y 0 0 N N 24824 0 ENSG00000125968 ENSG00000201770 - + 20 20 29657974 29632656 utr5p upstream ID1 U6 29656753 29632553 + + 0 29656835 29629245 - + N 2.09269160420568 - N HCC1954 1 1 1 0 1 N - - Y - LTR,LTR 0 1 1 4 0.849868031031224 0.792734045751814 0.849868031031224 0.792734045751814 1 0 - 2247 N Y 3.42424163912411 3.67440423364916 3.42424163912411 5 0.00408163265306127 0.039034966030659 N 0.897478991596639 0.926770708283313 N N 3567 10316 ENSG00000177951 ENSG00000144554 - + 11 3 197428 10118614 coding utr3p BET1L FANCD2 157784 10043113 - + 0 195612 10118201 + + Y - - N HCC1954 175 154.2 140 5 1 N 214 24.8339 N - SINE 0 1 1 5 0.778450549431962 0.299953422716903 0.778450549431962 0.299953422716903 0 - - 27412 Y Y 3.48081283043499 3.20976656280103 3.20976656280103 20 0.0386784754224271 0.864074785644607 Y 0.953233006912443 0.963625672043011 N N 4968 172 ENSG00000104731 ENSG00000205047 + - 16 16 86357056 86292831 coding upstream KLHDC4 AC010536.8 86298920 86291389 - - 0 86299067 86294541 - + N - - N HCC1954 2 1.14285714285714 1 1 3 N - - Y - - 0 0 0 7 0.607048593593732 0.928427260790413 0.928427260790413 0.607048593593732 3 - - 33035 Y Y 3.36609366414022 3.44040523365767 3.36609366414022 414 0 0.998495690674175 Y 0 0.994363929146538 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.994363929146538 14189 12612 - + N 0.550016932033967 0.807451493445787 N HCC1954 2 1.33333333333333 1 5 10 N - - Y - - 0 0 0 15 1.37835739486577 1.47120012094481 1.47120012094481 1.37835739486577 2 0 0 5927 N Y 3.18974812559266 3.4780843434859 3.18974812559266 0 0 0.534338786060766 N 0.450414327719861 0.862603581929965 N N 18437 0 ENSG00000163932 ENSG00000208079 - + 3 2 53201771 218758050 utr5p upstream PRKCD AC097483.3 53170263 218757949 + - 0 53174267 218761950 - - Y - - N HCC1954 20 20 20 7 1 N - - N - SINE 0 1 1 7 0.428504889595575 0.314236919036755 0.428504889595575 0.314236919036755 2 - - 9616 Y Y 3.50422665140011 3.19293127328835 3.19293127328835 309 0 0.0949578095252437 Y 0.986345701999379 0.99317285099969 N N 14866 497 ENSG00000188554 ENSG00000198496 - + 17 17 38719232 38549760 upstream downstream AC109326.11 NBR2 38576772 38531135 + + 0 38572524 38554327 - + N - - N HCC1954 7 3 1 6 3 N - - Y LTR LTR 1 0.864864864864865 1 10 1.07840397214886 0.792734045751814 1.07840397214886 0.792734045751814 1 - - 33673 N Y 3.50529022639353 3.1825606798934 3.1825606798934 220 0 0.574456382864696 Y 0 0.969526901669759 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0 10975 5449 - + N - 1.53136739020212 N HCC1954 2 1.5 1 3 4 N - - N - - 0 0 0 6 0.785592297591888 0.907002016310634 0.907002016310634 0.785592297591888 3 - 0 34303 Y Y 3.70144228268745 3.38230645903694 3.38230645903694 309 0 0.0107905205123793 Y 0.975286849073257 0.991762283024419 N N 111 0 ENSG00000188152 ENSG00000218062 - + 9 9 98744393 98721421 intron upstream FAM22G RP11-330M2.3 98721960 98721031 + + 0 98735899 98720930 - + N 1.24438055773419 - N HCC1954 8 2.51851851851852 1 26 2 N - - Y SINE - 0.274809160305344 0 0.274809160305344 27 0.93556900895034 1.29979816510658 1.29979816510658 0.93556900895034 1 0 - 10151 Y Y 3.49744043328497 3.83593234673454 3.49744043328497 166 0 0.0349115976839997 Y 0 0 N N 193 10798 ENSG00000221926 ENSG00000108448 - + 17 17 15463743 15528338 coding coding CDRT1 TRIM16 15432427 15471999 - - 0 15459848 15472786 + - N - - N HCC1954 4 2.66666666666667 2 6 1 N - - Y - - 0 0 0 6 0.93556900895034 0.664182578873142 0.93556900895034 0.664182578873142 3 - - 34902 Y Y 3.26360926716282 3.3080745951062 3.26360926716282 171 0.00829525985151336 0.0208747674574831 Y 0.00829525985151336 0.958923472301542 N N 553 5592 ENSG00000160323 ENSG00000148300 - - 9 9 135314329 135272985 utr5p upstream ADAMTS13 REXO4 135276941 135261009 + - 0 135277323 135273210 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.635615586233437 0.721316564152552 0.721316564152552 0.635615586233437 1 - - 35402 N Y 3.71617157986699 3.27717235582328 3.27717235582328 3 0 0.803580264973563 N 0 0.935032483758121 N N 8520 12 ENSG00000170832 ENSG00000205592 + + 17 12 55824368 39250827 intron downstream USP32 MUC19 55609473 39222629 - + 0 55652974 39372661 - + Y 0.753544430772631 - N HCC1954 17 12.25 7 12 1 N - - N SINE - 1 0 1 12 0.321378667196682 0.499922371194838 0.499922371194838 0.321378667196682 4 0 - 36444 Y Y 3.55401162459584 3.42208221362849 3.42208221362849 9 0.0329452563784988 0.762147888106622 Y 0.0329452563784988 0.992444884815457 N N 3074 122756 ENSG00000135477 ENSG00000135480 + + 12 12 50938438 50928976 upstream coding AC021066.37 KRT7 50932079 50913221 - + 0 50949728 50928691 - + N - - N HCC1954 6 2.25 1 1 3 N - - Y DNA,LTR - 0.278145695364238 0 0.278145695364238 4 0.857009779191151 0.871293275511003 0.871293275511003 0.857009779191151 2 - - 22173 N N 3.30488209984069 3.60256518892881 3.30488209984069 0 0 0.432543902545293 N 0 0.430875576036866 N N 57 0 ENSG00000172575 ENSG00000207623 + + 15 1 36644224 207672210 intron upstream RASGRP1 hsa-mir-205 36567590 207672101 - + 0.430875576036866 36644042 207670443 - + Y 1.67508964756034 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 16 0.278528178237124 0.564198104634174 0.564198104634174 0.278528178237124 2 0 - 31508 Y Y 3.27188321579446 3.54868263177367 3.27188321579446 157 0 0.173392855936905 Y 0.941551142750094 0.985387785687523 N N 0 8002 ENSG00000210957 ENSG00000172340 + - 3 3 67967650 67787728 downstream upstream AC113171.3 SUCLG2 67967527 67507835 - - 0 67879886 67788217 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.428504889595575 0.635615586233437 0.635615586233437 0.428504889595575 1 - - 37543 N Y 2.72146356525374 3.29868787111796 2.72146356525374 0 0.204166666666666 0.132492073618500 N 0.154427083333334 0.204166666666666 N N 0 8304 ENSG00000187141 ENSG00000087299 - + 17 14 67129172 49848697 upstream utr3p AC118653.6 L2HGDH 67128717 49774064 + - 0.204166666666666 66987118 49780404 - - Y - - N HCC1954 128 106 32 5 1 N - - N LINE LINE,LINE 1 1 1 5 0.278528178237124 0.392796148795944 0.392796148795944 0.278528178237124 1 - - 15511 N N 3.377215658101 3.74234439300473 3.377215658101 29 0 0.0994815835809816 N 0 0 N N 3170 2833 ENSG00000214194 ENSG00000133019 + + 7 1 112545845 238139338 upstream utr5p AC073346.12 CHRM3 112544018 237858996 - + 0.024872026498043 112696545 237859432 - + Y - - N HCC1954 23 22.3333333333333 22 6 1 N - - N LINE,LINE LINE 0.719512195121951 1 1 6 0.585623349113953 0.728458312312478 0.728458312312478 0.585623349113953 3 - - 14861 N N 3.61360747730288 3.45041445226185 3.45041445226185 0 0 0.0454709976146633 N 0 0 N N 49089 26899 ENSG00000117450 ENSG00000149428 - + 1 11 45760196 118433122 coding upstream PRDX1 HYOU1 45749295 118420110 - - 0 45757256 118436535 + - Y - - N HCC1954 40 19.0454545454545 5 22 1 N 31 23.0997 N - SINE 0 1 1 22 0.807017542071667 0.349945659836387 0.807017542071667 0.349945659836387 1 - - 13795 Y Y 3.45716081758364 3.49168728493972 3.45716081758364 148 0.475 0.00899574797984692 Y 0.475 0.971621621621622 N N 681 1381 ENSG00000100077 ENSG00000206062 - + 22 22 24455238 24187186 upstream coding ADRBK2 CRYBB2P1 24290861 24183283 + + 0 24246654 24183358 - + N - - N HCC1954 4 1.75 1 1 1 N - - Y LTR - 1 0 1 4 0.471355378555133 0.585623349113953 0.585623349113953 0.471355378555133 2 - - 24551 N N 3.47552369040616 3.48908677906663 3.47552369040616 2 0 0.26418940070605 N 0.873705468102734 0 N N 1992 8352 ENSG00000003436 ENSG00000197971 - - 2 18 188127464 72973788 utr5p intron TFPI MBP 188037202 72819771 - - 0 188127364 72870340 + + Y 19.2945621198005 1.27731152330312 N HCC1954 17 3.66666666666667 1 1 1 N - - N - Other 0 1 1 6 0.378512652476092 0.39993789695587 0.39993789695587 0.378512652476092 2 0 0 33128 N Y 3.20657406753552 3.21488786896051 3.20657406753552 365 0 0.223779736104569 Y 0 0.977961098917733 N N 247001 275222 ENSG00000198786 ENSG00000198763 - + MT MT 14149 5512 coding coding MT-ND5 MT-ND2 12338 4471 + + 0 13995 5227 - + N 1.4621269126378 0.971741044116378 N HCC1954 2 1.5 1 2 5 N - - N - - 0 0 0 4 1.12839620926835 0.971277749749971 1.12839620926835 0.971277749749971 1 0 0 17654 Y Y 3.52936639476796 3.34256120966892 3.34256120966892 0 0 0.308973740845192 Y 0.489952153110048 0.97384370015949 N N 208 68242 ENSG00000188206 ENSG00000153187 - + 1 1 243076776 243094450 coding downstream C1orf199 HNRNPU 243074714 243080225 - - 0 243076548 243078732 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.87843502367093 0.721316564152552 0.87843502367093 0.721316564152552 4 - - 5866 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.112280164649655 N 0 0.931476569407604 N N 20739 18789 ENSG00000143951 ENSG00000073849 - - 2 3 63669355 188279035 utr3p intron C2orf86 ST6GAL1 63202041 188131210 - + 0.897214854111406 63309485 188255502 + - Y - 1.11450078527912 N HCC1954 620 525.714285714286 420 7 1 N - - N LINE LINE 1 1 1 7 0.39993789695587 0.34280391167646 0.39993789695587 0.34280391167646 4 - 0 16430 N N 3.72448538129198 3.47907756046244 3.47907756046244 0 0 0.0738292759167765 N 0.00568181818181812 0 N N 1105 4363 ENSG00000163067 ENSG00000173436 - + 2 1 95213792 19839759 utr3p coding ZNF2 C1orf151 95194910 19796054 + + 0 95213340 19796178 - + Y - - N HCC1954 35 33.25 30 4 1 N - - N SINE - 1 0 1 4 0.321378667196682 0.528489363834543 0.528489363834543 0.321378667196682 1 - - 9619 Y Y 3.29908909870209 3.71720464963688 3.29908909870209 313 0 0.0322761710482404 Y 0 0.986529660651067 N N 0 3610 ENSG00000201849 ENSG00000198802 + - 17 17 59817128 59794509 downstream upstream Y_RNA PECAM1 59817023 59752964 - - 0 59812395 59804980 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.735099337748344 0 0.735099337748344 4 0.699891319672773 0.792734045751814 0.792734045751814 0.699891319672773 4 - - 22427 N Y 3.57696143724454 3.50529022639353 3.50529022639353 2 0 0.456427384917879 N 0.946183025130393 0.932728781412992 N N 553 3826 ENSG00000077782 ENSG00000160072 + + 8 1 38445509 1421444 utr3p coding FGFR1 ATAD3B 38387813 1397006 - + 0 38388773 1402593 - + Y - - N HCC1954 48 40.2857142857143 24 7 1 N - - N SINE - 1 0 1 7 0.335662163516534 0.721316564152552 0.721316564152552 0.335662163516534 4 - - 41297 N Y 2.99884535653422 3.40319013214585 2.99884535653422 253 0 0.020421931922059 N 0.933596837944664 0.933596837944664 N N 0 19569 ENSG00000147481 ENSG00000088812 - + 8 20 51867974 3579760 upstream coding SNTG1 ATRN 51469311 3399676 + + 0.0122529644268776 51048419 3544482 - + Y - - N HCC1954 20 17.7777777777778 2 9 1 N - - N LINE - 1 0 1 9 0.542772860154395 0.485638874874985 0.542772860154395 0.485638874874985 2 - - 18114 Y Y 3.40319013214585 3.46232197653647 3.40319013214585 292 0 0.074088438730808 Y 0.609674657534247 0.991695205479452 N N 0 0 ENSG00000208053 ENSG00000218362 + - 1 1 245434586 245439418 upstream intron AL390728.37-2 RP11-488L18.4 245434504 245419776 - - 0 245440613 245432017 - + N - 1 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 53 0.971277749749971 0.892718519990782 0.971277749749971 0.892718519990782 1 - 0 206 Y Y 3.39487633072086 3.49272035470961 3.39487633072086 0 0 0.780259376561762 Y 0.964101506086239 0.99102537652156 N N 1747 0 ENSG00000174804 ENSG00000197882 + - 11 11 86344081 86221791 downstream downstream FZD4 AP000654.4 86334370 86221278 - - 0 86327709 86212282 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 0.817073170731707 0.817073170731707 40 0.849868031031224 1.17124669822791 1.17124669822791 0.849868031031224 1 - - 9629 Y Y 3.33680806132367 2.84446999402795 2.84446999402795 355 0 0.00332102343772656 Y 0 0.988268434134217 N N 6267 9811 ENSG00000125450 ENSG00000189159 - - 17 17 70743449 70662373 upstream upstream NUP85 HN1 70713192 70642938 + - 0 70690067 70682707 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.5713398527941 0.307095170876829 0.5713398527941 0.307095170876829 3 - - 19146 Y Y 3.6052936758779 3.56079784271098 3.56079784271098 194 0.00844890054972502 0.661146111656199 Y 0.994268490754623 0.982805472263868 N N 1166 27007 ENSG00000154198 ENSG00000142973 + + 1 1 47138734 47057605 intron coding CYP4Z2P CYP4B1 47096493 47037257 - + 0 47107088 47053522 - + N 0.197481874237702 - N HCC1954 3 1.14563106796116 1 12 4 N - - Y LINE - 1 0 1 103 1.24980592798709 1.44977487646503 1.44977487646503 1.24980592798709 1 0 - 49514 N N 3.60525382308454 3.60785432895764 3.60525382308454 0 0 0.737558318824508 N 0.266047471620227 0 N N 59204 15837 ENSG00000150753 ENSG00000145780 + - 5 5 10319501 114908490 coding downstream CCT5 FEM1C 10303282 114884507 + - 0 10307903 114875977 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 9 0.435646637755502 0.271386430077198 0.435646637755502 0.271386430077198 2 - - 24542 N Y 3.75913982972405 3.52567938596249 3.52567938596249 1 0 0.156830953625200 N 0.0466798159105851 0.904667981591059 N N 13271 302 ENSG00000081923 ENSG00000212974 - + 18 2 53550037 105248500 coding coding ATP8B1 AC012360.7 53464656 105248138 - - 0.10387902695595 53549994 105248294 + - Y - - N HCC1954 35 27.25 24 4 1 Y - - N - SINE 0 1 1 4 0.614190341753658 0.328520415356608 0.614190341753658 0.328520415356608 2 - - 29138 Y Y 3.36295036923788 3.50844286886569 3.36295036923788 276 0 0.356760671730155 Y 0.0469439193446756 0.98916981726528 N N 871 5641 ENSG00000171462 ENSG00000124574 + + 6 6 43531764 43526142 intron utr3p EGFL9 ABCC10 43526068 43503270 - + 0.98916981726528 43527614 43526042 - + N 1.53632437823614 4.06334703418808 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.728458312312478 0.835584534711372 0.835584534711372 0.728458312312478 2 0 0 22256 N N 3.45976132345673 3.57336771439491 3.45976132345673 16 0 0.0416759742779753 N 0.638888888888889 0 N N 0 0 ENSG00000212456 ENSG00000202380 - + 1 20 146460937 5818858 intron intron U1 U1 146460770 5818701 + + 0 146460925 5818737 - + Y 1 1 N HCC1954 9 5.77777777777778 4 18 1 N - - N snRNA snRNA 0.175675675675676 1 1 18 0.528489363834543 0.28566992639705 0.528489363834543 0.28566992639705 2 0 0 13749 N N 3.44512531223303 2.63312463223808 2.63312463223808 0 0 0.0816088157703546 Y 0.0630564999190546 0 N N 19152 19152 ENSG00000182457 ENSG00000182457 - + 22 22 29702049 29702049 utr5p upstream TUG1 TUG1 29696663 29696663 + + 0.56432127246236 29697294 29695495 - + N 0.514016442254012 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 20 1.34264865406614 1.03555348318931 1.34264865406614 1.03555348318931 1 0 - 7413 N Y 3.47233119514066 3.37126417066287 3.37126417066287 4 0 0.101744415489461 N 0 0.937872023809524 Y N 20739 35 ENSG00000143951 ENSG00000186453 - - 2 2 63669355 24268070 utr3p downstream C2orf86 AC008073.8 63202041 24200740 - + 0.875744047619047 63309485 24272507 + - N - - N HCC1954 660 570 420 6 1 N - - N LINE LINE 1 1 1 6 0.392796148795944 0.371370904316165 0.392796148795944 0.371370904316165 4 - - 34081 N N 3.65281417044097 3.45720067037699 3.45720067037699 9 0 0.102474862244922 N 0 0.0687138454884576 N N 5530 3007 ENSG00000148154 ENSG00000182378 + + 9 X 113735168 160023 coding utr3p UGCG PLCXD1 113698867 132989 + + 0.0687138454884576 113728554 156846 + + Y - - N HCC1954 37 34.25 32 4 1 N - - N - SINE 0 1 1 4 0.807017542071667 0.564198104634174 0.807017542071667 0.564198104634174 2 - - 43098 N N 3.49168728493972 3.48743121468078 3.48743121468078 0 0 0.977392850552892 N 0 0 N N 9848 13 ENSG00000164134 ENSG00000152495 + + 4 5 140531972 110848645 coding intron NARG1 CAMK4 140442126 110587981 + + 0 140442434 110763555 + + Y 1.36446135228 1.00411712901805 N HCC1954 1 1 1 0 5 N 370 4.32528 N - - 0 0 0 5 0.685607823352921 1.04983697950916 1.04983697950916 0.685607823352921 1 0 0 48561 N N 3.52361324642271 3.59528445727371 3.52361324642271 3 0 0.379386620506522 N 0 0 N N 850768 27 ENSG00000075624 ENSG00000184188 - - 7 5 5536758 79631912 utr3p downstream ACTB AC026410.5-4 5533313 79631253 - - 0.00542516729231279 5533707 79631114 + + Y - - N HCC1954 3 1.5 1 1 1 N - - N - - 0 0 0 4 0.821301038391519 0.257102933757345 0.821301038391519 0.257102933757345 1 - - 36514 Y Y 3.48593413659447 3.53209488171704 3.48593413659447 0 0 0.877804137563426 Y 0 0 N N 5019 1961 ENSG00000081760 ENSG00000184992 - + 12 12 124193824 124076302 upstream coding AACS BRI3BP 124115878 124044147 + + 0 124101461 124063135 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.599906845433805 0.699891319672773 0.699891319672773 0.599906845433805 4 - - 7100 Y Y 3.39487633072086 3.62464976567696 3.39487633072086 173 0 0.0097773097780992 Y 0.952656206991467 0.976328103495734 N N 53 2713 ENSG00000125551 ENSG00000222041 - + 2 2 87840110 87687439 upstream utr3p PLGLB2 AC133644.1 87828721 87536002 + + 0 87784964 87687404 - + N - 53.8463918680519 N HCC1954 4 4 4 6 2 N - - Y - LINE 0 1 1 6 0.414221393275723 0.51420586751469 0.51420586751469 0.414221393275723 1 - 0 35632 N N 3.80144573217181 3.79040344379773 3.79040344379773 4 0 0.662954937979022 N 0 0.0262459990855055 N N 164905 94 ENSG00000123416 ENSG00000183785 + + 12 22 47811571 16994498 coding coding TUBA1B TUBA8 47807836 16973453 - + 0.0262459990855055 47808735 16989386 - + Y 0.488209187546538 1.60799922986838 N HCC1954 6 3.09090909090909 2 11 1 N 127 15.3989 N - - 0 0 0 11 0.771308801272036 0.371370904316165 0.771308801272036 0.371370904316165 1 0 0 47548 Y Y 3.46704205511183 3.53974633573272 3.46704205511183 110 0 0.0478151098991728 Y 0 0.996039333515433 N N 3991 6767 ENSG00000104872 ENSG00000161618 - - 19 19 54646879 54665657 utr5p utr5p PIH1D1 ALDH16A1 54641368 54648325 - + 0 54646662 54648341 + - N - 0.204060410926721 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 24 1.42834963198525 0.949852505270192 1.42834963198525 0.949852505270192 1 - 0 32542 N N 3.39271690522525 2.79947029975127 2.79947029975127 0 0 0.340430978581898 N 0 0 N N 0 5523 ENSG00000201818 ENSG00000051382 - + 4 3 170163070 139960875 downstream upstream Y_RNA PIK3CB 170162975 139856921 + - 0 170171904 140001772 - - Y - - N HCC1954 21 20.25 20 4 1 N 492 26.0165 N DNA SINE 0.5 1 1 4 0.385654400636018 0.28566992639705 0.385654400636018 0.28566992639705 4 - - 32616 N N 3.49065421516983 2.9699440564474 2.9699440564474 1 0 0.056143281900465 N 0 0 N N 186 0 ENSG00000212781 ENSG00000215164 - + 3 4 132070780 54489065 coding downstream AC055733.16 AC105384.3 132070406 54488423 - - 0 132070747 54441211 + - Y - - N HCC1954 414 357 308 4 1 N - - N Other LINE 1 1 1 4 0.628473838073511 0.357087407996313 0.628473838073511 0.357087407996313 3 - - 37223 N N 3.37973645838739 3.55397177180249 3.37973645838739 0 0 0.0628155999049729 N 0 0 N N 1716 551733 ENSG00000127328 ENSG00000204628 - + 12 5 68503251 180603512 utr3p coding RAB3IP GNB2L1 68418898 180596536 + - 0 68500438 180597265 - - Y - 0.562989757040652 N HCC1954 22 20 18 20 1 N - - N LINE,SINE - 0.459459459459459 0 0.459459459459459 20 0.264244681917271 0.564198104634174 0.564198104634174 0.264244681917271 1 - 0 40884 N N 3.40744620240479 3.29127915838687 3.29127915838687 0 0 0.61052247953471 N 0 0 N N 7139 59 ENSG00000155158 ENSG00000172264 + + 9 20 15297250 15981842 coding intron TTC39B C20orf133 15161561 13924365 - + 0 15182693 15049740 - + Y - 1.69126908760162 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 47 1.17124669822791 1.08554572030879 1.17124669822791 1.08554572030879 1 - 0 32984 N N 2.99376390316809 3.09715338883939 2.99376390316809 1 0 0.999984439118884 N 0 0 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0 8399 13869 - + N 0.806109216236245 1.03566449780506 N HCC1954 3 1.66666666666667 1 3 10 N 189 4.09957 N - - 0 0 0 6 1.15696320190805 1.07840397214886 1.15696320190805 1.07840397214886 2 0 0 49314 N Y 3.60103760561896 3.44615838200292 3.44615838200292 8 0 0.025451103762798 N 0 0.632121724429417 N N 232 12188 ENSG00000205464 ENSG00000168724 - - 5 5 81649981 34994825 utr5p utr3p ATP6AP1L DNAJA5 81611037 34965455 + + 0.0189912651451111 81636616 34991803 - - N - - Y HCC1954 814 782.5 748 4 1 N - - N SINE SINE 1 1 1 4 0.28566992639705 0.307095170876829 0.307095170876829 0.28566992639705 2 - - 34195 Y Y 3.51832410639388 3.48011063023233 3.48011063023233 287 0.123066202090592 0.108352456857351 Y 0.870452961672474 0.990034843205575 N N 3243 394 ENSG00000107099 ENSG00000183784 - - 9 9 455255 205741 upstream coding DOCK8 C9orf66 263048 202824 + - 0 261630 205032 - + N - 5.83809067207646 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 41 0.764167053112109 1.35693215038599 1.35693215038599 0.764167053112109 1 - 0 5253 N Y 3.35975787397237 3.30232144676095 3.30232144676095 11 0 0.0932544279401938 N 0 0.877712031558185 N N 864 0 ENSG00000048052 ENSG00000219468 + + 7 9 19003518 140250262 intron upstream HDAC9 RP11-885N19.5 18501894 140249980 + + 0.0522682445759368 18575126 140231529 + + Y 0.0960319548532015 - N HCC1954 84 23.5 8 8 1 N - - N SINE - 1 0 1 8 0.328520415356608 0.657040830713216 0.657040830713216 0.328520415356608 2 0 - 27172 Y Y 3.62401792349119 3.50120199000394 3.50120199000394 17 0.069071261682243 0.563440814476322 Y 0.990690712616822 0.990690712616822 N N 354 5009 ENSG00000151006 ENSG00000167397 - + 16 16 31007631 31014802 coding coding AC135050.5 VKORC1 31002246 31009664 - - 0 31007574 31012135 + - N - - N HCC1954 1 1 1 0 2 Y - - Y - - 0 0 0 7 0.914143764470561 0.814159290231593 0.914143764470561 0.814159290231593 3 - - 11723 N Y 3.68577320169385 3.6035982586987 3.6035982586987 243 0.0825312308007373 0.0309970911553621 N 0.764079459348761 0.755341661546863 N N 105 244 ENSG00000130653 ENSG00000184988 - + 9 17 139564807 38727115 intron downstream PNPLA7 TMEM106A 139474225 38719420 - + 0.781555054952557 139525383 38756719 + + Y 0.723832080433865 - N HCC1954 1 1 1 0 1 N 248 9.74144 N LTR LTR 1 1 1 4 0.335662163516534 0.749883556792257 0.749883556792257 0.335662163516534 1 0 - 47080 Y Y 3.7297745213208 3.47552369040616 3.47552369040616 371 0 0.00234646688334783 Y 0.0569704970937163 0.993215615087005 N N 2089 106 ENSG00000160336 ENSG00000213793 - + 19 19 58653326 58645397 utr5p downstream ZNF761 AC022137.6-2 58649710 58644449 + + 0 58649715 58646929 - + N 0.0397246869193302 - N HCC1954 20 3.5 1 2 1 N - - Y - SINE 0 1 1 8 0.771308801272036 0.771308801272036 0.771308801272036 0.771308801272036 1 0 - 49022 Y N 3.61355884632223 3.34831435801417 3.34831435801417 0 0 0.107294874076664 Y 0 0 N N 14973 18 ENSG00000069011 ENSG00000152705 + + 5 5 134397812 134375291 downstream downstream PITX1 CATSPER3 134392171 134331495 - + 0.0310195779303329 134385537 134380964 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.607048593593732 0.657040830713216 0.657040830713216 0.607048593593732 1 - - 11230 N Y 3.07101108092519 3.55231620741665 3.07101108092519 0 0 0.606699568043635 N 0.849653217987918 0.887239913490939 N N 1649619 4516 ENSG00000141736 ENSG00000144645 - + 17 3 35138441 31998242 coding intron ERBB2 OSBPL10 35104766 31674407 + - 0 35125066 31803965 - - Y - 0.80268147607642 N HCC1954 11 3 1 1 1 N - - N - SINE 0 1 1 5 0.51420586751469 0.299953422716903 0.51420586751469 0.299953422716903 2 - 0 36843 N N 3.51948515723976 3.50848272165904 3.50848272165904 0 0 0.0524874632057344 N 0 0 N N 0 2963 ENSG00000218553 ENSG00000133983 - + 12 14 113333712 69896147 downstream coding AC069240.23-1 COX16 113333477 69680762 + - 0 113375160 69879130 - - Y - - N HCC1954 10 3.66666666666667 1 5 1 N - - N SINE - 1 0 1 6 0.314236919036755 0.478497126715059 0.478497126715059 0.314236919036755 1 - - 23747 N Y 3.72824693801095 3.50848272165904 3.50848272165904 194 0.900515463917526 0.00472763149803013 N 0.966838487972509 0.950257731958763 N N 0 6544 ENSG00000215900 ENSG00000178980 - + 1 19 31340962 52979753 upstream coding AL356320.8 SEPW1 31340421 52973654 - + 0.104639175257732 31340972 52973883 + + Y - 0.691087754969216 N HCC1954 1 1 1 0 1 N 335 23.9758 N - - 0 0 0 7 0.428504889595575 0.607048593593732 0.607048593593732 0.428504889595575 3 - 0 47799 N N 3.22167408707565 3.4739867595265 3.22167408707565 0 0 0.0566434409136019 N 0 0.630612244897959 N N 6959 38037 ENSG00000105011 ENSG00000131446 + - 19 5 14108440 180175147 intron upstream ASF1B MGAT1 14091322 180150147 - - 0 14093013 180191394 - + Y 0.869932683569978 - N HCC1954 21 20.5 20 6 1 N - - N SINE - 1 0 1 6 0.349945659836387 0.914143764470561 0.914143764470561 0.349945659836387 1 0 - 30136 N N 3.74337746277462 3.39487633072086 3.39487633072086 6 0 0.621369744444106 N 0 0 N N 0 0 ENSG00000219374 ENSG00000196205 + + 6 9 49436052 134886082 intron intron RP1-142O9.1 AL593851.6-1 49433818 134884659 - + 0 49434164 134885717 - + Y 1 1 N HCC1954 10 5.8 3 20 1 N - - N - - 0 0 0 20 0.257102933757345 0.578481600954027 0.578481600954027 0.257102933757345 2 0 0 35755 N Y 3.75847748231474 3.45033474667515 3.45033474667515 0 0 0.0312241970551274 N 0.988434274343987 0.976868548687974 N N 64392 0 ENSG00000135486 ENSG00000212961 - + 12 16 52965295 50238192 downstream intron HNRPA1L3 AC084058.6-1 52960755 50237203 + + 0 52967002 50238184 - + Y - 1 N HCC1954 18 5.33333333333333 2 30 1 N - - N - - 0 0 0 30 0.742741808632331 0.721316564152552 0.742741808632331 0.721316564152552 1 - 0 418 Y Y 3.56232542602083 3.51679652308403 3.51679652308403 0 0 0.343189850835838 Y 0.993525993525993 0.993525993525993 N N 0 6352 ENSG00000221193 ENSG00000077514 - + 11 11 74041910 74031413 downstream coding AP001324.4-3 POLD3 74041830 73981277 + + 0 74057472 74029258 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE - 0.71505376344086 0 0.71505376344086 59 1.32836515774628 1.1426797055882 1.32836515774628 1.1426797055882 1 - - 33668 N N 3.01191908932792 3.0684105750521 3.01191908932792 0 0.167770554306384 0.185760841099357 N 0 0 Y N 171855 59837 ENSG00000198886 ENSG00000198695 - - MT MT 12138 14674 coding coding MT-ND4 MT-ND6 10761 14150 + - 0 10857 14204 - + N - 0.652044213910915 N HCC1954 2 1.2 1 1 2 N 189 4.09957 N - - 0 0 0 5 0.942710757110266 0.821301038391519 0.942710757110266 0.821301038391519 1 - 0 21873 N N 3.38233696426048 3.56079784271098 3.38233696426048 1 0 0.0744968802008065 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000185221 - + 12 1 6517797 213111649 coding intron GAPDH AC114496.2-1 6513918 213111223 + + 0 6517102 213111396 - + Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.614190341753658 0.507064119354764 0.614190341753658 0.507064119354764 1 - 0 14137 N Y 3.61311296376292 2.99611686958514 2.99611686958514 0 0 0.280653139416172 N 0.898334333733493 0.918667466986795 N N 0 8127 ENSG00000218995 ENSG00000109790 - + 22 4 22601761 38804810 intron utr5p AP000350.6 KLHL5 22599087 38723054 + + 0 22599109 38723110 - + Y 1 0.146398364682249 N HCC1954 1 1 1 0 1 N - - N - Low_complexity 0 0.372549019607843 0.372549019607843 4 0.328520415356608 0.364229156156239 0.364229156156239 0.328520415356608 1 0 0 18215 Y Y 3.31588453542141 3.35356364524965 3.31588453542141 270 0 0.239189810854933 Y 0 0.984059259259259 N N 0 3449 ENSG00000180867 ENSG00000131791 - - 1 1 145117830 145110753 upstream upstream AL356378.17-1 PRKAB2 145116308 145093314 + - 0 145116096 145112788 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE - 1 0 1 9 0.949852505270192 0.871293275511003 0.949852505270192 0.871293275511003 4 - - 47121 Y Y 3.34615493251855 3.65488030998075 3.34615493251855 222 0 0.309757337049264 Y 0.281031031031031 0.981564898231565 N N 1118 889 ENSG00000167744 ENSG00000196337 + - 19 19 54258936 54253929 coding utr5p NTF4 CGB7 54256216 54249344 - - 0 54256793 54253339 - + N 1.21995154686967 1.36715120089157 N HCC1954 2 1.28571428571429 1 2 3 N - - Y - - 0 0 0 7 0.907002016310634 0.928427260790413 0.928427260790413 0.907002016310634 2 0 0 32904 N N 3.63465898428114 3.56911164413597 3.56911164413597 0 0.00296735905044521 0.0781820758612464 N 0.766927434583221 0.71513353115727 N N 1400 100806 ENSG00000027847 ENSG00000163931 + - 5 3 176969929 53265078 downstream intron B4GALT7 TKT 176959778 53234715 + - 0 177012552 53244233 + + Y - 0.944486876321663 N HCC1954 20 10 6 4 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.628473838073511 0.628473838073511 0.271386430077198 1 - 0 46828 Y Y 3.35253057547976 3.4106386976703 3.35253057547976 260 0 0.735249204816463 Y 0.811837606837607 0.988931623931624 N N 746 2845 ENSG00000126460 ENSG00000142546 - - 19 19 54785999 54775625 upstream upstream PRRG2 NOSIP 54778280 54750782 + - 0.988931623931624 54778278 54776552 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 83 0.792734045751814 0.5713398527941 0.792734045751814 0.5713398527941 1 - - 44868 Y N 3.44768596531277 3.8333716936548 3.44768596531277 0 0 0.207502448496275 Y 0.721081081081081 0 N N 0 11 ENSG00000216230 ENSG00000178363 - + 10 10 5707095 5558225 upstream downstream RP11-336A10.7 CALML3 5706900 5556924 + + 0 5677117 5627110 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.51420586751469 0.407079645115797 0.51420586751469 0.407079645115797 1 - - 46938 Y Y 3.65913638023969 3.32589375402559 3.32589375402559 411 0 0.00280903149187550 Y 0 0.977831846444985 N N 10624 584 ENSG00000074219 ENSG00000197813 + - 19 19 54557526 54535371 coding intron TEAD2 AC011450.4 54535669 54523236 - - 0 54537507 54527619 - + N 0.989918838898032 25.4097405553027 N HCC1954 20 9.14285714285714 1 3 1 N - - Y - SINE 0 1 1 7 0.742741808632331 1.0069864905496 1.0069864905496 0.742741808632331 4 0 0 4496 N Y 3.76426113588353 3.38296880644625 3.38296880644625 1 0 0.569335069595253 N 0.947953957151512 0.970259404086578 N N 0 105 ENSG00000201959 ENSG00000188073 - + 7 7 76509001 74794884 upstream coding Y_RNA PMS2L2 76508900 74780722 + - 0 76507204 74787837 - - N - - Y HCC1954 16 10.625 7 8 1 N - - N - LTR 0 0.6328125 0.6328125 8 0.435646637755502 0.828442786551446 0.828442786551446 0.435646637755502 4 - - 31474 Y Y 3.18670434591002 3.66745018166468 3.18670434591002 0 0 0.890972170889547 Y 0.00819672131147553 0 N N 0 20663 ENSG00000198579 ENSG00000133657 + - 3 3 195703392 195670257 downstream intron AC108676.8 ATP13A3 195700704 195604698 - - 0 195689027 195664256 - + N - 168.228683185932 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.335662163516534 0.599906845433805 0.599906845433805 0.335662163516534 2 - 0 36268 Y Y 3.66273010308932 3.2159209387304 3.2159209387304 300 0 0.0204360006548977 Y 0.870296803652968 0.993173515981735 N N 0 847 ENSG00000215030 ENSG00000111671 - - 12 12 6863922 6852713 upstream upstream RPL13P5 SPSB2 6863421 6850365 + - 0 6861604 6853205 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE,LINE - 0.897637795275591 0 0.897637795275591 9 0.792734045751814 0.807017542071667 0.807017542071667 0.792734045751814 1 - - 49504 Y Y 3.55657227767559 3.19041047300197 3.19041047300197 239 0 0.132979832513632 Y 0 0.991340731307986 N Y 12147 1145 ENSG00000132356 ENSG00000113638 + - 5 5 40834054 40791829 coding intron PRKAA1 TTC33 40795238 40747439 - - 0 40800373 40782878 - + N - 0.245327224409686 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.821301038391519 0.5713398527941 0.821301038391519 0.5713398527941 4 - 0 16004 N Y 3.59321831773393 3.29908909870209 3.29908909870209 0 0 0.490943172745772 N 0 0 N N 2833 0 ENSG00000133019 ENSG00000221152 - + 1 7 238139338 124570287 utr5p downstream CHRM3 AC019155.4 237858996 124570222 + + 0 237859353 124580901 - + Y - - N HCC1954 23 22.3333333333333 22 6 1 N - - N LINE SINE 1 0.919354838709677 1 6 0.364229156156239 0.442788385915428 0.442788385915428 0.364229156156239 1 - - 30464 Y Y 3.32799974635873 3.64759957832565 3.32799974635873 255 0 0.161857170432144 Y 0.991338448422847 0.974015345268542 N N 0 0 ENSG00000220528 ENSG00000213468 + - X X 130765450 130757838 upstream downstream RP1-197O17.2 AL121572.14 130765021 130757360 - - 0 130786931 130756175 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.975609756097561 0.975609756097561 6 0.757025304952183 0.87843502367093 0.87843502367093 0.757025304952183 4 - - 38294 Y Y 3.51207644450867 3.34528969661801 3.34528969661801 3 0 0.719809251263058 Y 0 0.984180609180609 N N 1459 1187 ENSG00000206197 ENSG00000215394 - + 14 14 18757529 18754290 intron utr5p AL589743.4-3 AL589743.4-2 18754782 18720037 + + 0 18756377 18753753 - + N 0.781557611153834 - N HCC1954 12 8.33333333333333 6 6 1 N - - Y - SINE,LTR 0 0.457446808510638 0.457446808510638 6 0.485638874874985 0.671324327033068 0.671324327033068 0.485638874874985 4 0 - 41506 Y Y 3.43039601505348 3.36976709257655 3.36976709257655 269 0 0.796807268519958 Y 0.146043547530536 0.992509153925706 N N 0 0 ENSG00000222501 ENSG00000207110 + + 8 8 129092039 129080722 downstream upstream U4 U1 129091912 129080559 - + 0 129091019 129070720 - + N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 44 1.02841173502938 1.0069864905496 1.02841173502938 1.0069864905496 1 - - 14081 Y Y 3.74913061111987 3.79040344379773 3.74913061111987 0 0 0.482408929555354 Y 0 0.974751054852321 N N 8351 35913 ENSG00000100138 ENSG00000196419 + + 22 22 40416454 40389998 coding downstream NHP2L1 XRCC6 40399886 40347241 - + 0 40401144 40393033 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 15 1.07840397214886 1.05697872766909 1.07840397214886 1.05697872766909 2 - - 0 Y Y 2.86374637824031 3.31844518850115 2.86374637824031 351 0 0.000980011892111055 N 0 0.991549567820754 N N 14903 74591 ENSG00000185885 ENSG00000142089 - + 11 11 305271 310848 upstream upstream IFITM1 IFITM3 301317 309678 + - 0 300929 314563 - - N - - Y HCC1954 6 2.72727272727273 2 11 1 N 422 22.3018 N Low_complexity LTR 0.138297872340426 1 1 11 0.671324327033068 0.785592297591888 0.785592297591888 0.671324327033068 1 - - 29599 Y Y 3.80144573217181 3.6329237143086 3.6329237143086 2 0 0.0779299340657517 Y 0 0.98596884336321 N N 599 0 ENSG00000047936 ENSG00000219703 - - 6 6 117853711 117860298 coding downstream ROS1 RP1-92C8.2 117716223 117859447 - + 0 117846348 117870337 + - N - - N HCC1954 4 1.2 1 1 1 N - - Y - LTR 0 1 1 15 1.05697872766909 0.849868031031224 1.05697872766909 0.849868031031224 1 - - 4458 N Y 3.42424163912411 3.29037406969298 3.29037406969298 324 0.00308641975308632 0.058282423009044 Y 0 0 N N 4094 310 ENSG00000105997 ENSG00000105991 + - 7 7 27158458 27102150 coding upstream HOXA3 HOXA1 27112334 27099141 - - 0 27114636 27104264 - + N 0.548261429335359 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 6 1.02126998686945 0.892718519990782 1.02126998686945 0.892718519990782 1 0 - 49510 N Y 3.47804449069255 3.75169126419961 3.47804449069255 0 0 0.927572554524491 Y 0.197683981971905 0.955916702306149 N N 1955 5 ENSG00000205570 ENSG00000215159 + + 5 5 69590632 34232139 utr3p upstream AC140134.2-2 AC138409.1-1 69470446 34210910 - + 0 69528461 34205015 - + N - - N HCC1954 24 3.90909090909091 1 4 1 N - - N - LTR 0 1 1 11 0.785592297591888 0.928427260790413 0.928427260790413 0.785592297591888 4 - - 13524 N N 3.37192651807217 3.13957226198672 3.13957226198672 0 0.00632911392405078 0.156323479973718 N 0.00632911392405078 0 N N 24530 26452 ENSG00000186575 ENSG00000119139 - + 22 9 28424583 71059938 utr3p utr5p NF2 TJP2 28329563 70956382 + + 0.00632911392405078 28423577 70956411 - + Y - 0.292699056629818 N HCC1954 32 24.6666666666667 23 6 1 N - - N SINE - 1 0 1 6 0.364229156156239 0.528489363834543 0.528489363834543 0.364229156156239 2 - 0 42446 N N 3.11591748924604 3.58333708020574 3.11591748924604 12 0 0.0488394268728672 Y 0.130081300813008 0 N N 11166 1587 ENSG00000138796 ENSG00000164023 - + 4 4 109175780 109051558 upstream coding HADH SGMS2 109130319 108965168 + + 0.130081300813008 109130258 109051071 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 33 0.828442786551446 0.864151527351077 0.864151527351077 0.828442786551446 1 - - 35984 N N 3.63978029044062 3.68527868815389 3.63978029044062 0 0.267295597484277 0.328155150515266 N 0.417593936461861 0.248508305112079 N N 0 71224 ENSG00000215313 ENSG00000089009 + + X 12 16127335 111331793 intron coding AC078993.20 RPL6P27 16126472 111327378 - - 0.248508305112079 16126949 111329051 - - Y 1 - N HCC1954 6 3.7 1 7 1 N - - N - - 0 0 0 10 0.264244681917271 0.599906845433805 0.599906845433805 0.264244681917271 1 0 - 29559 Y N 3.2656754067026 2.74056850503289 2.74056850503289 0 0.27946127946128 0.137078404184473 Y 0.27946127946128 0.0542929292929294 N N 15464 20 ENSG00000124783 ENSG00000164304 - + 6 6 7258439 7334941 coding coding SSR1 CAGE1 7232803 7271886 - - 0.0542929292929294 7255226 7279292 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.757025304952183 0.642757334393363 0.757025304952183 0.642757334393363 3 - - 16337 N N 3.49896801659482 3.42936294528359 3.42936294528359 18 0 0.0504936278934447 N 0 0.039331179935398 N N 47769 0 ENSG00000170144 ENSG00000220375 - - 2 1 177796931 558984 coding intron HNRNPA3 RP5-857K21.14 177785668 558778 + + 0.039331179935398 177789663 558958 - - Y - 1 N HCC1954 10 7.25 4 4 1 N - - N Simple_repeat - 0.263473053892216 0 0.263473053892216 4 0.678466075192994 0.778450549431962 0.778450549431962 0.678466075192994 1 - 0 33132 N Y 3.45041445226185 3.40165320126619 3.40165320126619 313 0 0.0124315412783484 Y 0 0.990596178190367 N N 0 1291380 ENSG00000210194 ENSG00000198804 + + MT MT 14743 7446 intron coding AF347015.1-22 MT-CO1 14675 5905 - + 0 14721 6385 - + N 1 1.04294457008966 N HCC1954 3 1.77777777777778 1 6 1 N - - N - - 0 0 0 9 0.907002016310634 1.01412823870953 1.01412823870953 0.907002016310634 2 0 0 47208 Y N 3.42100929106525 3.11192253881228 3.11192253881228 9 0.0283042593566384 0.815854385703509 Y 0.822378197946912 0 N N 1423 1848 ENSG00000083842 ENSG00000198131 - + 19 19 63499066 63466822 upstream coding ZNF8 ZNF544 63482130 63431882 + + 0 63480316 63449916 - + N - - N HCC1954 2 1.08333333333333 1 1 3 N - - Y - SINE 0 0.0625 0.0625 12 1.09982921662864 1.50690886174444 1.50690886174444 1.09982921662864 3 - - 46394 N N 3.4748918482204 3.57800808738356 3.4748918482204 0 0 0.422480283390923 N 0.00409836065573788 0 N N 770 17943 ENSG00000173163 ENSG00000105141 - + 2 19 62216698 15027900 intron downstream COMMD1 CASP14 61986292 15024015 + + 0.00409836065573788 62080257 15029502 - + Y 1.14641889546328 - N HCC1954 20 8.21052631578947 1 35 1 N - - N SINE - 0.86046511627907 0 0.86046511627907 38 0.307095170876829 0.792734045751814 0.792734045751814 0.307095170876829 3 0 - 3083 N N 3.52101274054962 3.50120199000394 3.50120199000394 0 0 0.830458002724491 N 0.022872545244513 0 N N 8445 5068 ENSG00000110344 ENSG00000129347 - + 11 19 117775132 10537696 intron utr3p UBE4A KRI1 117735512 10525267 + - 0 117769315 10525297 - - Y 2.63342860561558 - N HCC1954 2 1.5 1 3 1 N - - N SINE,SINE SINE 0.575 1 1 6 0.28566992639705 0.364229156156239 0.364229156156239 0.28566992639705 3 0 - 31351 Y Y 3.34785034969775 3.65016023140539 3.34785034969775 277 0 0.0974449040276415 Y 0.991103661681279 0.982207323362558 N N 3580 0 ENSG00000080822 ENSG00000181828 + + 3 3 99724600 99700165 coding downstream CLDND1 OR5K2 99717008 99699215 - + 0 99718586 99708281 - + N 0.906298459003683 - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 6 0.828442786551446 0.87843502367093 0.87843502367093 0.828442786551446 4 0 - 13723 Y Y 3.35087501109391 3.6623288755052 3.35087501109391 340 0 0.753650756210528 Y 0 0.975381263616558 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 intron intron AP000347.3 AP000347.4 22321400 22310865 - - 0 22324842 22311129 - + N 1 1 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 4 0.5713398527941 0.51420586751469 0.5713398527941 0.51420586751469 2 0 0 36202 Y Y 3.40062947906611 3.26460248413936 3.26460248413936 0 0 0.815719916917955 Y 0.897397445820433 0.992671246130031 N N 16017 12 ENSG00000018236 ENSG00000205592 - + 12 12 39750361 39250827 utr5p downstream CNTN1 MUC19 39588423 39222629 + + 0 39588427 39372662 - + N 0.0257959138592769 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 355 1.0069864905496 1.09268746846872 1.09268746846872 1.0069864905496 1 0 - 40923 Y Y 3.49847350305486 3.02023289075291 3.02023289075291 225 0 0.0199661452269486 Y 0.984683760683761 0.984683760683761 N N 52353 525 ENSG00000088832 ENSG00000125775 + - 20 20 1321753 1257838 downstream intron FKBP1A SDCBP2 1297623 1238619 - - 0 1279060 1254414 - + N - 0.839232667631979 N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 4 0.592765097273879 0.792734045751814 0.792734045751814 0.592765097273879 1 - 0 17921 Y Y 3.53871326596283 3.39227582484777 3.39227582484777 103 0.0182874025775559 0.358882738907095 Y 0.99256278335286 0.99256278335286 N N 13170 33725 ENSG00000196187 ENSG00000143819 + + 1 1 224136671 224099884 utr3p intron TMEM63A EPHX1 224099863 224064459 - + 0 224101163 224095512 - + N - 0.913004889743209 N HCC1954 1 1 1 0 2 N - - Y - LINE 0 0.489208633093525 0.489208633093525 5 0.956994253430118 0.871293275511003 0.956994253430118 0.871293275511003 1 - 0 31397 Y Y 3.51529944499772 3.44193281696752 3.44193281696752 254 0 0.0362484337909859 Y 0.952188976377953 0.992031496062992 N N 512 1697 ENSG00000174928 ENSG00000114805 + - 3 3 157006755 156876522 downstream upstream C3orf33 PLCH1 156963095 156576063 - - 0 156945322 156904746 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.914143764470561 0.835584534711372 0.914143764470561 0.835584534711372 1 - - 39981 Y Y 3.4210491438586 3.47911741325579 3.4210491438586 231 0 0.13459629687192 Y 0.883485309017224 0.978815510730404 N N 0 4659 ENSG00000186690 ENSG00000173517 - - 15 15 75358134 75331928 downstream utr5p AC060773.10 AC107883.6 75357862 75187526 + - 0 75365820 75331923 - + N - 8.67194570135747 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.607048593593732 0.907002016310634 0.907002016310634 0.607048593593732 4 - 0 29400 Y Y 3.32064446679012 3.47911741325579 3.32064446679012 147 0 0.883180351418042 Y 0 0.996146132929867 N N 399 1730 ENSG00000221988 ENSG00000168452 - + 6 6 32244040 32239433 intron utr3p EGFL8 PPT2 32240360 32229279 + + 0 32241791 32238707 - + N 0.162096800549038 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 12 1.05697872766909 0.99270299422975 1.05697872766909 0.99270299422975 2 0 - 35193 N N 3.55976477294109 3.54872248456702 3.54872248456702 0 0.240414003889969 0.774596570968215 N 0.240414003889969 0.172895248680189 N N 712661 0 ENSG00000111640 ENSG00000213594 - - 12 2 6517797 38367062 coding intron GAPDH AC016995.7 6513918 38366056 + + 0.172895248680189 6515970 38366110 - - Y - 1 N HCC1954 5 3.6 3 5 1 N - - N - - 0 0 0 5 0.442788385915428 0.271386430077198 0.442788385915428 0.271386430077198 2 - 0 36158 N Y 3.45889608755619 3.3478104969044 3.3478104969044 5 0 0.253761392113546 N 0.432950191570881 0.831417624521073 N N 0 14514 ENSG00000222476 ENSG00000139289 - + 9 12 9432367 74711823 intron utr3p SRP_euk_arch PHLDA1 9432060 74705494 + - 0.371647509578544 9432090 74707711 - - Y 1 - N HCC1954 147 129.6 60 5 1 N - - N srpRNA SINE 1 1 1 5 0.51420586751469 0.378512652476092 0.51420586751469 0.378512652476092 2 0 - 22722 N N 3.40744620240479 3.21232721588077 3.21232721588077 1 0 0.168988583073703 N 0 0 N N 0 7324 ENSG00000220375 ENSG00000145247 - - 1 4 558984 48603572 intron utr5p RP5-857K21.14 OCIAD2 558778 48582164 + - 0 558959 48603527 - + Y 1 1.0710086070336 N HCC1954 3 2.25 2 8 1 N - - N - - 0 0 0 8 1.09982921662864 0.349945659836387 1.09982921662864 0.349945659836387 3 0 0 29148 Y Y 3.56335849579072 3.25360004855864 3.25360004855864 330 0 0.0214347268087564 Y 0.993526170798898 0.987052341597796 N N 820 9161 ENSG00000123552 ENSG00000132424 + - 6 6 100070029 99979881 downstream upstream USP45 SFRS18 99986911 99955137 - - 0 99985310 99980495 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 26 1.14982145374813 1.2783729206268 1.2783729206268 1.14982145374813 4 - - 36567 Y Y 3.52680574168822 3.45976132345673 3.45976132345673 178 0.125109668362871 0.975693335352113 Y 0.586857343393578 0.987848745393929 N Y 23800 55227 ENSG00000067182 ENSG00000111319 - + 12 12 6321522 6354976 coding coding TNFRSF1A SCNN1A 6308185 6326276 - - 0 6313671 6328154 + - N - 0.93979898501643 N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 85 1.37835739486577 0.635615586233437 1.37835739486577 0.635615586233437 4 - 0 31635 Y Y 3.24831090852981 3.1923087786724 3.1923087786724 11 0 0.943894460725735 Y 0.991407482533243 0.991407482533243 N Y 139 298 ENSG00000206552 ENSG00000182983 - + 3 3 42959283 42933958 utr5p coding C3orf41 ZNF662 42952856 42922406 + + 0 42955346 42925405 - + N - 0.495188534993101 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 18 1.15696320190805 0.871293275511003 1.15696320190805 0.871293275511003 4 - 0 9362 Y Y 3.63193049733206 3.45656882819122 3.45656882819122 353 0 0.055870244470807 Y 0.570986230977008 0.982607549904473 N N 5176 7182 ENSG00000141562 ENSG00000178927 - - 17 17 78039430 78001983 upstream upstream NARF C17orf62 78009349 77990056 + - 0 78008605 78005580 - + N - - N HCC1954 12 3.06451612903226 1 23 2 N - - Y LTR,LTR,LTR Other 0.761111111111111 1 1 31 1.2783729206268 1.16410495006798 1.2783729206268 1.16410495006798 3 - - 33292 N N 3.14484171727181 3.779528989293 3.14484171727181 0 0 0.822487609131254 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 14052 15834 - + N 1.73382696856726 - N HCC1954 2 1.2 1 1 4 N 189 4.09957 N - - 0 0 0 5 1.23552243166724 1.0069864905496 1.23552243166724 1.0069864905496 1 0 - 5566 N Y 3.25463311832853 3.8333716936548 3.25463311832853 0 0 0.781704003106328 N 0.108149405772496 0.985010914382731 N N 0 3966 ENSG00000221665 ENSG00000175772 - + X 2 94035248 110111006 upstream upstream AL591708.10 AC013268.5-1 94035156 110103138 + + 0 94007603 110102056 - + Y - - N HCC1954 40 39.4 34 20 1 N 380 26.7917 N LINE - 1 0 1 20 0.678466075192994 0.978419497909897 0.978419497909897 0.678466075192994 3 - - 44871 Y Y 3.56228557322748 3.64553343878587 3.56228557322748 167 0 0.0274181548888517 Y 0.0604544335985563 0.986383397588385 N N 906 917 ENSG00000148814 ENSG00000165752 - - 10 10 134109058 133995341 upstream intron LRRC27 STK32C 133995648 133870986 + - 0.986383397588385 133995632 133993978 - + N - 0.805901245586798 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.685607823352921 0.349945659836387 0.685607823352921 0.349945659836387 2 - 0 34651 N Y 3.48912663185998 3.4780843434859 3.4780843434859 0 0 0.951323343302708 Y 0 0 N N 22735 8003 ENSG00000119314 ENSG00000119471 - - 9 9 114135768 114274511 coding upstream ROD1 HSDL2 114020536 114182038 - + 0 114100017 114180801 + - N - - N HCC1954 1 1 1 0 2 N - - N - DNA 0 0.266666666666667 0.266666666666667 6 0.778450549431962 0.956994253430118 0.956994253430118 0.778450549431962 4 - - 40278 N Y 2.81826490538145 3.53296011761759 2.81826490538145 0 0.537131882202305 0.384177238872887 N 0.915842160400419 0.915842160400419 N N 5302 0 ENSG00000140157 ENSG00000173078 + - 15 8 20585849 82705924 utr5p downstream NIPA2 AC090255.4 20556790 82700847 - - 0.915842160400419 20585590 82693413 - + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.699891319672773 0.364229156156239 0.699891319672773 0.364229156156239 2 - - 33545 N Y 3.18871505582277 3.08507803069543 3.08507803069543 421 0 0.000212991671407758 Y 0 0.992874109263658 N N 247001 0 ENSG00000198786 ENSG00000210117 - + MT MT 14149 5580 coding intron MT-ND5 AF347015.1-9 12338 5513 + + 0 14009 5524 - + N - 1 N HCC1954 4 2 1 4 1 N - - N - - 0 0 0 6 0.771308801272036 0.785592297591888 0.785592297591888 0.771308801272036 0 - 0 5031 Y Y 3.45872825368684 3.45612774781375 3.45612774781375 248 0 0.0651124634954394 Y 0.983261046354025 0.991630523177013 N N 2975 4451 ENSG00000106603 ENSG00000164543 + + 7 7 43735620 43633502 utr3p downstream C7orf44 STK17A 43645381 43589217 - + 0 43645574 43637907 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE,DNA 0 0.754545454545455 0.754545454545455 6 0.799875793911741 0.785592297591888 0.799875793911741 0.785592297591888 1 - - 22597 N Y 3.50848272165904 3.70512929149291 3.50848272165904 236 0.279382247992863 0.185948694248236 N 0.72485504014273 0.921387154326494 N N 15774 0 ENSG00000197894 ENSG00000155816 - + 4 1 100240090 238711086 coding intron ADH5 FMN2 100211152 238321604 - + 0.921387154326494 100222284 238400212 + + Y 0.736785558298259 1 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 8 0.485638874874985 0.364229156156239 0.485638874874985 0.364229156156239 2 0 0 31608 Y Y 3.61616813038263 3.53362246502689 3.53362246502689 0 0 0.996466689823144 Y 0.33975138729596 0.990361334121109 N N 20663 0 ENSG00000133657 ENSG00000198579 - + 3 3 195670257 195703392 utr5p downstream ATP13A3 AC108676.8 195604698 195700704 - - 0 195664254 195687812 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 104 1.39978263934555 0.714174815992626 1.39978263934555 0.714174815992626 4 - - 47149 Y Y 3.4048456965317 3.53974633573272 3.4048456965317 254 0 0.476501815316921 Y 0.01538600778351 0.988551000090506 N N 1118 889 ENSG00000167744 ENSG00000196337 + - 19 19 54258936 54253929 downstream utr5p NTF4 CGB7 54256216 54249344 - - 0 54255785 54253418 - + N - 1.79965302332566 N HCC1954 1 1 1 0 3 N - - Y LINE - 0.511904761904762 0 0.511904761904762 4 0.87843502367093 0.549914608314322 0.87843502367093 0.549914608314322 2 - 0 19669 N Y 3.28399842673177 3.46807512488172 3.28399842673177 304 0 0.00383345222827058 N 0 0.969331983805668 N N 1894 3633 ENSG00000197568 ENSG00000136143 - + 1 13 70606291 47473463 utr3p upstream HHLA3 SUCLA2 70593081 47414792 + - 0 70606025 47487156 - - Y - - N HCC1954 168 40 21 8 1 N - - N LTR SINE 1 0.973333333333333 1 8 0.435646637755502 0.535631111994469 0.535631111994469 0.435646637755502 3 - - 379 Y Y 3.61889661733171 3.63040291402221 3.61889661733171 0 0 0.71806305865664 Y 0.394162073892631 0.978362931210451 N N 0 19435 ENSG00000213411 ENSG00000173933 - + 11 11 66186733 66170516 upstream coding AP001157.4-1 RBM4 66186447 66140673 + + 0 66181186 66170076 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE - 1 0 1 4 0.592765097273879 0.599906845433805 0.599906845433805 0.592765097273879 2 - - 36925 N Y 3.03589262417669 3.49744043328497 3.03589262417669 0 0 0.767736815397728 N 0 0.961652253072371 N N 0 542 ENSG00000219787 ENSG00000135482 - + 20 12 21683988 54802545 intron upstream RPL41P1 ZC3H10 21683908 54798297 + + 0.961652253072371 21683920 54796850 - + Y 1 - N HCC1954 9 6.86363636363636 2 22 1 N - - N - - 0 0 0 22 0.678466075192994 0.842726282871298 0.842726282871298 0.678466075192994 4 0 - 14867 N Y 3.61360747730288 3.3233729537392 3.3233729537392 0 0 0.0451127305348872 N 0 0 N N 49089 31 ENSG00000117450 ENSG00000186642 - - 1 11 45760196 72063113 coding downstream PRDX1 PDE2A 45749295 71964834 - - 0 45757256 71940390 + + Y - - N HCC1954 22 6.11111111111111 3 9 1 N - - N - SINE 0 1 1 9 0.692749571512847 0.257102933757345 0.692749571512847 0.257102933757345 1 - - 3404 Y Y 3.353603498043 3.45976132345673 3.353603498043 256 0.00390625 0.748964059768629 Y 0.00390625 0.990944602272727 N N 9282 1755 ENSG00000142197 ENSG00000159231 - + 21 21 36588442 36440728 upstream utr3p DOPEY2 CBR3 36458703 36429133 + + 0 36450388 36440702 - + N - 1.15952647467861 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.392796148795944 0.592765097273879 0.592765097273879 0.392796148795944 2 - 0 11896 N Y 3.48553290901035 3.58527523866953 3.48553290901035 8 0 0.338780028186459 N 0.869708631115998 0.879015157464855 N N 20793 244 ENSG00000141027 ENSG00000148057 - - 17 9 16059570 85448858 utr5p intron NCOR1 C9orf103 15875443 85427786 - + 0.627738946045708 16038677 85445454 + - Y - 0.296787537280795 N HCC1954 63 57.75 42 4 1 N - - N - SINE 0 1 1 4 0.499922371194838 0.314236919036755 0.499922371194838 0.314236919036755 1 - 0 3367 Y Y 3.43209143223268 3.60103760561896 3.43209143223268 137 0.0312609247640252 0.207080989897899 Y 0.0312609247640252 0.985648309996504 N N 2297 136 ENSG00000182093 ENSG00000157578 + + 21 21 39691685 39739573 coding coding WRB C21orf13 39674109 39699640 + - 0 39687076 39699710 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 1.37121564670584 0.828442786551446 1.37121564670584 0.828442786551446 4 - - 36599 Y Y 3.56807857436608 3.13379942889774 3.13379942889774 0 0 0.328318286068071 Y 0 0.994802989130435 N N 7855 6150 ENSG00000078246 ENSG00000171792 - + 12 12 2920558 2868885 coding intron TULP3 C12orf32 2870294 2856650 + + 0 2900266 2856888 - + N - 2.71188138455344 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 19 1.22838068350732 0.592765097273879 1.22838068350732 0.592765097273879 1 - 0 5132 N N 2.14166022353884 2.93912152275119 2.14166022353884 8 0 0.174472831844608 Y 0.55351724137931 0 N N 21370 3405 ENSG00000182158 ENSG00000170632 + + 7 7 137337386 102527432 utr3p utr3p CREB3L2 ARMC10 137210265 102502564 - + 0.0726896551724139 137211627 102527275 - + N - - N HCC1954 972 637.5 102 4 1 N - - N Simple_repeat SINE 0.925 0.865979381443299 0.925 4 0.28566992639705 0.692749571512847 0.692749571512847 0.28566992639705 2 - - 9448 N N 3.04380519801756 3.55025006787687 3.04380519801756 0 0 0.987602420756879 Y 0 0 N N 3927 0 ENSG00000176155 ENSG00000211264 + + 17 17 77763978 67836854 coding downstream CCDC57 AC005243.1 77652635 67836654 - + 0 77752839 67949146 - + N 0.780049370644783 - N HCC1954 1 1 1 0 4 N 449 0.607786 N - - 0 0 0 6 0.657040830713216 0.714174815992626 0.714174815992626 0.657040830713216 1 0 - 535 Y Y 3.55401162459584 3.29549537585246 3.29549537585246 8 0 0.413480800117686 Y 0 0.984722969338354 N N 2006 9059 ENSG00000134824 ENSG00000168496 - + 11 11 61391401 61321284 coding utr5p FADS2 FEN1 61340325 61316726 + + 0 61361920 61317008 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 149 1.1426797055882 0.921285512630487 1.1426797055882 0.921285512630487 2 - - 29104 Y Y 3.80144573217181 3.29553522864581 3.29553522864581 275 0 0.206930411952462 Y 0 0.98827807486631 N N 154 27657 ENSG00000124743 ENSG00000001084 + - 6 6 53638465 53517790 downstream upstream KLHL31 GCLC 53620658 53470098 - - 0 53589640 53546029 - + N - - N HCC1954 2 1.04347826086957 1 1 3 N - - Y LTR DNA 1 0.317647058823529 1 23 0.907002016310634 0.607048593593732 0.907002016310634 0.607048593593732 1 - - 3138 N N 2.99662073069491 3.17784060131804 2.99662073069491 288 0 0.00069324622120559 N 0.95667270531401 0.0901268115942029 N N 1814 8014 ENSG00000178229 ENSG00000149084 - + 19 11 62533956 43834736 utr3p utr3p ZNF543 HSD17B12 62523689 43658719 + + 0.205666264090177 62532693 43834022 - + Y - - N HCC1954 37 27.7352941176471 23 34 1 N - - N SINE - 1 0 1 34 0.93556900895034 1.02841173502938 1.02841173502938 0.93556900895034 0 - - 42505 Y Y 3.29231222815676 3.50575423470996 3.29231222815676 0 0 0.967112761745484 Y 0.993650729662178 0.993650729662178 N N 25208 10761 ENSG00000138757 ENSG00000138768 - - 4 4 76817629 76954388 utr5p upstream G3BP2 USO1 76786991 76869028 - + 0 76806257 76868484 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 129 1.16410495006798 0.985561246069823 1.16410495006798 0.985561246069823 4 - - 46983 Y Y 3.39062026046193 3.20231799727658 3.20231799727658 411 0 0.0582763677488128 Y 0 0 N N 675 793 ENSG00000179922 ENSG00000171443 + + 19 19 60827753 60806316 downstream downstream ZNF784 ZNF524 60823919 60803542 - + 0 60816769 60810271 - + N - - N HCC1954 1 1 1 0 4 N - - Y Simple_repeat LINE 0.301204819277108 0.738095238095238 0.738095238095238 6 1.02841173502938 1.14982145374813 1.14982145374813 1.02841173502938 3 - - 683 Y Y 3.30128837699106 3.01757895171733 3.01757895171733 168 0 0.155040852933405 Y 0 0.985163468372424 N N 138744 0 ENSG00000152558 ENSG00000210948 - - 11 11 101828985 101844353 utr5p upstream TMEM123 AP001830.5 101772268 101844288 - + 0 101828882 101837373 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.435646637755502 0.549914608314322 0.549914608314322 0.435646637755502 1 - - 6901 Y Y 3.54872248456702 3.57489529770476 3.54872248456702 246 0 0.0962276585525593 Y 0 0.977868112014453 N N 0 1 ENSG00000222130 ENSG00000204929 + + 2 2 65626338 65563784 downstream downstream SRP_euk_arch AC007389.7-3 65626041 65517368 - + 0 65597436 65593696 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR DNA 1 1 1 5 0.714174815992626 0.614190341753658 0.714174815992626 0.614190341753658 4 - - 31882 Y Y 3.37023110089298 3.2159209387304 3.2159209387304 0 0 0.914187787032424 Y 0.994333791208791 0.988667582417582 N N 2372 18789 ENSG00000163923 ENSG00000073849 + + 3 3 188339957 188279035 utr5p coding RPL39L ST6GAL1 188321435 188131210 - + 0 188328481 188243253 - + N - 0.823053281616687 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 16 1.29979816510658 1.3069399132665 1.3069399132665 1.29979816510658 4 - 0 45194 Y Y 3.45504124488137 3.50632329616342 3.45504124488137 4 0.00332225913621254 0.294258193191307 Y 0.00332225913621254 0.992829656540548 N N 4907 40 ENSG00000107957 ENSG00000107954 + + 10 10 105605154 105342292 coding intron SH3PXD2A NEURL 105343776 105244038 - + 0 105361329 105338687 - + N - 1.6372396260991 N HCC1954 5 2.18181818181818 1 5 1 N - - Y - SINE 0 1 1 11 1.14982145374813 0.907002016310634 1.14982145374813 0.907002016310634 1 - 0 30881 N Y 3.11192253881228 3.44768596531277 3.11192253881228 11 0 0.052038236002611 N 0 0 N N 78560 7874 ENSG00000112493 ENSG00000206560 - - 6 3 33390114 15876057 utr3p intron TAPBP ANKRD28 33375449 15683747 - - 0 33376428 15755320 + + Y - 1.58900631479787 N HCC1954 441 157.25 10 4 1 N - - N SINE LTR,LTR 1 1 1 4 0.542772860154395 0.835584534711372 0.835584534711372 0.542772860154395 2 - 0 48434 N N 3.60888739872753 3.51360402781852 3.51360402781852 0 0 0.0497949485793709 N 0.641296296296296 0.73787037037037 N N 116 3556 ENSG00000174469 ENSG00000146054 - - 7 5 147749019 180564783 intron downstream CNTNAP2 TRIM7 145444902 180553531 + - 0 147114763 180551745 - + Y 0.447182449456154 - N HCC1954 22 17.4 6 5 1 N - - N SINE - 1 0 1 5 0.314236919036755 0.821301038391519 0.821301038391519 0.314236919036755 2 0 - 5624 N Y 3.7297745213208 3.35616415112274 3.35616415112274 1 0 0.0208158259794318 N 0 0.79280661701411 N N 20739 0 ENSG00000143951 ENSG00000220973 - - 2 X 63669355 151602959 utr3p upstream C2orf86 RP1-14D6.2 63202041 151602143 - + 0.715109098394401 63309655 151596312 + - Y - - N HCC1954 660 553.333333333333 400 6 1 N - - N LINE LINE 1 1 1 6 0.414221393275723 0.378512652476092 0.414221393275723 0.378512652476092 1 - - 765 Y N 3.18974812559266 3.55504469436573 3.18974812559266 0 0.184039408866995 0.920627285264145 Y 0.263645320197044 0.184039408866995 N N 1172 1543 ENSG00000174165 ENSG00000174483 + + 11 11 66070247 66057660 coding intron ZDHHC24 BBS1 66063311 66034666 - + 0.184039408866995 66067794 66053478 - + N - 1.77735570313508 N HCC1954 1 1 1 0 4 N - - Y - LINE 0 1 1 9 1.39264089118562 0.778450549431962 1.39264089118562 0.778450549431962 4 - 0 5937 N Y 3.65760879692984 2.96581177736784 2.96581177736784 0 0.836629659583854 0.105866794486193 N 0.851481508712595 0.851481508712595 N N 1712 850768 ENSG00000196604 ENSG00000075624 - + 2 7 130603265 5536758 utr3p utr3p A26C1B ACTB 130547578 5533313 - - 0.851481508712595 130548136 5533752 + - Y - 0.974171826165781 N HCC1954 20 11.5555555555556 8 18 1 N - - N - Simple_repeat 0 0.266666666666667 0.266666666666667 18 0.357087407996313 0.821301038391519 0.821301038391519 0.357087407996313 3 - 0 33031 Y Y 3.0684105750521 3.17573460898491 3.0684105750521 473 0 0.990690606652541 Y 0 0.995525175627376 N N 59837 247001 ENSG00000198695 ENSG00000198786 + + MT MT 14674 14149 coding coding MT-ND6 MT-ND5 14150 12338 - + 0.995525175627376 14174 13076 - + N 0.388607403590434 0.838485276461348 N HCC1954 1 1 1 0 10 N - - Y - - 0 0 0 17 1.09982921662864 1.02126998686945 1.09982921662864 1.02126998686945 2 0 0 30535 Y Y 3.32320511986986 3.57336771439491 3.32320511986986 362 0 0.002854242347754 Y 0 0 N N 0 12932 ENSG00000207122 ENSG00000165175 + + X X 38825482 38550725 downstream downstream U6 MID1IP1 38825377 38545651 - + 0 38709200 38614992 - + N - - N HCC1954 1 1 1 0 2 N - - Y LINE - 1 0 1 6 0.592765097273879 0.657040830713216 0.657040830713216 0.592765097273879 2 - - 37573 N N 3.61104682422314 3.2395330987884 3.2395330987884 0 0 0.28661641561843 N 0 0 N N 2875 0 ENSG00000186532 ENSG00000222899 - - 17 14 1679925 26466821 utr3p downstream SMYD4 AL110292.4 1629582 26466699 - + 0 1630888 26616154 + - Y - - N HCC1954 23 22.6 22 5 1 N - - N SINE - 1 0 1 5 0.307095170876829 0.51420586751469 0.51420586751469 0.307095170876829 4 - - 312 Y Y 3.15103594599453 3.46869761949767 3.15103594599453 269 0 0.478752716709127 Y 0 0.990942886110172 N N 63500 30347 ENSG00000085733 ENSG00000131626 - + 11 11 69960337 69908148 upstream intron CTTN PPFIA1 69922292 69794471 + + 0 69921854 69890474 - + N - 1.82249192277887 N HCC1954 1 1 1 0 3 N - - Y LINE - 0.365217391304348 0 0.365217391304348 4 0.799875793911741 0.849868031031224 0.849868031031224 0.799875793911741 2 - 0 2521 N Y 3.26824964015148 3.52936639476796 3.26824964015148 13 0 0.392010091847852 N 0.94188679245283 0.94188679245283 N N 8014 4918 ENSG00000149084 ENSG00000080371 - + 11 12 43834736 70467417 utr3p utr3p HSD17B12 RAB21 43658719 70434925 + + 0.286037735849057 43834016 70466247 - + Y 1.56799368003871 - N HCC1954 105 63.4444444444444 36 9 1 N - - N - SINE 0 1 1 9 0.849868031031224 0.671324327033068 0.849868031031224 0.671324327033068 1 0 - 6933 Y Y 2.80355853614086 3.12848736092996 2.80355853614086 324 0 0.00384357099394594 Y 0.115099181578582 0.932792342904703 N N 1152 409 ENSG00000115350 ENSG00000204792 - + 2 2 75050366 75013659 utr5p intron POLE4 AC104135.5 75039283 75008874 + + 0 75039312 75011645 - + N 0.792214647613613 2.70748908846367 N HCC1954 1 1 1 0 2 N - - Y - DNA 0 1 1 32 1.31408166142643 0.907002016310634 1.31408166142643 0.907002016310634 1 0 0 24697 Y Y 3.49272035470961 3.11650947863845 3.11650947863845 339 0 0.386298141928425 Y 0.993883127929493 0.993883127929493 N N 10593 4475 ENSG00000134779 ENSG00000134775 + + 18 18 32663156 32614016 coding downstream C18orf10 FHOD3 32630033 32131700 - + 0 32632411 32621041 - + N 0.705229656616832 - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 92 1.22123893534739 1.31408166142643 1.31408166142643 1.22123893534739 1 0 - 26667 Y Y 3.45720067037699 3.37808089400154 3.37808089400154 232 0 0.0190781662665223 Y 0 0.977624951569159 N N 438 5 ENSG00000140660 ENSG00000048462 - + 16 16 12054642 11969426 upstream upstream RUNDC2A TNFRSF17 11978103 11966465 + + 0 11977871 11957596 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.923913043478261 0.923913043478261 6 0.664182578873142 0.628473838073511 0.664182578873142 0.628473838073511 1 - - 31766 Y Y 3.50785087947327 3.01654588194744 3.01654588194744 0 0 0.712988490213665 Y 0.992217432950191 0.984434865900383 N N 4792 2513 ENSG00000163882 ENSG00000114859 - - 3 3 185569057 185562085 coding upstream POLR2H CLCN2 185563888 185547034 + - 0 185565448 185562628 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.749883556792257 0.807017542071667 0.807017542071667 0.749883556792257 4 - - 30280 Y Y 3.55231620741665 3.73080759109069 3.55231620741665 177 0 0.462565554052502 Y 0.780317960846144 0.988437787412955 N N 0 0 ENSG00000188441 ENSG00000182707 - + X X 73168380 73013524 upstream downstream RP13-36G14.2 FXYD8 73168022 73011598 + + 0 73135331 73081225 - + N - - N HCC1954 1 1 1 0 4 N - - Y LINE - 1 0 1 9 0.557056356474248 0.507064119354764 0.557056356474248 0.507064119354764 1 - - 370 Y N 3.41600968859956 3.66488952858494 3.41600968859956 0 0 0.103721050165728 Y 0 0 N N 22748 13535 ENSG00000006118 ENSG00000110108 - + 11 11 60461207 60447489 upstream intron TMEM132A TMEM109 60448489 60438253 + + 0 60448409 60443190 - + N - 1.11924151866493 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 5 0.614190341753658 0.478497126715059 0.614190341753658 0.478497126715059 2 - 0 33877 N N 3.50422665140011 3.4782123245619 3.4782123245619 0 0 0.814718083086332 N 0 0 N N 59837 544065 ENSG00000198695 ENSG00000198744 - + MT MT 14674 9988 coding coding MT-ND6 MT-CO3 14150 8367 - + 0 14496 8800 + + N - - Y HCC1954 3 2 1 3 3 Y 316 3.86643 N - - 0 0 0 5 1.03555348318931 0.914143764470561 1.03555348318931 0.914143764470561 2 - - 18342 Y Y 3.74590761063082 3.26928270992137 3.26928270992137 177 0 0.00777261628808612 Y 0 0.979707137092125 N N 0 14389 ENSG00000219469 ENSG00000163113 - - 1 1 148293640 148249310 upstream upstream RP11-458I7.1 OTUD7B 148292470 148178855 + - 0 148287032 148259904 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 1 0 1 4 0.435646637755502 0.45707188223528 0.45707188223528 0.435646637755502 1 - - 29562 Y N 3.2656754067026 3.15831667764963 3.15831667764963 0 0.385210084033613 0.126045520682237 Y 0.385210084033613 0.464537815126051 N N 15464 20 ENSG00000124783 ENSG00000164304 - + 6 6 7258439 7334941 coding coding SSR1 CAGE1 7232803 7271886 - - 0.464537815126051 7255226 7279292 + - N - 2.4010389874965 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.649899082553289 0.507064119354764 0.649899082553289 0.507064119354764 3 - 0 37504 N N 3.31632561579888 3.04271869508518 3.04271869508518 0 0.668333333333333 0.0260884908312027 N 0.652539682539683 0 N N 3528 21399 ENSG00000163093 ENSG00000100852 + + 2 14 170071410 31698685 utr3p downstream BBS5 ARHGAP5 170044239 31616246 + + 0 170069806 31711460 + + Y - - N HCC1954 40 40 40 4 1 N - - N - SINE 0 1 1 4 0.549914608314322 0.407079645115797 0.549914608314322 0.407079645115797 2 - - 20447 N N 3.40062947906611 3.53039946453785 3.40062947906611 4 0 0.0388313383088755 N 0 0.00267379679144375 N N 37667 0 ENSG00000112473 ENSG00000212679 - - 6 1 33280191 559619 utr3p intron SLC39A7 RP5-857K21.10 33276581 558939 + + 0.00267379679144375 33280012 559164 - - Y - 1 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.278528178237124 0.335662163516534 0.335662163516534 0.278528178237124 0 - 0 45590 N N 3.24057974892742 3.35400472562712 3.24057974892742 0 0 0.118828021303898 N 0 0 N N 0 915 ENSG00000177051 ENSG00000204516 + + 19 6 50906933 31586880 upstream utr3p FBXO46 MICB 50906323 31573842 - + 0 50925782 31586405 - + Y - - N HCC1954 37 33 25 4 1 N - - N - SINE 0 1 1 4 0.335662163516534 0.292811674556976 0.335662163516534 0.292811674556976 3 - - 41102 N N 3.16038281718941 3.00927873066148 3.00927873066148 0 0 0.451596103587305 N 0.660193716040633 0 N N 696 6560 ENSG00000101307 ENSG00000198053 - + 20 20 1548689 1868543 coding coding SIRPB1 SIRPA 1493029 1822813 - + 0 1517259 1824105 + + N - 0.0476242706620857 Y HCC1954 1 1 1 0 2 N - - N - Low_complexity 0 0.148148148148148 0.148148148148148 4 0.307095170876829 0.578481600954027 0.578481600954027 0.307095170876829 2 - 0 46430 N N 3.64656650855576 3.58527523866953 3.58527523866953 0 0 0.789053890000755 N 0 0 N N 0 6649 ENSG00000149617 ENSG00000125503 + - 20 19 51925503 60320739 downstream intron AC005220.1 LENG3 51925198 60294095 - - 0.780549480590487 51897969 60308094 - + Y - 2.19379718282493 N HCC1954 21 20.1666666666667 20 6 1 N - - N SINE SINE 0.625 1 1 6 0.39993789695587 0.335662163516534 0.39993789695587 0.335662163516534 3 - 0 29747 Y Y 3.51935717616377 3.45976132345673 3.45976132345673 0 0 0.973077236702453 Y 0 0.936884669479606 N N 399 1730 ENSG00000221988 ENSG00000168452 - + 6 6 32244040 32239433 utr5p utr3p EGFL8 PPT2 32240360 32229279 + + 0 32240432 32238706 - + N - - N HCC1954 1 1 1 0 5 Y - - Y - - 0 0 0 17 0.928427260790413 1.10697096478857 1.10697096478857 0.928427260790413 1 - - 800 Y Y 3.40744620240479 3.38337003403037 3.38337003403037 0 0 0.674450466880454 Y 0.589151205702442 0.984783377988979 N N 7042 3010 ENSG00000160613 ENSG00000149591 + + 11 11 116608021 116580717 coding intron PCSK7 TAGLN 116581020 116575250 - + 0 116582607 116577845 - + N - 0.23192126714261 N HCC1954 2 2 2 4 1 N - - Y - - 0 0 0 4 1.0069864905496 0.607048593593732 1.0069864905496 0.607048593593732 4 - 0 25945 N Y 3.58743466416515 3.63552422018169 3.58743466416515 1 0 0.115830260750480 N 0 0.728779369627507 N N 21810 66 ENSG00000213699 ENSG00000175311 + + 2 16 26857603 21171251 utr3p utr3p C2orf18 ANKS4B 26840646 21152517 + + 0.593169054441261 26855583 21171043 + + Y - - N HCC1954 714 205.5 35 4 1 N - - N SINE SINE 1 1 1 4 0.921285512630487 0.349945659836387 0.921285512630487 0.349945659836387 1 - - 33007 N N 2.91783662205815 3.39483647792751 2.91783662205815 3 0 0.999998922788295 N 0 0 Y N 544065 171855 ENSG00000198744 ENSG00000198886 - + MT MT 9988 12138 coding coding MT-CO3 MT-ND4 8367 10761 + + 0 8407 12084 - + N 0.984947018030751 6.97806364728775 N HCC1954 4 1.58620689655172 1 27 12 N 189 4.09957 N - - 0 0 0 58 1.34264865406614 1.49262536542459 1.49262536542459 1.34264865406614 1 0 0 38265 N Y 3.47233119514066 3.58064844605001 3.47233119514066 263 0 0.225617405430738 Y 0.77536718109297 0.980466711399389 N N 681 25285 ENSG00000089775 ENSG00000100714 + + 14 14 64041055 63996474 coding intron ZBTB25 MTHFD1 64023310 63924821 - + 0 64023585 63986109 - + N 0.770248667424572 1.49735544871697 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.549914608314322 0.857009779191151 0.857009779191151 0.549914608314322 4 0 0 9338 Y Y 3.18292205468417 3.06316128781662 3.06316128781662 300 0.00333333333333341 0.00532764840998246 Y 0.978175182481752 0.992725060827251 N N 2083 9627 ENSG00000188878 ENSG00000204316 + - 17 17 71448714 71413089 downstream intron FBF1 MRPL38 71417582 71406319 - - 0 71417145 71412396 - + N - 4.5388423340961 N HCC1954 1 1 1 0 1 N - - Y SINE - 0.773049645390071 0 0.773049645390071 6 0.921285512630487 0.857009779191151 0.921285512630487 0.857009779191151 1 - 0 16364 N N 3.64809409186561 3.5246463161926 3.5246463161926 4 0 0.0271053670951253 N 0 0 N N 49089 5388 ENSG00000117450 ENSG00000198648 - - 1 2 45760196 168812365 coding intron PRDX1 STK39 45749295 168518777 - - 0 45757241 168726997 + + Y - 1.20782859481253 N HCC1954 6 4.2 3 5 1 N - - N - SINE 0 1 1 5 0.771308801272036 0.45707188223528 0.771308801272036 0.45707188223528 0 - 0 29971 N N 3.20384558058643 3.28638763610951 3.20384558058643 0 0.346062717770035 0.418632726415077 N 0.346062717770035 0.402926829268293 N N 59079 0 ENSG00000137309 ENSG00000170817 + + 6 X 34321986 26676390 utr3p downstream HMGA1 AC107293.4 34312628 26676067 + + 0.402926829268293 34321484 26677257 + + Y - - N HCC1954 2 1.1 1 1 1 N - - N - - 0 0 0 10 0.39993789695587 0.264244681917271 0.39993789695587 0.264244681917271 2 - - 1365 N Y 3.50000108636471 3.26824964015148 3.26824964015148 10 0 0.301745370059415 N 0.937731481481481 0.896219135802469 N N 15671 8014 ENSG00000115762 ENSG00000149084 - - 2 11 131827752 43834736 utr3p utr3p PLEKHB2 HSD17B12 131578890 43658719 + + 0 131621560 43834016 - - Y - 1.56799368003871 N HCC1954 99 64.0714285714286 38 14 1 N - - N SINE - 1 0 1 14 0.564198104634174 0.849868031031224 0.849868031031224 0.564198104634174 1 - 0 42582 N N 3.57336771439491 3.42311528339838 3.42311528339838 0 0 0.121305155192486 N 0.00534759358288761 0 Y N 12925 135 ENSG00000168924 ENSG00000174137 - + 4 4 1827772 1655516 coding coding LETM1 FAM53A 1784558 1611607 - - 0 1813241 1640204 + - N - - N HCC1954 1 1 1 0 1 Y 474 1.78937 N - - 0 0 0 4 0.778450549431962 0.771308801272036 0.778450549431962 0.771308801272036 2 - - 27151 Y Y 3.16952679989305 3.49065421516983 3.16952679989305 347 0 0.00614256390405976 Y 0 0.99117594552549 N N 54 0 ENSG00000168124 ENSG00000209499 - + 16 16 3195189 3186226 coding upstream OR1F1 AJ003147.1-2 3194248 3186154 + + 0 3194293 3181337 - + N - - N HCC1954 2 1.88888888888889 1 8 1 N - - Y - - 0 0 0 9 0.785592297591888 1.2783729206268 1.2783729206268 0.785592297591888 2 - - 45052 Y Y 3.23640338425519 3.51001030496889 3.23640338425519 337 0 0.0784246920336438 Y 0 0.993608765122118 N N 3745 753 ENSG00000189319 ENSG00000203791 - + 10 10 126422920 126470429 utr5p utr3p FAM53B METTL10 126297853 126437396 - - 0 126422572 126438878 + - N - 0.150439648602282 N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.0125 0 0.0125 23 1.1426797055882 1.36407389854591 1.36407389854591 1.1426797055882 3 - 0 20632 N N 3.40591861909494 2.8297941300109 2.8297941300109 0 0.0962812405901835 0.353708282571453 N 0.520475760313159 0.225383920505872 N N 78560 35 ENSG00000112493 ENSG00000084628 - + 6 1 33390114 31484986 utr3p downstream TAPBP NKAIN1 33375449 31425179 - - 0.225383920505872 33376420 31417441 + - Y - - N HCC1954 168 51 4 5 1 N - - N SINE SINE,LTR 1 0.794871794871795 1 5 0.385654400636018 0.278528178237124 0.385654400636018 0.278528178237124 2 - - 31126 N N 3.25616070163838 3.25993583872649 3.25616070163838 0 0 0.148248127714778 N 0 0 N N 7605 18437 ENSG00000134108 ENSG00000163932 - - 3 3 5197597 53201771 intron intron ARL8B PRKCD 5138930 53170263 + + 0 5166906 53187458 - - N 1.22353974727726 0.146924859574331 Y HCC1954 20 20 20 4 1 N - - N SINE,SINE - 1 0 1 4 0.271386430077198 0.614190341753658 0.614190341753658 0.271386430077198 2 0 0 34522 N N 3.59528445727371 3.28871850530713 3.28871850530713 0 0 0.761888441946225 Y 0 0 N N 11640 27825 ENSG00000137038 ENSG00000080503 + + 9 9 7789799 2183624 upstream coding C9orf123 SMARCA2 7786490 2005342 - + 0 7813335 2060469 - + N - - N HCC1954 1 1 1 0 1 N - - N LTR,LTR Low_complexity 1 0.185393258426966 1 24 1.37121564670584 1.22123893534739 1.37121564670584 1.22123893534739 3 - - 41410 N Y 3.47505968208974 3.5010341561346 3.47505968208974 299 0 0.0674260071628009 Y 0.910747267009435 0.992562272250786 N N 0 0 ENSG00000221176 ENSG00000207110 - + 8 8 129130666 129080722 downstream upstream hsa-mir-1207 U1 129130580 129080559 + + 0 129151586 129070717 - + N - - N HCC1954 1 1 1 0 2 N - - N LINE,LINE - 1 0 1 41 1.22123893534739 1.02126998686945 1.22123893534739 1.02126998686945 2 - - 607 Y Y 3.70719543103269 3.5816815158199 3.5816815158199 0 0 0.164941269915993 Y 0 0.995035858236412 N N 268 23658 ENSG00000110031 ENSG00000186660 - - 11 11 58099910 58149782 coding upstream LPXN ZFP91 58050925 58103163 - + 0 58094761 58101930 + - N - - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.825174825174825 0.825174825174825 11 1.33550690590621 0.835584534711372 1.33550690590621 0.835584534711372 1 - - 46791 Y Y 3.55397177180249 3.26932256271472 3.26932256271472 257 0 0.0968297788488457 Y 0 0.985970296487094 N N 692 912 ENSG00000175885 ENSG00000167766 + - 19 19 57930109 57833456 downstream upstream AC022150.6-2 ZNF83 57898675 57807432 - - 0 57885508 57850839 - + N - - N HCC1954 3 2.40909090909091 1 20 2 N - - Y - - 0 0 0 22 0.435646637755502 0.614190341753658 0.614190341753658 0.435646637755502 2 - - 26579 Y Y 3.6035982586987 3.60935140704395 3.6035982586987 305 0 0.0386136768627088 Y 0 0.993173141702223 N N 95267 76996 ENSG00000039068 ENSG00000062038 - + 16 16 67426943 67290440 upstream coding CDH1 CDH3 67328696 67236240 + + 0 67313827 67287325 - + N - 1.96433112792382 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 29 1.10697096478857 1.07840397214886 1.10697096478857 1.07840397214886 2 - 0 42091 N N 2.7889623777105 3.48383749183115 2.7889623777105 238 0.759634888438134 0.00956150765191643 N 0.914155317299333 0.450594030715735 N N 0 78560 ENSG00000216027 ENSG00000112493 + + 4 6 61212351 33390114 downstream utr3p AC095061.3 TAPBP 61212262 33375449 - - 0.0728774268328023 60902131 33376425 - - Y - - N HCC1954 37 16.2 2 10 1 N - - N SINE,SINE SINE 0.853658536585366 1 1 10 0.292811674556976 0.428504889595575 0.428504889595575 0.292811674556976 2 - - 33018 N N 2.77892265388278 3.5774559507845 2.77892265388278 0 0 0.224204289450511 N 0 0 Y N 544065 38150 ENSG00000198744 ENSG00000198840 - + MT MT 9988 10405 coding coding MT-CO3 MT-ND3 8367 10060 + + 0 8476 10405 - + N 0.675128136826734 130.041462815272 N HCC1954 2 1.125 1 1 1 N 189 4.09957 N - - 0 0 0 8 0.849868031031224 1.0069864905496 1.0069864905496 0.849868031031224 1 0 0 19595 N Y 3.77849591952311 3.24744567262926 3.24744567262926 0 0 0.689032258613831 N 0 0.932534037797196 N N 2418 0 ENSG00000142892 ENSG00000206696 + + 1 18 77457720 45272097 intron upstream PIGK SNORD58 77327254 45272032 - - 0.932534037797196 77367366 45272464 - - Y 0.349582486358079 - N HCC1954 4 2.83333333333333 2 6 3 N - - N - - 0 0 0 6 0.614190341753658 1.03555348318931 1.03555348318931 0.614190341753658 1 0 - 17560 Y Y 3.48912663185998 3.17564132302907 3.17564132302907 0 0 0.786319407410522 Y 0 0.969580009720673 N Y 38256 4774 ENSG00000171603 ENSG00000178585 - + 1 1 9807137 9892908 coding coding CLSTN1 CTNNBIP1 9711667 9830921 - - 0 9756039 9853832 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 15 0.964136001590045 0.87843502367093 0.964136001590045 0.87843502367093 4 - - 43132 N N 3.80041266240192 3.54296933622177 3.54296933622177 49 0 0.767853245576719 N 0 0.493004115226337 N N 0 71084 ENSG00000216505 ENSG00000134333 + + 10 11 120682797 18386341 intron coding RP11-498J9.1 LDHA 120682176 18372687 - + 0.493004115226337 120682720 18379119 - + Y 1 1.46088254996525 N HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.264244681917271 0.357087407996313 0.357087407996313 0.264244681917271 2 0 0 3399 N N 3.66592259835483 3.27192306858781 3.27192306858781 0 0 0.62649860527662 Y 0 0 N N 16900 0 ENSG00000185658 ENSG00000206102 + - 21 21 39607426 31332666 coding downstream BRWD1 KRTAP19-8 39479274 31332349 - - 0 39549443 31283781 - + N 0.479897642634047 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 17 1.33550690590621 1.17838844638783 1.33550690590621 1.17838844638783 2 0 - 34151 Y Y 3.63552422018169 3.20227814448323 3.20227814448323 311 0 0.3776146934879 Y 0.992505379203636 0.985010758407272 N N 0 11502 ENSG00000222760 ENSG00000159921 - - 9 9 36257919 36248450 downstream coding U4 GNE 36257780 36204430 + - 0 36266891 36236479 - + N - 2.62370890274306 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 66 0.999844742389676 1.31408166142643 1.31408166142643 0.999844742389676 4 - 0 21688 N N 3.56079784271098 3.25153390901886 3.25153390901886 7 0 0.0592399156359251 N 0.50187969924812 0.0766550522648084 N N 5963 0 ENSG00000158161 ENSG00000219468 - + 1 9 28287702 140250262 utr3p upstream EYA3 RP11-885N19.5 28169445 140249980 - + 0.0766550522648084 28170654 140231632 + + Y - - N HCC1954 152 135.571428571429 84 28 1 N - - N SINE - 1 0 1 28 0.364229156156239 0.599906845433805 0.599906845433805 0.364229156156239 2 - - 17914 Y Y 3.13081462029492 3.26460248413936 3.13081462029492 0 0 0.358947957636246 Y 0.972503650454903 0.993125912613726 N N 4429 3889 ENSG00000162885 ENSG00000116957 + + 1 1 233734404 233678901 coding coding B3GALNT2 TBCE 233679890 233597351 - + 0 233680177 233678361 - + N - 0.886804229372152 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 20 1.06412047582901 1.15696320190805 1.15696320190805 1.06412047582901 1 - 0 816 N N 2.66332467131833 3.48064499656564 2.66332467131833 0 0.00409836065573765 0.618407087985115 N 0.00409836065573765 0.425441361916772 N N 698 23248 ENSG00000183570 ENSG00000172927 + + 21 11 46186796 68821329 utr5p downstream PCBP3 MYEOV 45888036 68818198 + + 0.425441361916772 45979734 68911605 + + Y - - N HCC1954 1 1 1 0 2 N - - N Simple_repeat,Simple_repeat SINE 0.577464788732394 1 1 11 1.01412823870953 0.807017542071667 1.01412823870953 0.807017542071667 1 - - 42602 Y Y 3.38912318237562 3.37655331069169 3.37655331069169 0 0 0.368726359962769 Y 0.993127066603684 0.951889466225791 N N 1194 10290 ENSG00000145439 ENSG00000129116 + + 4 4 170167997 170086183 coding intron CBR4 PALLD 170145319 169654792 - + 0 170159798 170052492 - + N - 0.302841070787288 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.971277749749971 1.07840397214886 1.07840397214886 0.971277749749971 1 - 0 30217 N Y 3.48912663185998 3.3755202409218 3.3755202409218 5 0 0.0161875003533495 N 0 0.902188845132338 N N 6539 2 ENSG00000009413 ENSG00000165246 - - 6 Y 111911125 15466924 coding intron REV3L NLGN4Y 111726927 15144026 - + 0.0870958879018225 111736102 15237439 + - Y - 0.980413492927095 N HCC1954 620 590 520 4 1 N - - N LINE LINE 1 1 1 4 0.421363141435649 0.335662163516534 0.421363141435649 0.335662163516534 1 - 0 10245 Y N 2.8970552088742 3.19975734419684 2.8970552088742 0 0 0.070904887283427 Y 0.250857142857143 0.172 N N 23 8746 ENSG00000176927 ENSG00000141298 - - 17 17 25459595 25281144 coding intron EFCAB5 SSH2 25292812 24977091 + - 0.172 25294767 25281048 - + N - 2.97407413916396 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 10 0.771308801272036 0.792734045751814 0.792734045751814 0.771308801272036 1 - 0 16160 N Y 3.70719543103269 3.60256518892881 3.60256518892881 0 0 0.451499098541298 N 0.833979328165375 0.7786391042205 N N 26226 0 ENSG00000115310 ENSG00000207623 + - 2 1 55131468 207672210 intron upstream RTN4 hsa-mir-205 55052829 207672101 - + 0 55101561 207669147 - - Y 5.63299576227156 - N HCC1954 9 5.5 1 3 1 N - - N SINE - 1 0 1 4 0.271386430077198 0.421363141435649 0.421363141435649 0.271386430077198 1 0 - 6362 N Y 3.47552369040616 3.46079439322662 3.46079439322662 0 0 0.239420244972269 N 0.91187625492675 0.938313378448725 N N 1992 1926 ENSG00000003436 ENSG00000167081 - + 2 9 188127464 127769477 utr5p intron TFPI PBX3 188037202 127548372 - + 0.938313378448725 188127364 127583605 + + Y - 0.920054264220767 N HCC1954 20 17.5714285714286 3 7 1 N - - N - Other 0 1 1 7 0.807017542071667 0.507064119354764 0.807017542071667 0.507064119354764 2 - 0 41122 N Y 3.58441000276898 3.66016945000958 3.58441000276898 250 0.849090909090909 0.0453498096778155 N 0.954727272727273 0.849090909090909 N Y 696 6560 ENSG00000101307 ENSG00000198053 - + 20 20 1548689 1868543 coding coding SIRPB1 SIRPA 1493029 1822813 - + 0.200181818181818 1507340 1824172 + + N - - Y HCC1954 1 1 1 0 2 Y - - N - Low_complexity 0 0.255813953488372 0.255813953488372 4 0.392796148795944 0.307095170876829 0.392796148795944 0.307095170876829 4 - - 3169 N N 2.31222350987905 2.7313276114062 2.31222350987905 0 0 0.315307739690766 N 0 0.0796296296296297 N N 551733 22054 ENSG00000204628 ENSG00000166889 + - 5 11 180603512 59182996 coding intron GNB2L1 PATL1 180596536 59160770 - - 0.0796296296296297 180597309 59177166 - + Y 0.772523368513563 0.839682778820193 N HCC1954 21 8.61764705882353 1 21 2 N 395 21.2836 N - - 0 0 0 34 0.714174815992626 0.28566992639705 0.714174815992626 0.28566992639705 2 0 0 6723 Y Y 3.64656650855576 3.52105259334297 3.52105259334297 1 0 0.548083652480187 Y 0.700777202072539 0.993766191709845 N N 603 2838 ENSG00000163126 ENSG00000168763 + + 2 2 96873485 96864848 coding utr3p ANKRD23 CNNM3 96867379 96845718 - + 0 96869464 96863007 - + N - 0.862187867848867 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 8 1.09982921662864 0.956994253430118 1.09982921662864 0.956994253430118 1 - 0 29497 Y Y 3.70360170818306 3.34673757434116 3.34673757434116 30 0.0242971805459031 0.894196442454811 Y 0.02974803428587 0.989098292520066 N N 6450 0 ENSG00000135540 ENSG00000216802 - + 6 6 138934741 139013803 coding upstream NHSL1 RP11-390P2.2 138784876 139013056 - - 0 138859201 139055306 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 98 1.49262536542459 1.3069399132665 1.49262536542459 1.3069399132665 4 - - 12996 N Y 3.49528100778935 3.61257440753299 3.49528100778935 0 0 0.0468467540644216 N 0 0 N N 7525 23283 ENSG00000173894 ENSG00000213585 - - 17 5 75375973 133368723 upstream intron CBX2 VDAC1 75366588 133335505 + - 0 75358159 133362669 - + Y - 5.54407148977073 N HCC1954 21 16 12 4 1 N - - N LTR SINE 1 1 1 4 0.392796148795944 0.28566992639705 0.392796148795944 0.28566992639705 1 - 0 22356 N N 3.57696143724454 3.31588453542141 3.31588453542141 0 0 0.048402629125843 N 0 0 N N 553 6058 ENSG00000077782 ENSG00000197785 - - 8 1 38445509 1459928 utr3p coding FGFR1 ATAD3A 38387813 1437394 - + 0 38388811 1442564 + - Y - - N HCC1954 48 43.3333333333333 36 6 1 N 324 23.0992 N SINE - 1 0 1 6 0.392796148795944 0.978419497909897 0.978419497909897 0.392796148795944 1 - - 18106 N Y 3.03020225656374 2.8182878333204 2.8182878333204 348 0 0.00733083372494447 Y 0 0.993919960751332 N N 0 0 ENSG00000212678 ENSG00000217866 - + 1 1 560165 555926 intron intron RP5-857K21.11 RP5-857K21.8 559619 554883 + + 0 559656 555846 - + N 1 1 N HCC1954 4 3.6 2 5 1 N - - N - - 0 0 0 5 0.649899082553289 0.557056356474248 0.649899082553289 0.557056356474248 3 0 0 16550 N Y 3.30591516961058 3.43681151080804 3.30591516961058 260 0 0.0329357606488596 N 0.981204644412192 0.971806966618287 N N 2844 0 ENSG00000198860 ENSG00000217731 - + 1 17 182309969 17301298 downstream intron TSEN15 AC073621.3 182287434 17300466 + + 0 182331447 17301135 - + Y - 1 N HCC1954 40 5.33333333333333 2 12 1 N 482 25.2474 N LTR - 1 0 1 12 0.907002016310634 0.714174815992626 0.907002016310634 0.714174815992626 3 - 0 9315 N Y 3.35356364524965 3.19872427442695 3.19872427442695 283 0 0.014415504131019 Y 0.071784694322087 0.959049324749504 N N 2602 117 ENSG00000006062 ENSG00000184922 + + 17 17 40750197 40680464 intron downstream MAP3K14 FMNL1 40696271 40655075 - + 0 40700203 40681143 - + N 0.772065578393814 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 30 1.06412047582901 0.528489363834543 1.06412047582901 0.528489363834543 3 0 - 23106 N Y 3.55703628599201 3.61360747730288 3.55703628599201 0 0 0.179347537022947 N 0.848860182370821 0.839969604863222 N N 136 1878 ENSG00000218327 ENSG00000138185 + + 1 10 225153888 97627013 intron utr3p AL391628.18 ENTPD1 225151212 97461526 + + 0 225153110 97626407 + + Y - - N HCC1954 26 24 22 4 1 N - - N SINE - 1 0 1 4 0.39993789695587 0.692749571512847 0.692749571512847 0.39993789695587 2 - - 41580 Y Y 3.56911164413597 3.48912663185998 3.48912663185998 284 0 0.0367543651923006 Y 0.961301791330507 0.990325447832627 N N 0 23415 ENSG00000212451 ENSG00000168672 - - 8 8 127753081 127639648 upstream upstream U11 FAM84B 127752949 127633871 + - 0 127698814 127670715 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.949852505270192 0.699891319672773 0.949852505270192 0.699891319672773 2 - - 19573 N Y 3.25463311832853 3.53296011761759 3.25463311832853 0 0 0.459890507536508 N 0.902360944377751 0.882833133253301 N N 11670 0 ENSG00000117360 ENSG00000216876 - + 1 1 148592292 185950489 coding upstream PRPF3 RP5-925F19.1 148560642 185949997 + - 0 148571779 185954739 - - N - - Y HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.621332089913584 0.371370904316165 0.621332089913584 0.371370904316165 3 - - 1339 N Y 3.41844863798551 3.2720510496638 3.2720510496638 107 0.0936567906144361 0.0127726660470699 N 0.0725790415589579 0.810300258500696 N N 13069 12566 ENSG00000055332 ENSG00000173039 - - 2 11 37405184 65186959 utr3p upstream EIF2AK2 RELA 37179857 65177649 - - 0.0936567906144361 37184724 65187086 + + Y - - N HCC1954 36 33.5384615384615 26 13 1 N - - N SINE,SINE Low_complexity 1 0.0121951219512195 1 13 0.349945659836387 0.585623349113953 0.585623349113953 0.349945659836387 1 - - 35110 N Y 3.62717056596335 3.62464976567696 3.62464976567696 298 0.88003355704698 0.0139455257395993 N 0.88003355704698 0.806208053691275 N N 34637 0 ENSG00000197111 ENSG00000220595 - + 12 21 52159872 39465902 coding intron PCBP2 AF129408.11 52132161 39464926 + - 0.400167785234899 52147272 39465257 - - Y - 1 N HCC1954 2 1.5 1 2 1 N - - N - SINE 0 0.806201550387597 0.806201550387597 4 1.0069864905496 0.635615586233437 1.0069864905496 0.635615586233437 3 - 0 19180 Y Y 2.58702666784781 2.31441296411064 2.31441296411064 2 0.00367647058823528 0.471650853989203 Y 0.847621107266436 0.976557093425606 N N 0 582 ENSG00000220338 ENSG00000153363 - + 1 1 209657899 209638102 downstream coding RP11-318L16.4 C1orf97 209656990 209622768 + + 0 209666176 209636796 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 40 0.599906845433805 1.19981369086761 1.19981369086761 0.599906845433805 4 - - 3866 N N 3.32320511986986 2.74559290026932 2.74559290026932 0 0.60161943319838 0.276518544635361 N 0.60161943319838 0.203238866396761 N N 30666 0 ENSG00000147684 ENSG00000172400 + - 8 7 125631407 131089320 utr3p downstream NDUFB9 AC093106.3-2 125620524 131089045 + - 0.203238866396761 125631389 131088956 + + Y - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.87843502367093 0.357087407996313 0.87843502367093 0.357087407996313 2 - - 48068 N N 3.55401162459584 3.44615838200292 3.44615838200292 0 0 0.145712098922698 N 0.0481746031746031 0 N N 0 51629 ENSG00000208525 ENSG00000165671 + + 8 5 130372654 176655369 downstream coding AC103833.2-1 NSD1 130372411 176493532 + + 0 130419959 176571802 + + Y - 1.41929569714202 N HCC1954 1 1 1 0 1 N 221 23.615 N LINE - 0.189189189189189 0 0.189189189189189 9 1.02841173502938 0.549914608314322 1.02841173502938 0.549914608314322 2 - 0 39842 N Y 3.60256518892881 3.46232197653647 3.46232197653647 272 0 0.00987088102216538 Y 0 0.35071050892267 N N 964 964 ENSG00000128928 ENSG00000128928 - + 15 15 38498355 38498355 upstream upstream IVD IVD 38484978 38484978 + + 0 38481689 38479353 - + N - - N HCC1954 3 1.375 1 2 1 N - - N SINE LTR,LINE 1 0.919786096256685 1 8 0.657040830713216 1.33550690590621 1.33550690590621 0.657040830713216 1 - - 39503 N N 3.44296588673741 3.56232542602083 3.44296588673741 9 0 0.0444248079127448 N 0 0.332172439759036 N N 24 4 ENSG00000140678 ENSG00000103569 - + 16 15 31301819 56265402 utr3p downstream ITGAX AQP9 31274010 56217700 + + 0 31301154 56339667 - + Y - - N HCC1954 414 40.6086956521739 21 23 1 N - - N SINE LTR 1 1 1 23 0.328520415356608 0.39993789695587 0.39993789695587 0.328520415356608 1 - - 3997 Y Y 3.60256518892881 3.03383583220673 3.03383583220673 303 0 0.00644220753645242 Y 0 0.9530964861192 N N 0 0 ENSG00000177418 ENSG00000201515 + - 7 7 65659784 65653116 downstream downstream AC006001.2-1 5S_rRNA 65659267 65652992 - - 0 65657074 65648180 - + N - - N HCC1954 2 1.6 1 3 1 N - - Y - SINE 0 0.176470588235294 0.176470588235294 5 0.785592297591888 0.971277749749971 0.971277749749971 0.785592297591888 1 - - 6520 Y Y 3.37655331069169 3.24575025545007 3.24575025545007 0 0 0.112996378852011 Y 0 0.983943621040395 N N 3612 5 ENSG00000079308 ENSG00000188282 - - 2 2 218517041 218663548 utr5p upstream TNS1 RUFY4 218372757 218607956 - + 0 218480212 218563868 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.628473838073511 0.835584534711372 0.835584534711372 0.628473838073511 1 - - 31431 N Y 3.47705127371601 3.69209541149257 3.47705127371601 0 0 0.898422576465506 Y 0 0 N N 24565 174 ENSG00000169908 ENSG00000163762 + - 3 3 150578258 150534160 upstream downstream TM4SF1 TM4SF18 150569495 150519452 - - 0 150586845 150485659 - + N - - N HCC1954 1 1 1 0 1 N - - N - LTR,LTR 0 0.395833333333333 0.395833333333333 6 0.607048593593732 0.685607823352921 0.685607823352921 0.607048593593732 4 - - 4096 N Y 3.04376534522421 3.37655331069169 3.04376534522421 283 0 0.81877493428384 Y 0.992393386022172 0.992393386022172 N N 524 0 ENSG00000218609 ENSG00000201515 - - 7 7 65743252 65653116 upstream upstream KCTD7 5S_rRNA 65731380 65652992 + - 0 65694681 65675974 - + N - - N HCC1954 4 2.34090909090909 1 27 5 N - - N - - 0 0 0 44 0.971277749749971 1.09268746846872 1.09268746846872 0.971277749749971 2 - - 7158 Y Y 3.56335849579072 3.54296933622177 3.54296933622177 283 0 0.0704502610460032 N 0 0.991181712999156 Y N 3966 2842 ENSG00000175772 ENSG00000204588 - + 2 2 110111006 110111006 downstream downstream AC013268.5-1 AC013268.5-2 110103138 110108526 + + 0 110122107 110112195 - + N - - N HCC1954 30 12.6666666666667 4 9 2 N - - N SINE - 1 0 1 9 0.857009779191151 0.849868031031224 0.857009779191151 0.849868031031224 3 - - 39835 Y Y 3.74913061111987 3.71720464963688 3.71720464963688 264 0 0.267555425281907 Y 0.971263111888112 0.980842074592075 N N 589 4202 ENSG00000074621 ENSG00000138614 - - 15 15 63735652 63690522 upstream upstream SLC24A1 C15orf44 63703472 63658173 + - 0 63698271 63692004 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 0.807017542071667 1.16410495006798 1.16410495006798 0.807017542071667 4 - - 49445 N N 3.5774559507845 3.28655907981151 3.28655907981151 0 0 0.912486751604251 Y 0 0 N N 19497 193 ENSG00000134970 ENSG00000080709 + + 5 5 114989757 113860096 coding intron TICAM2 KCNN2 114942238 113725565 - + 0 114984275 113811264 - + N - 5.30673728194955 N HCC1954 1 1 1 0 2 N 242 8.77589 N - - 0 0 0 76 1.29979816510658 1.26408942430695 1.29979816510658 1.26408942430695 2 - 0 46330 N N 3.63296356710195 3.22117957353569 3.22117957353569 0 0 0.235753223418624 N 0 0 N N 1992 246 ENSG00000003436 ENSG00000197013 - + 2 19 188127464 21512919 intron intron TFPI ZNF429 188037202 21480277 - + 0 188120722 21486667 + + Y 11.2383441972674 0.268803173058492 N HCC1954 20 20 20 15 2 N - - N - Other 0 1 1 15 0.764167053112109 0.321378667196682 0.764167053112109 0.321378667196682 2 0 0 39791 Y Y 3.40591861909494 3.15782216410967 3.15782216410967 304 0 0.0126086045104423 Y 0.992213199013158 0.992213199013158 N N 530 3915 ENSG00000128845 ENSG00000214882 + - 15 15 53587724 53487866 intron upstream DYX1C1 CCPG1 53497250 53434730 - - 0 53497712 53488275 - + N 2.89406436140274 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 43 1.10697096478857 0.999844742389676 1.10697096478857 0.999844742389676 1 0 - 4103 Y Y 3.21228736308742 3.28871850530713 3.21228736308742 366 0 0.0386013839953525 Y 0.0778688524590165 0.965846994535519 N N 0 0 ENSG00000223022 ENSG00000209951 + - 7 7 86961 86960 downstream downstream U6 AC097646.2-1 86858 86858 - - 0 82428 73209 - + N - - N HCC1954 196 62.8571428571429 15 7 3 N - - Y LTR,SINE - 0.536423841059603 0 0.536423841059603 7 0.985561246069823 0.807017542071667 0.985561246069823 0.807017542071667 3 - - 36336 Y Y 3.55334927718654 3.33424740824393 3.33424740824393 260 0 0.154518650427034 Y 0.721076923076923 0.984061538461539 N N 1240 0 ENSG00000139354 ENSG00000012504 - + 12 12 99542812 99481775 upstream downstream GAS2L3 NR1H4 99512769 99391810 + + 0 99509645 99491694 - + N - - N HCC1954 1 1 1 0 2 N - - Y SINE Simple_repeat 0.965811965811966 0.1796875 0.965811965811966 16 0.835584534711372 0.914143764470561 0.914143764470561 0.835584534711372 4 - - 17859 Y Y 3.70889084821189 3.33528047801382 3.33528047801382 357 0 0.00137510270668606 Y 0 0.99109643857543 N N 2564 16774 ENSG00000143554 ENSG00000143624 - + 1 1 152019257 152013179 utr5p utr3p SLC27A3 INTS3 152013454 151967167 + + 0.99109643857543 152013640 152012540 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.956994253430118 0.821301038391519 0.956994253430118 0.821301038391519 1 - - 4073 N Y 3.37973645838739 3.49744043328497 3.37973645838739 211 0 0.105558312149291 Y 0.640012100433599 0.894121206009882 N N 0 0 ENSG00000223189 ENSG00000212568 - + 7 7 128054565 65993713 downstream upstream U6 U6 128054462 65993610 + + 0 128069507 65992833 - + N - - N HCC1954 20 18 16 4 1 N 299 24.4666 N - - 0 0 0 4 0.321378667196682 0.499922371194838 0.499922371194838 0.321378667196682 4 - - 36362 Y Y 3.36613351693357 3.50844286886569 3.36613351693357 248 0 0.440956395929992 Y 0 0.991186126177562 N N 10492 2365 ENSG00000211584 ENSG00000079337 - - 12 12 46461719 46439128 upstream upstream SLC48A1 RAPGEF3 46453258 46417296 + - 0 46452222 46444006 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 6 0.835584534711372 0.892718519990782 0.892718519990782 0.835584534711372 2 - - 43488 N Y 3.8333716936548 3.1986844216336 3.1986844216336 0 0 0.699533700443131 N 0.172703964236408 0.962395634738019 N N 0 3627 ENSG00000183846 ENSG00000138193 + + 2 10 110575338 96078139 upstream intron AC112229.4-1 PLCE1 110574935 95743736 - + 0 110576429 95911853 - + Y - 0.616740273311221 N HCC1954 60 43.8285714285714 34 35 1 N - - N - LINE 0 1 1 35 1.02126998686945 0.528489363834543 1.02126998686945 0.528489363834543 3 - 0 30354 N Y 3.63296356710195 3.55231620741665 3.55231620741665 282 0 0.094189705470314 Y 0 0.990035460992908 N N 0 18 ENSG00000207820 ENSG00000215107 + + X X 73423769 73353624 downstream intron hsa-mir-545 AC004386.1-2 73423664 73334464 - + 0 73416956 73340515 - + N - 0.179897201599086 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 17 0.907002016310634 1.22838068350732 1.22838068350732 0.907002016310634 2 - 0 34419 N Y 3.68680627146374 3.5816815158199 3.5816815158199 0 0 0.262647618561115 Y 0 0 N N 8003 22735 ENSG00000119471 ENSG00000119314 - - 9 9 114274511 114135768 upstream intron HSDL2 ROD1 114182038 114020536 + - 0 114180617 114070299 - + N - 0.954587645715677 N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 4 0.492780623034912 0.578481600954027 0.578481600954027 0.492780623034912 1 - 0 37705 N Y 3.81657625693547 3.07311707325832 3.07311707325832 0 0 0.096141664921904 N 0 0.776753625639508 N N 2 0 ENSG00000140015 ENSG00000215401 - - 14 18 62638337 1353874 downstream upstream KCNH5 AP005119.2 62243052 1352441 - - 0 62072369 1504575 + + Y - - N HCC1954 23 22.2 22 5 1 N 291 27.0468 N LINE - 1 0 1 5 0.321378667196682 0.485638874874985 0.485638874874985 0.321378667196682 2 - - 8771 N N 3.48656597878024 3.49744043328497 3.48656597878024 0 0 0.199090002663810 N 0.257256570369862 0 N N 0 37 ENSG00000184565 ENSG00000173826 + - Y 17 19698690 59160897 intron intron TTTY14 KCNH6 19553973 58954427 - + 0 19612778 58990751 - - Y 1 0.291111557913296 N HCC1954 13 8.75 1 3 1 N - - N SINE SINE 0.403846153846154 1 1 4 0.371370904316165 0.307095170876829 0.371370904316165 0.307095170876829 1 0 0 22136 N N 3.21910408642609 3.46977054206092 3.21910408642609 0 0.210606833248343 0.573948196096454 N 0.229401908647192 0.210606833248343 N N 18713 2299 ENSG00000158864 ENSG00000173867 + - 1 15 159450806 86811623 utr3p downstream NDUFS2 MRPL46 159435729 86803713 + - 0.210606833248343 159450696 86786965 + + Y - - N HCC1954 4 2.28571428571429 1 4 1 N - - N - Simple_repeat 0 0.651162790697674 0.651162790697674 7 0.507064119354764 0.307095170876829 0.507064119354764 0.307095170876829 3 - - 39948 Y Y 3.40272612382943 3.54036883034868 3.40272612382943 187 0.0557097407432477 0.00608380081728643 Y 0.785960874568469 0.98740946320991 N N 7018 1244 ENSG00000169032 ENSG00000075131 - - 15 15 64570935 64436083 upstream intron MAP2K1 TIPIN 64466674 64416230 + - 0 64466043 64432348 - + N - 0.734837917684037 N HCC1954 2 1.28571428571429 1 2 1 N - - Y - - 0 0 0 7 0.735600060472404 0.671324327033068 0.735600060472404 0.671324327033068 1 - 0 39443 N N 3.43101850966944 3.71976530271662 3.43101850966944 0 0 0.0444069968961657 N 0 0 N N 5333 4 ENSG00000119537 ENSG00000103569 + + 18 15 59185486 56265402 utr3p downstream FVT1 AQP9 59145951 56217700 - + 0 59146654 56339885 - + Y - - N HCC1954 33 30.75 25 4 1 N - - N SINE,SINE LTR 1 1 1 4 0.357087407996313 0.378512652476092 0.378512652476092 0.357087407996313 1 - - 36482 Y Y 3.5465630590714 3.56249325989018 3.5465630590714 258 0 0.037737602570988 Y 0.990234078127375 0.990234078127375 N N 1758 1574 ENSG00000139624 ENSG00000178449 + + 12 12 48847412 48800501 intron utr5p LASS5 C12orf62 48809875 48792167 - + 0 48845073 48792348 - + N 2.3815356301981 - N HCC1954 7 1.19354838709677 1 1 2 N - - Y SINE - 0.341880341880342 0 0.341880341880342 31 0.835584534711372 0.771308801272036 0.835584534711372 0.771308801272036 1 0 - 9728 Y Y 3.53296011761759 3.51679652308403 3.51679652308403 48 0 0.108260068263184 Y 0 0.99531569085665 N N 0 22430 ENSG00000209051 ENSG00000133030 - + 17 17 17022710 17029599 downstream utr3p AC055811.20-1 MPRIP 17022458 16886799 + + 0 17032264 17028939 - + N - - N HCC1954 2 1.2 1 1 1 N - - Y - - 0 0 0 5 0.807017542071667 0.928427260790413 0.928427260790413 0.807017542071667 1 - - 25827 N Y 3.82911562339586 3.61360747730288 3.61360747730288 1 0 0.661103899805332 N 0.894383162165589 0.864206922784329 N N 0 487 ENSG00000177418 ENSG00000168447 - + 7 16 65659784 23300121 downstream intron AC006001.2-1 SCNN1B 65659267 23221092 - + 0 65657259 23254411 + + Y - 0.466999195088946 N HCC1954 36 15.8333333333333 4 6 1 N - - N - SINE 0 1 1 6 0.45707188223528 0.328520415356608 0.45707188223528 0.328520415356608 4 - 0 20024 N N 3.64553343878587 3.48809356209009 3.48809356209009 0 0 0.0897457026845164 N 0 0 N N 23349 45068 ENSG00000117139 ENSG00000205336 + + 1 16 201045186 56256445 intron upstream JARID1B GPR56 200963156 56220023 - + 0 201035896 56211646 - + Y 6.75580400953017 - N HCC1954 21 20.25 20 4 1 N - - N SINE - 1 0 1 4 0.278528178237124 0.299953422716903 0.299953422716903 0.278528178237124 1 0 - 42236 Y Y 3.69102248892932 3.43246215459326 3.43246215459326 370 0 0.0224702848258552 Y 0 0 N N 0 13648 ENSG00000187821 ENSG00000151726 - - 4 4 186178920 185984209 upstream upstream HELT ACSL1 186177077 185913744 + - 0 186117485 186052884 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 29 1.36407389854591 0.978419497909897 1.36407389854591 0.978419497909897 4 - - 46215 N Y 3.56591914887046 3.76426113588353 3.56591914887046 4 0.33267841971113 0.26896391102342 N 0.321367884451996 0.785099830076466 N N 11455 20782 ENSG00000119487 ENSG00000205246 + + 9 19 127509334 23802761 intron downstream MAPKAP1 RPSAP8 127239494 23801726 - + 0.321367884451996 127378882 23803140 - + Y 0.767643800081096 - N HCC1954 42 22.2 3 5 1 N 226 4.34896 N Other LINE 1 0.918604651162791 1 5 0.492780623034912 0.614190341753658 0.614190341753658 0.492780623034912 1 0 - 48507 N Y 3.75169126419961 3.48805370929674 3.48805370929674 0 0 0.266554809816121 N 0.520888577575424 0.924350828038225 N N 12 19481 ENSG00000156475 ENSG00000198074 + + 5 7 146415783 133876693 intron downstream PPP2R2B AKR1B10 145949260 133862884 - + 0 146366810 133884542 - + Y 1.36163522012579 - N HCC1954 20 4.76923076923077 2 13 1 N - - N LTR LTR 1 1 1 13 0.299953422716903 0.578481600954027 0.578481600954027 0.299953422716903 0 0 - 19175 N N 3.25828027434064 3.25993583872649 3.25828027434064 1 0 0.0666022284697482 N 0 0 N N 0 179175 ENSG00000220375 ENSG00000163191 - + 1 1 558984 150276135 intron utr3p RP5-857K21.14 S100A11 558778 150271606 + - 0 558921 150271648 - - N 1 - Y HCC1954 3 2.4 2 5 1 N - - N - - 0 0 0 5 0.535631111994469 0.635615586233437 0.635615586233437 0.535631111994469 1 0 - 23985 N N 3.12747721909902 1.77814393520486 1.77814393520486 35 0.0293781975600158 0.0603372545785182 N 0.0429850452577725 0 N N 551733 13691 ENSG00000204628 ENSG00000143842 + + 5 1 180603512 202363490 utr3p intron GNB2L1 SOX13 180596536 202308866 - + 0 180596544 202351434 - + Y - 0.918941854059962 N HCC1954 19 14.125 2 8 1 N - - N - Simple_repeat 0 0.5 0.5 8 0.542772860154395 0.257102933757345 0.542772860154395 0.257102933757345 3 - 0 28009 N Y 3.47336426491055 3.63193049733206 3.47336426491055 30 0.0194859038142621 0.174252146559508 N 0.272042564953013 0 N N 66 17179 ENSG00000175311 ENSG00000177189 - + 16 X 21171251 20194671 utr3p utr3p ANKS4B RPS6KA3 21152517 20077951 + - 0 21170964 20081912 - - Y - 0.534777094007045 N HCC1954 36 32.3333333333333 29 6 1 N - - N SINE - 1 0 1 6 0.371370904316165 0.542772860154395 0.542772860154395 0.371370904316165 1 - 0 38123 Y Y 3.032709476481 3.58849823915857 3.032709476481 312 0 0.0263780041206455 Y 0 0.986529799029799 N N 0 830 ENSG00000200693 ENSG00000140006 + - 14 14 63187970 63177878 intron upstream U3 WDR89 63187768 63133510 - - 0 63187803 63178668 - + N 1 - N HCC1954 1 1 1 0 1 N - - Y snRNA - 1 0 1 61 1.19267194270768 1.07126222398894 1.19267194270768 1.07126222398894 4 0 - 47954 N Y 3.47336426491055 3.48912663185998 3.47336426491055 7 0 0.0474429006093473 N 0.631930443548387 0.855972782258065 N N 4992 3556 ENSG00000197892 ENSG00000146054 + - 8 5 29176529 180564783 intron downstream KIF13B TRIM7 28980715 180553531 - - 0.0878276209677419 29145788 180551726 - + Y 1.11948510126859 - N HCC1954 24 23.8 23 5 1 N - - N SINE - 1 0 1 5 0.292811674556976 0.549914608314322 0.549914608314322 0.292811674556976 2 0 - 8840 N N 3.32163768376666 3.51001030496889 3.32163768376666 1 0 0.436474741032012 N 0 0.63420961604981 N N 313916 0 ENSG00000131748 ENSG00000177673 + + 17 2 35073248 232167236 intron downstream STARD3 C2orf57 35046938 232165856 + + 0 35047013 232171515 + + Y 1.09830374749134 - N HCC1954 1 1 1 0 1 N - - N - SINE 0 1 1 6 0.607048593593732 0.257102933757345 0.607048593593732 0.257102933757345 1 0 - 10850 N N 3.71041843152174 3.20807114562183 3.20807114562183 16 0 0.625782674829291 N 0 0.0440047757120928 N N 343 3866 ENSG00000178729 ENSG00000198740 + + 6 17 48144384 44794834 utr3p utr3p C6orf138 ZNF652 47953998 44727485 - - 0.0440047757120928 47976635 44727791 - - Y - - N HCC1954 36 26.6 23 5 1 N 511 21.5589 N SINE - 1 0 1 5 0.799875793911741 0.921285512630487 0.921285512630487 0.799875793911741 3 - - 10277 Y Y 3.64297278570613 3.51100352194543 3.51100352194543 1 0 0.244092579129437 Y 0 0 N N 408 0 ENSG00000069188 ENSG00000177338 - + 17 17 69015332 69336254 coding downstream SDK2 C17orf54 68842118 69258158 - - 0 69015332 69151760 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.899860268150708 0.692749571512847 0.899860268150708 0.692749571512847 1 - - 4061 N Y 3.41423242051993 3.31422897103557 3.31422897103557 0 0 0.996057082907596 Y 0 0.992153042725329 N N 3729 0 ENSG00000178234 ENSG00000208257 - - 7 7 151450178 151353493 utr5p upstream GALNT11 AC006017.2-1 151407293 151353212 + - 0 151407306 151353903 - + N 0.00860285461523994 - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 14 0.921285512630487 0.785592297591888 0.921285512630487 0.785592297591888 1 0 - 7515 Y Y 3.33680806132368 3.34615493251855 3.33680806132368 162 0.0244676131322095 0.649437208897941 Y 0.0244676131322095 0.992879325643301 N N 17694 466 ENSG00000153827 ENSG00000153832 - - 2 2 230494912 230586068 utr5p intron TRIP12 FBXO36 230340174 230495262 - + 0 230494840 230495843 + - N - 0.600688791064477 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 40 1.29979816510658 0.899860268150708 1.29979816510658 0.899860268150708 1 - 0 41950 Y Y 3.11807691474166 3.35513108135285 3.11807691474166 0 0 0.390475681602476 Y 0.992452197249245 0.992452197249245 N N 18418 2418 ENSG00000066777 ENSG00000104218 + + 8 8 68418466 68271048 coding intron ARFGEF1 CSPP1 68272451 68139157 - + 0 68275186 68250362 - + N - 2.21533081660345 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.914143764470561 0.87843502367093 0.914143764470561 0.87843502367093 1 - 0 31235 Y Y 2.96595182135875 3.38908332958226 2.96595182135875 245 0 0.329097369259889 Y 0.967524401064774 0.967524401064774 N N 95 2906 ENSG00000215837 ENSG00000214135 - + 3 3 196900773 196895854 coding downstream AC069513.28-2 AC069513.28-1 196900191 196874647 + + 0 196900585 196897991 - + N 0.999453193350831 - N HCC1954 8 4.8 2 5 2 N - - Y LINE - 0.876190476190476 0 0.876190476190476 5 0.728458312312478 0.742741808632331 0.742741808632331 0.728458312312478 4 0 - 33735 N Y 3.14168907479965 3.29231222815676 3.14168907479965 236 0 0.0259029874160168 Y 0 0.777542372881356 N N 339915 0 ENSG00000198727 ENSG00000210151 - - MT MT 15882 7517 coding intron MT-CYB AF347015.1-14 14748 7446 + - 0.226694915254237 14767 7451 - + N - 1 N HCC1954 2 2 2 4 1 N - - N - - 0 0 0 4 0.557056356474248 0.607048593593732 0.607048593593732 0.557056356474248 2 - 0 47156 Y Y 3.43937216388778 3.59425138750382 3.43937216388778 323 0 0.0343276107688483 Y 0 0.989827509951349 N N 106 280 ENSG00000213793 ENSG00000183022 - + 19 19 58645397 58637941 upstream intron AC022137.6-2 AC022137.6-1 58644449 58627067 + + 0 58641293 58627242 - + N - 0.269063083904262 N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 4 0.542772860154395 1.02841173502938 1.02841173502938 0.542772860154395 0 - 0 44239 N N 3.41848849077886 3.09087103183403 3.09087103183403 0 0 0.0776375274056257 N 0 0 N N 7240 3891 ENSG00000165271 ENSG00000166295 + + 9 10 33463941 73665622 upstream intron NOL6 C10orf104 33451354 73645812 - + 0 33471981 73645953 - + Y - 0.744979490524871 N HCC1954 34 24.5 20 6 1 N - - N SINE - 1 0 1 6 0.578481600954027 0.464213630395207 0.578481600954027 0.464213630395207 1 - 0 8254 N N 3.2802368700128 3.50678730447985 3.2802368700128 0 0.279335912314636 0.531431637608951 N 0.427707930367505 0.258139909735654 N N 2 551733 ENSG00000115705 ENSG00000204628 - + 2 5 1525502 180603512 intron utr3p TPO GNB2L1 1396242 180596536 + - 0.258139909735654 1483758 180596557 - - Y 0.822222222222222 - N HCC1954 22 15.9090909090909 2 22 1 N - - N SINE - 0.804878048780488 0 0.804878048780488 22 0.292811674556976 0.678466075192994 0.678466075192994 0.292811674556976 2 0 - 14390 N N 3.64656650855576 2.97888035248834 2.97888035248834 0 0 0.401401798463346 N 0 0.0901066706730769 N N 2003 251 ENSG00000160781 ENSG00000197580 - - 1 11 154484471 111594853 coding downstream PAQR6 BCO2 154479831 111551418 - + 0.0901066706730769 154484374 111598073 + - Y - - N HCC1954 2 1.25 1 1 1 N - - N - - 0 0 0 4 0.635615586233437 0.34280391167646 0.635615586233437 0.34280391167646 2 - - 47691 Y Y 3.74913061111987 3.21547985835293 3.21547985835293 3 0 0.91305426287651 Y 0.899209964569442 0.989920996456944 N N 4775 0 ENSG00000127527 ENSG00000219228 + - 19 19 16443762 16330138 coding downstream EPS15L1 AC020917.4-2 16333408 16329998 - - 0 16356940 16327662 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 44 1.78543703998156 1.44977487646503 1.78543703998156 1.44977487646503 4 - - 6435 Y Y 2.77742557579647 3.33424740824393 2.77742557579647 316 0 0.0554415107831857 Y 0.993172359979192 0.993172359979192 N N 603 812 ENSG00000163126 ENSG00000213337 - + 2 2 96873485 96887475 coding utr3p ANKRD23 ANKRD39 96867379 96877505 - - 0 96873430 96877734 + - N - 0.569984389251158 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 58 1.02841173502938 1.2783729206268 1.2783729206268 1.02841173502938 2 - 0 33103 N N 3.26100876128973 2.92871107656288 2.92871107656288 0 0.157407407407407 0.999658965541487 N 0 0.157407407407407 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0.157407407407407 8781 15553 - + N 0.579906997707467 1.31915801544436 N HCC1954 2 1.75 1 3 8 Y 189 4.09957 N - - 0 0 0 4 0.785592297591888 0.842726282871298 0.842726282871298 0.785592297591888 1 0 0 25165 Y Y 3.41319935075004 3.08404496092554 3.08404496092554 323 0 0.0407699149219202 Y 0.931718902413164 0.993171890241316 N N 0 846 ENSG00000207652 ENSG00000102743 - + 13 13 40282997 40282246 downstream downstream hsa-mir-621 SLC25A15 40282902 40261597 + + 0.993171890241316 40283592 40282335 - + N - - N HCC1954 2 1.18181818181818 1 2 1 N - - Y SINE SINE 0.340540540540541 0.215827338129496 0.340540540540541 11 1.20695543902754 0.99270299422975 1.20695543902754 0.99270299422975 3 - - 37302 N Y 3.39384326095097 3.53209488171704 3.39384326095097 0 0 0.0681055977929239 N 0 0.817626527050611 N N 4 3 ENSG00000181552 ENSG00000214960 - - 14 7 20308947 16427472 upstream intron FAM12B AC004741.2 20306426 16097683 + - 0 20301963 16145048 - + Y - 0.84 N HCC1954 20 20 20 4 1 N - - N LTR SINE 1 1 1 4 0.364229156156239 0.299953422716903 0.364229156156239 0.299953422716903 1 - 0 29318 N Y 3.44086924197409 3.33996070379583 3.33996070379583 230 0 0.0289428877402556 Y 0 0.983124539425203 N N 3388 0 ENSG00000198315 ENSG00000219891 - + 6 6 28233215 28168598 upstream upstream ZNF192 ZSCAN12L1 28217695 28168305 + + 0 28212557 28167253 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.557056356474248 0.849868031031224 0.849868031031224 0.557056356474248 3 - - 37926 N Y 3.684245618384 3.52001952357308 3.52001952357308 253 0 0.0277266142989202 N 0.928853754940711 0.914624505928854 N N 1542 1633 ENSG00000205664 ENSG00000022976 - + X 14 3771898 101878797 coding upstream RP11-706O15.1 ZNF839 3745569 101855849 - + 0 3757428 101853756 + + Y 2.70263168866007 - N HCC1954 4 3.66666666666667 3 6 1 Y - - N - - 0 0 0 6 0.364229156156239 0.335662163516534 0.364229156156239 0.335662163516534 4 0 - 39854 Y Y 3.18825104750635 3.21700744166278 3.18825104750635 0 0 0.240337030984893 Y 0.852836571825121 0.98867973629424 N N 3392 0 ENSG00000140382 ENSG00000186690 - + 15 15 75564998 75358134 upstream downstream HMG20A AC060773.10 75500285 75357862 + + 0 75499402 75365900 - + N - - N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.176795580110497 0 0.176795580110497 22 1.29265641694665 0.642757334393363 1.29265641694665 0.642757334393363 1 - - 41484 Y Y 3.43358851031899 3.58320909912975 3.43358851031899 274 0 0.0308157086770384 Y 0.94593447631981 0.992276353759973 N N 0 0 ENSG00000221176 ENSG00000222501 - - 8 8 129130666 129092039 downstream downstream hsa-mir-1207 U4 129130580 129091912 + - 0 129177945 129091871 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 19 1.06412047582901 0.971277749749971 1.06412047582901 0.971277749749971 1 - - 32306 N Y 2.84550306379784 3.44768596531277 2.84550306379784 0 0 0.292062616470385 N 0.948277809147374 0.935347261434218 N N 0 0 ENSG00000218352 ENSG00000207650 - - 9 3 109337264 196911548 upstream upstream RP11-438P9.1 hsa-mir-570 109336492 196911452 + + 0 109322076 196911079 - - Y - - N HCC1954 20 19.1428571428571 17 7 1 N 561 26.106 N LINE - 1 0 1 7 0.385654400636018 0.642757334393363 0.642757334393363 0.385654400636018 2 - - 18569 Y Y 3.27551679143744 3.44256465915329 3.27551679143744 110 0 0.0292626864900185 Y 0.952813852813853 0.976406926406927 N N 15448 81453 ENSG00000143294 ENSG00000143321 - - 1 1 155037226 154988864 upstream upstream PRCC HDGF 155003898 154978526 + - 0 155003257 154992013 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE,SINE 0 0.659090909090909 0.659090909090909 6 0.521347615674617 0.628473838073511 0.628473838073511 0.521347615674617 1 - - 33077 N Y 3.06572194089636 3.00455865208612 3.00455865208612 332 0 0.973377476084998 Y 0 0.990030120481928 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0 14080 9120 - + N 1.97871975092609 0.551657607152432 N HCC1954 3 1.85714285714286 1 5 7 Y - - N - - 0 0 0 7 1.03555348318931 1.28551466878673 1.28551466878673 1.03555348318931 2 0 0 36770 N N 3.25203261245543 3.31332388234167 3.25203261245543 0 0 0.491380427468806 N 0 0 Y N 11392 2251 ENSG00000175203 ENSG00000123297 + + 12 12 56227245 56476784 coding intron DCTN2 TSFM 56210361 56462826 - + 0 56214471 56465960 - + N - 0.881451311801125 N HCC1954 3 1.04166666666667 1 1 3 N 463 0.0544881 N - DNA,DNA 0 1 1 48 0.692749571512847 0.899860268150708 0.899860268150708 0.692749571512847 1 - 0 31566 Y Y 3.24831090852981 3.15674924154643 3.15674924154643 0 0 0.982101474620616 Y 0.321441363994556 0.992931680874943 N Y 139 298 ENSG00000206552 ENSG00000182983 - + 3 3 42959283 42933958 intron coding C3orf41 ZNF662 42952856 42922406 + + 0 42955346 42925405 - + N 0.0582648691514671 - N HCC1954 1 1 1 0 2 N - - Y Simple_repeat - 0.280821917808219 0 0.280821917808219 14 0.899860268150708 1.03555348318931 1.03555348318931 0.899860268150708 4 0 - 11181 N N 3.67593181695901 3.71041843152174 3.67593181695901 0 0 0.374306421825225 N 0 0 N N 14820 7874 ENSG00000108639 ENSG00000206560 - + 17 3 73680604 15876057 coding utr5p SYNGR2 ANKRD28 73676266 15683747 + - 0 73678499 15875888 - - Y 0.764099905789465 3.71463627210652 N HCC1954 14 6 1 3 1 N - - N - Simple_repeat 0 1 1 4 0.685607823352921 0.264244681917271 0.685607823352921 0.264244681917271 2 0 0 31797 Y Y 3.18615440274303 3.53296011761759 3.18615440274303 0 0 0.972041938781214 Y 0 0.745977011494253 N N 1907 18718 ENSG00000160799 ENSG00000160796 - - 3 3 46993242 47026197 coding upstream CCDC12 AC094020.2 46938225 46996177 - + 0 46993168 46995885 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 11 0.742741808632331 0.942710757110266 0.942710757110266 0.742741808632331 2 - - 47623 N Y 3.42953077915294 3.09359951878311 3.09359951878311 0 0 0.808468961077712 Y 0 0 N N 538 0 ENSG00000182310 ENSG00000207550 - + 19 19 56900254 56887746 utr5p upstream AC018755.3-4 hsa-mir-99b 56888409 56887677 + + 0 56889543 56884647 - + N - - N HCC1954 1 1 1 0 1 N - - N - Low_complexity,Low_complexity 0 0.318181818181818 0.318181818181818 4 0.735600060472404 0.557056356474248 0.735600060472404 0.557056356474248 4 - - 9376 Y Y 3.66488952858494 3.31229081257178 3.31229081257178 271 0 0.139977056529535 Y 0.0365354202992577 0 N N 19270 0 ENSG00000170921 ENSG00000207552 - + 17 17 58858799 58375405 utr5p downstream TANC2 hsa-mir-633 58440630 58375308 + + 0 58440630 58397842 - + N 0.00795866198796268 - N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.146739130434783 0.146739130434783 66 0.699891319672773 1.31408166142643 1.31408166142643 0.699891319672773 4 0 - 33053 N Y 3.28871850530713 3.16414437390839 3.16414437390839 458 0 0.95863947711605 Y 0 0.938460650597311 N N 544065 275222 ENSG00000198744 ENSG00000198763 - + MT MT 9988 5512 coding coding MT-CO3 MT-ND2 8367 4471 + + 0.00657907392801482 9225 5379 - + N 0.519064467778772 1.31413227598792 N HCC1954 4 2.5 2 12 9 Y - - N - - 0 0 0 12 1.07840397214886 0.799875793911741 1.07840397214886 0.799875793911741 2 0 0 19674 N N 3.35872480420248 3.38759559906577 3.35872480420248 17 0.00359712230215825 0.0377529120613654 N 0.00359712230215825 0.00359712230215825 N N 1894 2546 ENSG00000197568 ENSG00000136159 - - 1 13 70606291 47519283 coding utr5p HHLA3 NUDT15 70593081 47509704 + + 0.00359712230215825 70605907 47509742 - - Y - - N HCC1954 22 21.625 21 8 1 N - - N LTR - 1 0 1 8 0.39993789695587 0.699891319672773 0.699891319672773 0.39993789695587 0 - - 16532 N N 3.30062602958175 3.58593758607883 3.30062602958175 4 0 0.137761438255732 N 0 0.0043103448275863 N N 0 317991 ENSG00000209352 ENSG00000171346 - - 1 17 558776 36932191 intron coding AC114498.2-9 KRT15 558707 36923523 + - 0.0043103448275863 558759 36928245 - + Y 1 8.51812938738204 N HCC1954 2 2 2 7 1 N - - N - - 0 0 0 7 0.664182578873142 0.642757334393363 0.664182578873142 0.642757334393363 2 0 0 29112 Y Y 3.59272380419397 3.34256120966892 3.34256120966892 309 0 0.315095136863617 Y 0.947074490935647 0.991179081822608 N N 1789 0 ENSG00000204599 ENSG00000203481 - - 6 6 30419485 30360468 upstream upstream TRIM39 AL662795.5 30402600 30360104 + - 0 30401908 30371994 - + N - - N HCC1954 1 1 1 0 5 N - - Y LINE LTR 0.6125 1 1 8 0.99270299422975 0.785592297591888 0.99270299422975 0.785592297591888 1 - - 4677 N Y 3.09872082494259 3.63552422018169 3.09872082494259 0 0 0.672823284411602 N 0.944034651342311 0.932841581610773 N N 6576 6389 ENSG00000106635 ENSG00000006451 - + 7 7 72609960 39714240 coding downstream BCL7B RALA 72588622 39629687 - + 0 72609753 39726190 + + N - - Y HCC1954 21 20.25 20 4 1 N - - N - SINE 0 1 1 4 0.542772860154395 0.292811674556976 0.542772860154395 0.292811674556976 3 - - 29369 N N 3.49065421516983 3.58064844605001 3.49065421516983 3 0.0077403058608746 0.827533382593417 Y 0 0 N N 343 52571 ENSG00000178729 ENSG00000096433 + + 6 6 48144384 33772324 intron coding C6orf138 ITPR3 47953998 33697139 - + 0 48100371 33697391 - + N 5.08738813241339 - N HCC1954 1 1 1 0 4 N 104 11.3593 N - Low_complexity 0 0.0219435736677116 0.0219435736677116 157 1.38549914302569 1.66402732126282 1.66402732126282 1.38549914302569 1 0 - 30468 Y Y 3.43528392749819 3.49528100778935 3.43528392749819 313 0 0.164576202421775 Y 0 0.993484933909666 N N 0 0 ENSG00000199168 ENSG00000207820 + - X X 73423917 73423769 upstream downstream hsa-mir-374a hsa-mir-545 73423846 73423664 - - 0 73428988 73421505 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 1.05697872766909 1.08554572030879 1.08554572030879 1.05697872766909 1 - - 16011 N Y 3.22526780992528 3.54296933622177 3.22526780992528 9 0 0.210947821857394 N 0.921129134190015 0.911270275963767 N N 11670 37 ENSG00000117360 ENSG00000181016 - - 1 7 148592292 111918171 coding intron PRPF3 C7orf53 148560642 111908282 + + 0 148567549 111913943 - - Y - 0.536222777107139 N HCC1954 40 25 20 4 1 N - - N - SINE 0 1 1 4 0.471355378555133 0.364229156156239 0.471355378555133 0.364229156156239 1 - 0 9696 N Y 3.47080361183081 3.23999710710482 3.23999710710482 8 0 0.148458967787691 N 0.347878264208909 0 Y N 11059 1649619 ENSG00000160551 ENSG00000141736 - + 17 17 24895628 35138441 intron coding TAOK1 ERBB2 24742069 35104766 + + 0 24863851 35122226 - + N 1.43506673329209 - N HCC1954 11 5.5 3 8 1 N 230 25.8166 N SINE - 1 0 1 8 0.278528178237124 0.449930134075354 0.449930134075354 0.278528178237124 1 0 - 22103 N Y 3.76951977068882 3.56807857436608 3.56807857436608 60 0 0.215060991759637 N 0.969809203142536 0.969809203142536 N N 1 0 ENSG00000166206 ENSG00000208317 - - 15 1 24767329 172101447 intron downstream GABRB3 SNORD78 24339786 172101383 - - 0.969809203142536 24441869 172101309 + + Y 1.01325966850829 - N HCC1954 2 1.18518518518519 1 5 1 N - - N - - 0 0 0 27 0.849868031031224 0.999844742389676 0.999844742389676 0.849868031031224 1 0 - 33032 N Y 2.87060295437234 3.47655676017605 2.87060295437234 419 0 0.00145571357508956 Y 0 0.992822925430539 N N 339915 247001 ENSG00000198727 ENSG00000198786 - + MT MT 15882 14149 coding coding MT-CYB MT-ND5 14748 12338 + + 0.188990573650864 14764 12616 - + N 0.343791605542793 0.802885937219944 N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 4 0.864151527351077 0.521347615674617 0.864151527351077 0.521347615674617 1 0 0 14320 N Y 3.47911741325579 3.56079784271098 3.47911741325579 13 0 0.0215332601392811 N 0 0.894459298871064 N N 2 14 ENSG00000196844 ENSG00000042781 - + 11 1 125153924 214663361 utr3p intron PATE2 USH2A 125151268 213862859 - - 0 125151456 214602678 + - Y - 1.06013304698549 N HCC1954 462 449.142857142857 420 7 1 N - - N LINE SINE 1 1 1 7 0.449930134075354 0.335662163516534 0.449930134075354 0.335662163516534 1 - 0 49529 Y Y 3.40591861909494 3.5465630590714 3.40591861909494 0 0 0.732460122686668 Y 0 0.993023218081223 N N 39024 4089 ENSG00000169223 ENSG00000213347 + - 5 5 176711254 176671502 coding upstream LMAN2 MXD3 176691357 176666821 - - 0 176693893 176672700 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 1.02126998686945 0.914143764470561 1.02126998686945 0.914143764470561 2 - - 21345 N N 2.42750191356991 3.16783138271386 2.42750191356991 0 0 0.0506769521353597 N 0 0 N N 0 41507 ENSG00000207623 ENSG00000188846 - + 1 3 207672210 40478862 downstream coding hsa-mir-205 RPL14 207672101 40473834 + + 0 207672269 40478645 - + Y - - N HCC1954 44 6.28571428571429 1 11 1 N - - N Simple_repeat Simple_repeat 0.233918128654971 0.00709219858156028 0.233918128654971 14 1.12839620926835 1.0069864905496 1.12839620926835 1.0069864905496 1 - - 31661 Y Y 3.35662815943916 3.55976477294109 3.35662815943916 0 0 0.950223752967863 Y 0.990333110143957 0.980666220287914 N N 2709 98 ENSG00000163947 ENSG00000186451 - - 3 3 57044217 57084500 coding downstream ARHGEF3 SPATA12 56736489 57069509 - + 0 56967957 57087615 + - N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 14 1.13553795742827 0.749883556792257 1.13553795742827 0.749883556792257 4 - - 13650 Y Y 3.46141688784258 2.64358364964939 2.64358364964939 205 0 0.0680573887848483 Y 0 0.988428814520703 N N 26397 1 ENSG00000197077 ENSG00000206069 - - 22 22 23923415 23672662 upstream upstream CTA-221G9.5 TMEM211 23753158 23661077 + - 0 23740420 23678720 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE - 1 0 1 58 0.721316564152552 0.635615586233437 0.721316564152552 0.635615586233437 1 - - 3857 N N 2.68847799505532 3.39487633072086 2.68847799505532 0 0 0.104513841697950 N 0 0 N N 71032 3563 ENSG00000160932 ENSG00000171130 + + 8 7 144175199 149208720 intron downstream LY6E ATP6V0E2 144171300 149200990 + + 0 144171537 149230880 + + Y 1.33866756416173 - N HCC1954 20 20 20 5 1 N 559 25.4837 N Low_complexity SINE 0.0714285714285714 1 1 5 0.599906845433805 0.264244681917271 0.599906845433805 0.264244681917271 3 0 - 41834 Y Y 3.69255941980899 3.6052936758779 3.6052936758779 0 0 0.999671332038982 Y 0.109265614275909 0.98586135895676 N N 2237 3297 ENSG00000147408 ENSG00000104613 - - 8 8 19584374 19753864 utr5p upstream CSGALNACT1 INTS10 19305952 19719198 - + 0 19503656 19659641 + - N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 8 0.799875793911741 0.907002016310634 0.907002016310634 0.799875793911741 4 - - 24257 N N 2.99190065211955 3.36447795254773 2.99190065211955 3 0 0.202537959080227 N 0 0 N N 41 0 ENSG00000197370 ENSG00000209703 + - 5 1 69832484 26841467 downstream upstream AC146944.1-1 AL627082.8 69826551 26841366 - - 0.00403225806451624 69751859 26843364 - + Y - - N HCC1954 6 6 6 4 1 N 93 25.8398 N - SINE 0 1 1 4 0.385654400636018 0.257102933757345 0.385654400636018 0.257102933757345 1 - - 31314 Y Y 3.09872082494259 3.377215658101 3.09872082494259 381 0 0.00141659098014235 Y 0.525059367579053 0.993215133822558 N N 13421 425 ENSG00000153560 ENSG00000153558 + + 3 3 33456874 33403121 intron utr3p UBP1 FBXL2 33404835 33293938 - + 0 33419649 33402210 - + N 0.803179148579714 1.47105651121808 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 1.0069864905496 0.971277749749971 1.0069864905496 0.971277749749971 2 0 0 35684 N Y 3.51207644450867 3.55657227767558 3.51207644450867 0 0 0.183619210749644 N 0 0.620559334845049 N N 235 3329 ENSG00000134757 ENSG00000151233 - - 18 12 27312661 40824940 utr3p intron DSG3 GLT8D3 27281730 40761917 + - 0 27310889 40769000 - + Y - 0.50062173148844 N HCC1954 32 24.1111111111111 23 9 1 N - - N SINE - 1 0 1 9 0.385654400636018 0.578481600954027 0.578481600954027 0.385654400636018 2 - 0 49156 Y Y 3.45343911365801 3.46551447180198 3.45343911365801 308 0 0.00294144384000983 Y 0 0 N N 10 27039 ENSG00000186334 ENSG00000196743 + + 5 5 150663520 150629000 intron coding SLC36A3 GM2A 150636516 150612837 - + 0 150640728 150626655 - + N 1.40221302929405 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.778450549431962 0.771308801272036 0.778450549431962 0.771308801272036 1 0 - 19263 Y Y 3.55081912933034 3.67849247003875 3.55081912933034 111 0 0.622776270447392 Y 0 0 N Y 169 24350 ENSG00000134256 ENSG00000134247 - + 1 1 117380690 117334495 intron coding IGSF2 PTGFRN 117345905 117254207 + + 0 117353995 117318468 - + N 0.209124552569314 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.778450549431962 0.807017542071667 0.807017542071667 0.778450549431962 4 0 - 31675 N N 3.61616813038263 2.97423997949968 2.97423997949968 0 0 0.0404725215330330 Y 0 0 N N 151 12271 ENSG00000214271 ENSG00000177479 - + 3 3 143204805 48997971 coding intron AC128648.5 ARIH2 143179267 48931285 + + 0 143181232 48931497 - + N - 0.684981992063489 N HCC1954 30 23.875 21 16 1 N 295 24.0715 N SINE - 1 0 1 16 0.428504889595575 0.978419497909897 0.978419497909897 0.428504889595575 1 - 0 26587 Y Y 3.38908332958226 3.52577267191832 3.38908332958226 293 0 0.0622101666468149 Y 0 0.992981781473826 N N 48 6328 ENSG00000185669 ENSG00000167508 + - 16 16 87280383 87257019 downstream upstream SNAI3 MVD 87271591 87245849 - - 0 87265184 87257933 - + N - - N HCC1954 1 1 1 0 1 N - - Y DNA - 1 0 1 8 0.899860268150708 0.964136001590045 0.964136001590045 0.899860268150708 2 - - 27819 N Y 3.06886100299938 3.22536109588112 3.06886100299938 0 0.278514588859416 0.0582830279221316 N 0.209801692560313 0.793861311102691 N N 18920 8 ENSG00000082781 ENSG00000153446 - + 3 16 126088834 5056112 utr5p intron ITGB5 C16orf89 125964488 5034125 - - 0 126088579 5051405 + - Y - 1.11901595744681 N HCC1954 21 20.1428571428571 20 7 1 N 592 22.7499 N - SINE 0 1 1 7 0.521347615674617 0.278528178237124 0.521347615674617 0.278528178237124 1 - 0 36387 Y Y 3.43784458057793 3.3012485241977 3.3012485241977 267 0 0.0968120741758715 Y 0.553677902621723 0.992029962546816 N Y 2251 1532 ENSG00000123297 ENSG00000123427 - + 12 12 56476784 56462588 coding intron TSFM FAM119B 56462826 56452650 + + 0 56463160 56453178 - + N 0.888136429544554 0.563192722212695 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.757025304952183 0.628473838073511 0.757025304952183 0.628473838073511 4 0 0 33973 N Y 3.28399842673177 3.17138525277014 3.17138525277014 372 0.00268817204301075 0.00903275354532096 Y 0.0425806451612905 0.953458781362007 N N 59837 544065 ENSG00000198695 ENSG00000198744 + + MT MT 14674 9988 coding coding MT-ND6 MT-CO3 14150 8367 - + 0 14300 9125 - + N - 0.546746183351487 N HCC1954 4 2.25 1 3 1 N - - N - - 0 0 0 4 0.707033067832699 0.87843502367093 0.87843502367093 0.707033067832699 3 - 0 38275 Y Y 3.52105259334297 3.51679652308403 3.51679652308403 271 0 0.818082214637941 Y 0 0.977611012065177 N N 438 333 ENSG00000126790 ENSG00000181619 + - 14 14 59020826 59001813 coding upstream C14orf149 GPR135 59009159 58965493 - - 0 59012340 59002198 - + N 0.316761790973107 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.635615586233437 0.735600060472404 0.735600060472404 0.635615586233437 4 0 - 33111 N Y 2.76022891149302 3.41576000382978 2.76022891149302 292 0.00342465753424659 0.828632619471474 Y 0.00342465753424659 0.952991729128974 N N 544065 1291380 ENSG00000198744 ENSG00000198804 - + MT MT 9988 7446 coding coding MT-CO3 MT-CO1 8367 5905 + + 0.952991729128974 8492 6702 - + N 0.619501286280727 0.999958986709105 N HCC1954 2 1.75 1 3 5 N - - N - - 0 0 0 4 0.999844742389676 0.87843502367093 0.999844742389676 0.87843502367093 2 0 0 26264 N Y 3.46232197653647 3.59948328967027 3.46232197653647 10 0.137742053343077 0.309815680688135 N 0.267080745341615 0.956887102667154 N N 7487 8652 ENSG00000188603 ENSG00000182628 - + 16 17 28411124 54587582 coding utr3p CLN3 FAM33A 28396101 54542090 - - 0 28410304 54542809 + - Y - - N HCC1954 21 21 21 5 1 N - - N - SINE 0 1 1 5 0.542772860154395 0.28566992639705 0.542772860154395 0.28566992639705 2 - - 33158 N N 3.08035795212007 3.0888395874144 3.08035795212007 2 0 0.705576182683584 N 0 0 Y N 151141 275222 ENSG00000198888 ENSG00000198763 - + MT MT 4264 5512 coding coding MT-ND1 MT-ND2 3308 4471 + + 0 3498 5490 - + N 0.876637446768272 43.930336276942 N HCC1954 2 1.2 1 1 2 N 128 10.5705 N - - 0 0 0 5 0.907002016310634 0.842726282871298 0.907002016310634 0.842726282871298 1 0 0 48820 Y Y 3.32952732966858 3.0431827034016 3.0431827034016 309 0 0.050992276282197 Y 0.992980536943343 0.992980536943343 N N 10798 12549 ENSG00000113761 ENSG00000087206 - - 5 5 176426349 176366358 upstream intron ZNF346 UIMC1 176382303 176264612 + - 0 176382072 176342231 - + N - 4.9833844996012 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 26 1.16410495006798 1.06412047582901 1.16410495006798 1.06412047582901 1 - 0 31977 N N 3.19975734419684 3.73233517440054 3.19975734419684 0 0 0.115265345942635 N 0 0.164414414414414 N N 15 386 ENSG00000181722 ENSG00000196295 + - 3 7 116348817 30570758 upstream upstream ZBTB20 AC005154.1 115540230 30566129 - - 0.164414414414414 116386873 30585457 - + Y - - N HCC1954 7 4.75 3 4 1 N 558 28.0997 N LTR LTR,LTR 1 0.541666666666667 1 4 0.335662163516534 0.34280391167646 0.34280391167646 0.335662163516534 1 - - 36686 N Y 3.16931911323036 3.41103992525442 3.16931911323036 9 0.0172541547581242 0.938318974310412 Y 0.0470343318866659 0.970219822871458 N N 9765 351 ENSG00000139182 ENSG00000205885 - + 12 12 7202793 7165701 utr5p intron CLSTN3 AC018653.29-1 7174234 7152443 + + 0 7174450 7164503 - + N - 15.5779209940653 N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 6 1.26408942430695 0.821301038391519 1.26408942430695 0.821301038391519 2 - 0 29122 Y Y 3.43784458057793 3.35885278527847 3.35885278527847 308 0 0.00131071065675059 Y 0 0.984665334665335 N N 14 1219 ENSG00000164691 ENSG00000130363 + - 6 6 159386172 159341207 downstream upstream TAGAP RSPH3 159376017 159317300 - - 0 159366844 159341340 - + N - - N HCC1954 7 2.85714285714286 1 3 1 N - - Y LTR - 1 0 1 7 0.442788385915428 0.542772860154395 0.542772860154395 0.442788385915428 1 - - 3837 N Y 3.61360747730288 3.01105607394689 3.01105607394689 0 0.210201149425287 0.339371380678812 N 0.210201149425287 0.553591954022988 N N 6271 0 ENSG00000170381 ENSG00000212451 - + 7 8 83116262 127753081 utr3p downstream SEMA3E U11 82831158 127752949 - + 0.553591954022988 82831376 128107233 + + Y - - N HCC1954 34 26.4 23 15 1 N 79 19.6116 N SINE LTR 1 1 1 15 1.07126222398894 0.728458312312478 1.07126222398894 0.728458312312478 2 - - 32978 N N 3.30960217841605 3.21804051143267 3.21804051143267 0 0 0.99998906795051 N 0 0 Y N 544065 59837 ENSG00000198744 ENSG00000198695 - - MT MT 9988 14674 coding coding MT-CO3 MT-ND6 8367 14150 + - 0 8868 14442 - + N 0.57514237935253 1.37319647595014 N HCC1954 2 1.4 1 2 10 N 189 4.09957 N - - 0 0 0 5 1.19267194270768 0.799875793911741 1.19267194270768 0.799875793911741 1 0 0 41451 Y Y 3.4944157718888 3.58320909912975 3.4944157718888 333 0 0.057496444988064 Y 0.872564293616925 0.992503781977466 N N 0 0 ENSG00000221176 ENSG00000222501 - - 8 8 129130666 129092039 downstream downstream hsa-mir-1207 U4 129130580 129091912 + - 0 129151587 129091871 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE,LINE - 1 0 1 47 1.40692438750547 0.985561246069823 1.40692438750547 0.985561246069823 1 - - 24604 N Y 3.48759904855013 3.45612774781375 3.45612774781375 0 0 0.365683747073291 N 0 0.817481481481482 N N 0 13271 ENSG00000208432 ENSG00000081923 - - 4 18 191052067 53550037 upstream upstream AF250324.1-1 ATP8B1 191051869 53464656 + - 0 191013370 53550060 - + Y - - N HCC1954 6 3.5 1 3 1 N 611 23.2452 N SINE - 1 0 1 4 0.271386430077198 0.378512652476092 0.378512652476092 0.271386430077198 1 - - 7000 Y Y 2.93760751981047 3.39743698380061 2.93760751981047 268 0 0.205995330748963 Y 0.991260801256874 0.991260801256874 N N 676 2952 ENSG00000144401 ENSG00000118260 + + 2 2 208198276 208171806 intron intron FAM119A CREB1 208185086 208102917 - + 0 208194774 208155128 - + N 1.07256906523847 3.86540137913076 N HCC1954 1 1 1 0 3 N - - Y - LINE 0 1 1 11 0.964136001590045 0.999844742389676 0.999844742389676 0.964136001590045 1 0 0 46365 N Y 3.33098455496154 3.2232016703855 3.2232016703855 227 0 0.0229920165689929 N 0 0.875550660792952 N N 1303 20739 ENSG00000197573 ENSG00000143951 - + 19 2 46148403 63669355 downstream utr3p CYP2B7P1 C2orf86 46122010 63202041 + - 0.806412139011258 46162184 63309318 - - Y - - N HCC1954 62 32 21 15 1 N 358 19.5442 N LINE LINE 1 1 1 15 0.899860268150708 0.542772860154395 0.899860268150708 0.542772860154395 2 - - 47419 N Y 3.63978029044062 3.18974812559266 3.18974812559266 0 0 0.435186446416676 Y 0 0 N N 12053 259 ENSG00000075702 ENSG00000105270 - - 19 19 41287852 41215635 coding intron WDR62 CLIP3 41237623 41197402 + - 0 41241523 41202127 - + N - 2.14899069776909 N HCC1954 1 1 1 0 1 N - - N - SINE 0 0.202898550724638 0.202898550724638 8 0.792734045751814 0.985561246069823 0.985561246069823 0.792734045751814 1 - 0 41697 Y N 3.17088654933356 3.72717401544771 3.17088654933356 0 0 0.731863134638965 N 0 0 N N 19339 79632 ENSG00000177570 ENSG00000182197 + + 8 8 119703365 119193119 utr3p coding SAMD12 EXT1 119270880 118875910 - - 0 119271701 119191505 - - N 0.660159916998196 - Y HCC1954 1 1 1 0 1 N 166 4.4797 N - - 0 0 0 41 1.18553019454776 1.24980592798709 1.24980592798709 1.18553019454776 4 0 - 13662 Y Y 3.73808832274579 3.6623288755052 3.6623288755052 336 0 0.97507680229468 Y 0.951533564814815 0.986152447089947 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 upstream intron AP000347.3 AP000347.4 22321400 22310865 - - 0 22332052 22311129 - + N - 1 N HCC1954 9 4.46511627906977 1 25 6 N - - Y - - 0 0 0 43 1.1141127129485 1.36407389854591 1.36407389854591 1.1141127129485 4 - 0 39379 N Y 3.41844863798551 3.38552945952599 3.38552945952599 327 0 0.00475762259272283 N 0.358029839681216 0.93957927902882 N N 1278 110 ENSG00000214611 ENSG00000198312 - + 15 22 19634453 20993088 intron upstream AC126335.16-4 D87018.1-3 19624910 20991471 + + 0 19630173 20982575 - + Y 0.729398619962815 - N HCC1954 8 4.53846153846154 3 26 2 N 364 23.3546 N - Satellite 0 0.932773109243697 0.932773109243697 26 0.978419497909897 0.699891319672773 0.978419497909897 0.699891319672773 1 0 - 26808 N Y 3.53824925764641 3.30335451653084 3.30335451653084 224 0.0561804267161411 0.183809700585695 Y 0.0561804267161411 0.987070964749536 N N 1173 0 ENSG00000140987 ENSG00000209508 + + 16 16 3391026 3357718 coding upstream ZNF434 AC025283.6-2 3372087 3357649 - + 0 3387205 3355184 - + N 0.735970542697945 - N HCC1954 1 1 1 0 2 N - - N - - 0 0 0 5 0.749883556792257 0.378512652476092 0.749883556792257 0.378512652476092 1 0 - 23087 N Y 3.59001826628863 3.50575423470996 3.50575423470996 0 0 0.270955145084354 N 0 0 N N 7120 3891 ENSG00000143337 ENSG00000166295 + + 1 10 178157206 73665622 utr3p intron TOR1AIP1 C10orf104 178117800 73645812 + + 0 178156757 73645977 + + Y - 0.744979490524871 N HCC1954 36 32.4444444444444 28 9 1 N 340 22.3611 N SINE - 1 0 1 9 0.464213630395207 0.742741808632331 0.742741808632331 0.464213630395207 2 - 0 28597 N N 3.42208221362849 2.45397090115473 2.45397090115473 0 0.00555555555555565 0.212243550814146 N 0.00555555555555565 0.0246794871794871 N N 6894 1 ENSG00000159792 ENSG00000104967 - - 16 19 66521078 51168497 utr5p upstream PSKH1 NOVA2 66484705 51134631 + - 0.0246794871794871 66500093 51168573 - + Y 0.136187067634458 - N HCC1954 17 12 7 4 1 N - - N - Simple_repeat 0 1 1 4 0.364229156156239 0.299953422716903 0.364229156156239 0.299953422716903 2 0 - 46741 Y N 3.21228736308742 2.65034422448047 2.65034422448047 211 0 0.0156698747066312 Y 0 0 N N 16692 12189 ENSG00000079432 ENSG00000105722 - - 19 19 47491789 47451093 upstream upstream CIC ERF 47480657 47443564 + - 0.421800947867299 47467840 47465348 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 177 1.09268746846872 0.971277749749971 1.09268746846872 0.971277749749971 1 - - 9479 Y Y 3.53209488171704 3.51207644450867 3.51207644450867 514 0 0.000300356351474185 Y 0 0 N N 600 5160 ENSG00000167363 ENSG00000141560 - + 17 17 78302362 78279142 upstream downstream FN3K FN3KRP 78286797 78267895 + + 0.995752959682093 78284162 78282625 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE SINE 0.0123456790123457 0.475113122171946 0.475113122171946 4 1.04269523134923 0.628473838073511 1.04269523134923 0.628473838073511 2 - - 16757 N Y 3.12804628055249 3.60422075331465 3.12804628055249 0 0 0.553182601852266 N 0.759518010511473 0.811049865401871 N N 1649619 2043 ENSG00000141736 ENSG00000197056 - - 17 1 35138441 35354047 coding intron ERBB2 ZMYM1 35104766 35317559 + + 0 35122227 35348998 - - Y - 1.80081736146951 N HCC1954 4 2 1 6 1 N - - N - SINE 0 1 1 12 1.04983697950916 0.349945659836387 1.04983697950916 0.349945659836387 2 - 0 6946 Y Y 3.08255723040904 3.86682523844763 3.08255723040904 256 0 0.0137579392175071 Y 0.209449404761905 0.984188988095238 N N 0 2144 ENSG00000222119 ENSG00000144006 + - 2 2 96034328 95956704 downstream upstream SRP_euk_arch AC073995.6-2 96034040 95905442 - - 0 96007600 95988263 - + N - - N HCC1954 6 2.5 1 2 1 N - - Y - - 0 0 0 4 0.307095170876829 0.321378667196682 0.321378667196682 0.307095170876829 1 - - 9308 Y Y 3.5580693557619 3.48809356209009 3.48809356209009 252 0 0.679911126822131 Y 0 0.97857996245093 N N 1312 5490 ENSG00000120093 ENSG00000173917 + - 17 17 44006809 43977392 downstream upstream HOXB3 HOXB2 43981232 43975020 - - 0 43980734 43977745 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 15 0.671324327033068 0.921285512630487 0.921285512630487 0.671324327033068 2 - - 38545 Y Y 3.48743121468078 3.42572936964061 3.42572936964061 0 0 0.475687729945588 Y 0 0.992329360780065 N N 2273 1811 ENSG00000187097 ENSG00000119723 + + 14 14 73552387 73499564 coding intron ENTPD5 COQ6 73502946 73486396 - + 0 73506469 73496012 - + N - 0.864561442968397 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.964136001590045 1.17124669822791 1.17124669822791 0.964136001590045 1 - 0 18835 Y Y 3.41423242051993 3.78208964237274 3.41423242051993 212 0 0.035077266196444 Y 0 0.987862402208928 N N 2732 0 ENSG00000168275 ENSG00000138396 - - 1 1 232586416 232559510 upstream intron C1orf31 RP5-827C21.1 232575836 232559073 + - 0 232567879 232559488 - + N - 1 N HCC1954 3 2.375 1 6 2 N - - Y - - 0 0 0 8 0.657040830713216 0.714174815992626 0.714174815992626 0.657040830713216 1 - 0 2666 N Y 3.41741556821562 3.60103760561896 3.41741556821562 0 0 0.389473601401273 N 0.985599556909443 0.971199113818887 N N 319 2 ENSG00000166415 ENSG00000082175 - - 15 11 51842367 100506465 coding upstream WDR72 PGR 51593230 100414313 - - 0 51602811 100657077 + + Y - - N HCC1954 24 22.5 20 4 1 N 327 25.6129 N - LINE 0 1 1 4 0.428504889595575 0.34280391167646 0.428504889595575 0.34280391167646 4 - - 4994 N Y 3.52208566311286 3.54396255319831 3.52208566311286 0 0 0.323599545865479 Y 0.978548793369627 0.978548793369627 N N 650 0 ENSG00000127957 ENSG00000067601 + - 7 7 74995330 66404852 utr3p downstream PMS2L3 AC006480.3-1 74975006 66389963 - - 0 74975039 66378671 - + N - - N HCC1954 108 43.8 1 4 1 N - - N LTR SINE 0.38125 0.943661971830986 0.943661971830986 5 1.05697872766909 0.742741808632331 1.05697872766909 0.742741808632331 4 - - 35131 N Y 3.41103992525442 3.63759035972147 3.41103992525442 0 0.14242530447735 0.635832685169506 N 0.832427933058793 0.832427933058793 N N 34637 0 ENSG00000197111 ENSG00000220595 + - 12 21 52159872 39465902 coding intron PCBP2 AF129408.11 52132161 39464926 + - 0.615569964076053 52142616 39465258 + + Y - 1 N HCC1954 2 1.1875 1 3 2 N - - N SINE SINE 0.350515463917526 0.2578125 0.350515463917526 16 1.19267194270768 0.657040830713216 1.19267194270768 0.657040830713216 2 - 0 332 Y Y 3.61360747730288 3.7061623612628 3.61360747730288 249 0 0.00173469508325064 Y 0.95951284814053 0.991902569628106 N N 3 85 ENSG00000154096 ENSG00000036672 + - 11 11 118800048 118757575 downstream upstream THY1 USP2 118794097 118732163 - - 0 118785450 118771069 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE LINE 1 1 1 6 1.07126222398894 0.742741808632331 1.07126222398894 0.742741808632331 2 - - 9342 Y Y 3.25828027434064 3.52357339362936 3.25828027434064 277 0 0.304273092368474 Y 0.0700361010830325 0 N N 679 0 ENSG00000183308 ENSG00000201849 - - 17 17 59895221 59817128 upstream downstream C17orf60 Y_RNA 59875702 59817023 + - 0 59860910 59812481 - + N - - N HCC1954 13 1.71428571428571 1 2 3 N - - Y LTR,LTR LINE 1 0.190839694656489 1 21 0.928427260790413 0.93556900895034 0.93556900895034 0.928427260790413 4 - - 37850 N Y 3.11192253881228 3.62192127872787 3.11192253881228 10 0 0.0595703374462424 N 0 0.750485436893204 N N 78560 0 ENSG00000112493 ENSG00000222639 - + 6 14 33390114 49123344 utr3p downstream TAPBP SRP_euk_arch 33375449 49123048 - + 0.675631067961165 33376428 49123349 + + Y - - N HCC1954 189 71.1111111111111 10 9 1 N - - N SINE srpRNA 1 1 1 9 0.928427260790413 1.0069864905496 1.0069864905496 0.928427260790413 1 - - 9111 N N 3.07101108092519 3.43528392749819 3.07101108092519 0 0 0.595750278491176 N 0.193127413127413 0.711119691119691 N N 1649619 0 ENSG00000141736 ENSG00000221388 - + 17 2 35138441 213336644 coding downstream ERBB2 AC093865.2 35104766 213336539 + - 0.711119691119691 35125066 213260021 - - Y - - N HCC1954 17 13 3 5 1 N - - N - SINE 0 1 1 5 0.335662163516534 0.264244681917271 0.335662163516534 0.264244681917271 1 - - 31623 Y Y 3.43209143223268 3.68527868815389 3.43209143223268 3 0 0.996884345802436 Y 0.538490353998876 0.989511144409065 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 utr5p upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42836124 42826025 - + N - - N HCC1954 1 1 1 0 6 N - - Y - LTR 0 1 1 148 1.35693215038599 0.749883556792257 1.35693215038599 0.749883556792257 1 - - 41678 N Y 3.52208566311286 3.69937614314766 3.52208566311286 223 0 0.0078118249032606 Y 0 0 N N 2253 38251 ENSG00000156795 ENSG00000156802 - - 8 8 124523441 124477868 upstream coding WDYHV1 ATAD2 124498146 124401922 + - 0 124497668 124462097 - + N - 1.12974123625469 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 12 0.721316564152552 0.87843502367093 0.87843502367093 0.721316564152552 1 - 0 45175 Y Y 3.55231620741665 3.37808089400154 3.37808089400154 116 0 0.159209739271048 Y 0 0 N N 4023 5872 ENSG00000107897 ENSG00000120539 + + 10 10 27571065 27515854 coding intron ACBD5 MASTL 27524149 27484298 - + 0 27533377 27513252 - + N - 2.66597982100246 N HCC1954 1 1 1 0 1 N - - Y - LINE 0 1 1 4 0.621332089913584 0.5713398527941 0.621332089913584 0.5713398527941 3 - 0 38982 N N 3.36551102231762 3.33424740824393 3.33424740824393 0 0 0.888060824573919 N 0 0 N N 0 5111 ENSG00000184565 ENSG00000181827 + - Y 15 19698690 54322775 intron downstream TTTY14 RFX7 19553973 54170024 - - 0 19613132 54152365 - + Y 1 - N HCC1954 1 1 1 0 3 N - - N - - 0 0 0 6 0.985561246069823 0.328520415356608 0.985561246069823 0.328520415356608 2 0 - 31195 Y Y 3.69784855983781 3.51104337473878 3.51104337473878 282 0.0139258274231678 0.169828582612511 Y 0.750886524822695 0.989620271867612 N N 1033 0 ENSG00000196639 ENSG00000213964 - - 3 3 11280243 11251366 utr5p downstream HRH1 AC083855.3 11269385 11250939 + - 0 11275687 11242743 - + N 0.106002789547093 - N HCC1954 1 1 1 0 3 N - - Y - LINE 0 1 1 27 1.07126222398894 0.649899082553289 1.07126222398894 0.649899082553289 2 0 - 47199 Y Y 3.36663737804334 3.21332043285731 3.21332043285731 0 0 0.694550158444102 Y 0.619036173536835 0.993650602892281 N Y 14186 4002 ENSG00000171570 ENSG00000167578 - + 19 19 46006176 45994687 utr5p utr3p EGLN2 RAB4B 45996959 45976011 + + 0 45998084 45984723 - + N 0.386701714469743 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.921285512630487 1.12839620926835 1.12839620926835 0.921285512630487 4 0 - 29860 Y Y 3.27291628556435 3.68953475841283 3.27291628556435 0 0 0.648846424246078 Y 0.950170068027211 0.985762876579203 N N 41 0 ENSG00000164520 ENSG00000217733 + + 6 6 150253863 150244349 coding downstream RAET1E RP11-350J20.6 150251014 150242810 - + 0 150251368 150247333 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.215277777777778 0.215277777777778 5 0.885576771830856 0.985561246069823 0.985561246069823 0.885576771830856 4 - - 47377 Y Y 3.25679254382414 3.57952209032428 3.25679254382414 169 0 0.312607113352571 Y 0 0.875739644970414 N N 4159 60677 ENSG00000012061 ENSG00000125740 - - 19 19 50619017 50670254 utr5p upstream ERCC1 FOSB 50604712 50663093 - + 0 50618890 50645792 + - N - - N HCC1954 26 11.8888888888889 2 9 4 N - - Y - SINE 0 1 1 9 0.792734045751814 0.728458312312478 0.792734045751814 0.728458312312478 1 - - 15687 N Y 3.62093606475077 3.64297278570613 3.62093606475077 0 0 0.0516634544575965 N 0.205194805194805 0.503246753246753 N N 3 850768 ENSG00000162779 ENSG00000075624 - + 1 7 177790491 5536758 intron utr3p C1orf125 ACTB 177601478 5533313 + - 0 177647129 5533865 - - Y 0.979415906833497 1.01371244516945 N HCC1954 11 3.5 1 1 1 N - - N Simple_repeat - 0.777777777777778 0 0.777777777777778 4 0.257102933757345 0.535631111994469 0.535631111994469 0.257102933757345 1 0 0 10755 N Y 3.60785432895764 3.04640570389065 3.04640570389065 3 0.0244932432432433 0.130909312266442 N 0.0244932432432433 0.0244932432432433 N N 19823 20747 ENSG00000204435 ENSG00000073605 - + 6 17 31749302 35328429 utr3p intron CSNK2B GSDMB 31740992 35314374 + - 0.0244932432432433 31748883 35319858 - - Y - 1.12508004904349 N HCC1954 29 24 21 4 1 N 339 25.6301 N SINE - 1 0 1 4 0.364229156156239 0.299953422716903 0.364229156156239 0.299953422716903 3 - 0 42002 N Y 3.38652267650252 3.47233119514066 3.38652267650252 0 0.845404435328804 0.383574492260614 N 0.845404435328804 0.845404435328804 N N 22644 0 ENSG00000167110 ENSG00000170289 - + 9 8 130078089 87825017 coding intron GOLGA2 CNGB3 130057932 87655277 - - 0.845404435328804 130068423 87741188 + - Y - 1 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 30 1.09268746846872 0.407079645115797 1.09268746846872 0.407079645115797 2 - 0 3457 N N 3.53354275944019 3.16316473730098 3.16316473730098 0 0 0.247444960864034 Y 0 0 N N 5734 6113 ENSG00000160194 ENSG00000154640 - - 21 21 43202841 17907086 coding upstream NDUFV3 BTG3 43186447 17887844 + - 0 43202084 17983904 - + N 1.74003519746462 - N HCC1954 1 1 1 0 2 N - - N - LINE 0 1 1 11 0.578481600954027 0.492780623034912 0.578481600954027 0.492780623034912 2 0 - 19594 N Y 3.69359248957888 3.24893340314576 3.24893340314576 0 0 0.971327813113497 N 0.264138721411131 0.964622053913997 N N 2418 0 ENSG00000142892 ENSG00000206696 + + 1 18 77457720 45272097 intron upstream PIGK SNORD58 77327254 45272032 - - 0.964622053913997 77367378 45272639 - - Y 0.349582486358079 - N HCC1954 6 4.59090909090909 1 65 3 N - - N - - 0 0 0 66 0.921285512630487 0.757025304952183 0.921285512630487 0.757025304952183 3 0 - 36716 Y Y 3.2420632466446 2.9935562165054 2.9935562165054 105 0 0.0938172564179321 Y 0.665626815915833 0.976939780407988 N N 4974 4945 ENSG00000152556 ENSG00000079387 - - 12 12 46826154 46785886 coding upstream PFKM SENP1 46787424 46722948 + - 0 46788142 46786285 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.671324327033068 0.928427260790413 0.928427260790413 0.671324327033068 2 - - 36304 N Y 3.41529599551336 3.64549358599252 3.41529599551336 0 0 0.763171219108336 Y 0.918701906992305 0.898377383740382 N N 124 2520 ENSG00000174456 ENSG00000123268 + + 12 12 108989883 49501174 intron intron AC007546.6-1 ATF1 108963366 49444086 - + 0 108970551 49486478 - + N 8.34876281104222 1.74501076380473 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.51420586751469 0.357087407996313 0.51420586751469 0.357087407996313 3 0 0 368 Y Y 3.4780843434859 3.33680806132367 3.33680806132367 303 0 0.00203258240586368 Y 0.501650165016502 0 N N 2853 10556 ENSG00000174775 ENSG00000023191 + - 11 11 525591 497273 downstream upstream HRAS RNH1 522242 484513 - - 0 518160 509108 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.942710757110266 0.93556900895034 0.942710757110266 0.93556900895034 1 - - 40060 Y Y 3.41216628098015 3.60831833727406 3.41216628098015 0 0 0.107756993109918 Y 0 0.979671245930279 N N 5276 2960 ENSG00000169118 ENSG00000166803 - + 15 15 62435495 62460755 utr5p coding CSNK1G1 KIAA0101 62244769 62444266 - - 0 62379910 62456109 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.857009779191151 0.971277749749971 0.971277749749971 0.857009779191151 1 - - 28021 N N 3.48809356209009 3.56488607910057 3.48809356209009 0 0 0.330969805937150 N 0 0 N N 45068 201 ENSG00000205336 ENSG00000173698 + - 16 X 56256445 19050676 upstream intron GPR56 GPR64 56220023 18917348 + - 0 56211646 19034875 + + Y - 3.36503073775745 N HCC1954 22 18.9090909090909 5 33 2 N - - N - SINE 0 1 1 33 0.821301038391519 0.435646637755502 0.821301038391519 0.435646637755502 1 - 0 30538 N Y 3.57489529770476 3.26041677189731 3.26041677189731 249 0 0.0168097883657777 Y 0.988551908784563 0.988551908784563 N N 0 0 ENSG00000208964 ENSG00000209002 - + X X 101951770 101914855 downstream upstream AL590407.8-9 AL035427.17-1 101951702 101914785 + + 0 101958577 101910926 - + N - - N HCC1954 1 1 1 0 2 N - - N SINE - 0.0752688172043011 0 0.0752688172043011 7 0.664182578873142 1.37121564670584 1.37121564670584 0.664182578873142 1 - - 45405 N N 2.995317129762 2.42680847320244 2.42680847320244 0 0.143276036400405 0.238444267496447 N 0.397977755308392 0 N N 20790 5996 ENSG00000099204 ENSG00000187678 - - 10 5 116434404 141684750 utr3p utr3p ABLIM1 SPRY4 116180862 141670189 - - 0.143276036400405 116184048 141671703 + + Y - - N HCC1954 35 34.6 34 5 1 N - - N Simple_repeat - 1 0 1 5 0.299953422716903 0.321378667196682 0.321378667196682 0.299953422716903 1 - - 30344 Y Y 3.59784511035345 3.60785432895764 3.59784511035345 174 0 0.149780584366771 Y 0.988438920074846 0.976877840149693 N N 0 0 ENSG00000188441 ENSG00000182707 - + X X 73168380 73013524 upstream downstream RP13-36G14.2 FXYD8 73168022 73011598 + + 0 73131399 73081002 - + N - - N HCC1954 2 1.77777777777778 1 7 4 N - - Y SINE - 1 0 1 9 0.542772860154395 0.792734045751814 0.792734045751814 0.542772860154395 1 - - 48551 N N 3.52361324642271 3.2965682984157 3.2965682984157 7 0 0.915923064901281 N 0 0 N N 27 850768 ENSG00000184188 ENSG00000075624 + + 5 7 79631912 5536758 coding coding AC026410.5-4 ACTB 79631253 5533313 - - 0 79631390 5534175 - - Y 1.62698094634082 - N HCC1954 2 1.66666666666667 1 4 3 Y - - N - - 0 0 0 6 0.521347615674617 0.39993789695587 0.521347615674617 0.39993789695587 2 0 - 25139 Y Y 3.61633596425197 2.9265652314364 2.9265652314364 347 0 0.00287476510244467 Y 0.951190020354285 0.993027145764898 N N 1066 6669 ENSG00000120688 ENSG00000120690 - - 13 13 40556137 40491450 upstream intron WBP4 ELF1 40533662 40404170 + - 0 40532976 40454420 - + N - 2.87842396206544 N HCC1954 16 1.35526315789474 1 4 1 N - - Y Simple_repeat - 0.242857142857143 0 0.242857142857143 76 1.49976711358451 1.12839620926835 1.49976711358451 1.12839620926835 1 - 0 32851 N Y 2.88274380859372 3.38908332958226 2.88274380859372 0 0 0.800203376264011 N 0.935006723442403 0.913342297923203 N N 1131 45909 ENSG00000214116 ENSG00000073578 - + 3 5 197173943 309794 coding utr3p AC024937.21-2 SDHA 197171055 271439 - + 0 197171354 309570 + + Y - - N HCC1954 8 2.71428571428571 1 4 1 N 78 18.8125 N LINE - 0.597402597402597 0 0.597402597402597 7 0.685607823352921 0.692749571512847 0.692749571512847 0.685607823352921 4 - - 34360 Y Y 3.39384326095097 3.54400240599166 3.39384326095097 244 0 0.0188988085225702 Y 0 0 N N 0 22539 ENSG00000219149 ENSG00000187210 + + 9 9 78354504 78312150 upstream downstream AL161626.20-1 GCNT1 78354018 78263888 - + 0 78357836 78332632 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 0.693333333333333 0.693333333333333 5 0.599906845433805 0.535631111994469 0.599906845433805 0.535631111994469 1 - - 49466 Y Y 3.32679884271949 3.43681151080804 3.32679884271949 0 0 0.976954557951594 Y 0 0 N N 32583 247 ENSG00000131504 ENSG00000214574 + + 5 5 140978806 140872730 coding intron DIAPH1 PCDHGA8 140874767 140751667 - + 0 140883894 140816150 - + N - 0.194212665568841 N HCC1954 7 1.26206896551724 1 22 2 N - - Y - LTR 0 1 1 145 1.4426331283051 1.43549138014518 1.4426331283051 1.43549138014518 4 - 0 41925 N N 3.47552369040616 3.2378376816092 3.2378376816092 0 0 0.750966618581289 Y 0 0 N N 8783 0 ENSG00000147697 ENSG00000221261 + + 8 8 130868316 129231616 coding upstream GSDMC hsa-mir-1208 130829625 129231544 - + 0 130834165 129182494 - + N - - N HCC1954 1 1 1 0 4 N 6 9.04195 N - LTR 0 1 1 4 0.364229156156239 0.28566992639705 0.364229156156239 0.28566992639705 1 - - 2773 N N 3.48167806633553 3.71976530271662 3.48167806633553 1 0 0.478164580405524 N 0.00431034482758619 0 N N 84 23415 ENSG00000214650 ENSG00000168672 - + 11 8 66059237 127639648 coding utr3p AP002748.4-1 FAM84B 66040318 127633871 + - 0 66059198 127635704 - - Y - 0.593161417104792 N HCC1954 37 34 31 4 1 N - - N SINE - 1 0 1 4 0.28566992639705 0.442788385915428 0.442788385915428 0.28566992639705 2 - 0 29115 Y N 3.49938906222957 3.53209488171704 3.49938906222957 0 0 0.324399276072809 Y 0.339130434782609 0.0387351778656129 N N 3388 788 ENSG00000198315 ENSG00000196812 - + 6 6 28233215 28205833 upstream upstream ZNF192 ZNF435 28217695 28200366 + + 0.0387351778656129 28212570 28196355 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.528489363834543 0.792734045751814 0.792734045751814 0.528489363834543 2 - - 12876 N Y 3.4701412644215 3.46704205511183 3.46704205511183 0 0 0.192270790666557 N 0 0.575276603139663 N N 8421 60677 ENSG00000012048 ENSG00000125740 - + 17 19 38530994 50670254 utr5p upstream BRCA1 FOSB 38449840 50663093 - + 0.575276603139663 38530370 50644469 + + Y - - N HCC1954 29 25.1 24 10 1 N - - N SINE SINE 1 1 1 10 0.292811674556976 0.471355378555133 0.471355378555133 0.292811674556976 3 - - 17936 Y Y 3.43465208531242 3.4748918482204 3.43465208531242 244 0 0.0341234252673829 Y 0.5531210592686 0.961696090794452 N N 7645 216 ENSG00000182134 ENSG00000143450 + + 1 1 150030516 150010429 utr3p intron TDRKH OAZ3 150010674 150002236 - + 0 150013482 150009664 - + N - 0.8206275240758 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.357087407996313 0.435646637755502 0.435646637755502 0.357087407996313 1 - 0 4039 Y Y 3.44040523365767 3.48167806633553 3.44040523365767 340 0 0.0165982345154563 Y 0.551323529411765 0.992878151260504 N N 0 1 ENSG00000202035 ENSG00000077800 + + 7 7 72456155 72410577 downstream intron Y_RNA FKBP6 72456054 72380236 - + 0 72452559 72380678 - + N - 1.23376623376623 N HCC1954 9 8.6 3 15 1 N - - Y - - 0 0 0 15 0.885576771830856 0.928427260790413 0.928427260790413 0.885576771830856 3 - 0 291 Y Y 3.35087501109391 3.42936294528359 3.35087501109391 227 0 0.273019536544539 Y 0 0 N N 5 2102 ENSG00000176029 ENSG00000166452 + + 11 11 8911129 8898202 intron utr3p C11orf16 C11orf17 8898200 8889277 - + 0 8900116 8897643 - + N 1.10802231220829 1.19212285352767 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.699891319672773 0.435646637755502 0.699891319672773 0.435646637755502 4 0 0 25783 N Y 3.33168675516419 3.70144228268744 3.33168675516419 280 0 0.00526363540906294 N 0.957778450363196 0.983111380145279 N N 0 0 ENSG00000209951 ENSG00000221151 - - 7 16 86960 88689322 upstream upstream AC097646.2-1 AC133919.3-4 86858 88689218 - - 0 116554 88705392 + + Y - - N HCC1954 144 28.7727272727273 9 22 1 N 143 3.42047 N - SINE 0 1 1 22 1.25694767614702 0.649899082553289 1.25694767614702 0.649899082553289 2 - - 31681 Y Y 3.49896801659482 3.52936639476796 3.49896801659482 0 0 0.436635513639969 Y 0.994169046647627 0.994169046647627 N N 13534 186 ENSG00000017260 ENSG00000212781 - - 3 3 132218243 132070780 coding downstream ATP2C1 AC055733.16 132096124 132070406 + - 0 132131952 132052464 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 63 1.32122340958636 1.2783729206268 1.32122340958636 1.2783729206268 2 - - 12144 N N 3.48064499656564 3.00935843624818 3.00935843624818 0 0 0.155036970620836 N 0 0 N N 505 0 ENSG00000108474 ENSG00000217620 - - 17 8 16170286 103888783 intron upstream PIGL AP003356.2 16061234 103888246 + + 0 16145997 103838036 - - Y 0.996291053936328 - N HCC1954 34 18.6764705882353 7 34 1 N - - N SINE - 1 0 1 34 0.28566992639705 0.714174815992626 0.714174815992626 0.28566992639705 2 0 - 35242 N Y 3.33896748681929 3.55657227767559 3.33896748681929 271 0 0.0125785282608586 N 0 0 N N 2742 3418 ENSG00000196912 ENSG00000177425 + - 2 12 97572761 78608921 utr3p downstream ANKRD36B PAWR 97475562 78509878 - - 0.712927637750954 97487984 78478762 - + Y - - N HCC1954 100 64.5 25 4 1 N - - N SINE SINE 1 0.82051282051282 1 4 0.364229156156239 0.278528178237124 0.364229156156239 0.278528178237124 1 - - 30015 N Y 3.44871903508266 3.63825270713077 3.44871903508266 50 0.231062151502788 0.268939810197482 N 0.143682850537196 0.938834489324085 N N 67499 0 ENSG00000124614 ENSG00000213280 + - 6 7 34501814 127997978 intron intron RPS10 RPS10P15 34493209 127997576 - - 0.938834489324085 34501784 127997925 - + Y 0.3170471100253 1 N HCC1954 11 8.9 5 10 1 N 393 24.9286 N - - 0 0 0 10 0.478497126715059 0.349945659836387 0.478497126715059 0.349945659836387 1 0 0 73 Y Y 3.53312795148693 3.20438413681636 3.20438413681636 220 0 0.0355984734985746 Y 0 0 N N 4525 1952 ENSG00000179119 ENSG00000151116 + - 11 11 18612596 18566857 downstream upstream SPTY2D1 UEVLD 18584527 18509821 - - 0 18581898 18567121 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 13 0.742741808632331 0.828442786551446 0.828442786551446 0.742741808632331 2 - - 43817 N Y 3.40591861909494 3.58441000276898 3.40591861909494 0 0 0.157904659382158 N 0.0187421907538526 0.493544356518117 N N 4519 6142 ENSG00000085415 ENSG00000215153 - + 18 10 12977533 38780939 intron upstream SEH1L AL133216.10-2 12937983 38777208 + + 0.145356101624323 12944554 38774755 - + Y 0.946649041420742 - N HCC1954 40 10 2 5 1 N - - N SINE SINE,DNA 1 0.86046511627907 1 5 0.364229156156239 0.307095170876829 0.364229156156239 0.307095170876829 3 0 - 49052 Y Y 3.48167806633553 3.35257042827311 3.35257042827311 259 0 0.107608579416640 Y 0.278307461980931 0.979670632731857 N N 3639 13832 ENSG00000181904 ENSG00000145833 - + 5 5 134223326 134194708 utr5p utr3p C5orf24 DDX46 134209577 134122360 + + 0 134218487 134192452 - + N 1.0130599673363 21.7257892971794 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 1.18553019454776 0.742741808632331 1.18553019454776 0.742741808632331 4 0 0 32106 N Y 2.30597118160966 2.80981554559588 2.30597118160966 0 0.207714596160811 0.320166154787531 N 0.592538935168417 0.592538935168417 N N 850768 1106 ENSG00000075624 ENSG00000198919 + + 7 3 5536758 109896382 utr3p intron ACTB DZIP3 5533313 109791274 - + 0.592538935168417 5533792 109836923 - + Y 0.965958621896059 - N HCC1954 56 8.7 1 5 1 N - - N Simple_repeat - 0.135 0 0.135 10 1.42834963198525 0.357087407996313 1.42834963198525 0.357087407996313 3 0 - 34333 Y Y 3.40125197368207 3.51310951427856 3.40125197368207 298 0 0.0283609453970577 Y 0.0766383734701935 0.992671733122779 N N 6 3495 ENSG00000167094 ENSG00000136854 - + 9 9 129536272 129494816 intron downstream TTC16 STXBP1 129506775 129414389 + + 0 129517074 129497240 - + N 0.885865257595773 - N HCC1954 16 2.875 1 1 1 N - - Y - Simple_repeat 0 0.539568345323741 0.539568345323741 8 1.06412047582901 0.857009779191151 1.06412047582901 0.857009779191151 1 0 - 39861 Y Y 3.22845095762097 3.40744620240479 3.22845095762097 314 0 0.00526888244123269 Y 0.993264761576863 0.993264761576863 N N 1007 0 ENSG00000128891 ENSG00000223313 + + 15 15 38644544 38609164 intron downstream C15orf57 U6 38632592 38609061 - + 0 38636705 38611791 - + N 0.538183008762087 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 27 1.21409718718746 1.12839620926835 1.21409718718746 1.12839620926835 1 0 - 18171 Y Y 3.30950889246021 3.43465208531242 3.30950889246021 0 0 0.531431813771995 Y 0.402448979591837 0.977868480725624 N N 0 1 ENSG00000217689 ENSG00000127074 - + 1 1 190952401 190896013 downstream upstream RP11-92K2.2 RGS13 190951936 190871869 + + 0 190975144 190863174 - + N - - N HCC1954 2 1.02439024390244 1 1 1 N - - Y LINE,LTR Low_complexity 0.782894736842105 0.0319148936170213 0.782894736842105 41 1.08554572030879 0.671324327033068 1.08554572030879 0.671324327033068 4 - - 67 Y Y 3.49744043328497 3.56911164413597 3.49744043328497 368 0 0.00127432779046543 Y 0.980943644419828 0.993647881473276 N N 0 5225 ENSG00000184669 ENSG00000166689 - - 11 11 17030421 16992535 upstream coding AC116533.11-2 PLEKHA7 17030154 16765791 + - 0 17030153 16992488 - + N - 1.89374881724119 N HCC1954 17 4.58823529411765 1 20 1 N - - Y - Low_complexity 0 0.248520710059172 0.248520710059172 34 1.549759350704 1.20695543902754 1.549759350704 1.20695543902754 1 - 0 42409 Y Y 3.63655728995158 3.58630830843942 3.58630830843942 250 0 0.0421624617884776 Y 0 0 N N 12251 9622 ENSG00000134851 ENSG00000128039 - + 4 4 55987095 55932235 upstream downstream TMEM165 SRD5A2L 55956877 55907166 + + 0 55947267 55943904 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR,LTR DNA 1 0.774193548387097 1 4 0.87843502367093 0.442788385915428 0.87843502367093 0.442788385915428 4 - - 3636 Y Y 3.56335849579072 3.6272104187567 3.56335849579072 4 0 0.852910998555872 Y 0 0 N Y 5041 4793 ENSG00000160221 ENSG00000160220 - + 21 21 44390033 44375490 coding coding C21orf33 PWP2H 44377922 44351636 + + 0 44380370 44372935 - + N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 4 0.578481600954027 0.899860268150708 0.899860268150708 0.578481600954027 4 - - 9634 Y Y 3.22639416565101 3.4446613039166 3.22639416565101 187 0 0.0140354234434454 Y 0 0 N N 29705 2092 ENSG00000108292 ENSG00000179294 - - 17 17 34139557 34084703 intron upstream MLLT6 C17orf96 34115399 34081482 + - 0 34115833 34091903 - + N 0.582869563704414 - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 1 1 6 0.307095170876829 0.528489363834543 0.528489363834543 0.307095170876829 3 0 - 44713 Y Y 3.75016368088976 3.66592259835483 3.66592259835483 245 0 0.0773427777689184 Y 0.989516648764769 0.989516648764769 N N 6 1878 ENSG00000173088 ENSG00000138185 - + 10 10 97783497 97627013 upstream utr3p C10orf131 ENTPD1 97657655 97461526 + + 0 97654579 97626409 - + N - 12.1344362460959 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 11 0.735600060472404 0.899860268150708 0.899860268150708 0.735600060472404 1 - 0 49461 Y Y 3.67849247003875 3.5816815158199 3.5816815158199 0 0 0.893227127406954 Y 0.941428932087857 0.985357233021964 N N 1658 551733 ENSG00000183718 ENSG00000204628 + - 5 5 180620725 180603512 utr3p upstream TRIM52 GNB2L1 180615994 180596536 - - 0 180616792 180606990 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 9 0.39993789695587 0.714174815992626 0.714174815992626 0.39993789695587 1 - - 40933 Y Y 3.60000453584907 3.34256120966892 3.34256120966892 260 0 0.045970175759968 Y 0 0 N N 0 0 ENSG00000210843 ENSG00000210835 - + 20 20 54697157 54675994 downstream upstream AL121920.21-2 AL121920.21-1 54696864 54675893 + + 0 54697245 54668543 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE SINE 1 0.024 1 4 0.592765097273879 0.771308801272036 0.771308801272036 0.592765097273879 2 - - 2561 N N 3.44785379918211 3.38805025981237 3.38805025981237 33 0.142138686442484 0.108862968941262 N 0.0916762562332182 0.179985509099433 N N 936 10477 ENSG00000151338 ENSG00000213593 - + 14 11 37090214 57265020 downstream intron MIPOL1 TMX2 36736907 57236618 + + 0.179985509099433 37105946 57241679 - + Y - 1.02580969506116 N HCC1954 24 21.6 20 5 1 N - - N SINE Other 1 1 1 5 0.721316564152552 0.671324327033068 0.721316564152552 0.671324327033068 1 - 0 48201 N N 2.55674721891456 2.89848053225909 2.55674721891456 0 0.539094650205761 0.0875090260083605 N 0.553497942386831 0.539094650205761 N N 19184 78560 ENSG00000083312 ENSG00000112493 - + 5 6 72248316 33390114 utr3p utr3p TNPO1 TAPBP 72148171 33375449 + - 0.539094650205761 72247685 33377413 - - Y - - N HCC1954 32 29 25 4 1 N - - N SINE LINE 1 1 1 4 0.39993789695587 0.864151527351077 0.864151527351077 0.39993789695587 4 - - 44657 Y Y 3.17142510556349 3.61360747730288 3.17142510556349 0 0 0.554212929882 Y 0.994064199495954 0.994064199495954 N N 0 3919 ENSG00000222374 ENSG00000150054 - - 10 10 28639894 28611073 upstream intron AC022021.10-3 MPP7 28639788 28379928 + - 0 28631798 28567672 - + N - 33.4492517318265 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 84 1.42834963198525 1.20695543902754 1.42834963198525 1.20695543902754 1 - 0 43991 N Y 3.51782959285392 3.53615261288309 3.51782959285392 3 0 0.106207414038972 N 0.00325732899022813 0.838762214983713 N N 75177 2242 ENSG00000125107 ENSG00000107968 + + 16 10 57221251 30790768 utr5p intron CNOT1 MAP3K8 57111359 30762872 - + 0 57190783 30781314 - + Y - 2.94400210490786 N HCC1954 21 20.3333333333333 20 6 1 N - - N - SINE 0 1 1 6 0.371370904316165 0.321378667196682 0.371370904316165 0.321378667196682 2 - 0 48558 N N 3.59425138750382 3.15678909433978 3.15678909433978 0 0.258585293019784 0.375365134007032 N 0.311543486375513 0.0785274356103024 N N 0 28646 ENSG00000209202 ENSG00000164880 + + 5 7 119701247 1510772 downstream coding AC113418.2 INTS1 119701143 1476439 - - 0.0785274356103024 119546918 1499960 - - Y - - N HCC1954 7 3.25 1 7 1 N - - N LINE - 1 0 1 8 0.407079645115797 0.892718519990782 0.892718519990782 0.407079645115797 1 - - 26843 Y Y 3.51525959220437 3.75744441254485 3.51525959220437 283 0 0.066395209393297 Y 0 0.992882382635033 N N 3394 1124 ENSG00000140961 ENSG00000103150 - + 16 16 82557438 82507286 upstream coding OSGIN1 MLYCD 82540173 82490231 + + 0 82536335 82503470 - + N - 1.29009389519488 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.814159290231593 0.956994253430118 0.956994253430118 0.814159290231593 2 - 0 36841 N N 3.36295036923788 3.20972671000768 3.20972671000768 20 0 0.775580979437189 N 0 0.0409043581734343 N N 173971 0 ENSG00000170421 ENSG00000199285 + + 12 14 51585127 38526338 utr3p upstream KRT8P9 Y_RNA 51577238 38526231 - + 0.0409043581734343 51577374 38267556 - + Y 0.522472643493426 - N HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.39993789695587 0.271386430077198 0.39993789695587 0.271386430077198 2 0 - 327 Y Y 3.44615838200292 3.82232940528072 3.44615838200292 153 0 0.0230430454300481 Y 0 0.958022645677989 N N 9875 47 ENSG00000189057 ENSG00000166840 - + 11 11 58651443 58481092 upstream downstream FAM111B GLYATL1 58631286 58451750 + + 0 58577528 58546165 - + N - - N HCC1954 2 1.25 1 1 1 N - - Y - SINE 0 1 1 4 0.728458312312478 0.51420586751469 0.728458312312478 0.51420586751469 2 - - 24673 Y Y 3.85425536676371 3.58271458558979 3.58271458558979 11 0.0300393272529494 0.916381936963574 Y 0.993264161994812 0.993264161994812 N N 4163 124 ENSG00000141644 ENSG00000172361 + - 18 18 46062142 46046863 coding upstream MBD1 CCDC11 46049215 46007564 - - 0 46053043 46048029 - + N - - N HCC1954 1 1 1 0 3 N - - Y DNA - 0.0109289617486339 0 0.0109289617486339 26 1.24266417982717 1.10697096478857 1.24266417982717 1.10697096478857 3 - - 49186 N Y 3.67320333000993 3.09462324098319 3.09462324098319 0 0 0.467065763109939 Y 0.993568177320404 0.980704531961211 N N 397 4794 ENSG00000145779 ENSG00000172869 - + 5 5 118756975 118612721 coding downstream TNFAIP8 DMXL1 118752897 118434983 + + 0 118756410 118632501 - + N - - N HCC1954 1 1 1 0 1 N - - N LINE - 0.0172413793103448 0 0.0172413793103448 184 1.24266417982717 1.12125446110842 1.24266417982717 1.12125446110842 4 - - 48906 N N 3.64809409186561 3.33528047801382 3.33528047801382 0 0 0.783570645209818 Y 0 0 N N 19497 193 ENSG00000134970 ENSG00000080709 + + 5 5 114989757 113860096 intron intron TICAM2 KCNN2 114942238 113725565 - + 0 114989194 113811263 - + N 0.297252844097792 5.30673728194955 N HCC1954 1 1 1 0 2 N 242 8.77589 N - - 0 0 0 76 1.28551466878673 1.24980592798709 1.28551466878673 1.24980592798709 0 0 0 39547 N N 3.54144175291192 3.29231222815676 3.29231222815676 5 0 0.0598949588749673 N 0 0 N N 11826 18 ENSG00000137313 ENSG00000214896 + + 6 15 30289183 50965962 utr3p upstream TRIM26 RPSAP55 30260211 50963988 - + 0 30260227 50948944 - + Y 0.142297036188965 - N HCC1954 1 1 1 0 1 N - - N LINE LINE 1 1 1 5 0.657040830713216 0.257102933757345 0.657040830713216 0.257102933757345 1 0 - 35169 N Y 2.86791432021661 2.82404098166565 2.82404098166565 10 0 0.0333383397811297 N 0 0.0448028673835126 N N 1673 1084 ENSG00000212774 ENSG00000023697 - + 7 12 23644794 16081581 coding upstream AC006026.2-1 DERA 23643291 16000968 - + 0.0448028673835126 23644441 15990785 + + Y - - N HCC1954 414 280 21 8 1 N - - N Other LINE 1 1 1 8 0.45707188223528 0.307095170876829 0.45707188223528 0.307095170876829 2 - - 1603 N Y 3.07101108092519 3.62039369541802 3.07101108092519 8 0 0.417016021721022 N 0.874197689345314 0.895164741121095 N N 1649619 2298 ENSG00000141736 ENSG00000133818 - - 17 11 35138441 14337305 coding upstream ERBB2 RRAS2 35104766 14256042 + - 0 35125066 14382842 - + Y - - N HCC1954 21 18 2 9 1 N - - N - SINE 0 1 1 9 0.87843502367093 0.449930134075354 0.87843502367093 0.449930134075354 1 - - 27166 N N 3.65760879692984 3.6272104187567 3.6272104187567 0 0 0.0470200336078562 N 0.658181179775281 0.658181179775281 N N 24 6328 ENSG00000140678 ENSG00000167508 - + 16 16 31301819 87257019 utr3p coding ITGAX MVD 31274010 87245849 + - 0 31301118 87252606 - - N - - Y HCC1954 35 28.5833333333333 21 12 1 N 121 22.1599 N SINE - 1 0 1 12 0.34280391167646 0.614190341753658 0.614190341753658 0.34280391167646 2 - - 16931 N Y 3.64400585547602 3.07101108092519 3.07101108092519 8 0.00369003690036906 0.284511864501132 N 0.862212451911753 0.894009578393656 N N 4498 1649619 ENSG00000117222 ENSG00000141736 - - 1 17 203357766 35138441 utr3p coding RBBP5 ERBB2 203314400 35104766 - + 0 203322131 35125066 + - Y - - N HCC1954 28 23.8589743589744 2 78 1 N 613 26.5117 N SINE - 1 0 1 78 0.428504889595575 1.19981369086761 1.19981369086761 0.428504889595575 1 - - 13476 N Y 3.49793494682493 3.62770493229666 3.49793494682493 0 0.362591093117409 0.515435091198721 N 0.38251012145749 0.661376518218624 N N 1414 0 ENSG00000100336 ENSG00000220215 + + 22 7 34930825 156119199 utr3p upstream APOL4 AC005534.6 34915123 156118810 - + 0.362591093117409 34916432 156076989 - + Y - - N HCC1954 21 20.75 20 4 1 N - - N LTR LTR,LTR 1 1 1 4 0.349945659836387 0.314236919036755 0.349945659836387 0.314236919036755 1 - - 10218 Y Y 3.40744620240479 3.41166241987037 3.40744620240479 324 0 0.00269145550790417 Y 0.993264097430764 0.993264097430764 N N 6028 48 ENSG00000196704 ENSG00000183600 - + 17 17 63776634 63708031 utr5p downstream AMZ2 AC005332.1-3 63755740 63706572 + + 0 63756440 63713972 - + N - - N HCC1954 3 1.4 1 3 1 N - - Y - Low_complexity 0 0.421621621621622 0.421621621621622 10 1.09268746846872 1.18553019454776 1.18553019454776 1.09268746846872 1 - - 104 Y Y 3.34512186274866 3.58337693299909 3.34512186274866 360 0 0.0115489842281863 Y 0.654296296296296 0.993351851851852 N N 10802 1147 ENSG00000221844 ENSG00000174516 - + 11 11 66033706 66001381 upstream intron DPP3 PELI3 66004456 65990912 + + 0 66004089 65999154 - + N - 1.51725961488016 N HCC1954 20 2.46153846153846 1 2 1 N - - Y - SINE,SINE 0 0.529032258064516 0.529032258064516 26 1.549759350704 1.10697096478857 1.549759350704 1.10697096478857 1 - 0 9415 Y Y 3.31336373513502 3.18871505582277 3.18871505582277 300 0 0.00287749825781358 Y 0.117704918032787 0.983661202185793 N N 15759 7339 ENSG00000108312 ENSG00000087152 + - 17 17 39653776 39631055 upstream upstream UBTF ATXN7L3 39637928 39624700 - - 0 39655299 39631774 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 34 1.05697872766909 0.842726282871298 1.05697872766909 0.842726282871298 1 - - 8831 N Y 3.23739660123173 3.72551845106187 3.23739660123173 0 0 0.343854734740364 N 0.347282347282347 0 N N 313916 18846 ENSG00000131748 ENSG00000138095 + - 17 2 35073248 44076648 utr5p intron STARD3 LRPPRC 35046938 43968391 + - 0 35047010 44049889 + + Y 1.09044475696202 0.816023041121228 N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.592765097273879 0.314236919036755 0.592765097273879 0.314236919036755 4 0 0 5239 N N 2.49231235839227 2.89362312503792 2.49231235839227 7 0 0.0566422694367533 N 0.757144352559405 0 N N 12 3405 ENSG00000188394 ENSG00000170632 - + 9 7 124837796 102527432 intron utr3p GPR21 ARMC10 124836627 102502564 + + 0.0771485397257408 124837764 102527276 - + Y - - N HCC1954 972 799 532 4 1 N - - N Simple_repeat SINE 0.840909090909091 1 1 4 0.314236919036755 0.478497126715059 0.478497126715059 0.314236919036755 2 - - 19199 N Y 3.51104337473878 3.48167806633553 3.48167806633553 302 0 0.0137000789649551 N 0.985962130398284 0.992981065199142 N N 0 454 ENSG00000208674 ENSG00000215863 + + 1 1 147939600 142535935 downstream coding AL358813.13-2 BX284650.8-1 147939529 142439162 - - 0 147938928 142455717 - - N - - Y HCC1954 12 9.35714285714286 2 14 1 N - - N - - 0 0 0 14 1.12125446110842 1.17124669822791 1.17124669822791 1.12125446110842 1 - - 4371 N Y 3.43614916339873 2.55080478331253 2.55080478331253 0 0 0.462264623227172 N 0.931808581256412 0.945446865005129 Y N 7862 0 ENSG00000091073 ENSG00000196898 - - 7 7 75973241 76436410 intron upstream DTX2 AC114737.3-1 75928954 76435514 + - 0 75947671 76442537 - + N 0.546186459524847 - N HCC1954 2 1.6 1 3 2 N 249 9.15227 N - Simple_repeat 0 0.62 0.62 5 0.721316564152552 0.357087407996313 0.721316564152552 0.357087407996313 1 0 - 10452 Y Y 3.42316871656087 3.48383749183115 3.42316871656087 0 0 0.391402446211348 Y 0.99373034591195 0.987460691823899 N N 182 0 ENSG00000188825 ENSG00000222250 + - 17 17 38822096 38800981 coding upstream AC087650.12-3 U2 38810460 38800793 - - 0 38810565 38804320 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE LINE 0.0609756097560976 1 1 9 1.1426797055882 0.942710757110266 1.1426797055882 0.942710757110266 4 - - 31936 Y Y 3.50525037360018 3.34785034969775 3.34785034969775 0 0 0.846033783574843 Y 0 0.990410673337503 N N 4437 873 ENSG00000126062 ENSG00000114395 + + 3 3 50371943 50366477 coding coding TMEM115 CYB561D2 50367186 50363301 - + 0 50367934 50363995 - + N - 0.656793950283327 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.599906845433805 0.51420586751469 0.599906845433805 0.51420586751469 3 - 0 159 Y Y 3.33528047801382 3.44615838200292 3.33528047801382 292 0 0.0463027380577914 Y 0 0.992274609748327 N N 745 9059 ENSG00000149485 ENSG00000168496 + + 11 11 61340886 61321284 intron utr5p FADS1 FEN1 61323679 61316726 - + 0 61333415 61317073 - + N 0.800607890108977 0.363538864217911 N HCC1954 1 1 1 0 2 N - - Y SINE - 0.822695035460993 0 0.822695035460993 6 0.885576771830856 0.678466075192994 0.885576771830856 0.678466075192994 1 0 0 23159 N N 3.24359082995445 3.45868840089349 3.24359082995445 24 0 0.501419538145586 N 0 0.0642929715515179 N N 0 282831 ENSG00000212679 ENSG00000099194 - + 1 10 559619 102114577 intron coding RP5-857K21.10 SCD 558939 102096762 + + 0.0642929715515179 559619 102097946 - + Y 1 - N HCC1954 4 2.33333333333333 2 6 1 N - - N - - 0 0 0 6 0.771308801272036 1.03555348318931 1.03555348318931 0.771308801272036 2 0 - 33118 N N 2.87266909391212 3.03482904918326 2.87266909391212 3 0.0347727272727273 0.222994379241869 N 0.0347727272727273 0.0347727272727273 Y N 275222 171855 ENSG00000198763 ENSG00000198886 - + MT MT 5512 12138 coding coding MT-ND2 MT-ND4 4471 10761 + + 0.0347727272727273 5291 12063 - + N 1.01674672186686 3.64404823230828 N HCC1954 4 1.875 1 5 1 Y 106 8.09281 N - - 0 0 0 8 0.292811674556976 0.585623349113953 0.585623349113953 0.292811674556976 1 0 0 33353 N N 3.47911741325579 2.98933999903981 2.98933999903981 5 0 0.99993844630267 N 0 0.0187932739861523 Y N 544065 247001 ENSG00000198744 ENSG00000198786 - + MT MT 9988 14149 coding coding MT-CO3 MT-ND5 8367 12338 + + 0.0187932739861523 8756 13901 - + N - 1.10433892238253 N HCC1954 2 2 2 4 10 N 189 4.09957 N - - 0 0 0 4 0.378512652476092 1.12125446110842 1.12125446110842 0.378512652476092 1 - 0 38679 N Y 3.34458749641535 3.87361145656277 3.34458749641535 1 0 0.0674438984603735 N 0.833967046894804 0.858871989860583 N N 0 2963 ENSG00000213766 ENSG00000133983 + + 8 14 93225728 69896147 downstream coding AC104339.10-1 COX16 93225660 69680762 - - 0 93204079 69895990 - - Y - 0.802254886786784 N HCC1954 20 20 20 4 1 N - - N SINE - 1 0 1 4 0.349945659836387 0.421363141435649 0.421363141435649 0.349945659836387 1 - 0 34442 Y Y 3.19806192701765 3.05206556628006 3.05206556628006 395 0 0.000940826701995467 Y 0 0 N N 20685 0 ENSG00000070214 ENSG00000205741 - - 9 9 107241273 106988859 intron upstream SLC44A1 RP11-112N13.1 107046724 106984582 + - 0 107047122 107001655 - + N 0.578924537299816 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.51420586751469 0.485638874874985 0.51420586751469 0.485638874874985 2 0 - 21845 N N 3.58337693299909 3.60103760561896 3.58337693299909 0 0 0.0476664148485274 N 0 0 N N 6180 0 ENSG00000176915 ENSG00000207623 + - 12 1 131848524 207672210 intron upstream ANKLE2 hsa-mir-205 131812328 207672101 - + 0 131815549 207670394 - - Y 0.405896106492869 - N HCC1954 35 19.2857142857143 6 14 1 N - - N SINE - 1 0 1 14 0.392796148795944 0.478497126715059 0.478497126715059 0.392796148795944 1 0 - 47 Y Y 3.55297855482595 3.47695798776018 3.47695798776018 313 0 0.832956222182647 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.99208884831888 1816504 1814664 - + N - 0.679260286911601 N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 60 1.32122340958636 0.971277749749971 1.32122340958636 0.971277749749971 1 - 0 40027 Y Y 3.38230645903694 3.39487633072086 3.38230645903694 95 0 0.384120755432925 Y 0 0.990862239116927 N N 2960 2047 ENSG00000166803 ENSG00000103671 - - 15 15 62460755 62534530 coding upstream KIAA0101 TRIP4 62444266 62467073 - + 0 62460580 62466716 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 13 0.914143764470561 0.828442786551446 0.914143764470561 0.828442786551446 2 - - 4540 Y Y 3.69937614314766 3.64656650855576 3.64656650855576 1 0 0.67738658690926 Y 0.112483969616257 0.990850350202229 N N 36 2583 ENSG00000214173 ENSG00000135245 - + 7 7 127896489 127885707 coding coding AC010655.7-2 C7orf68 127893850 127883120 + + 0 127893851 127884587 - + N 0.139947628745999 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 7 0.692749571512847 0.785592297591888 0.785592297591888 0.692749571512847 2 0 - 5332 N Y 3.48440655328462 2.90397256077916 2.90397256077916 0 0 0.564219379547068 N 0 0.917921568627451 N N 1 13029 ENSG00000169659 ENSG00000124664 + - 2 6 106374599 34632069 upstream intron PLGLA1 SPDEF 106364994 34613558 + - 0 106327962 34620241 + + Y - 1.59566412409274 N HCC1954 2 2 2 35 1 N - - N - - 0 0 0 35 0.607048593593732 1.34264865406614 1.34264865406614 0.607048593593732 1 - 0 1017 N Y 3.64081336021051 3.67849247003875 3.64081336021051 1 0 0.848429072059281 N 0.351441860465116 0.942093023255814 N N 81 3301 ENSG00000214248 ENSG00000070081 - - 7 11 100913300 17309646 coding coding AC004965.2 NUCB2 100906891 17254860 + + 0 100907044 17273447 - - Y - - N HCC1954 35 26.25 21 8 1 N - - N SINE - 1 0 1 8 0.39993789695587 0.499922371194838 0.499922371194838 0.39993789695587 4 - - 10331 Y Y 3.19247661254175 3.33424740824393 3.19247661254175 247 0.0354814814814814 0.999995631287027 Y 0.0354814814814814 0 N N 443941 20747 ENSG00000172057 ENSG00000073605 + - 17 17 35337380 35328429 utr3p intron ORMDL3 GSDMB 35330822 35314374 - - 0 35332229 35327757 - + N - 9.44764878355004 N HCC1954 1 1 1 0 14 N - - Y - LTR 0 0.141242937853107 0.141242937853107 8 1.21409718718746 1.07840397214886 1.21409718718746 1.07840397214886 2 - 0 41751 N N 3.71617157986699 3.54296933622177 3.54296933622177 1 0 0.883034847214738 N 0 0 N Y 19339 8537 ENSG00000177570 ENSG00000129292 - + 8 8 119703365 133930234 coding coding SAMD12 PHF20L1 119270880 133856786 - + 0 119279152 133886167 + + N - 7.62810223615346 Y HCC1954 1 1 1 0 1 N 252 7.30508 N - - 0 0 0 195 1.35693215038599 0.999844742389676 1.35693215038599 0.999844742389676 4 - 0 34582 Y Y 3.57489529770476 3.329991337985 3.329991337985 129 0 0.0674871537010846 Y 0.986153455284553 0.993076727642276 N N 16658 15197 ENSG00000136930 ENSG00000119408 + + 9 9 126217542 126155407 intron coding PSMB7 NEK6 126155566 126059706 - + 0 126177869 126149921 - + N 0.945414057446564 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 6 0.956994253430118 1.09268746846872 1.09268746846872 0.956994253430118 1 0 - 33004 N Y 3.08511788348878 3.55913293075533 3.08511788348878 503 0 0.000951516006912123 Y 0 0.995336392857806 N N 59837 171855 ENSG00000198695 ENSG00000198886 + + MT MT 14674 12138 coding coding MT-ND6 MT-ND4 14150 10761 - + 0.435703535794578 14595 11942 - + N 1.79058182994885 1.89465916999389 N HCC1954 2 1.2 1 1 2 N - - N - - 0 0 0 5 0.757025304952183 0.921285512630487 0.921285512630487 0.757025304952183 2 0 0 21114 N N 3.03276290964348 3.56129235625094 3.03276290964348 0 0 0.329188335056003 N 0 0 N N 53009 2 ENSG00000131236 ENSG00000185008 + + 1 3 40310908 77779351 coding intron CAP1 ROBO2 40278492 76069335 + + 0 40308069 76566633 + + Y - 0.970242214532872 N HCC1954 2 1.2 1 1 1 N - - N - - 0 0 0 5 0.5713398527941 0.28566992639705 0.5713398527941 0.28566992639705 2 - 0 10637 N Y 3.54975555433691 3.45612774781375 3.45612774781375 0 0 0.3897712618592 N 0 0.826162628794208 N N 42814 13271 ENSG00000170315 ENSG00000081923 - - 17 18 16226779 53550037 downstream upstream UBB ATP8B1 16225092 53464656 + - 0 16239363 53550060 - + Y - - N HCC1954 6 4 1 3 1 N 386 21.0755 N SINE - 1 0 1 4 0.307095170876829 0.378512652476092 0.378512652476092 0.307095170876829 1 - - 27198 Y Y 3.60888739872753 3.63825270713077 3.60888739872753 87 0 0.625948471862319 Y 0.983393719806763 0.983393719806763 N Y 50387 29027 ENSG00000134419 ENSG00000170540 - + 16 16 18709157 18720367 utr5p coding RPS15A ARL6IP1 18701779 18710492 - - 0 18707941 18713422 + - N - - N HCC1954 3 1.75 1 2 1 Y - - Y - - 0 0 0 4 0.742741808632331 0.585623349113953 0.742741808632331 0.585623349113953 4 - - 31759 Y Y 3.37295958784206 3.5010341561346 3.37295958784206 2 0 0.993666420557434 Y 0 0.984424603174603 N N 6749 46 ENSG00000118855 ENSG00000214217 - + 3 3 160030198 159943998 coding downstream MFSD1 AC080013.17 160002606 159940900 + + 0 160004802 159948532 - + N - - N HCC1954 2 1.25 1 2 3 N - - Y - LTR 0 1 1 8 1.0069864905496 0.942710757110266 1.0069864905496 0.942710757110266 4 - - 40376 N N 3.66592259835483 3.24209375186814 3.24209375186814 5 0 0.246774326684796 N 0 0 N N 7644 3154 ENSG00000028528 ENSG00000204604 - + 15 19 62223486 58119222 utr3p coding SNX1 ZNF468 62175230 58033598 + - 0 62219941 58037124 - - Y - - N HCC1954 294 165.6 21 5 1 N - - N SINE - 1 0 1 5 0.278528178237124 0.699891319672773 0.699891319672773 0.278528178237124 3 - - 38480 Y N 3.44040523365767 3.49528100778935 3.44040523365767 21 0.239572192513369 0.0961134284473307 Y 0.239572192513369 0.239572192513369 N N 10952 931 ENSG00000184916 ENSG00000183828 - + 14 14 104706206 104718686 coding coding JAG2 NUDT14 104679121 104710321 - - 0.239572192513369 104695114 104714008 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.28551466878673 0.928427260790413 1.28551466878673 0.928427260790413 2 - - 40109 Y Y 3.35616415112274 3.65128658713112 3.35616415112274 0 0 0.984866287239892 Y 0 0.940799689440994 N Y 524 1874 ENSG00000203289 ENSG00000187951 - + 15 15 28848794 28765101 utr5p utr3p AC004460.1-2 ARHGAP11B 28795810 28705695 + + 0 28828071 28727209 - + N - - N HCC1954 2 1.18181818181818 1 2 3 N - - Y - DNA 0 0.0410958904109589 0.0410958904109589 11 0.821301038391519 0.521347615674617 0.821301038391519 0.521347615674617 4 - - 41445 N Y 3.60785432895764 3.28296535696188 3.28296535696188 0 0 0.825411825479424 Y 0.599942073060353 0.987690525324934 N N 1572 2561 ENSG00000155792 ENSG00000136982 - - 8 8 121131937 120937330 upstream utr5p DEPDC6 DSCC1 120955143 120915398 + - 0 120950084 120937300 - + N - 3.96449298624662 N HCC1954 16 2.5 1 4 1 N - - N LTR - 1 0 1 30 1.19267194270768 1.29979816510658 1.29979816510658 1.19267194270768 4 - 0 25323 N N 3.31804396091703 3.63465898428114 3.31804396091703 0 0 0.0436069057777525 N 0 0 N N 23303 7 ENSG00000136149 ENSG00000144847 + + 13 3 53913472 120347588 upstream utr5p RPL13AP20 IGSF11 53912798 120102173 - - 0 54053779 120314244 - - Y - - N HCC1954 23 22.125 22 8 1 N - - N LTR LINE 1 1 1 8 0.864151527351077 0.299953422716903 0.864151527351077 0.299953422716903 1 - - 9073 N N 3.07101108092519 3.62977107183644 3.07101108092519 0 0 0.344262898555104 N 0.169835234474018 0 N N 1649619 277 ENSG00000141736 ENSG00000135960 - + 17 2 35138441 108972260 coding upstream ERBB2 EDAR 35104766 108877359 + - 0 35125066 109080066 - - Y - - N HCC1954 17 2.4375 1 9 1 N - - N - SINE 0 1 1 32 0.692749571512847 0.28566992639705 0.692749571512847 0.28566992639705 1 - - 46751 Y Y 3.20487865035632 3.45720067037699 3.20487865035632 68 0 0.0408486341644805 Y 0 0.492525252525252 N N 10334 20161 ENSG00000170892 ENSG00000125505 - - 19 19 59389337 59385478 intron utr5p TSEN34 LENG4 59386009 59368921 + - 0.492525252525252 59386870 59385159 - + N 0.0465702667382263 3.21479186618807 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.778450549431962 0.721316564152552 0.778450549431962 0.721316564152552 1 0 0 9976 Y Y 3.58424216889964 3.3070415253363 3.3070415253363 317 0 0.99999777509981 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 utr5p utr3p GSDMB ORMDL3 35314374 35330822 - - 0 35327099 35331925 + - N - - N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 69 1.57118459518378 1.1426797055882 1.57118459518378 1.1426797055882 1 - - 31349 Y Y 3.56911164413597 3.23846952379497 3.23846952379497 428 0 0.00151461689150800 Y 0 0.993023331808378 N N 1844 1031 ENSG00000179021 ENSG00000175105 - + 3 3 88289801 88276504 upstream intron C3orf38 ZNF654 88281583 88270952 + + 0 88281219 88272900 - + N - 2.30081462380602 N HCC1954 2 1.25 1 1 2 N - - Y - - 0 0 0 4 0.542772860154395 0.542772860154395 0.542772860154395 0.542772860154395 1 - 0 36984 N N 3.72146071989581 3.65016023140539 3.65016023140539 11 0.233509234828496 0.245190933294465 N 0.0395778364116096 0.00263852242744056 N N 0 712661 ENSG00000183663 ENSG00000111640 + + 8 12 97151085 6517797 intron coding AC007992.12 GAPDH 97150133 6513918 - + 0.298153034300791 97150577 6517033 - + Y 1 - N HCC1954 7 2.1 1 5 1 N - - N - - 0 0 0 10 0.51420586751469 1.03555348318931 1.03555348318931 0.51420586751469 1 0 - 2164 N N 3.55041790174621 3.69462555934877 3.55041790174621 17 0.0302220927220925 0.131237461678391 N 0.0302220927220925 0.0720830095830096 N N 152129 0 ENSG00000109971 ENSG00000168875 + + 11 3 122438054 138967086 coding downstream HSPA8 SOX14 122433413 138966269 - + 0.0720830095830096 122434686 139083245 - + Y - - N HCC1954 2 1.5 1 2 1 N - - N - - 0 0 0 4 0.34280391167646 0.321378667196682 0.34280391167646 0.321378667196682 1 - - 23656 N Y 3.61360747730288 3.5016965035439 3.5016965035439 0 0 0.0457414183840383 N 0 0 N N 49089 23 ENSG00000117450 ENSG00000173809 - + 1 19 45760196 37998367 coding intron PRDX1 TDRD12 45749295 37902499 - + 0 45757256 37920826 + + Y - 0.715625339536354 N HCC1954 40 20.6086956521739 16 23 1 N - - N - SINE 0 1 1 23 0.792734045751814 0.314236919036755 0.792734045751814 0.314236919036755 1 - 0 28268 N Y 3.25099954268554 3.0066299492991 3.0066299492991 298 0 0.00110290349615427 N 0.671990485090477 0.810763741398352 N N 0 0 ENSG00000207986 ENSG00000207985 + - 16 20 33869267 26136914 upstream upstream AC136932.4-2 hsa-mir-663 33869153 26136822 + - 0.810763741398352 33868977 26137104 + + Y - - N HCC1954 1 1 1 0 1 N 588 9.57492 N - - 0 0 0 14 0.414221393275723 0.51420586751469 0.51420586751469 0.414221393275723 1 - - 33778 N N 2.80150174417089 3.48374420587532 2.80150174417089 0 0 0.999657910477623 N 0 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8463 15843 - + N - 2.51112346367471 N HCC1954 2 1.3 1 3 8 N - - N - - 0 0 0 10 0.721316564152552 0.921285512630487 0.921285512630487 0.721316564152552 2 - 0 13126 N Y 3.56129235625094 3.38599346784241 3.38599346784241 31 0 0.0632700254133333 N 0.149012010848508 0.0818287485470747 N N 1410 317991 ENSG00000183323 ENSG00000171346 - + 5 17 68664392 36932191 utr3p intron CCDC125 KRT15 68612278 36923523 - - 0 68614028 36924805 + - Y - 1.61822492111163 N HCC1954 32 30.75 29 4 1 N - - N SINE SINE 1 0.18 1 4 0.264244681917271 0.357087407996313 0.357087407996313 0.264244681917271 1 - 0 44997 Y Y 3.67423639977982 3.53296011761759 3.53296011761759 235 0 0.408438269261866 Y 0 0 N N 828 4690 ENSG00000138347 ENSG00000148634 - - 10 10 69641464 69505109 coding upstream MYPN HERC4 69535918 69351663 + - 0 69572705 69517757 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 7 0.585623349113953 0.728458312312478 0.728458312312478 0.585623349113953 1 - - 36409 Y N 3.49777964526717 3.64656650855576 3.49777964526717 0 0.293924466338259 0.244767210786960 Y 0.293924466338259 0.293924466338259 N N 1758 1574 ENSG00000139624 ENSG00000178449 + + 12 12 48847412 48800501 downstream utr5p LASS5 C12orf62 48809875 48792167 - + 0.293924466338259 48809703 48792297 - + N - 0.209781386919918 N HCC1954 1 1 1 0 2 N - - Y SINE - 0.261904761904762 0 0.261904761904762 4 0.5713398527941 0.592765097273879 0.592765097273879 0.5713398527941 2 - 0 31340 Y Y 3.53209488171704 3.06736392491307 3.06736392491307 279 0 0.00935569261454605 Y 0 0.991899058775534 N N 100806 0 ENSG00000163931 ENSG00000222060 + + 3 3 53265078 53219102 downstream downstream TKT AC097015.2-2 53234715 53219009 - + 0 53229043 53220906 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR 0 1 1 4 0.635615586233437 0.664182578873142 0.664182578873142 0.635615586233437 1 - - 47119 Y Y 3.54975555433691 3.54400240599166 3.54400240599166 294 0 0.553133872338303 Y 0 0.982203595724004 N N 2469 421 ENSG00000142252 ENSG00000170684 - - 19 19 50286622 50271528 utr5p coding GEMIN7 ZNF296 50274370 50266599 + - 0 50285205 50270920 - + N 0.944343774497746 1.56268899744127 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 15 0.814159290231593 1.2783729206268 1.2783729206268 0.814159290231593 4 0 0 46888 Y Y 3.37651345789834 3.1158869840225 3.1158869840225 327 0 0.0107294930059531 Y 0 0.826618800691397 N N 22 5830 ENSG00000174788 ENSG00000076924 + - 19 19 7604636 7600439 downstream upstream PCP2 XAB2 7602509 7590412 - - 0.826618800691397 7602357 7600873 - + N - - N HCC1954 2 1.18181818181818 1 10 2 N - - Y - - 0 0 0 55 0.857009779191151 0.471355378555133 0.857009779191151 0.471355378555133 2 - - 43690 N Y 3.13073491470822 3.09504739650626 3.09504739650626 0 0 0.625952588720361 N 0.935437323493641 0.94261095421657 N N 4310 559 ENSG00000183011 ENSG00000108187 - - 17 10 7701897 69762690 coding downstream LSMD1 PBLD 7700730 69712423 - - 0.00286532951289409 7701243 69709080 + + Y 11.8312907194667 - N HCC1954 4 1.75373134328358 1 56 1 N - - N - - 0 0 0 134 1.02841173502938 0.999844742389676 1.02841173502938 0.999844742389676 2 0 - 48066 N N 3.52361324642271 3.20024908666147 3.20024908666147 0 0 0.078486283306306 N 0 0 N N 19339 0 ENSG00000177570 ENSG00000170549 - + 8 5 119703365 3654517 upstream upstream SAMD12 IRX1 119270880 3649168 - + 0 119845989 3260997 + + Y - - N HCC1954 1 1 1 0 1 N 287 4.21238 N LTR LINE 1 1 1 6 0.549914608314322 0.642757334393363 0.642757334393363 0.549914608314322 2 - - 266 Y Y 3.11543655607521 3.39487633072086 3.11543655607521 326 0 0.156567155114864 Y 0.993218146154167 0.986436292308334 N N 8 13917 ENSG00000150676 ENSG00000137501 - - 11 11 85308699 85146692 upstream coding CCDC83 SYTL2 85243792 85082915 + - 0 85199645 85137114 - + N - 0.827413164395625 N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 14 1.02126998686945 0.914143764470561 1.02126998686945 0.914143764470561 4 - 0 33104 N N 2.98272161479402 3.28569384391097 2.98272161479402 0 0 0.99995896818028 N 0.0595888720425938 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8408 15658 - + N 1.00286059173194 1.51968490524322 N HCC1954 2 1.15 1 3 8 Y 189 4.09957 N - - 0 0 0 20 1.19267194270768 1.61403508414333 1.61403508414333 1.19267194270768 3 0 0 35954 N N 3.19975734419684 3.17784060131804 3.17784060131804 2 0 0.158481334975018 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000216624 + + 12 6 6517797 166398773 utr3p downstream GAPDH RP11-459F1.3 6513918 166397775 + + 0 6517678 166398871 + + Y - - N HCC1954 20 5.77777777777778 1 8 1 N - - N - - 0 0 0 9 0.535631111994469 0.292811674556976 0.535631111994469 0.292811674556976 2 - - 4864 N N 3.00037293984407 3.66228902271184 3.00037293984407 6 0.00392156862745108 0.328075139132373 Y 0.988932461873638 0.00392156862745108 N N 911 1837 ENSG00000219545 ENSG00000106399 - - 7 7 7885379 7724763 utr5p intron AC006465.3 RPA3 7778517 7642874 + - 0 7807827 7679610 - + N - 93.5307591623037 N HCC1954 1 1 1 0 1 N - - N - Simple_repeat 0 0.0222222222222222 0.0222222222222222 17 0.928427260790413 0.642757334393363 0.928427260790413 0.642757334393363 1 - 0 36964 N N 3.78105657260285 3.60426060610801 3.60426060610801 0 0 0.99996885367515 N 0 0 N N 12084 3 ENSG00000177119 ENSG00000179242 + + 12 20 44112391 59945671 coding intron ANO6 CDH4 43896170 59260965 + + 0 44047841 59576104 + + Y - 0.929733246584255 N HCC1954 1 1 1 0 8 N - - N - LTR 0 0.719512195121951 0.719512195121951 7 1.0069864905496 1.17124669822791 1.17124669822791 1.0069864905496 2 - 0 25119 Y Y 3.80144573217181 3.73233517440054 3.73233517440054 0 0 0.941566970201296 Y 0.993484224965706 0.941358024691358 N N 2873 2546 ENSG00000136146 ENSG00000136159 + + 13 13 47567268 47519283 coding downstream MED4 NUDT15 47548093 47509704 - + 0 47549290 47525628 - + N - - N HCC1954 1 1 1 0 2 N - - Y - SINE 0 0.751592356687898 0.751592356687898 19 1.25694767614702 1.0069864905496 1.25694767614702 1.0069864905496 4 - - 6562 N N 3.42953077915294 3.62192127872787 3.42953077915294 0 0 0.287687811903213 N 0 0 N N 356 16967 ENSG00000073734 ENSG00000144283 - + 2 2 169596079 159246184 coding coding ABCB11 PK4P 169487694 159021722 - + 0 169529002 159185794 + + N - - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.728458312312478 0.671324327033068 0.728458312312478 0.671324327033068 2 - - 33576 N N 3.12486313285679 3.70463477795295 3.12486313285679 0 0 0.919192874939544 N 0 0 Y N 247001 339915 ENSG00000198786 ENSG00000198727 - + MT MT 14149 15882 coding coding MT-ND5 MT-CYB 12338 14748 + + 0 13775 15824 - + N - - N HCC1954 2 1.25 1 1 4 N 189 4.09957 N - - 0 0 0 4 0.742741808632331 0.464213630395207 0.742741808632331 0.464213630395207 2 - - 6665 N Y 3.54292948342842 3.3675771618574 3.3675771618574 1 0 0.361286947326613 Y 0 0.990419708029197 N N 307 884 ENSG00000214184 ENSG00000187627 + + 2 2 108517107 87094615 intron intron AC012487.12-1 RGPD1 108492643 86988587 - + 0 108494817 87083790 - + N - 6.38566237099179 N HCC1954 8 7.5 7 6 1 N 294 25.0315 N SINE LTR 0.413793103448276 1 1 6 0.971277749749971 0.849868031031224 0.971277749749971 0.849868031031224 1 - 0 29278 Y N 2.91894106454618 3.30591516961058 2.91894106454618 0 0 0.591871674776892 Y 0 0 N N 0 61 ENSG00000183239 ENSG00000181577 + + 6 6 44165423 44080864 downstream downstream AL109615.42-1 C6orf223 44164963 44076317 - + 0.0595000000000002 44125040 44119391 - + N - - N HCC1954 1 1 1 0 3 N - - Y LINE SINE 0.620689655172414 0.415584415584416 0.620689655172414 7 0.621332089913584 0.549914608314322 0.621332089913584 0.549914608314322 2 - - 30768 Y Y 3.46448140203209 3.24169252428402 3.24169252428402 110 0 0.265181371143007 Y 0 0.986529799029799 N N 36635 54 ENSG00000198918 ENSG00000187808 + + X X 118809620 118778155 coding downstream RPL39 ANKRD58 118804497 118776604 - + 0 118807899 118787333 - + N - - N HCC1954 5 2.33333333333333 2 18 1 N - - Y - SINE,LTR 0 0.578034682080925 0.578034682080925 18 1.0069864905496 0.649899082553289 1.0069864905496 0.649899082553289 4 - - 8260 N N 2.95112233298165 3.50678730447985 2.95112233298165 0 0.257847012322716 0.602319111323971 N 0.433620088351546 0.0820739362938849 N N 12 551733 ENSG00000169554 ENSG00000204628 + + 2 5 144994386 180603512 intron utr3p ZEB2 GNB2L1 144862055 180596536 - - 0.0820739362938849 144892749 180596557 - - Y 1.09860914087147 - N HCC1954 9 5.8 2 10 1 N - - N SINE - 0.622222222222222 0 0.622222222222222 10 0.321378667196682 0.45707188223528 0.45707188223528 0.321378667196682 2 0 - 9947 Y Y 3.5920919620082 3.57639237579107 3.57639237579107 3 0 0.99999992759166 Y 0 0 N N 20747 443941 ENSG00000073605 ENSG00000172057 - + 17 17 35328429 35337380 utr5p utr3p GSDMB ORMDL3 35314374 35330822 - - 0 35328405 35331915 + - N - 2.86071547682629 N HCC1954 1 1 1 0 14 N - - Y - - 0 0 0 14 1.63546032862311 1.50690886174444 1.63546032862311 1.50690886174444 1 - 0 18625 Y Y 3.70040921291756 3.19702885724776 3.19702885724776 316 0 0.00245034936484689 Y 0 0.991178447406744 N N 12 0 ENSG00000116147 ENSG00000219660 + + 1 1 173979529 173533000 downstream downstream TNR RP5-1114G22.1 173558558 173532839 - + 0 173556768 173543236 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE - 0.326241134751773 0 0.326241134751773 5 0.814159290231593 0.721316564152552 0.814159290231593 0.721316564152552 1 - - 30532 Y Y 3.47695798776018 3.44040523365767 3.44040523365767 0 0 0.484110112852806 Y 0.275261324041812 0 N N 0 0 ENSG00000217920 ENSG00000214009 + - X X 46033507 45803461 downstream upstream RP1-30G7.1 AL034410.9 46032395 45803125 - - 0 45946068 45870613 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 6 0.45707188223528 0.607048593593732 0.607048593593732 0.45707188223528 3 - - 36590 Y Y 3.54193626645188 3.72551845106187 3.54193626645188 1 0 0.34392443748748 Y 0 0.995248292036301 N N 30837 3495 ENSG00000062485 ENSG00000144785 - + 12 12 54980442 54996387 utr5p coding CS CNPY2 54951750 54990484 - - 0 54980278 54991338 + - N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.87843502367093 0.828442786551446 0.87843502367093 0.828442786551446 1 - - 27477 Y Y 3.77274277117786 3.39077874676146 3.39077874676146 0 0 0.73714387015493 Y 0 0 N N 29300 0 ENSG00000167522 ENSG00000205014 + + 16 16 88084470 87828005 coding downstream ANKRD11 AC009113.8-1 87861536 87826786 - + 0 87864726 87837997 - + N - - N HCC1954 2 1.85714285714286 1 6 1 N - - Y - LTR 0 1 1 7 0.978419497909897 0.949852505270192 0.978419497909897 0.949852505270192 4 - - 41964 N N 3.54040868314203 3.23999710710482 3.23999710710482 6 0 0.123813610755419 N 0 0 N N 0 462279 ENSG00000218877 ENSG00000070756 + + X 8 73720106 101803491 intron coding CTD-2530H13.2 PABPCP5 73719648 101784320 - - 0 73719652 101785738 - - Y 1 - N HCC1954 2 1.85714285714286 1 6 1 N - - N - - 0 0 0 7 0.521347615674617 0.585623349113953 0.585623349113953 0.521347615674617 2 0 - 3463 N N 3.60153211915892 3.2305569499541 3.2305569499541 0 0 0.721681197441038 N 0 0 Y N 0 542 ENSG00000209722 ENSG00000160191 - + 21 21 17725836 43068688 upstream downstream AP000952.2 PDE9A 17725745 42946931 + + 0 17709368 43084678 - + N - - N HCC1954 1 1 1 0 2 N 55 7.82755 N LINE LINE,LTR 1 0.91304347826087 1 7 1.24266417982717 0.657040830713216 1.24266417982717 0.657040830713216 2 - - 693 N Y 3.48908677906663 2.50861328157163 2.50861328157163 0 0.0140648286140088 0.628346414766321 Y 0.98866741182315 0.98866741182315 N N 8913 0 ENSG00000134909 ENSG00000209294 - - 11 11 128567303 128665093 coding upstream AP000751.4-1 AP002886.3-1 128343052 128665009 - + 0 128567188 128654252 + - N - - N HCC1954 1 1 1 0 2 N - - N - Low_complexity 0 0.433333333333333 0.433333333333333 9 1.47120012094481 0.642757334393363 1.47120012094481 0.642757334393363 1 - - 33246 N Y 3.18871505582277 3.48081283043499 3.18871505582277 478 0 0.0021029697741054 Y 0 0.995084197291671 N N 247001 171855 ENSG00000198786 ENSG00000198886 - + MT MT 14149 12138 coding coding MT-ND5 MT-ND4 12338 10761 + + 0 14010 11230 - + N 1.47881856565883 - N HCC1954 1 1 1 0 2 Y - - N - - 0 0 0 4 0.842726282871298 1.02126998686945 1.02126998686945 0.842726282871298 3 0 - 6929 Y Y 3.47705127371601 3.27345065189766 3.27345065189766 269 0 0.0363070168579629 Y 0 0.986716232961586 N N 4140 4147 ENSG00000152117 ENSG00000173272 - - 2 2 131995615 131966775 upstream coding AC093838.3-2 FAM128A 131967133 131958003 + - 0 131967039 131958253 - + N - 1.7589466873706 N HCC1954 2 1.5 1 2 1 N - - Y - - 0 0 0 4 0.435646637755502 0.692749571512847 0.692749571512847 0.435646637755502 3 - 0 44123 N N 3.09087103183403 3.41848849077886 3.09087103183403 0 0 0.0710035368208806 N 0 0 N N 3891 111946 ENSG00000166295 ENSG00000147065 + + 10 X 73665622 64878517 intron upstream C10orf104 MSN 73645812 64804283 + + 0 73645953 64760902 + + Y 0.744979490524871 - N HCC1954 23 20.6 20 5 1 N - - N - SINE 0 1 1 5 0.392796148795944 0.464213630395207 0.464213630395207 0.392796148795944 1 0 - 19633 N N 3.53399318738748 3.36720643949681 3.36720643949681 4 0 0.347070349758443 N 0 0.017881241565452 N N 1134 25026 ENSG00000175984 ENSG00000133313 - + 1 18 115014255 70339336 intron utr5p DENND2C CNDP2 114926992 70314577 - + 0.017881241565452 114957102 70314642 + + Y 1.33188705481777 0.525643774951007 N HCC1954 21 10.75 1 2 1 N - - N SINE,SINE - 0.923076923076923 0 0.923076923076923 4 0.278528178237124 0.442788385915428 0.442788385915428 0.278528178237124 1 0 0 44270 N N 3.51104337473878 3.17983219294431 3.17983219294431 4 0 0.266143046330579 N 0.00403225806451601 0.00403225806451601 N N 3 18434 ENSG00000075891 ENSG00000136868 - + 10 9 102579688 115068495 upstream utr3p PAX2 SLC31A1 102495458 115023638 + + 0.00403225806451601 102398233 115066274 - + Y - - N HCC1954 2 1.4 1 2 1 N - - N SINE SINE 1 0.339285714285714 1 5 0.257102933757345 0.39993789695587 0.39993789695587 0.257102933757345 1 - - 38252 Y Y 3.21704729445613 3.65594388497418 3.21704729445613 308 0 0.0789985031425209 Y 0.210571428571429 0.984051948051948 N N 0 46 ENSG00000201358 ENSG00000214900 - - 14 14 49605358 49543988 upstream upstream 7SK C14orf182 49605036 49518180 + - 0 49575483 49547626 - + N - - N HCC1954 1 1 1 0 1 N - - Y - LTR,LTR 0 0.628930817610063 0.628930817610063 7 0.771308801272036 0.771308801272036 0.771308801272036 0.771308801272036 4 - - 45355 N Y 3.75016368088976 3.10915419906985 3.10915419906985 259 0.372432432432433 0.00286803687225812 N 0.99003861003861 0.87050193050193 N N 23703 1903 ENSG00000095787 ENSG00000113580 - + 10 5 28949703 142795270 upstream intron WAC NR3C1 28861706 142637689 + - 0.382393822393822 28854512 142694108 - - Y - 1.09298681427716 N HCC1954 6 3.8 2 5 1 N - - N SINE SINE 1 0.5 1 5 1.09982921662864 0.721316564152552 1.09982921662864 0.721316564152552 1 - 0 43765 N Y 3.18296190747752 3.66848325143457 3.18296190747752 178 0 0.205410847046531 N 0.954076729745713 0.940955795387345 N Y 238 10094 ENSG00000211643 ENSG00000165733 - + 22 10 21003581 42646855 coding coding IGLV5-52 BMS1 21003021 42598265 + + 0 21003254 42639238 - + Y 0.043242452348241 - N HCC1954 14 9.72972972972973 1 36 1 N - - N - - 0 0 0 37 1.09268746846872 0.685607823352921 1.09268746846872 0.685607823352921 4 0 - 7341 Y Y 3.61464054707278 3.48912663185998 3.48912663185998 0 0.112115927050363 0.052288380468291 Y 0.133949141958961 0 N N 3 7189 ENSG00000152086 ENSG00000152082 + + 2 2 130672510 130664769 upstream coding TUBA3E FAM128B 130665790 130656173 - + 0 130676351 130656722 - + N - - N HCC1954 4 3.4 2 30 1 N - - Y - Low_complexity 0 0.161048689138577 0.161048689138577 30 0.914143764470561 1.18553019454776 1.18553019454776 0.914143764470561 1 - - 27510 N N 3.37655331069169 3.32895826821511 3.32895826821511 0 0 0.0863236967880338 N 0 0 N N 975 180 ENSG00000198487 ENSG00000140807 + - 6 16 42218335 49226142 intron upstream AL512274.9 NKD1 42183124 49139742 - + 0 42204322 49082900 - - Y 0.755947860259476 - N HCC1954 23 18 9 4 1 N - - N - SINE 0 1 1 4 0.349945659836387 0.307095170876829 0.349945659836387 0.307095170876829 2 0 - 34765 Y Y 3.19975734419684 3.52833332499807 3.19975734419684 0 0 0.767694639833664 Y 0 0 N N 526 3337 ENSG00000177943 ENSG00000054148 - + 9 9 138875070 138865308 utr5p downstream MAMDC4 PHPT1 138866640 138862997 + + 0.854469596827495 138866653 138865450 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 10 0.699891319672773 0.814159290231593 0.814159290231593 0.699891319672773 2 - - 43197 N Y 3.37977631118074 3.54296933622177 3.37977631118074 1 0 0.291789418014472 N 0 0 N N 5301 14402 ENSG00000107771 ENSG00000156689 - + 10 11 86268256 58368833 utr3p intron KIAA1128 GLYATL2 86078322 58358118 + - 0 86265235 58368479 - - Y - 0.958134545874787 N HCC1954 76 41.375 34 8 1 N 103 24.8192 N SINE - 1 0 1 8 0.307095170876829 0.5713398527941 0.5713398527941 0.307095170876829 3 - 0 41497 Y Y 3.49950657282475 3.54292948342842 3.49950657282475 248 0 0.0207006991995770 Y 0 0 N N 0 0 ENSG00000213791 ENSG00000222697 - + 8 8 81376271 81279688 upstream downstream AC104212.3-2 SRP_euk_arch 81375668 81279396 + + 0 81332224 81324603 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,LINE - 0.902173913043478 0 0.902173913043478 8 0.657040830713216 0.671324327033068 0.671324327033068 0.657040830713216 2 - - 18959 Y Y 3.36079094374226 3.54296933622177 3.36079094374226 367 0 0.000580598222183482 Y 0 0.991015538699462 N N 0 0 ENSG00000212157 ENSG00000219021 + + 1 1 222230574 222204741 upstream downstream U6 RP11-504P24.1 222230471 222201925 - + 0 222231217 222219036 - + N - - N HCC1954 162 76 6 4 1 N - - Y - SINE 0 1 1 4 0.735600060472404 0.485638874874985 0.735600060472404 0.485638874874985 1 - - 5065 Y Y 3.31233066536513 3.39231567764112 3.31233066536513 337 0 0.087264785477063 Y 0.993883235331598 0.993883235331598 N N 1135 1279 ENSG00000153807 ENSG00000078399 + - 7 7 27186405 27175794 utr3p upstream HOXA10 HOXA9 27176736 27168583 - - 0.993883235331598 27177450 27175906 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Simple_repeat 0 0.188235294117647 0.188235294117647 175 1.27123117246687 1.21409718718746 1.27123117246687 1.21409718718746 2 - - 4859 Y Y 3.33996070379583 3.5278388114581 3.33996070379583 272 0 0.400436925092878 Y 0 0 N N 650 4345 ENSG00000175873 ENSG00000136213 - + 7 7 2454008 2440740 utr5p downstream AC004840.4 CHST12 2443924 2274908 + + 0 2443965 2441361 - + N - - N HCC1954 13 5.22222222222222 1 5 2 N - - Y - SINE 0 1 1 9 0.671324327033068 1.08554572030879 1.08554572030879 0.671324327033068 4 - - 16521 N N 3.05682218208888 2.25637033799751 2.25637033799751 0 0 0.440723860814342 N 0 0 N N 0 317991 ENSG00000212678 ENSG00000171346 - - 1 17 560165 36932191 intron coding RP5-857K21.11 KRT15 559619 36923523 + - 0 559652 36928358 - + Y 1 11.3024445482699 N HCC1954 3 2.1 2 10 2 N - - N - - 0 0 0 10 0.307095170876829 0.635615586233437 0.635615586233437 0.307095170876829 2 0 0 30747 Y Y 3.47233119514066 3.50120199000394 3.47233119514066 1 0.0042918454935621 0.805066862193048 Y 0 0.980665861077545 N N 1011 1542 ENSG00000205663 ENSG00000205664 + - X X 3810322 3771898 utr3p intron BX890604.9-1 RP11-706O15.1 3792439 3745569 - - 0 3793055 3750621 - + N - 1.1490492744088 N HCC1954 84 40.25 6 4 2 N - - Y SINE - 1 0 1 4 0.892718519990782 0.478497126715059 0.892718519990782 0.478497126715059 4 - 0 9505 Y Y 3.40381262676181 3.48743121468078 3.40381262676181 325 0 0.0193177239495813 Y 0 0 N N 6556 3927 ENSG00000141526 ENSG00000176155 - - 17 17 77790658 77763978 intron upstream SLC16A3 CCDC57 77779582 77652635 + - 0 77787147 77769348 - + N 0.15467835909463 - N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.418478260869565 0.418478260869565 15 1.05697872766909 1.29979816510658 1.29979816510658 1.05697872766909 1 0 - 19235 Y N 3.32408779740342 3.48639814491089 3.32408779740342 0 0.00338983050847452 0.103356897784190 Y 0.00338983050847452 0.00338983050847452 N N 6231 1659 ENSG00000156875 ENSG00000117620 - + 1 1 100321515 100261594 coding coding HIAT1 SLC35A3 100276377 100208128 + + 0 100288106 100260573 - + N 0.534929987334119 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.664182578873142 0.956994253430118 0.956994253430118 0.664182578873142 1 0 - 755 N Y 3.48081283043499 3.55231620741665 3.48081283043499 236 0.0042372881355931 0.150517641646801 Y 0.0628115653040877 0.988285144566301 N N 821 219 ENSG00000132275 ENSG00000179532 + + 11 11 6581387 6498664 coding intron RRP8 C11orf47 6577732 6475107 - + 0 6581212 6492740 - + N - 1.82112241717428 N HCC1954 1 1 1 0 1 N - - N - LTR 0 1 1 5 0.649899082553289 0.449930134075354 0.649899082553289 0.449930134075354 2 - 0 47243 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 0 0 0.761335808083477 Y 0 0.993521594684385 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 132 1.5783263433437 1.15696320190805 1.5783263433437 1.15696320190805 4 - - 42421 Y Y 3.60426060610801 3.57848902055439 3.57848902055439 334 0 0.00715896457457832 Y 0.993567703303071 0.987135406606142 N N 735 2700 ENSG00000198515 ENSG00000170448 + - 4 4 47678276 47611390 downstream upstream CNGA1 NFXL1 47632753 47544017 - - 0 47623515 47611478 - + N - - N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 4 0.685607823352921 0.785592297591888 0.785592297591888 0.685607823352921 4 - - 19587 N Y 3.73808832274579 3.24893340314576 3.24893340314576 0 0 0.950250860214061 N 0.977075351213282 0.977075351213282 N N 35256 0 ENSG00000212664 ENSG00000206696 - + 1 18 109337022 45272097 utr5p upstream RPL17 SNORD58 109336399 45272032 + - 0.977075351213282 109336418 45272639 - - Y 0.959657026618176 - N HCC1954 9 4.98701298701299 4 154 2 N - - N - - 0 0 0 154 1.19981369086761 1.45691662462496 1.45691662462496 1.19981369086761 3 0 - 12546 N N 2.91828252592479 3.53824925764641 2.91828252592479 0 0 0.0825759495220688 N 0.0539529914529916 0.300747863247863 N N 7722 3184 ENSG00000090661 ENSG00000161542 - + 19 17 8233302 71861526 coding upstream LASS4 PRPSAP1 8180257 71818610 + - 0.300747863247863 8222081 71873507 - - Y - - N HCC1954 20 12.6666666666667 6 6 1 N - - N - SINE 0 1 1 6 0.542772860154395 0.385654400636018 0.542772860154395 0.385654400636018 2 - - 44972 N Y 3.59425138750382 2.8753230329477 2.8753230329477 313 0 0.0219055652823492 Y 0.992025559105431 0.992025559105431 N N 6115 253 ENSG00000089876 ENSG00000203780 - - 10 10 127559874 127688151 utr5p upstream DHX32 FANK1 127514896 127575098 - + 0 127559632 127574779 + - N - - N HCC1954 1 1 1 0 2 N - - N LINE Low_complexity 0.406060606060606 0.05 0.406060606060606 97 1.17838844638783 0.999844742389676 1.17838844638783 0.999844742389676 1 - - 24840 N N 2.35275713669329 3.02457708929449 2.35275713669329 0 0 0.380937540944231 N 0.149060222477944 0 N N 1 21616 ENSG00000220008 ENSG00000074657 + - 19 18 2259156 54804663 upstream intron LINGO3 ZNF532 2240774 54681041 - + 0 2259163 54681747 - - Y - 0.0429844556081304 N HCC1954 6 2.25 1 1 1 N - - N Simple_repeat,Low_complexity Simple_repeat 0.666666666666667 0.606741573033708 0.666666666666667 4 0.278528178237124 0.635615586233437 0.635615586233437 0.278528178237124 1 - 0 34780 Y Y 3.6052936758779 3.60256518892881 3.60256518892881 0 0 0.967409457228307 Y 0.0158881315156375 0.918955493183641 N N 4263 0 ENSG00000187764 ENSG00000218102 - - 9 9 91260688 91277427 utr5p downstream SEMA4D RP13-93L13.1 91181972 91276972 - + 0 91260623 91279275 + - N - - N HCC1954 1 1 1 0 4 N - - Y - - 0 0 0 4 0.928427260790413 0.585623349113953 0.928427260790413 0.585623349113953 2 - - 39370 N N 3.28189243439864 3.7527243339695 3.28189243439864 0 0.0377168888591142 0.154594753245779 N 0.257184966838615 0.0377168888591142 N N 12320 4948 ENSG00000108587 ENSG00000157823 + - 17 15 25877957 88238206 utr3p intron GOSR1 AP3S2 25828552 88177793 + - 0.0377168888591142 25874014 88211336 + + Y - 1.13403203753708 N HCC1954 4 1.75 1 1 1 N - - N - Other 0 1 1 4 0.557056356474248 0.271386430077198 0.557056356474248 0.271386430077198 1 - 0 26078 N Y 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.254863244402521 N 0 0 N N 8418 45068 ENSG00000074755 ENSG00000205336 + + 17 16 3993002 56256445 intron upstream ZZEF1 GPR56 3854489 56220023 - + 0 3874342 56211646 - + Y 0.964575783316972 - N HCC1954 24 21.0857142857143 20 35 2 N - - N SINE - 1 0 1 35 0.407079645115797 0.599906845433805 0.599906845433805 0.407079645115797 1 0 - 44801 Y Y 3.15678909433978 3.51849194026323 3.15678909433978 322 0 0.0132973578460506 Y 0.893773546482028 0.983657468689543 N N 0 24224 ENSG00000178775 ENSG00000151208 - - 10 10 79357961 79356384 downstream coding AL391421.27-4 DLG5 79357395 79220555 + - 0 79359353 79356041 - + N - 2.90586348732889 N HCC1954 1 1 1 0 1 N - - Y LTR - 1 0 1 13 0.921285512630487 1.29979816510658 1.29979816510658 0.921285512630487 4 - 0 33816 N N 3.30232144676095 3.26464233693271 3.26464233693271 0 0 0.999757879005492 N 0 0 Y N 544065 339915 ENSG00000198744 ENSG00000198727 - + MT MT 9988 15882 coding coding MT-CO3 MT-CYB 8367 14748 + + 0 8386 15338 - + N - - N HCC1954 2 1.22222222222222 1 2 8 Y 189 4.09957 N - - 0 0 0 9 1.1141127129485 1.27123117246687 1.27123117246687 1.1141127129485 2 - - 497 Y Y 3.04011818921209 3.40012561795634 3.04011818921209 9 0 0.713668645101513 Y 0.0118834682287706 0.99522649018468 N N 95337 3156 ENSG00000172757 ENSG00000172732 - - 11 11 65382380 65390485 utr5p coding CFL1 MUS81 65378884 65384801 - + 0 65382207 65385103 + - N - 0.464220174550779 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 4 0.39993789695587 0.492780623034912 0.492780623034912 0.39993789695587 2 - 0 36234 Y Y 3.77104735399867 3.58271458558979 3.58271458558979 363 0 0.0455936238773371 Y 0.979224058769514 0.989612029384757 N N 35326 55227 ENSG00000111321 ENSG00000111319 - - 12 12 6370994 6354976 intron upstream LTBR SCNN1A 6363595 6326276 + - 0 6364012 6355018 - + N 0.527277963947244 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 12 0.735600060472404 1.20695543902754 1.20695543902754 0.735600060472404 1 0 - 33449 N N 3.1416492220063 3.50422665140011 3.1416492220063 0 0 0.183614131511824 N 0 0 Y N 240508 59837 ENSG00000198899 ENSG00000198695 - - MT MT 9208 14674 coding coding MT-ATP6 MT-ND6 8528 14150 + - 0 8648 14496 - + N - 1.40918744733293 N HCC1954 3 2 1 6 1 N 189 4.09957 N - - 0 0 0 9 1.17838844638783 1.1141127129485 1.17838844638783 1.1141127129485 3 - 0 31144 Y Y 3.63193049733206 3.67593181695901 3.63193049733206 304 0 0.534752177957676 Y 0.791895604395604 0.989047137073453 N N 6473 7313 ENSG00000144648 ENSG00000181061 - - 3 3 42883778 42820986 intron upstream CCBP2 HIGD1D 42836115 42800797 + - 0 42880958 42826024 - + N 0.0692123342775211 - N HCC1954 1 1 1 0 6 N - - Y - LTR 0 1 1 255 1.56404284702385 0.742741808632331 1.56404284702385 0.742741808632331 1 0 - 47951 N N 3.63552422018169 3.76017289949394 3.63552422018169 0 0 0.999999634402327 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 intron downstream RAD21 IRX2 117927355 2798959 - - 0 117944548 2617784 - + Y 1.0363918474073 - N HCC1954 4 2.45454545454545 1 19 12 N 282 1.61558 N - - 0 0 0 22 0.871293275511003 1.36407389854591 1.36407389854591 0.871293275511003 2 0 - 49008 Y Y 3.6550481438501 3.52361324642271 3.52361324642271 258 0 0.88374759825086 Y 0.992217781007752 0.992217781007752 N N 6117 11413 ENSG00000171368 ENSG00000112877 + + 5 5 746510 706664 downstream downstream TPPP CEP72 712978 665405 - + 0.992217781007752 710042 708698 - + N - - N HCC1954 1 1 1 0 6 N - - Y LINE - 1 0 1 13 0.771308801272036 0.921285512630487 0.921285512630487 0.771308801272036 2 - - 13648 Y Y 3.61360747730288 3.55913293075533 3.55913293075533 277 0 0.0137915895330225 Y 0.758450935346242 0.98490318345914 N N 0 49214 ENSG00000216570 ENSG00000100219 + - 22 22 27562125 27526560 downstream upstream CTA-292E10.7 XBP1 27561881 27520545 - - 0 27547958 27526723 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,SINE - 0.506410256410256 0 0.506410256410256 21 1.07126222398894 0.34280391167646 1.07126222398894 0.34280391167646 3 - - 34505 N Y 3.30335451653084 2.85484058742291 2.85484058742291 0 0 0.485308964203992 Y 0 0.992880873279544 N N 0 10544 ENSG00000222760 ENSG00000122705 - + 9 9 36257919 36202055 upstream coding U4 CLTA 36257780 36180892 + + 0 36255416 36194174 - + N - - N HCC1954 2 1.16666666666667 1 1 1 N - - N DNA - 0.0593220338983051 0 0.0593220338983051 6 0.842726282871298 1.01412823870953 1.01412823870953 0.842726282871298 1 - - 4615 N Y 3.65488030998075 3.34359427943881 3.34359427943881 395 0 0.157703747744838 Y 0.994489125113644 0.994489125113644 N N 3729 0 ENSG00000178234 ENSG00000208257 - - 7 7 151450178 151353493 utr5p upstream GALNT11 AC006017.2-1 151407293 151353212 + - 0.189901391705714 151407426 151353901 - + N - - N HCC1954 1 1 1 0 4 N - - N - - 0 0 0 82 1.34264865406614 1.10697096478857 1.34264865406614 1.10697096478857 1 - - 22779 N Y 3.52101274054962 3.51104337473878 3.51104337473878 0 0 0.477496348602745 N 0.893693693693694 0.946846846846847 N N 73 39 ENSG00000109743 ENSG00000171357 - - 4 1 15343508 46537834 upstream intron BST1 C1orf190 15313739 46441593 + + 0 15292074 46447302 - - Y - 0.38148697309892 N HCC1954 12 3.75 1 1 1 N - - N - SINE 0 1 1 4 0.956994253430118 0.492780623034912 0.956994253430118 0.492780623034912 3 - 0 398 Y Y 3.56591914887046 3.24255776018456 3.24255776018456 130 0 0.385398242827075 Y 0.00342465753424659 0.992214255136986 N N 2663 642 ENSG00000137478 ENSG00000168010 + + 11 11 72530954 72218326 intron coding FCHSD2 ATG16L2 72225439 72203099 - + 0 72231309 72217676 - + N 0.543552347619288 - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 5 0.892718519990782 0.871293275511003 0.892718519990782 0.871293275511003 1 0 - 28160 N N 3.49168728493972 3.02495296932827 3.02495296932827 4 0 0.154867431439721 N 0 0 N N 1584 15518 ENSG00000130958 ENSG00000103534 - + 9 16 98185797 19417936 intron utr3p SLC35D2 TMC5 98122834 19329558 - + 0 98159162 19417743 + + Y 1.17127643470723 2.46477552407063 N HCC1954 3 1.22222222222222 1 1 1 N - - N SINE snRNA,SINE 1 0.35632183908046 1 9 0.271386430077198 0.621332089913584 0.621332089913584 0.271386430077198 1 0 0 39879 Y Y 3.31063524818594 3.42576922243396 3.31063524818594 286 0 0.117234901446405 Y 0 0.992334588488435 N N 7 1228 ENSG00000206125 ENSG00000186031 + - 15 15 31274189 31147377 downstream upstream AC019278.6 FMN1 31229284 30853637 - - 0 31193163 31168466 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.785592297591888 0.814159290231593 0.814159290231593 0.785592297591888 1 - - 28549 N Y 3.48639814491089 3.20174893582312 3.20174893582312 238 0.0404125286478229 0.00406392437592318 N 0.547364400305577 0.0947288006111535 N N 0 10339 ENSG00000216027 ENSG00000177200 - + 4 16 61212351 51918914 downstream intron AC095061.3 CHD9 61212262 51646446 - + 0.782734912146677 60902269 51784739 + + Y - 1.27613943306093 N HCC1954 168 47 20 10 1 N - - N SINE,SINE SINE 0.842105263157895 1 1 10 0.271386430077198 0.292811674556976 0.292811674556976 0.271386430077198 1 - 0 44668 Y Y 3.04483826778745 3.34256120966892 3.04483826778745 335 0 0.00642326502678181 Y 0.981536760641238 0.993845586880413 N N 9499 13 ENSG00000107485 ENSG00000197308 - - 10 10 8157170 8135453 utr5p upstream GATA3 AL390294.19 8136673 8132419 + - 0.993845586880413 8137258 8135749 - + N 0.756750419018155 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 76 1.14982145374813 1.22838068350732 1.22838068350732 1.14982145374813 1 0 - 16221 N N 3.60103760561896 3.53039946453785 3.53039946453785 0 0 0.687098680444535 N 0 0 N N 14038 30525 ENSG00000115183 ENSG00000134202 - + 2 1 159797412 110085183 intron coding TANC1 GSTM3 159533392 110078077 + - 0 159621514 110082480 - - Y 0.680008452721304 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 6 0.257102933757345 0.535631111994469 0.535631111994469 0.257102933757345 2 0 - 10746 N N 3.56704550459619 3.65281417044097 3.56704550459619 0 0 0.0465880278987157 N 0 0 N N 16264 78560 ENSG00000177885 ENSG00000112493 - + 17 6 70913385 33390114 utr3p utr3p GRB2 TAPBP 70825752 33375449 - - 0 70827392 33376013 + - Y - - N HCC1954 39 37.5 35 4 1 N - - N SINE DNA 1 0.80952380952381 1 4 0.278528178237124 0.735600060472404 0.735600060472404 0.278528178237124 1 - - 29902 N N 3.44040523365767 3.60103760561896 3.44040523365767 7 0 0.040379685790737 N 0 0 N N 975 241 ENSG00000198487 ENSG00000101842 + + 6 X 42218335 107209069 coding utr3p AL512274.9 VSIG1 42183124 107174856 - + 0 42204405 107208379 - + Y 0.811586469073095 - N HCC1954 39 35.7777777777778 33 9 1 N - - N - SINE 0 1 1 9 0.585623349113953 0.492780623034912 0.585623349113953 0.492780623034912 1 0 - 36667 Y Y 3.63080414160633 3.49065421516983 3.49065421516983 118 0 0.923789995917728 Y 0 0.991627877916966 N Y 2025 1204 ENSG00000176894 ENSG00000176876 - + 12 12 131805819 131791649 coding coding PGAM5 PXMP2 131797509 131774265 + + 0 131801517 131777035 - + N - - N HCC1954 1 1 1 0 2 N - - Y - - 0 0 0 4 0.892718519990782 0.707033067832699 0.892718519990782 0.707033067832699 4 - - 48992 Y Y 3.53035871401856 3.41319935075004 3.41319935075004 0 0 0.420402643306897 N 0.0654952076677314 0.0654952076677314 Y N 0 1302 ENSG00000196570 ENSG00000131187 + - 5 5 176760183 176769183 upstream intron PFN3 F12 176759770 176761747 - - 0.0654952076677314 176771470 176763297 - + N - 8.17408796905862 N HCC1954 1 1 1 0 2 N - - N LTR - 1 0 1 4 0.628473838073511 0.5713398527941 0.628473838073511 0.5713398527941 2 - 0 47604 N Y 3.66488952858494 3.21704729445613 3.21704729445613 0 0 0.8353883383526 N 0.887264150943396 0.887264150943396 N Y 298 763 ENSG00000197044 ENSG00000197857 - + 19 19 11754301 12266637 utr5p intron ZNF441 ZNF44 11738907 12196503 + - 0 11749426 12266507 - - N - 1.03849242196126 Y HCC1954 3 2.33333333333333 1 4 1 N - - N - - 0 0 0 6 0.321378667196682 0.592765097273879 0.592765097273879 0.321378667196682 4 - 0 9775 N N 2.83814778422924 3.39384326095097 2.83814778422924 0 0 0.217825845497869 N 0 0 Y N 2887 27122 ENSG00000159266 ENSG00000171634 + + 17 17 60263719 63410956 downstream coding PLEKHM1P FALZ 60205839 63252242 - + 0 60185020 63320674 - + N - - N HCC1954 2 1.75 1 3 1 N - - N - - 0 0 0 4 0.607048593593732 0.778450549431962 0.778450549431962 0.607048593593732 1 - - 12721 N Y 2.39788152983156 3.10447397328784 2.39788152983156 0 0 0.0635996380192989 N 0 0.870171890798787 N N 0 610 ENSG00000182225 ENSG00000176170 + + 19 17 5527949 71895536 downstream downstream AC011533.6 SPHK1 5527671 71892326 - + 0 5518621 71896476 - + Y - - N HCC1954 23 22.4 21 5 1 N 610 25.885 N - SINE 0 1 1 5 0.557056356474248 0.335662163516534 0.557056356474248 0.335662163516534 1 - - 17856 N Y 3.71041843152174 3.48639814491089 3.48639814491089 0 0.342115832596996 0.0764897938617702 N 0.342115832596996 0 N N 9561 5414 ENSG00000143753 ENSG00000135763 + + 1 1 222447763 227862569 utr3p intron DEGS1 URB2 222437551 227828604 + + 0 222447127 227847430 + + N - 1.69437638019124 Y HCC1954 2 2 2 5 1 N - - N - SINE 0 1 1 5 0.549914608314322 0.271386430077198 0.549914608314322 0.271386430077198 2 - 0 33300 N Y 3.00500908003341 2.96167010781576 2.96167010781576 320 0 0.916558791778637 Y 0 0.961658653846154 N N 247001 544065 ENSG00000198786 ENSG00000198744 - + MT MT 14149 9988 coding coding MT-ND5 MT-CO3 12338 8367 + + 0 13972 8456 - + N 1.39700444604868 - N HCC1954 2 1.2 1 1 7 Y - - N - - 0 0 0 5 0.814159290231593 0.599906845433805 0.814159290231593 0.599906845433805 2 0 - 22080 N N 3.41741556821562 3.51729103662399 3.41741556821562 0 0 0.453465422378069 N 0.939936738102854 0 N N 319 2833 ENSG00000166415 ENSG00000133019 - + 15 1 51842367 238139338 coding utr5p WDR72 CHRM3 51593230 237858996 - + 0 51602811 237859191 + + Y - - N HCC1954 25 23.7692307692308 22 13 2 N - - N - LINE 0 1 1 13 0.849868031031224 0.5713398527941 0.849868031031224 0.5713398527941 4 - - 14067 Y Y 3.4048456965317 3.50848272165904 3.4048456965317 294 0.0197390431582468 0.0135687775373285 Y 0.0360767257722761 0.885636221701795 N N 7983 1794 ENSG00000100227 ENSG00000182841 + - 22 22 41340906 41307988 utr3p intron POLDIP3 Z93241.11-1 41309671 41281173 - - 0 41309687 41307443 - + N - 0.378130738183779 N HCC1954 2 2 2 4 1 N - - Y - LINE 0 1 1 4 0.578481600954027 0.649899082553289 0.649899082553289 0.578481600954027 2 - 0 17053 N N 3.26564714070074 3.43152237077921 3.26564714070074 0 0.0847131716696934 0.390695969381256 N 0.0847131716696934 0.138553573336182 N N 0 0 ENSG00000221534 ENSG00000212875 + + 17 1 48969964 557859 upstream intron AC090079.6 RP5-857K21.6 48969873 556317 + + 0.138553573336182 48538384 557371 + + Y - 1 N HCC1954 2 2 2 7 1 N - - N - - 0 0 0 7 0.271386430077198 0.585623349113953 0.585623349113953 0.271386430077198 1 - 0 551 N Y 3.31216283149579 3.07317050642081 3.07317050642081 134 0 0.965963336591208 Y 0.957260596546311 0.992876766091052 N N 9074 0 ENSG00000166444 ENSG00000202276 - + 11 11 8817478 8855641 utr5p downstream ST5 Y_RNA 8671478 8855540 - - 0 8817475 8849079 + - N - - N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 7 0.871293275511003 1.02841173502938 1.02841173502938 0.871293275511003 3 - - 9361 Y Y 3.68577320169385 3.5580693557619 3.5580693557619 456 0 0.26146891032645 Y 0 0.994425659119867 N N 170868 1649619 ENSG00000141741 ENSG00000141736 + + 17 17 35140314 35138441 intron utr3p C17orf37 ERBB2 35138937 35104766 - + 0.994425659119867 35139768 35138232 - + N 1.35620378426741 2.37973796965433 N HCC1954 1 1 1 0 6 N - - Y SINE - 0.22972972972973 0 0.22972972972973 15 1.05697872766909 1.20695543902754 1.20695543902754 1.05697872766909 1 0 0 504 Y Y 3.60394554157413 3.23999710710482 3.23999710710482 0 0.0913234005258546 0.909442628785992 Y 0.0913234005258546 0.971603856266433 N N 1594 103869 ENSG00000188082 ENSG00000117984 - + 11 11 1728397 1741798 coding coding AC068580.3 CTSD 1710216 1730561 - - 0 1725489 1735295 + - N - - N HCC1954 1 1 1 0 4 Y - - Y - - 0 0 0 4 0.678466075192994 1.02126998686945 1.02126998686945 0.678466075192994 2 - - 40825 N N 3.65657572715995 3.41319935075004 3.41319935075004 1 0 0.405685291913729 N 0 0 N N 0 0 ENSG00000220165 ENSG00000179460 + + 20 7 18712334 22640794 intron intron RP5-1068E13.4 AC002480.1-1 18711068 22516494 - - 0 18711402 22517121 - - Y 1 1 N HCC1954 3 3 3 7 1 N - - N - - 0 0 0 7 0.264244681917271 0.357087407996313 0.357087407996313 0.264244681917271 2 0 0 44747 Y Y 3.2965682984157 3.7527243339695 3.2965682984157 247 0 0.0536615735020353 Y 0.769054743883119 0.985565921492695 N N 40 36 ENSG00000165429 ENSG00000204043 - + 10 10 81600608 81462701 upstream downstream AL135925.10 FAM22C 81591094 81453188 + + 0 81554224 81516240 - + N - - N HCC1954 16 10.75 4 16 2 N - - Y - SINE 0 0.597014925373134 0.597014925373134 16 0.414221393275723 0.956994253430118 0.956994253430118 0.414221393275723 1 - - 36391 Y Y 3.65384724021086 3.22489708756469 3.22489708756469 348 0 0.00812304635146188 Y 0 0.989278210357187 N N 2438 1815 ENSG00000188026 ENSG00000184209 + + 12 12 122584457 122516894 downstream intron RILPL1 AC145423.8 122522316 122508604 - + 0 122520668 122508880 - + N - 1.14655907857906 N HCC1954 1 1 1 0 2 N - - Y SINE - 0.643564356435644 0 0.643564356435644 4 0.649899082553289 0.564198104634174 0.649899082553289 0.564198104634174 2 - 0 40478 N N 3.27291628556435 3.56232542602083 3.27291628556435 1 0 0.119709586886773 N 0 0.0429968363531781 N N 45374 4 ENSG00000160007 ENSG00000103569 + + 19 15 52199404 56265402 upstream downstream GRLF1 AQP9 52113773 56217700 + + 0.0429968363531781 52084445 56339667 + + Y - - N HCC1954 46 25 20 10 1 N 165 25.8144 N SINE LTR 1 1 1 10 0.314236919036755 0.407079645115797 0.407079645115797 0.314236919036755 3 - - 31039 N Y 3.39128260787123 3.55334927718654 3.39128260787123 0 0 0.103635221807137 N 0.946165677872995 0.946165677872995 N N 12271 2428 ENSG00000177479 ENSG00000018610 - + 3 X 48997971 118583392 intron utr3p ARIH2 CXorf56 48931285 118556140 + - 0 48939897 118557399 - - Y 0.963247002497696 - N HCC1954 56 27.12 3 25 1 N - - N - SINE 0 1 1 25 0.557056356474248 0.364229156156239 0.557056356474248 0.364229156156239 1 0 - 34174 Y Y 3.55231620741665 3.16510289576477 3.16510289576477 327 0 0.354007621846542 Y 0.829290771228687 0.986343261698295 N N 1727 0 ENSG00000147905 ENSG00000216536 - + 9 9 37348143 37037234 upstream downstream ZCCHC7 RP11-297B17.2 37110469 37036832 + + 0 37076665 37070027 - + N - - N HCC1954 2 1.35922330097087 1 37 3 N - - Y - - 0 0 0 103 1.31408166142643 1.16410495006798 1.31408166142643 1.16410495006798 4 - - 27945 N N 3.66745018166468 3.48809356209009 3.48809356209009 0 0 0.0747582384061586 N 0 0 N N 36 45068 ENSG00000126752 ENSG00000205336 - + X 16 48185976 56256445 intron upstream SSX1 GPR56 47957054 56220023 + + 0 48028021 56211646 - + Y 2.68272318561336 - N HCC1954 24 20.6666666666667 20 15 1 N - - N SINE - 1 0 1 15 0.357087407996313 0.485638874874985 0.485638874874985 0.357087407996313 1 0 - 30371 N N 3.39380340815762 3.71145150129163 3.39380340815762 0 0 0.315870911115855 Y 0.719114219114219 0 N N 4 0 ENSG00000215253 ENSG00000215269 - + X X 49129941 49082313 coding upstream GAGE2B GAGE13 49122652 49047069 + + 0 49129845 49042858 - + N 1.63436123348018 - N HCC1954 187 63.875 1 7 1 N - - N - LINE,LINE 0 1 1 8 0.392796148795944 0.557056356474248 0.557056356474248 0.392796148795944 1 0 - 48118 N N 3.63552422018169 3.78208964237274 3.63552422018169 0 0 0.999999831157503 N 0 0 N N 159165 19352 ENSG00000164754 ENSG00000170561 + - 8 5 117956182 2804774 coding downstream RAD21 IRX2 117927355 2798959 - - 0 117943358 2617783 - + Y - - N HCC1954 4 2.18181818181818 1 24 12 N 282 1.61558 N - - 0 0 0 33 1.22838068350732 1.16410495006798 1.22838068350732 1.16410495006798 1 - - 21716 N Y 3.61360747730288 3.54872248456702 3.54872248456702 0 0 0.452614126412418 N 0.696053630154313 0.679167720718441 N N 33725 0 ENSG00000143819 ENSG00000210611 - + 1 9 224099884 32059981 utr5p downstream EPHX1 AL589825.8 224064459 32059823 + + 0 224083049 32154402 - + Y - - N HCC1954 21 5.21052631578947 1 4 1 N - - N - LTR 0 1 1 19 0.849868031031224 0.34280391167646 0.849868031031224 0.34280391167646 3 - - 45947 N N 3.65384724021086 3.5010341561346 3.5010341561346 0 0 0.144112732728752 N 0 0 N N 20035 40617 ENSG00000117868 ENSG00000130164 + + 7 19 158315080 11105490 utr3p utr3p FAM62B LDLR 158216450 11061132 - + 0 158217010 11104135 - + Y - - N HCC1954 39 38 37 4 1 N - - N SINE SINE 0.278947368421053 0.540816326530612 0.540816326530612 4 0.528489363834543 0.592765097273879 0.592765097273879 0.528489363834543 3 - - 11718 N Y 3.53933576057879 3.72079837248651 3.53933576057879 0 0 0.846448883427801 N 0.923289417764556 0.956165381579746 N N 0 275 ENSG00000217435 ENSG00000204303 + + 9 17 104867701 72068110 downstream utr5p RP11-341A22.1 SNORD1C 104867519 72065446 + + 0 105007049 72066277 + + Y - 1.16101690535844 N HCC1954 2 1.4 1 2 3 N - - N - - 0 0 0 5 0.885576771830856 0.435646637755502 0.885576771830856 0.435646637755502 3 - 0 2698 N Y 3.353603498043 3.6491271616355 3.353603498043 10 0 0.222211504167933 N 0.921645113419546 0.932838668645325 N N 3567 2180 ENSG00000177951 ENSG00000124217 - + 11 20 197428 49011227 coding intron BET1L MOCS3 157784 49008770 - + 0 195611 49010829 + + Y - - N HCC1954 195 166 128 22 1 N - - N - SINE 0 1 1 22 0.864151527351077 0.464213630395207 0.864151527351077 0.464213630395207 3 - - 11053 N Y 3.52936639476796 3.53871326596283 3.52936639476796 0 0 0.293657434828007 N 0.0181211784324623 0 N N 45 5881 ENSG00000212659 ENSG00000112664 - + 17 6 36676419 34468419 intron downstream KRTAP9-6 NUDT3 36675117 34363982 + - 0 36675928 34362776 - - Y - - N HCC1954 35 32.25 30 4 1 N - - N SINE - 1 0 1 4 0.371370904316165 0.842726282871298 0.842726282871298 0.371370904316165 2 - - 8005 N Y 3.47233119514066 3.37126417066287 3.37126417066287 3 0 0.0851640324571021 N 0 0.936899862825789 N N 20739 0 ENSG00000143951 ENSG00000211560 - - 2 4 63669355 38186151 utr3p upstream C2orf86 AC096739.3 63202041 38186025 - + 0 63309485 38123530 + - Y - - N HCC1954 620 560 420 4 1 N - - N LINE LINE 1 1 1 4 0.357087407996313 0.407079645115797 0.407079645115797 0.357087407996313 4 - - 48582 N Y 3.17407904459906 3.44719145177281 3.17407904459906 15 0.0957457609909635 0.119612314909257 N 0 0.421870240633567 N N 6896 1870 ENSG00000158604 ENSG00000153044 - - 7 5 44588352 68541939 utr3p upstream TMED4 CENPH 44584435 68521131 - + 0.258808000812265 44584845 68519063 + - Y - - N HCC1954 29 27.6 27 5 1 N - - N SINE SINE 1 0.608695652173913 1 5 0.34280391167646 0.657040830713216 0.657040830713216 0.34280391167646 1 - - 3403 Y Y 3.3984700535705 3.37973645838739 3.37973645838739 151 0.00662251655629142 0.268753584444586 Y 0.0668272125225768 0.984948826008429 N N 9282 1755 ENSG00000142197 ENSG00000159231 - + 21 21 36588442 36440728 upstream coding DOPEY2 CBR3 36458703 36429133 + + 0 36450445 36440500 - + N - 1.14346936946479 N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 33 0.592765097273879 0.814159290231593 0.814159290231593 0.592765097273879 2 - 0 30243 Y Y 3.27551679143744 3.58593758607883 3.27551679143744 222 0 0.0229872156889013 Y 0.121621621621622 0.988288288288288 N N 217 4501 ENSG00000156500 ENSG00000156504 - - X X 133816282 133758830 upstream utr5p FAM122C FAM122B 133768890 133731262 + - 0 133765803 133758488 - + N - 1.13868446796403 N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.282608695652174 0.282608695652174 9 0.999844742389676 0.985561246069823 0.999844742389676 0.985561246069823 1 - 0 33094 N Y 3.48337348351473 3.47336426491055 3.47336426491055 318 0.0171848702276555 0.0953339826425483 Y 0.00314465408805042 0.985959783860395 N N 171855 275222 ENSG00000198886 ENSG00000198763 - + MT MT 12138 5512 coding coding MT-ND4 MT-ND2 10761 4471 + + 0.0171848702276555 10973 5078 - + N 0.536334839507319 0.96456179033856 N HCC1954 4 1.71428571428571 1 3 4 Y - - N - - 0 0 0 7 1.39978263934555 0.99270299422975 1.39978263934555 0.99270299422975 1 0 0 30571 Y Y 3.41103992525442 3.30062602958175 3.30062602958175 81 0 0.0987048532503957 Y 0.993919283115483 0.993919283115483 N N 0 466 ENSG00000215269 ENSG00000049769 - + X X 49082313 49031501 upstream coding GAGE13 PPP1R3F 49047069 49013261 + + 0 49042695 49025467 - + N - - N HCC1954 20 4.58823529411765 1 14 1 N - - Y LINE,LINE - 1 0 1 17 1.08554572030879 1.40692438750547 1.40692438750547 1.08554572030879 1 - - 27936 N Y 3.43887765034782 3.74487454086093 3.43887765034782 0 0 0.602463988474041 N 0.927563636363636 0.909454545454545 N N 5945 100806 ENSG00000003249 ENSG00000163931 + + 16 3 88613438 53265078 utr5p coding DBNDD1 TKT 88598782 53234715 - - 0 88603976 53249307 - - Y - - N HCC1954 39 33.75 29 4 1 N 9 26.613 N SINE - 1 0 1 4 0.271386430077198 0.271386430077198 0.271386430077198 0.271386430077198 4 - - 36620 Y Y 3.32886498225927 3.18040125439778 3.18040125439778 233 0 0.256495937202444 Y 0 0.986360162267035 N N 10492 2365 ENSG00000211584 ENSG00000079337 - - 12 12 46461719 46439128 utr5p upstream SLC48A1 RAPGEF3 46453258 46417296 + - 0 46459079 46440452 - + N - - N HCC1954 1 1 1 0 3 N - - Y - DNA 0 0.0355029585798817 0.0355029585798817 5 0.421363141435649 0.707033067832699 0.707033067832699 0.421363141435649 1 - - 13663 Y Y 3.69425483698818 3.51104337473878 3.51104337473878 354 0.0091762927777177 0.229969246137891 Y 0.650671128863939 0.987297131958689 N N 4291 30294 ENSG00000075240 ENSG00000075275 - - 22 22 45454352 45311731 utr5p upstream DIP CELSR1 45394963 45134397 + - 0 45401312 45351851 - + N 0.0152608685699692 - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.652941176470588 0.652941176470588 46 1.37121564670584 1.21409718718746 1.37121564670584 1.21409718718746 4 0 - 2053 N Y 3.26824964015148 3.16463888744835 3.16463888744835 0 0 0.0420606707723878 N 0.292517006802721 0.778911564625851 N N 8014 4577 ENSG00000149084 ENSG00000146263 - + 11 6 43834736 97837773 utr3p utr3p HSD17B12 C6orf167 43658719 97696758 + - 0 43834016 97698450 - - Y - - N HCC1954 70 44.75 34 4 1 N 411 21.7753 N - SINE 0 1 1 4 0.385654400636018 0.328520415356608 0.385654400636018 0.328520415356608 1 - - 6779 Y Y 3.13842622151726 3.47336426491055 3.13842622151726 1 0.00207468879668049 0.108985978720662 Y 0.00207468879668049 0.995584401277861 N N 26165 2840 ENSG00000143870 ENSG00000143882 + + 2 2 10895554 10842679 utr3p intron PDIA6 ATP6V1C2 10840970 10779226 - + 0 10841836 10827779 - + N - 0.0190746589255255 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.478497126715059 0.449930134075354 0.478497126715059 0.449930134075354 1 - 0 9756 N Y 3.59425138750382 3.60103760561896 3.59425138750382 0 0 0.584476202494287 N 0.82615539759451 0.935951988587451 N N 473 7721 ENSG00000154251 ENSG00000108854 + + 17 17 63635979 60088854 downstream coding AC005332.1-1 SMURF2 63633345 59971197 - - 0 63633122 59988084 - - N - - Y HCC1954 12 4.64285714285714 2 28 2 N - - N - - 0 0 0 28 1.39264089118562 0.442788385915428 1.39264089118562 0.442788385915428 1 - - 35965 N N 3.46551447180198 3.51001030496889 3.46551447180198 3 0 0.552181018891582 N 0 0 N N 712661 0 ENSG00000111640 ENSG00000219951 + + 12 6 6517797 84160059 coding intron GAPDH RP11-378G13.2 6513918 84158544 + + 0 6517076 84159458 + + Y - 1 N HCC1954 3 2.2 1 3 1 N - - N - - 0 0 0 5 0.735600060472404 0.278528178237124 0.735600060472404 0.278528178237124 3 - 0 48933 N N 3.4561676006071 3.72079837248651 3.4561676006071 0 0 0.981823711165823 N 0 0.00312500000000004 Y N 19497 22 ENSG00000134970 ENSG00000172901 + + 5 5 114989757 115391199 intron intron TICAM2 AC034236.1 114942238 115326170 - + 0.00312500000000004 114989149 115388480 - + N 0.297252844097792 0.493778452200303 N HCC1954 1 1 1 0 5 N - - N - - 0 0 0 53 0.99270299422975 1.01412823870953 1.01412823870953 0.99270299422975 0 0 0 42294 Y Y 3.6052936758779 3.27614863362321 3.27614863362321 0 0 0.319136071302899 Y 0.8774049561336 0.986378328459289 N N 0 6139 ENSG00000213466 ENSG00000164056 - + 4 4 125203592 124544357 upstream downstream AC108075.3 SPRY1 125203103 124537406 + + 0 124969698 124802436 - + N - - N HCC1954 1 1 1 0 2 N - - Y - LINE 0 1 1 4 0.728458312312478 0.421363141435649 0.728458312312478 0.421363141435649 2 - - 9599 Y Y 3.11080976345569 3.43824580816205 3.11080976345569 271 0 0.0359064114004906 Y 0.980073800738007 0.990036900369004 N N 64784 2188 ENSG00000170004 ENSG00000182224 - + 17 17 7756803 7721124 upstream intron CHD3 CYB5D1 7728849 7702038 + + 0 7727280 7702876 - + N - 0.719341995259983 N HCC1954 3 3 3 7 1 N - - Y - - 0 0 0 7 0.678466075192994 0.99270299422975 0.99270299422975 0.678466075192994 2 - 0 27061 Y Y 2.6465826677615 3.23697244570866 2.6465826677615 3 0.0100815185287285 0.944805043046293 Y 0 0.985114007797425 N N 4999 5945 ENSG00000141013 ENSG00000003249 - - 16 16 88638880 88613438 coding upstream GAS8 DBNDD1 88616509 88598782 + - 0 88621545 88613677 - + N - - N HCC1954 1 1 1 0 2 N - - Y - Low_complexity 0 0.118279569892473 0.118279569892473 13 1.08554572030879 1.22123893534739 1.22123893534739 1.08554572030879 4 - - 4045 Y Y 3.58271458558979 3.58697065584872 3.58271458558979 296 0 0.044713902832786 Y 0 0.979018492176387 N N 1841 1688 ENSG00000196652 ENSG00000160908 - - 7 7 98969380 98935840 upstream upstream ZKSCAN5 ZNF394 98940209 98928806 + - 0 98939106 98937068 - + N - - N HCC1954 6 2.25 1 1 1 N - - Y - LTR 0 1 1 4 0.678466075192994 0.814159290231593 0.814159290231593 0.678466075192994 4 - - 3922 N Y 3.73080759109069 3.66695566812472 3.66695566812472 0 0 0.0630804061116348 N 0.882985452245414 0.859582542694497 N N 0 0 ENSG00000182707 ENSG00000177329 + + X 7 73013524 32478262 downstream upstream FXYD8 AC018641.3 73011598 32477585 + + 0 73081224 32421558 + + Y - - N HCC1954 20 13.8333333333333 8 6 1 N 284 23.0148 N - SINE 0 1 1 6 0.449930134075354 0.335662163516534 0.449930134075354 0.335662163516534 2 - - 47163 Y Y 3.48743121468078 3.28292550416853 3.28292550416853 0 0.633384932920537 0.105144619495743 N 0.947626418988648 0.947626418988648 Y N 20782 267 ENSG00000205246 ENSG00000213967 - + 19 19 23802761 23910101 downstream coding RPSAP8 AC011503.4 23801726 23889552 + + 0.319143446852425 23806246 23906991 - + N - - N HCC1954 2 1.75 1 3 1 N - - N - - 0 0 0 4 0.764167053112109 0.414221393275723 0.764167053112109 0.414221393275723 1 - - 47094 Y Y 3.42783536197374 2.95393894821337 2.95393894821337 238 0 0.00565362821823745 Y 0.246656923639021 0.991340884179759 N N 13744 6959 ENSG00000072071 ENSG00000105011 + - 19 19 14177972 14108440 intron upstream LPHN1 ASF1B 14119547 14091322 - - 0 14127014 14109016 - + N 0.605239954802675 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 1.01412823870953 0.842726282871298 1.01412823870953 0.842726282871298 2 0 - 4252 Y Y 3.57535930602118 3.21232721588077 3.21232721588077 239 0 0.369352071350336 Y 0 0.859286883754775 N N 0 31271 ENSG00000209275 ENSG00000146701 - + 7 7 75554801 75533864 upstream downstream AC005077.5-1 MDH2 75554699 75515329 + + 0.978351828269965 75544360 75542572 - + N - - N HCC1954 2 1.16666666666667 1 1 1 N - - Y DNA,DNA,SINE LTR 0.711111111111111 0.032258064516129 0.711111111111111 6 0.642757334393363 0.664182578873142 0.664182578873142 0.642757334393363 4 - - 46693 N Y 3.10616939046704 3.44871903508266 3.10616939046704 0 0 0.110879372346626 N 0 0.820197868374516 N N 342 0 ENSG00000219665 ENSG00000210638 + - 19 4 11999553 58053296 intron downstream AC008770.7-4 AC013724.8 11959471 58053193 + - 0 11959800 57901395 + + Y 1.86793252820982 - N HCC1954 20 6.25 1 2 1 N - - N - SINE 0 0.837209302325581 0.837209302325581 4 0.557056356474248 0.307095170876829 0.557056356474248 0.307095170876829 2 0 - 16601 N N 3.70512929149291 3.18937740323207 3.18937740323207 0 0 0.058898969795908 N 0.574057843996494 0 N N 170 0 ENSG00000187595 ENSG00000207623 + - 17 1 37459533 207672210 intron upstream ZNF385C hsa-mir-205 37431120 207672101 - + 0 37435312 207670368 - - Y 1.39692234311101 - N HCC1954 35 21.2307692307692 20 13 1 N - - N SINE - 1 0 1 13 0.271386430077198 0.478497126715059 0.478497126715059 0.271386430077198 3 0 - 30521 Y Y 3.71041843152174 3.20487865035633 3.20487865035633 184 0 0.00498377552376061 Y 0.784510869565217 0.983423913043478 N N 4858 44136 ENSG00000169093 ENSG00000169100 + - X X 1531844 1470993 downstream upstream ASMTL SLC25A6 1482032 1465144 - - 0.983423913043478 1477712 1476050 - + N - - N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.602941176470588 0.602941176470588 4 0.478497126715059 0.485638874874985 0.485638874874985 0.478497126715059 1 - - 32646 N Y 3.28552601004162 3.33420755545058 3.28552601004162 293 0 0.00201794765811414 N 0.8945917563665 0.8945917563665 N N 42439 1 ENSG00000138674 ENSG00000172139 - - 4 3 84040715 113495795 intron intron SEC31A SLC9A10 83958839 113342424 - - 0.798766080336046 84035020 113483247 + + Y 5.28288539994045 1.0255297421496 N HCC1954 1 1 1 0 1 N - - N DNA - 1 0 1 4 0.421363141435649 0.578481600954027 0.578481600954027 0.421363141435649 1 0 0 45423 N N 3.77208042376856 3.54400240599166 3.54400240599166 32 0 0.643900807200698 N 0.00440528634361237 0.257829395274329 N N 0 175 ENSG00000218744 ENSG00000182578 + - 10 5 36026971 149473128 downstream intron RP11-382K22.1 CSF1R 36026234 149413051 + - 0.257829395274329 36026992 149454794 + + Y - 2.46861848455443 N HCC1954 12 11 10 4 1 N - - N - - 0 0 0 4 0.257102933757345 0.314236919036755 0.314236919036755 0.257102933757345 2 - 0 28739 N N 3.65384724021086 3.5010341561346 3.5010341561346 3 0 0.116441812795395 N 0 0 N N 886 40617 ENSG00000197162 ENSG00000130164 - + 16 19 30504511 11105490 utr3p utr3p ZNF688 LDLR 30008266 11061132 - + 0 30500048 11104135 + + Y - 2.27267372255859 N HCC1954 39 38 37 7 1 N - - N SINE SINE 1 0.0317460317460317 1 7 0.314236919036755 0.449930134075354 0.449930134075354 0.314236919036755 3 - 0 42092 N N 2.8972397758265 3.48383749183115 2.8972397758265 47 0.485589519650655 0.18624239512135 N 0.634934497816594 0.502183406113537 N N 1 78560 ENSG00000163116 ENSG00000112493 + + 4 6 99283414 33390114 intron utr3p C4orf37 TAPBP 98699050 33375449 - - 0.502183406113537 99124334 33376425 - - Y 0.907096774193548 - N HCC1954 63 30.1666666666667 9 6 1 N - - N LINE,SINE SINE 0.921052631578947 1 1 6 0.271386430077198 0.535631111994469 0.535631111994469 0.271386430077198 2 0 - 13764 Y Y 3.18296190747752 3.43358851031899 3.18296190747752 296 0 0.02007070777651 Y 0.993079016516516 0.993079016516516 N N 238 110 ENSG00000211643 ENSG00000198312 - + 22 22 21003581 20993088 coding downstream IGLV5-52 D87018.1-3 21003021 20991471 + + 0 21003255 20994249 - + N 0.0469079334214729 - N HCC1954 7 2.6 1 3 2 N - - Y - - 0 0 0 5 0.842726282871298 0.999844742389676 0.999844742389676 0.842726282871298 1 0 - 31032 N Y 3.36869417001331 3.66848325143457 3.36869417001331 238 0 0.0319212323120991 N 0.924845409862058 0.924845409862058 N N 41549 0 ENSG00000164054 ENSG00000217820 + - 3 X 48516665 41067308 intron upstream SHISA5 RP13-13A3.1 48484201 41066798 - - 0 48489428 41067532 - + Y 1.11512714644717 - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 14 1.20695543902754 0.428504889595575 1.20695543902754 0.428504889595575 4 0 - 26735 Y Y 3.53615261288309 3.60785432895764 3.53615261288309 0 0 0.281132705628324 Y 0.00276243093922657 0.993881978103922 N N 5 40802 ENSG00000196585 ENSG00000205609 - - 16 16 28333958 28322701 downstream upstream AC138894.2-1 EIF3CL 28332525 28298403 + - 0 28345008 28322810 - + N - - N HCC1954 6 6 6 5 1 N - - Y LTR - 0.643564356435644 0 0.643564356435644 5 1.01412823870953 0.764167053112109 1.01412823870953 0.764167053112109 1 - - 36292 Y N 3.53615261288309 3.47552369040616 3.47552369040616 0 0 0.0528366177718486 Y 0.801905425816196 0 N N 75 0 ENSG00000064763 ENSG00000222481 - - 12 12 29378272 29165082 utr5p upstream FAR2 AC012150.16 29267865 29164983 + - 0 29314629 29193643 - + N 0.276219567460816 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 11 0.921285512630487 0.914143764470561 0.921285512630487 0.914143764470561 2 0 - 20497 N N 3.50641658211926 3.43937216388778 3.43937216388778 30 0.155365566037736 0.0707254085456831 N 0.174135220125786 0.155365566037736 N N 950 78560 ENSG00000185436 ENSG00000112493 + + 1 6 24387036 33390114 utr3p utr3p IL28RA TAPBP 24353234 33375449 - - 0.155365566037736 24353718 33375989 - - Y - - N HCC1954 36 35 34 4 1 N 572 27.019 N SINE DNA 1 0.795081967213115 1 4 0.278528178237124 0.599906845433805 0.599906845433805 0.278528178237124 3 - - 24762 Y Y 3.07680408206379 3.72655152083176 3.07680408206379 350 0 0.00117547758356806 Y 0.002857142857143 0 N N 4823 1271 ENSG00000141627 ENSG00000101665 + - 18 18 45241077 44731079 downstream upstream DYM SMAD7 44824170 44700222 - - 0 44801612 44776089 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 0.592765097273879 0.857009779191151 0.857009779191151 0.592765097273879 2 - - 28726 N N 3.64127736852694 3.02692582291221 3.02692582291221 6 0 0.048606892612552 N 0 0.0208412277377793 N N 2191 6328 ENSG00000131943 ENSG00000167508 - + 19 16 34898292 87257019 utr3p intron C19orf12 MVD 34881634 87245849 - - 0.0208412277377793 34881985 87256823 + - Y - 1.07307248473141 N HCC1954 33 30.5555555555556 22 9 1 N 19 15.41 N SINE - 1 0 1 9 0.321378667196682 0.442788385915428 0.442788385915428 0.321378667196682 1 - 0 48263 N N 3.06362529613304 3.15678909433978 3.06362529613304 0 0.00290697674418616 0.124316008749331 N 0.0998465762273901 0 N N 551733 0 ENSG00000204628 ENSG00000217268 + - 5 6 180603512 74771248 utr3p upstream GNB2L1 RP11-374N7.1 180596536 74770956 - - 0 180596546 74812633 - + Y - - N HCC1954 19 13.6 1 19 1 N - - N - SINE,Low_complexity 0 0.42 0.42 20 0.914143764470561 0.357087407996313 0.914143764470561 0.357087407996313 3 - - 216 Y Y 3.46824295875106 3.50529022639353 3.46824295875106 305 0 0.0445840141318476 Y 0 0 N Y 5767 4805 ENSG00000110237 ENSG00000171631 - + 11 11 72757783 72687292 coding intron ARHGEF17 P2RY6 72697317 72653218 + + 0 72735576 72661159 - + N 0.693474575474322 0.693440573389612 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.54 0.54 11 0.585623349113953 1.07126222398894 1.07126222398894 0.585623349113953 4 0 0 13688 Y Y 3.13379942889774 3.4439989565073 3.13379942889774 280 0 0.840622978419093 Y 0 0.904452054794521 N N 0 0 ENSG00000220101 ENSG00000218145 + - 22 22 22325521 22312612 intron intron AP000347.3 AP000347.4 22321400 22310865 - - 0 22324574 22312557 - + N 1 1 N HCC1954 2 1.125 1 1 6 N - - Y - - 0 0 0 8 0.549914608314322 0.599906845433805 0.599906845433805 0.549914608314322 2 0 0 24092 N Y 3.44143830342756 3.50785087947327 3.44143830342756 0 0 0.232286274044503 N 0.915917616250265 0.887890155000354 N N 0 2470 ENSG00000208696 ENSG00000151883 + + 1 5 147554054 50173926 upstream coding AL356957.27-7 PARP8 147553983 49998570 - + 0 147557827 49998776 - + Y - - N HCC1954 12 5 1 6 1 N - - N LTR - 1 0 1 9 0.871293275511003 0.621332089913584 0.871293275511003 0.621332089913584 1 - - 29359 N Y 3.707857778442 3.37080016234644 3.37080016234644 262 0 0.00770531451333634 N 0.478189749182115 0.794438386041439 N N 185 95833 ENSG00000204600 ENSG00000204525 - + 6 6 30342707 31432935 utr5p coding HLA-L HLA-C 30335353 31344505 + - 0.794438386041439 30335790 31347406 - - N 0.564890559363254 - Y HCC1954 1 1 1 0 1 N - - N - - 0 0 0 4 0.34280391167646 0.335662163516534 0.34280391167646 0.335662163516534 1 0 - 33129 N Y 3.29595938416888 3.59102838701478 3.29595938416888 403 0 0.0133149322353486 Y 0 0.993917569448647 N N 171855 539404 ENSG00000198886 ENSG00000198712 - + MT MT 12138 8270 coding coding MT-ND4 MT-CO2 10761 7587 + + 0 10907 7782 - + N 0.418313462819904 1.03546587000528 N HCC1954 2 1.33333333333333 1 2 3 Y - - N - - 0 0 0 6 1.18553019454776 0.842726282871298 1.18553019454776 0.842726282871298 2 0 0 29957 N Y 3.47911741325579 3.50744965188915 3.47911741325579 0 0 0.0479241350118371 N 0 0 N N 975 0 ENSG00000198487 ENSG00000210180 + - 6 X 42218335 3987693 coding upstream AL512274.9 AC073493.27-1 42183124 3987629 - - 0 42183205 4202000 - + Y - - N HCC1954 22 7.85714285714286 2 7 1 N - - N - SINE 0 1 1 7 0.51420586751469 0.299953422716903 0.51420586751469 0.299953422716903 1 - - 40188 Y Y 3.68783934123363 3.4561676006071 3.4561676006071 283 0 0.181590700257548 Y 0.0268882508833922 0 N N 1602 563 ENSG00000177082 ENSG00000176700 + + 15 15 82998525 82985249 coding utr3p WDR73 SCAND2 82987018 82975695 - + 0 82990419 82984451 - + N - 0.664303798839279 N HCC1954 1 1 1 0 1 N - - Y - SINE 0 0.0655737704918033 0.0655737704918033 5 0.971277749749971 0.857009779191151 0.971277749749971 0.857009779191151 4 - 0 28815 N N 3.47336426491055 3.11125084383316 3.11125084383316 0 0 0.0432333653087208 N 0 0 N N 1848 4096 ENSG00000198131 ENSG00000103121 + + 19 16 63466822 79597997 utr3p coding ZNF544 C16orf61 63431882 79567206 + - 0 63466549 79572941 + - Y - - N HCC1954 26 24 21 7 1 N - - N SINE - 1 0 1 7 0.299953422716903 0.764167053112109 0.764167053112109 0.299953422716903 1 - - 31297 Y Y 3.48167806633553 3.56232542602083 3.48167806633553 261 0 0.0533823502194177 Y 0.175215259753635 0.98928850986693 N N 12276 2379 ENSG00000163655 ENSG00000169359 - - 3 3 157138215 157054889 upstream upstream GMPS SLC33A1 157071019 157027032 + - 0.196638240019775 157063129 157058813 - + N - - N HCC1954 9 3.8 1 2 1 N - - Y LTR LINE 1 1 1 5 1.09982921662864 0.542772860154395 1.09982921662864 0.542772860154395 1 - - 18336 Y Y 3.29549537585246 3.66592259835483 3.29549537585246 292 0 0.339127853618464 Y 0.0118702112839562 0 N N 14045 0 ENSG00000117859 ENSG00000218025 - - 1 1 52026729 51833157 utr5p intron OSBPL9 RP11-191G24.2 51815439 51800126 + - 0 51855134 51812392 - + N 0.00670793950779787 1 N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.160220994475138 0 0.160220994475138 9 1.29265641694665 0.814159290231593 1.29265641694665 0.814159290231593 4 0 0 13679 Y Y 2.80253481394078 3.32207876414413 2.80253481394078 166 0 0.0466381202362405 Y 0 0 N N 51 14981 ENSG00000182057 ENSG00000100207 - - 22 22 41000811 40941389 intron utr5p Z83851.17 TCF20 40995703 40885963 + - 0 40996291 40941293 - + N 3.07360415790882 90.2271956765243 N HCC1954 1 1 1 0 2 N - - Y Low_complexity - 0.449438202247191 0 0.449438202247191 6 0.635615586233437 0.635615586233437 0.635615586233437 0.635615586233437 1 0 0 4877 Y N 3.59887818012334 3.62613749619346 3.59887818012334 0 0 0.225939116723424 N 0 0 Y N 16361 188 ENSG00000198420 ENSG00000159860 - - 7 7 143230181 143146099 coding downstream FAM115B AC099548.6 143180984 143138257 - + 0 143204020 143161168 + - N - - N HCC1954 4 3 2 4 1 N - - N - - 0 0 0 4 0.892718519990782 0.828442786551446 0.892718519990782 0.828442786551446 2 - - 17717 N Y 3.2965682984157 3.48167806633553 3.2965682984157 0 0 0.562507454788852 N 0.947602339181287 0.930136452241715 N N 5400 0 ENSG00000122482 ENSG00000202394 - - 1 1 91260358 172100206 upstream downstream ZNF644 SNORD47 91153447 172100130 - - 0.930136452241715 91287825 172100065 + + N - - Y HCC1954 3 2.45 1 17 1 N - - N - - 0 0 0 20 0.657040830713216 0.849868031031224 0.849868031031224 0.657040830713216 3 - - 29189 Y Y 3.40951234194457 3.76273355257368 3.40951234194457 336 0 0.0212417094502518 Y 0.540764790764791 0.987914862914863 N N 23280 891 ENSG00000124767 ENSG00000183826 + - 6 6 38778930 38673848 downstream upstream GLO1 BTBD9 38751682 38250713 - - 0 38715554 38673875 - + N - - N HCC1954 1 1 1 0 1 N - - Y Simple_repeat - 0.605095541401274 0 0.605095541401274 20 1.12125446110842 1.19981369086761 1.19981369086761 1.12125446110842 4 - - 2193 N Y 3.6491271616355 3.39128260787123 3.39128260787123 0 0 0.0803247194464694 N 0.841866571189879 0 N N 3619 12271 ENSG00000174669 ENSG00000177479 + - 11 3 65895867 48997971 upstream intron SLC29A2 ARIH2 65886569 48931285 - + 0 65904559 48939897 - - Y - 0.963247002497696 N HCC1954 21 20.7142857142857 20 7 1 N - - N SINE - 1 0 1 7 0.299953422716903 0.614190341753658 0.614190341753658 0.299953422716903 1 - 0 28339 N Y 3.63399663687184 3.2159209387304 3.2159209387304 0 0 0.406878894339469 N 0.941898148148148 0.941898148148148 N N 2710 11 ENSG00000196678 ENSG00000176406 - + 16 8 20819172 105333263 coding intron ERI2 RIMS2 20699017 104582291 - + 0.0537698412698414 20722492 104702850 + + Y - 1.06909912995821 N HCC1954 20 20 20 4 1 N - - N - LTR 0 1 1 4 0.707033067832699 0.521347615674617 0.707033067832699 0.521347615674617 1 - 0 3522 N N 3.61720120015252 3.47705127371601 3.47705127371601 0 0 0.480528890716597 N 0 0 N N 6 166846 ENSG00000157554 ENSG00000142192 + + 21 21 38955488 26465003 upstream coding ERG APP 38673819 26174733 - - 0 39019355 26384132 - - N - - Y HCC1954 1 1 1 0 1 N - - N LTR - 0.879746835443038 0 0.879746835443038 9 1.12125446110842 0.785592297591888 1.12125446110842 0.785592297591888 2 - - 29131 Y Y 3.41737571542227 3.48696720636436 3.41737571542227 334 0 0.0307952070804437 Y 0 0 N N 2787 97 ENSG00000197657 ENSG00000137338 + + 6 6 28429951 28378305 downstream downstream ZNF323 PGBD1 28400493 28357328 - + 0 28391349 28389282 - + N - - N HCC1954 1 1 1 0 1 N - - Y - Simple_repeat 0 0.134502923976608 0.134502923976608 33 1.16410495006798 1.22123893534739 1.22123893534739 1.16410495006798 4 - - 45747 N N 3.47655676017605 3.57800808738356 3.47655676017605 0 0 0.461775180796998 N 0.00398406374501981 0 N N 7329 17943 ENSG00000176095 ENSG00000105141 + + 3 19 49798977 15027900 intron downstream IP6K1 CASP14 49736732 15024015 - + 0.00398406374501981 49744390 15029502 - + Y 0.772383765861644 - N HCC1954 3 2.25 1 3 1 N - - N SINE - 1 0 1 4 0.242819437437493 0.471355378555133 0.471355378555133 0.242819437437493 3 0 - 277 N Y 3.6272104187567 3.5816815158199 3.5816815158199 257 0.0038910505836578 0.0160712112660456 Y 0.986893303297153 0.986893303297153 N N 2208 19435 ENSG00000173914 ENSG00000173933 + + 11 11 66201851 66170516 intron coding RBM4B RBM4 66189048 66140673 - + 0 66189901 66164168 - + N 0.699848265632176 0.843545639785394 N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 6 0.485638874874985 0.292811674556976 0.485638874874985 0.292811674556976 1 0 0 38112 N Y 3.53089397807781 3.18991595946201 3.18991595946201 0 0 0.471746907916341 Y 0 0.984485815602837 N N 2024 2004 ENSG00000129538 ENSG00000181784 + + 14 14 20340876 20238597 downstream downstream RNASE1 RNASE4 20339355 20222212 - + 0 20337955 20251168 - + N - - N HCC1954 1 1 1 0 2 N - - N LTR,SINE LTR 0.529411764705882 1 1 7 0.728458312312478 0.728458312312478 0.728458312312478 0.728458312312478 2 - - 29283 Y Y 3.40744620240479 3.61832755587824 3.40744620240479 307 0 0.0161621462921038 Y 0.989046783835057 0.989046783835057 N N 0 1384 ENSG00000209924 ENSG00000124787 + - 6 6 4991334 4949270 downstream upstream AL359643.27 RPP40 4991186 4940280 - - 0 4987740 4966707 - + N - - N HCC1954 20 5.57142857142857 1 16 2 N - - Y LTR,LTR,LTR SINE 0.706185567010309 1 1 21 1.38549914302569 0.614190341753658 1.38549914302569 0.614190341753658 1 - - 23775 N N 3.50000108636471 3.33680806132368 3.33680806132368 35 0 0.437276489410979 N 0.970415841584158 0.359009900990099 N N 1814 2806 ENSG00000178229 ENSG00000143674 + + 19 1 62533956 231587517 utr3p utr3p ZNF543 MAP3K19 62523689 231530137 + + 0.457623762376238 62532991 231585767 + + Y - 2.37004660865496 N HCC1954 34 23.8333333333333 22 12 1 N - - N SINE - 1 0 1 12 0.499922371194838 0.692749571512847 0.692749571512847 0.499922371194838 3 - 0 47013 N Y 3.11232376639641 3.25613019641484 3.11232376639641 376 0 0.00748728306469082 Y 0 0.992208277925532 N N 1118 1118 ENSG00000167744 ENSG00000167744 + - 19 19 54258936 54258936 upstream utr5p NTF4 NTF4 54256216 54256216 - - 0.992208277925532 54259898 54258930 - + N - 10.3380307635627 N HCC1954 1 1 1 0 1 N - - N Low_complexity - 0.0854700854700855 0 0.0854700854700855 26 0.835584534711372 0.807017542071667 0.835584534711372 0.807017542071667 2 - 0 26780 N Y 3.35766122920905 3.45297510534159 3.35766122920905 93 0 0.0365206628652819 Y 0.956033452807646 0.978016726403823 N N 23840 6229 ENSG00000102898 ENSG00000102901 - - 16 16 66462727 66425300 intron upstream NUTF2 CENPT 66438331 66419565 + - 0.0986857825567502 66439048 66426992 - + N 1.0809318228776 - N HCC1954 4 1.6 1 1 2 N - - N - SINE 0 1 1 5 0.678466075192994 0.664182578873142 0.678466075192994 0.664182578873142 1 0 - 38216 N Y 3.60103760561896 3.61616813038263 3.60103760561896 0 0 0.99955141508395 Y 0 0.977390485162506 N N 10274 0 ENSG00000197555 ENSG00000207444 - + 14 14 71275871 70934877 upstream downstream SIPA1L1 SNORD56 71065795 70934807 + + 0 71049214 70937390 - + N - - N HCC1954 1 1 1 0 6 N - - N LTR - 1 0 1 5 0.664182578873142 0.664182578873142 0.664182578873142 0.664182578873142 2 - - 42556 Y Y 3.23896403733493 3.57848902055439 3.23896403733493 0 0 0.993057975652888 Y 0 0.985763042418333 N N 1615 108 ENSG00000156219 ENSG00000169248 - - 4 4 77252964 77176376 utr5p upstream ART3 CXCL11 77214887 77173975 + - 0 77216058 77194451 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 36 1.05697872766909 1.1426797055882 1.1426797055882 1.05697872766909 4 - - 24654 Y Y 3.85425536676371 3.58271458558979 3.58271458558979 0 0 0.857812843807965 Y 0.993171890241316 0.993171890241316 N N 4163 124 ENSG00000141644 ENSG00000172361 + - 18 18 46062142 46046863 coding upstream MBD1 CCDC11 46049215 46007564 - - 0 46051907 46048029 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 33 1.36407389854591 1.09982921662864 1.36407389854591 1.09982921662864 1 - - 42573 N N 3.55401162459584 3.40740634961144 3.40740634961144 244 0.5531210592686 0.0115778281053275 Y 0.73187263556116 0.680800756620429 N Y 532 207 ENSG00000131127 ENSG00000215383 - + 4 4 359047 146496 utr5p intron ZNF141 ZNF718 321622 43358 + + 0.182849936948298 321775 49323 - + N - 0.823742306121539 N HCC1954 4 3.6 2 5 1 N - - N - - 0 0 0 5 0.428504889595575 0.521347615674617 0.521347615674617 0.428504889595575 2 - 0 1183 N N 3.50272957331379 3.18768198605288 3.18768198605288 0 0.0926399545325376 0.124202752413303 N 0 0 N N 12635 0 ENSG00000109919 ENSG00000212455 - - 11 2 47620640 18085480 utr5p upstream MTCH2 SNORA40 47595444 18085353 - - 0 47620596 18214990 + + Y - - N HCC1954 3 1.33333333333333 1 1 1 N - - N - LTR 0 1 1 6 0.314236919036755 0.321378667196682 0.321378667196682 0.314236919036755 3 - - 31410 N Y 3.51633251476761 3.84168549507978 3.51633251476761 253 0 0.0114483678251157 Y 0 0 N N 2195 4350 ENSG00000058056 ENSG00000136521 - + 3 3 180984675 180824981 upstream intron USP13 NDUFB5 180853635 180805269 + + 0 180840366 180819006 - + N - 2.21188169535504 N HCC1954 3 1.22222222222222 1 1 1 N - - N SINE - 1 0 1 9 0.885576771830856 0.814159290231593 0.885576771830856 0.814159290231593 2 - 0 33212 N N 3.21588108593705 3.22064101730576 3.21588108593705 0 0 0.661130535126877 N 0 0 Y N 171855 247001 ENSG00000198886 ENSG00000198786 - + MT MT 12138 14149 coding coding MT-ND4 MT-ND5 10761 12338 + + 0 11079 14051 - + N 0.624828569119596 - N HCC1954 1 1 1 0 3 Y 189 4.09957 N - - 0 0 0 7 1.29265641694665 1.07126222398894 1.29265641694665 1.07126222398894 1 0 - 44403 N N 3.39487633072086 3.18615440274303 3.18615440274303 1 0 0.244793056930430 N 0 0 N N 1 0 ENSG00000137872 ENSG00000218380 - + 15 10 45853709 33387341 intron downstream SEMA6D RPL7AP53 45797978 33386549 + - 0 45809642 33386530 - - Y 0.988474467744517 - N HCC1954 11 4.66666666666667 3 15 1 N 535 27.0704 N - - 0 0 0 15 0.478497126715059 0.257102933757345 0.478497126715059 0.257102933757345 1 0 - 47226 N Y 3.76170048280379 3.58999531724489 3.58999531724489 1 0 0.8612075099253 N 0.61439205955335 0.892886683209264 N N 2089 970 ENSG00000160336 ENSG00000182986 - + 19 19 58653326 58157833 utr5p coding ZNF761 ZNF320 58649710 58071237 + - 0 58649716 58078705 - - N 0.0427693509999645 - Y HCC1954 3 1.4 1 1 1 Y - - N - SINE 0 0.555555555555556 0.555555555555556 5 0.699891319672773 0.5713398527941 0.699891319672773 0.5713398527941 4 0 - 42268 Y Y 3.48271113610542 3.68321254861411 3.48271113610542 227 0 0.0213000350687151 Y 0.882338806567881 0.99094913896676 N N 2970 735 ENSG00000163293 ENSG00000198515 - - 4 4 47736947 47678276 upstream utr5p NPAL1 CNGA1 47713548 47632753 + - 0 47707570 47678276 - + N - 22.7593014426727 N HCC1954 3 1.27272727272727 1 2 2 N - - Y LTR Low_complexity 1 0.0353982300884956 1 11 0.51420586751469 0.807017542071667 0.807017542071667 0.51420586751469 1 - 0 14238 N Y 3.58849823915857 3.31489131844487 3.31489131844487 0 0 0.587238340592883 N 0.902429773616214 0.944245584923551 N N 21 480 ENSG00000205561 ENSG00000159496 - - 5 22 70185264 22371363 coding upstream AC139834.2 RGL4 70127358 22360329 + + 0 70127362 22355914 - - Y - - N HCC1954 9 7.87096774193548 3 31 1 N 36 25.6481 N - - 0 0 0 31 0.764167053112109 1.1141127129485 1.1141127129485 0.764167053112109 2 - - 30247 Y Y 3.32799974635873 3.70719543103269 3.32799974635873 0 0 0.999777605733333 Y 0.755161807532476 0.994028336769085 N N 3500 2920 ENSG00000131089 ENSG00000186767 + - X X 62922138 62487936 downstream upstream ARHGEF9 SPIN4 62771572 62483832 - - 0 62697435 62569094 - + N - - N HCC1954 1 1 1 0 7 N - - Y - LTR 0 1 1 65 1.4426331283051 1.27123117246687 1.4426331283051 1.27123117246687 1 - - 29176 Y Y 3.54296933622177 3.37345410138202 3.37345410138202 245 0 0.0396048519988559 Y 0.977868480725624 0.988934240362812 N N 387 8928 ENSG00000164674 ENSG00000146425 - - 6 6 159105889 158985759 utr5p upstream SYTL3 DYNLT1 158991034 158977494 + - 0 158992774 158986255 - + N 0.0918439279839765 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.664182578873142 0.671324327033068 0.671324327033068 0.664182578873142 1 0 - 49492 N Y 3.46128890676658 3.45144752203174 3.45144752203174 0 0 0.407343820738955 Y 0 0.86827137604877 N N 551733 0 ENSG00000204628 ENSG00000087116 + - 5 5 180603512 178704936 coding downstream GNB2L1 ADAMTS2 180596536 178473457 - - 0.86827137604877 180601100 178458708 - + N - - N HCC1954 20 20 20 4 1 N - - N - SINE 0 1 1 4 0.771308801272036 0.321378667196682 0.771308801272036 0.321378667196682 1 - - 37128 N Y 3.56890511773614 3.54400240599166 3.54400240599166 221 0 0.0278885092162257 N 0 0.668174962292609 N N 6175 0 ENSG00000221983 ENSG00000222458 + + 19 12 18546960 114640199 coding upstream UBA52 SRP_euk_arch 18545111 114639906 + + 0.668174962292609 18546888 114514863 + + Y - - N HCC1954 1 1 1 0 1 N 484 22.3649 N - - 0 0 0 9 0.621332089913584 0.278528178237124 0.621332089913584 0.278528178237124 2 - - 36250 Y N 3.30062602958175 3.20583169014299 3.20583169014299 0 0 0.264878471198913 Y 0 0.435897435897436 N N 0 3246 ENSG00000222159 ENSG00000111615 + - 12 12 74638177 74191685 downstream upstream SRP_euk_arch KRR1 74637881 74177686 - - 0.435897435897436 74505804 74374905 - + N - - N HCC1954 1 1 1 0 1 N - - Y LINE DNA 1 1 1 4 0.364229156156239 0.414221393275723 0.414221393275723 0.364229156156239 4 - - 37197 N N 3.54080991072615 3.13487235146098 3.13487235146098 0 0 0.0373326024719838 N 0 0 N N 0 712661 ENSG00000213376 ENSG00000111640 - + 5 12 173873916 6517797 intron coding AC108104.2 GAPDH 173872917 6513918 + + 0 173873298 6517090 - + Y 1 - N HCC1954 6 4.2 1 4 1 N - - N - - 0 0 0 5 0.492780623034912 0.735600060472404 0.735600060472404 0.492780623034912 0 0 - 27039 Y N 3.29383981146661 2.93868044237372 2.93868044237372 0 0 0.565686797141442 Y 0 0 N N 23054 0 ENSG00000131149 ENSG00000220991 - + 16 16 84267311 83906889 coding downstream KIAA0182 AC092275.3 84202524 83906768 + + 0 84239721 83948691 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 10 1.02841173502938 0.899860268150708 1.02841173502938 0.899860268150708 1 - - 24340 N N 3.53871326596283 3.35583426102209 3.35583426102209 0 0 0.296647845405080 N 0.325491873396065 0.00598802395209586 N N 64411 0 ENSG00000151914 ENSG00000206696 + + 6 18 56927363 45272097 intron upstream DST SNORD58 56430744 45272032 - - 0.00598802395209586 56843939 45272184 - - Y 16.6542368297408 - N HCC1954 6 6 6 8 1 N - - N - - 0 0 0 8 0.271386430077198 0.678466075192994 0.678466075192994 0.271386430077198 3 0 - 29695 N N 3.39487633072086 2.9548541897103 2.9548541897103 0 0.245714285714286 0.0770075506018163 Y 0.245714285714286 0.245714285714286 N N 37 8087 ENSG00000146147 ENSG00000137269 - + 6 6 54239040 53896878 coding downstream C6orf142 LRRC1 53991673 53767737 + + 0.245714285714286 54094217 53902197 - + N - - N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 5 0.671324327033068 0.614190341753658 0.671324327033068 0.614190341753658 2 - - 42073 N N 3.39384326095097 3.7297745213208 3.39384326095097 0 0 0.995680146118451 N 0 0 N N 29840 61 ENSG00000164830 ENSG00000038295 + + 8 4 107834093 167244443 coding upstream OXR1 TLL1 107739270 167013860 + + 0 107823719 166921167 + + Y - - N HCC1954 2 1.07692307692308 1 1 4 N - - N - LTR,LTR 0 1 1 13 1.12125446110842 1.02126998686945 1.12125446110842 1.02126998686945 2 - - 29613 Y Y 3.60103760561896 3.38127338926705 3.38127338926705 0 0 0.532373136918285 Y 0 0.949577875721646 N N 1837 2007 ENSG00000026297 ENSG00000213066 - - 6 6 167290669 167374055 coding upstream RNASET2 FGFR1OP 167263003 167332806 - + 0 167286026 167332396 + - N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.12125446110842 1.0069864905496 1.12125446110842 1.0069864905496 4 - - 40168 Y Y 3.57063922744582 3.48912663185998 3.48912663185998 244 0.00409836065573788 0.051610138371287 Y 0.00409836065573788 0 N N 980 35 ENSG00000169857 ENSG00000198838 + + 15 15 32118595 31945591 utr3p intron AVEN RYR3 31945721 31390469 - + 0.990946348733234 31946058 31944476 - + N - 0.489223765052261 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 4 0.914143764470561 0.907002016310634 0.914143764470561 0.907002016310634 2 - 0 38151 Y Y 3.51001030496889 3.56488607910057 3.51001030496889 267 0 0.519162117541854 Y 0 0.991336915811757 N N 4 4 ENSG00000181552 ENSG00000181562 - + 14 14 20308947 20286379 upstream downstream FAM12B FAM12A 20306426 20283939 + + 0 20301958 20293943 - + N - - N HCC1954 20 8.875 1 19 3 N - - Y LTR SINE 1 1 1 24 0.93556900895034 0.814159290231593 0.93556900895034 0.814159290231593 1 - - 29864 Y Y 3.5246463161926 3.43209143223268 3.43209143223268 0 0 0.873874086558347 Y 0.501760563380282 0.925264084507042 N Y 1837 5274 ENSG00000026297 ENSG00000071242 + - 6 6 167290669 167195648 coding intron RNASET2 RPS6KA2 167263003 166742844 - - 0 167272373 167191737 - + N - 65.9174251199735 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 9 0.971277749749971 0.792734045751814 0.971277749749971 0.792734045751814 4 - 0 13704 Y Y 3.36191729946799 3.39483647792751 3.36191729946799 262 0.00381679389312983 0.0154849382937505 Y 0.129461522591294 0 N N 91 112 ENSG00000213784 ENSG00000167087 + - 22 22 41158345 41158345 upstream intron NFAM1 AL022316.2 41106357 41106357 - - 0 41162909 41137689 - + N - 2.00324640505174 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 7 0.842726282871298 0.671324327033068 0.842726282871298 0.671324327033068 2 - 0 54 Y Y 3.69784855983781 3.53404662054996 3.53404662054996 377 0 0.0118780030276869 Y 0 0.990678995513027 N N 0 0 ENSG00000129586 ENSG00000222048 + - 11 11 10836165 10836196 upstream upstream AC069360.7 ZBED5 10830921 10830827 - - 0 10856505 10836599 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 13 0.821301038391519 0.421363141435649 0.821301038391519 0.421363141435649 1 - - 1151 N Y 3.00935843624818 2.1493974703477 2.1493974703477 0 0.531928279333124 0.193948130834973 N 0.531928279333124 0 N N 74637 0 ENSG00000089597 ENSG00000206951 - - 11 2 62170680 33024022 coding downstream GANAB Y_RNA 62148876 33023910 - - 0 62163779 32994807 + + Y - - N HCC1954 3 2 1 6 2 N 257 17.9495 N - Simple_repeat 0 1 1 7 1.15696320190805 0.707033067832699 1.15696320190805 0.707033067832699 3 - - 35864 N N 3.67489874718912 3.2965682984157 3.2965682984157 4 0 0.105703463719919 N 0 0 N N 712661 17333 ENSG00000111640 ENSG00000169180 + - 12 16 6517797 28130691 coding upstream GAPDH XPO6 6513918 28016817 + - 0.0163150850806195 6517537 28158798 + + Y - - N HCC1954 2 1.42857142857143 1 3 1 N 234 13.6434 N - - 0 0 0 7 0.871293275511003 0.521347615674617 0.871293275511003 0.521347615674617 2 - - 1204 N Y 2.32501121082418 1.68892254108627 1.68892254108627 20 0 0.132511424494633 N 0.283829787234043 0 N N 0 0 ENSG00000203360 ENSG00000211547 + - 11 2 71057232 132755208 downstream downstream AP003498.2-1 AC097532.3-1 71056959 132755117 + - 0.482765957446808 71059417 132745891 + + Y - - N HCC1954 3 2 1 3 1 N 391 8.61162 N Simple_repeat Low_complexity 1 1 1 4 0.292811674556976 0.328520415356608 0.328520415356608 0.292811674556976 1 - - 9391 Y Y 3.425274708894 3.70719543103269 3.425274708894 254 0.049909145972138 0.00467049878307435 Y 0.984675953967293 0.984675953967293 N N 1521 1133 ENSG00000179036 ENSG00000179094 + - 17 17 8007017 7996427 downstream intron VAMP2 PER1 8003146 7984534 - - 0 8000351 7994889 - + N - 17.0982729253317 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 18 0.464213630395207 0.87843502367093 0.87843502367093 0.464213630395207 1 - 0 30253 Y Y 3.41952156054875 3.70040921291755 3.41952156054875 0 0.00403225806451613 0.690984265024362 Y 0 0 N N 0 726 ENSG00000216283 ENSG00000011677 - - X X 151400152 151370993 upstream utr5p AC108171.5 GABRA3 151398705 151086290 + - 0 151387314 151283728 - + N - 20.9408421897565 N HCC1954 15 3 1 1 1 N - - Y SINE - 1 0 1 7 0.714174815992626 0.764167053112109 0.764167053112109 0.714174815992626 2 - 0 44687 Y N 3.45612774781375 2.98528226787376 2.98528226787376 0 0 0.126245391731567 Y 0 0 N N 82 1726 ENSG00000214562 ENSG00000165874 - + 10 10 88984892 88941200 downstream downstream FAM22A FAM35A 88975185 88844933 + + 0 88995707 88957472 - + N - - N HCC1954 8 3.2 2 5 1 N - - Y SINE LINE 1 1 1 5 0.664182578873142 0.757025304952183 0.757025304952183 0.664182578873142 3 - - 20894 N Y 3.47552369040616 3.29549537585246 3.29549537585246 273 0 0.0235590870327543 N 0.872030110562221 0.881170816950633 N N 3880 667 ENSG00000137955 ENSG00000206530 - - 1 3 76033688 114643030 coding intron RABGGTB WDR52 76024474 114493094 + - 0.881170816950633 76029750 114562456 - + Y - 1.41101489475111 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 8 0.835584534711372 0.614190341753658 0.835584534711372 0.614190341753658 2 - 0 25715 N N 3.51832410639388 3.47804449069255 3.47804449069255 0 0 0.0710786682156974 N 0 0 N N 41 3590 ENSG00000172533 ENSG00000128609 - + 16 7 29003535 122985194 coding coding AC009093.10-2 NDUFA5 28993829 122968319 + - 0 28993940 122984717 - - Y - - N HCC1954 105 75 20 6 1 N - - N SINE - 1 0 1 6 0.335662163516534 0.357087407996313 0.357087407996313 0.335662163516534 2 - - 48097 N N 3.51935717616377 3.14471373619582 3.14471373619582 0 0.441506583207425 0.129406736675119 N 0.562918195553637 0 N N 551733 70 ENSG00000204628 ENSG00000042832 + + 5 8 180603512 134216325 utr3p intron GNB2L1 TG 180596536 133948387 - + 0 180596558 134072353 - + Y - 1.00910561485727 N HCC1954 22 15.75 1 3 1 N - - N - LTR 0 1 1 4 0.707033067832699 0.357087407996313 0.707033067832699 0.357087407996313 2 - 0 17151 N Y 3.18188898491428 3.64553343878587 3.18188898491428 275 0 0.0128259892367245 N 0.934202401372213 0.915403087478559 N N 20793 1154 ENSG00000141027 ENSG00000180488 + + 17 1 16059570 78116667 utr5p utr3p NCOR1 FAM73A 15875443 78017897 - + 0 16059401 78116660 - + Y - - N HCC1954 31 27.5333333333333 23 15 1 N - - N Simple_repeat SINE 0.312056737588652 1 1 15 0.721316564152552 0.564198104634174 0.721316564152552 0.564198104634174 4 - - 29090 N Y 3.61360747730288 3.01105607394689 3.01105607394689 0 0.213505747126437 0.231727498922866 N 0.658045977011494 0.623850574712644 N N 343 0 ENSG00000178729 ENSG00000212451 + + 6 8 48144384 127753081 utr3p downstream C6orf138 U11 47953998 127752949 - + 0.623850574712644 47976637 128107233 - + Y - - N HCC1954 37 26.8571428571429 24 14 1 N 545 25.1276 N SINE LTR 1 1 1 14 0.814159290231593 0.728458312312478 0.814159290231593 0.728458312312478 2 - - 47079 Y Y 3.63825270713077 3.33416770265723 3.33416770265723 357 0 0.148078375409767 Y 0.0206082432973189 0.99406429238362 N N 16146 7111 ENSG00000167491 ENSG00000129933 - + 19 19 19480736 19339989 intron downstream GATAD2A KIAA0892 19399336 19292614 + + 0 19399504 19357946 - + N 0.0116756738608158 - N HCC1954 5 1.85714285714286 1 3 3 N - - Y SINE Low_complexity,Simple_repeat 1 0.221649484536082 1 7 0.821301038391519 1.05697872766909 1.05697872766909 0.821301038391519 1 0 - 17698 N Y 3.32423818963975 3.29855989004197 3.29855989004197 312 0 0.00465101780672228 Y 0 0.983386752136752 N N 98 5290 ENSG00000085465 ENSG00000116455 - + 1 1 111771922 111793353 coding utr3p OVGP1 WDR77 111758461 111784036 - - 0 111770693 111785175 + - N - - N HCC1954 1 1 1 0 1 Y - - N - - 0 0 0 4 0.971277749749971 0.607048593593732 0.971277749749971 0.607048593593732 1 - - 403 Y Y 2.84123764596909 3.47695798776018 2.84123764596909 105 0 0.992391634754405 Y 0 0 N N 2920 11955 ENSG00000130598 ENSG00000149043 - + 11 11 1819484 1815327 upstream coding TNNI2 SYT8 1816795 1809259 + + 0.979365079365079 1816335 1814664 - + N - - N HCC1954 1 1 1 0 6 N - - Y - - 0 0 0 5 0.785592297591888 0.678466075192994 0.785592297591888 0.678466075192994 1 - - 29162 Y Y 3.63296356710195 3.60103760561896 3.60103760561896 361 0 0.46741956534014 Y 0 0.98840430329189 N N 1789 0 ENSG00000204599 ENSG00000203481 - - 6 6 30419485 30360468 upstream upstream TRIM39 AL662795.5 30402600 30360104 + - 0 30401920 30370722 - + N - - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 9 0.607048593593732 0.592765097273879 0.607048593593732 0.592765097273879 3 - - 19790 N N 3.47336426491055 3.38912318237562 3.38912318237562 0 0 0.323543428956051 N 0.23813689044391 0 N N 16390 0 ENSG00000140950 ENSG00000208366 - + 16 1 83095794 169717771 intron upstream KIAA1609 AL049762.20-1 83068608 169717670 - + 0 83089222 169717255 + + Y 1.98970794067006 - N HCC1954 2 1.09090909090909 1 1 2 N - - N - SINE 0 0.846153846153846 0.846153846153846 11 0.542772860154395 0.278528178237124 0.542772860154395 0.278528178237124 1 0 - 35268 N N 3.8552884365336 3.80144573217181 3.80144573217181 0 0 0.653776170425 N 0 0 N N 13659 103375 ENSG00000127824 ENSG00000167553 + + 2 12 219827574 47953383 coding coding TUBA1 TUBA1C 219822677 47945132 - + 0 219824024 47952556 - + Y 0.544183119701614 - N HCC1954 3 2.63636363636364 2 11 1 N 145 22.3825 N - - 0 0 0 11 0.385654400636018 0.34280391167646 0.385654400636018 0.34280391167646 1 0 - 29160 Y Y 3.13639993477083 3.38656252929588 3.13639993477083 289 0 0.0752354123444645 Y 0.982818279441594 0.991409139720797 N N 0 0 ENSG00000221559 ENSG00000218208 - + 6 6 114132819 114009842 upstream downstream AL357519.19 RP11-367G18.2 114132752 114009396 + + 0 114077909 114055569 - + N - - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 20 1.2783729206268 0.885576771830856 1.2783729206268 0.885576771830856 1 - - 25939 N Y 3.57336771439491 3.234707967076 3.234707967076 0 0 0.268079808571751 N 0 0.886206896551724 N N 2010 0 ENSG00000119004 ENSG00000221151 + - 2 16 203878808 88689322 utr3p upstream CYP20A1 AC133919.3-4 203811419 88689218 + - 0 203871945 88700643 + + Y - - N HCC1954 160 142.5 116 32 1 N - - N SINE - 1 0 1 32 0.392796148795944 0.828442786551446 0.828442786551446 0.392796148795944 2 - - 13256 N Y 3.48383749183115 2.91403521254583 2.91403521254583 245 0.800816326530612 0.0146213949049175 N 0.950204081632653 0.817414965986395 N N 78560 2205 ENSG00000112493 ENSG00000184979 + + 6 22 33390114 17040164 utr3p intron TAPBP USP18 33375449 17012758 - + 0.817414965986395 33376425 17026426 - + Y 0.848669951896309 1.09112016915679 N HCC1954 36 14.75 6 4 1 N - - N SINE SINE 1 1 1 4 0.349945659836387 0.271386430077198 0.349945659836387 0.271386430077198 2 0 0 26841 Y Y 3.59272380419397 3.50951579142893 3.50951579142893 217 0 0.0848039493914586 Y 0 0.989296863386354 N N 5 24977 ENSG00000048462 ENSG00000103342 - - 16 16 11969426 11917313 upstream upstream TNFRSF17 GSPT1 11966465 11874040 + - 0 11965247 11939024 - + N - - N HCC1954 17 9.625 1 7 2 N - - Y SINE - 1 0 1 8 0.857009779191151 0.814159290231593 0.857009779191151 0.814159290231593 1 - - 35068 N Y 3.29797209054617 2.59073931993733 2.59073931993733 244 0 0.00420725471487293 Y 0 0.989174982181041 N N 8087 7080 ENSG00000148297 ENSG00000148296 + - 9 9 135204793 135192868 coding coding MED22 SURF6 135197577 135187390 - - 0 135200886 135191227 - + N - 0.731075033692978 N HCC1954 1 1 1 0 1 N - - N - - 0 0 0 14 1.29979816510658 1.2783729206268 1.29979816510658 1.2783729206268 1 - 0 36246 Y Y 3.68680627146374 3.46720988898117 3.46720988898117 0 0 0.969710107342576 Y 0 0.993397986590942 N N 756 0 ENSG00000139132 ENSG00000207176 - - 12 12 32684940 32440348 intron upstream FGD4 Y_RNA 32546361 32440251 + - 0 32608337 32444159 - + N 0.0876523220302632 - N HCC1954 1 1 1 0 3 N - - Y - - 0 0 0 39 1.12839620926835 1.2783729206268 1.2783729206268 1.12839620926835 1 0 - 18476 Y Y 3.41000685548453 3.45612774781375 3.41000685548453 239 0 0.0174149229061441 Y 0.991340731307986 0.974022193923959 N N 3535 15221 ENSG00000159596 ENSG00000159592 - - 1 1 45932685 45924795 upstream utr5p TMEM69 GPBP1L1 45926434 45865563 + - 0 45926242 45899484 - + N - 2.8210607456026 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 16 0.714174815992626 0.928427260790413 0.928427260790413 0.714174815992626 4 - 0 47739 Y Y 3.27824527838653 3.6491271616355 3.27824527838653 318 0 0.0932634001581995 Y 0.045265302506865 0 N Y 512 89 ENSG00000105227 ENSG00000160396 + - 19 19 45611113 45587934 coding intron PRX HIPK4 45591512 45577019 - - 0 45601453 45581886 - + N - 3.90340091917432 N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 8 1.09982921662864 1.10697096478857 1.10697096478857 1.09982921662864 4 - 0 47840 N N 3.71976530271662 3.58630830843942 3.58630830843942 0 0 0.0478260507361067 N 0 0 N N 4159 4 ENSG00000012061 ENSG00000164509 - + 19 5 50619017 55254435 utr5p utr5p ERCC1 IL31RA 50604712 55182964 - + 0 50618535 55183846 + + Y - - N HCC1954 35 33.75 32 4 1 N - - N - SINE 0 1 1 4 0.39993789695587 0.378512652476092 0.39993789695587 0.378512652476092 1 - - 28480 N N 3.47911741325579 3.21808036422602 3.21808036422602 0 0 0.195631136649783 N 0 0 N N 4060 45068 ENSG00000138698 ENSG00000205336 - + 4 16 99584031 56256445 intron upstream RAP1GDS1 GPR56 99401550 56220023 + + 0 99578854 56211249 - + Y 3.13456894155132 - N HCC1954 21 20.5 20 4 1 N - - N SINE - 1 0 1 4 0.307095170876829 0.549914608314322 0.549914608314322 0.307095170876829 2 0 - 48085 N N 3.54569782317086 3.59528445727371 3.54569782317086 0 0 0.979960474418484 N 0 0.0286082602012993 N N 12549 0 ENSG00000087206 ENSG00000212451 + + 5 8 176366358 127753081 coding downstream UIMC1 U11 176264612 127752949 - + 0.0286082602012993 176270994 128072280 - + Y - - N HCC1954 1 1 1 0 5 N 573 7.11156 N Low_complexity - 0.0285714285714286 0 0.0285714285714286 7 0.499922371194838 0.764167053112109 0.764167053112109 0.499922371194838 2 - - 44333 N Y 3.51104337473878 3.6272104187567 3.51104337473878 4 0 0.503080513653491 N 0.773651145602365 0.88229859571323 N N 23800 1260 ENSG00000067182 ENSG00000156398 - + 12 10 6321522 104488930 coding utr3p TNFRSF1A SFXN2 6308185 104464288 - + 0.88229859571323 6310353 104488186 + + Y - - N HCC1954 22 16.75 3 4 1 N 236 26.1752 N - SINE 0 1 1 4 0.549914608314322 0.307095170876829 0.549914608314322 0.307095170876829 3 - - 2729 N N 3.54040868314203 3.49424793801946 3.49424793801946 0 0 0.084167717222915 N 0 0 N N 2 0 ENSG00000169946 ENSG00000222048 - - 8 11 106885939 10836196 upstream intron ZFPM2 ZBED5 106400323 10830827 + - 0 106345553 10833215 - + Y - 1 N HCC1954 1 1 1 0 1 N - - N - DNA 0 1 1 6 0.335662163516534 0.414221393275723 0.414221393275723 0.335662163516534 2 - 0 47267 Y Y 3.44615838200292 3.30232144676095 3.30232144676095 157 0 0.252736182087986 Y 0 0.986717363751584 N Y 1457 7761 ENSG00000169035 ENSG00000129455 - + 19 19 56179106 56196770 coding coding KLK7 KLK8 56171541 56191076 - - 0 56176982 56196166 + - N - - N HCC1954 1 1 1 0 1 Y - - Y - - 0 0 0 14 0.742741808632331 0.485638874874985 0.742741808632331 0.485638874874985 4 - - 18515 Y Y 3.40654111371089 3.78105657260285 3.40654111371089 269 0 0.0192908774178854 Y 0 0 N N 362 2252 ENSG00000162913 ENSG00000181873 + + 1 1 226467988 226436581 downstream coding C1orf145 C1orf69 226457831 226420139 - + 0 226451891 226420480 - + N - 0.775647416686638 N HCC1954 1 1 1 0 1 N - - Y - Low_complexity 0 0.276923076923077 0.276923076923077 4 0.778450549431962 0.807017542071667 0.807017542071667 0.778450549431962 1 - 0 24967 N Y 3.65488030998075 3.485365075141 3.485365075141 2 0 0.365370302540367 N 0 0.892491779320424 N N 1493 559 ENSG00000123179 ENSG00000153234 - + 13 2 49163612 156907106 coding downstream EBPL NR4A2 49132860 156889194 - - 0.81430398246255 49140543 156819538 + - Y - - N HCC1954 150 58.5 23 4 1 N - - N SINE LINE 1 1 1 4 0.407079645115797 0.542772860154395 0.542772860154395 0.407079645115797 1 - - 31424 Y Y 3.37767966641742 3.66745018166468 3.37767966641742 2 0 0.31819079241936 Y 0.970248097262034 0.992562024315509 N N 1241 480 ENSG00000073803 ENSG00000113790 - - 3 3 186683293 186454531 utr5p upstream MAP3K13 EHHADH 186529396 186391108 + - 0 186628981 186486127 - + N 0.186945846051621 - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 5 0.956994253430118 0.814159290231593 0.956994253430118 0.814159290231593 1 0 - 11212 N Y 3.12804628055249 3.60422075331465 3.12804628055249 0 0 0.143866076028087 N 0.908034188034188 0.908034188034188 N N 1649619 3364 ENSG00000141736 ENSG00000033867 - + 17 3 35138441 27473249 coding intron ERBB2 SLC4A7 35104766 27389218 + - 0 35122227 27423851 - - Y - 0.753276788839154 N HCC1954 22 10.8181818181818 1 15 1 N - - N - SINE 0 1 1 22 1.34264865406614 0.407079645115797 1.34264865406614 0.407079645115797 2 - 0 30434 Y Y 3.52567938596249 3.53039946453785 3.52567938596249 231 0 0.00885385874290479 Y 0.907379442263163 0.988422430282895 N N 4474 49 ENSG00000056998 ENSG00000124343 - + X X 2810858 2743955 upstream utr3p GYG2 XG 2756859 2680115 + + 0 2752050 2743780 - + N - 2.72168284789644 N HCC1954 2 1.5 1 2 2 N - - Y - - 0 0 0 4 0.692749571512847 0.564198104634174 0.692749571512847 0.564198104634174 1 - 0 46464 N Y 3.15737173616238 3.57800808738356 3.15737173616238 0 0 0.403254620866823 N 0.0042372881355931 0 N N 0 17943 ENSG00000165078 ENSG00000105141 + + 8 19 68821134 15027900 intron downstream CPA6 CASP14 68496963 15024015 - + 0 68618596 15029502 - + Y 1 - N HCC1954 14 9.7027027027027 1 36 1 N - - N Simple_repeat,SINE SINE 0.82051282051282 0.201550387596899 0.82051282051282 37 0.278528178237124 0.914143764470561 0.914143764470561 0.278528178237124 3 0 - 7228 Y Y 2.94740481895264 2.36569501539269 2.36569501539269 303 0 0.00662013416271778 Y 0.984898489848985 0 N N 1516 3083 ENSG00000168395 ENSG00000168393 - - 2 2 242317560 242274900 upstream upstream ING5 DTYMK 242290129 242263830 + - 0 242282518 242275633 - + N - - N HCC1954 1 1 1 0 1 N - - Y SINE,LINE SINE 0.641221374045801 0.134502923976608 0.641221374045801 7 0.899860268150708 1.22123893534739 1.22123893534739 0.899860268150708 1 - - 4382 Y Y 3.40843941938133 3.53039946453785 3.40843941938133 290 0 0.0115373269869868 Y 0.44078392458447 0.928305631356984 N N 6508 42 ENSG00000184863 ENSG00000216895 - - 7 7 155266940 155129856 intron utr5p RBM33 AC009403.2 155129906 155096686 + - 0.928305631356984 155130546 155129059 - + N 0.830298874877254 0.422768081591611 N HCC1954 1 1 1 0 1 N - - Y - LINE 0 0.339449541284404 0.339449541284404 6 0.764167053112109 0.778450549431962 0.778450549431962 0.764167053112109 3 0 0 29231 Y Y 3.63296356710195 3.38656252929588 3.38656252929588 331 0 0.080661801133398 Y 0.046368054643373 0.99277551556548 N N 0 0 ENSG00000221559 ENSG00000218208 - + 6 6 114132819 114009842 upstream downstream AL357519.19 RP11-367G18.2 114132752 114009396 + + 0 114077298 114055569 - + N - - N HCC1954 1 1 1 0 3 N - - Y SINE - 0.302702702702703 0 0.302702702702703 14 1.32122340958636 0.985561246069823 1.32122340958636 0.985561246069823 1 - - 49262 Y Y 3.68953475841283 3.56129235625094 3.56129235625094 144 0 0.311724569094158 Y 0.982048224695284 0.991024112347642 N N 3135 2529 ENSG00000086200 ENSG00000086189 - - 5 5 61960165 61735485 coding upstream IPO11 DIMT1L 61744351 61720108 + - 0 61768860 61735689 - + N - - N HCC1954 1 1 1 0 1 N - - Y - - 0 0 0 12 0.921285512630487 0.585623349113953 0.921285512630487 0.585623349113953 3 - - 21553 N Y 3.5727053669856 3.29504071510585 3.29504071510585 0 0 0.665916823665561 N 0.885663189269747 0.877496274217586 N N 4626 108 ENSG00000133059 ENSG00000204054 + + 1 9 203447322 131325878 utr3p intron DSTYK AL391056.25-1 203378255 131291741 - + 0 203382344 131295695 - + Y - 4.50715835140998 N HCC1954 37 35.7142857142857 34 7 1 N - - N SINE SINE,LINE 1 0.610619469026549 1 7 0.407079645115797 0.807017542071667 0.807017542071667 0.407079645115797 4 - 0 32262 N N 3.55401162459584 3.26088078021373 3.26088078021373 1 0 0.0757253543878725 N 0.528867388789568 0.0711957093280049 N N 5744 0 ENSG00000155034 ENSG00000213113 + + 7 3 5523646 199332046 utr3p downstream FBXL18 AC073135.3-1 5481955 199330983 - + 0.0711957093280049 5486778 199368972 - + Y - - N HCC1954 136 121.142857142857 84 7 1 N - - N SINE - 1 0 1 7 0.28566992639705 0.542772860154395 0.542772860154395 0.28566992639705 2 - - 9764 Y Y 3.43784458057793 3.38080938095063 3.38080938095063 0 0 0.979947927701168 Y 0 0.973519751847459 N N 138 10722 ENSG00000181350 ENSG00000175061 + + 17 17 16336192 16286063 intron utr3p C17orf76 C17orf45 16286053 16283081 - + 0 16306711 16285119 - + N 3.43189971253672 - N HCC1954 1 1 1 0 5 N - - Y - - 0 0 0 15 0.742741808632331 1.09982921662864 1.09982921662864 0.742741808632331 2 0 - 30469 Y Y 3.10972326052331 3.45769518391695 3.10972326052331 266 0 0.0185337708528674 Y 0 0 N N 5963 137 ENSG00000123575 ENSG00000176274 - - X X 103322781 103288364 upstream upstream CXorf39 MCART6 103297957 103230555 + - 0 103294148 103288542 - + N - - N HCC1954 1 1 1 0 2 N - - Y LTR - 1 0 1 9 0.885576771830856 0.678466075192994 0.885576771830856 0.678466075192994 1 - - 44815 Y Y 3.51782959285392 3.39384326095097 3.39384326095097 403 0 0.000400941595100401 N 0 0.993120561307436 Y N 0 0 ENSG00000222314 ENSG00000209826 - + 10 10 38752662 38752662 downstream downstream U6 AL133216.10-1 38752559 38752560 + + 0 38764141 38757289 - + N - - N HCC1954 224 172.272727272727 16 22 1 N - - N SINE,LTR SINE,LTR 0.797709923664122 0.954545454545455 0.954545454545455 22 1.19981369086761 0.628473838073511 1.19981369086761 0.628473838073511 1 - - 29350 N N 3.74337746277462 3.39487633072086 3.39487633072086 6 0 0.866571798065925 N 0 0 N N 0 568998 ENSG00000219374 ENSG00000156508 + + 6 6 49436052 74288344 intron coding RP1-142O9.1 EEF1A1 49433818 74282194 - - 0 49434164 74284803 - - N 1 - Y HCC1954 10 5.85714285714286 3 21 2 N - - N - - 0 0 0 21 0.257102933757345 0.792734045751814 0.792734045751814 0.257102933757345 2 0 -