# Properties associated with genes included in deletion MPRA # # # column descriptions # tss_id - FANTOM5 tss_id # oligo_coords - oligo_coords - hg19 coordinates of the designed oligonucleotide sequence, each 114bp long # tss_description - FANTOM5 tss_description for TSSs, FANTOM5 enhancer_id for enhancers # tss_start - FANTOM5 TSS start (1bp) # gene_type - defined biotype based on Gencode or FANTOM5 gene type # gene_name - Gencode v19 gene_name # gene_id - Gencode v19 gene_id # name - custom name defined for TSS/gene combination # closest_divergent_tss - gene_id for closest annotated antisense TSS # distance_to_next_tss - distance between the TSS and the aforementioned closest divergent TSS # divergent_tss_selected - whether or not the divergent TSS was added to the MPRA as well # is_flipped - whether or not the flipped (antisense) sequence was added to the MPRA as well # mean_cage_exp_all - mean CAGE expression across all FANTOM5 samples # K562_rep1 - FANTOM5 CAGE expression # K562_rep2 - FANTOM5 CAGE expression # K562_rep3 - FANTOM5 CAGE expression # HeLa_rep1 - FANTOM5 CAGE expression # HeLa_rep2 - FANTOM5 CAGE expression # HeLa_rep3 - FANTOM5 CAGE expression # HepG2_rep1 - FANTOM5 CAGE expression # HepG2_rep2 - FANTOM5 CAGE expression # HepG2_rep3 - FANTOM5 CAGE expression # mean_cage_exp_cell_lines - mean CAGE expression across the previously noted FANTOM5 K562, HeLa, and HepG2 cell line samples tss_id oligo_coords tss_description tss_start gene_type gene_name gene_id name closest_divergent_tss distance_to_next_tss divergent_tss_selected is_flipped mean_cage_exp_all K562_rep1 K562_rep2 K562_rep3 HeLa_rep1 HeLa_rep2 HeLa_rep3 HepG2_rep1 HepG2_rep2 HepG2_rep3 mean_cage_exp_cell_line chr11:65187544..65187545,- chr11:65187510..65187718,- chr11:65187297-65188198 chr11:65187544..65187545,- Enhancer NA NA enh.NEAT1 NA 2472 no noflip 6.046389497 1.318987755 1.33697341 2.45246763 6.498367061 3.875310779 6.291857459 1.348996888 0.86775787 0.968860914 2.773286641 chr11:65265055..65265056,- chr11:65265021..65265229,- chr11:65264635-65265953 chr11:65265055..65265056,- Enhancer NA NA enh.MALAT1 NA 0 no noflip 13.2262035 13.18987755 12.79674549 18.80225183 5.848530355 5.566355483 5.505375276 4.046990665 3.865466874 4.392169477 8.223751445 chr20:47893131..47893132,- chr20:47893097..47893305,- chr20:47893075-47893400 chr20:47893131..47893132,- Enhancer NA NA enh.ZFAS NA 1790 no noflip 0.828068928 0 0 0 0.18566763 0.070460196 0.078648218 0 0.078887079 0 0.045962569 chr3:169482113..169482114,- chr3:169482079..169482287,- chr3:169482089-169482431 chr3:169482113..169482114,- Enhancer NA NA enh.TERC NA 585 no noflip 0.874595186 0 0.190996201 0.163497842 0.18566763 0.35230098 0.157296436 0.224832815 0.078887079 0 0.150386554 chr7:130796123..130796124,- chr7:130796089..130796297,- chr7:130795999-130796263 chr7:130796123..130796124,- Enhancer NA NA enh.LINCPINT NA 1260 no noflip 0.338626368 0 0 0 0.557002891 1.127363136 0.707833964 0 0 0 0.265799999 chr1:150488205..150488251,+ chr1:150488076..150488284,+ p1@ENST00000416894 chr1:150488227..150488228,+ Lincrna LINC00568 ENSG00000228126.1 FALEC ENSG00000203804.3 45735 no noflip 0.576464812 1.804765285 0.392125069 0.335643174 0.483781656 0.438535903 0.574808199 0.551482276 0.49449515 0.539228351 0.623873896 chr1:153518270..153518290,- chr1:153518247..153518455,- p1@S100A4 chr1:153518281..153518282,- control S100A4 ENSG00000196154.7 S100A4 ENSG00000238279.1 16532 no noflip 192.1078431 0.676786982 2.352750412 1.342572696 583.247165 455.4195348 548.6133686 4.569424574 4.120792919 4.313826807 178.2951359 chr1:173837113..173837137,- chr1:173837092..173837300,- p1@GAS5 chr1:173837126..173837127,- Antisense GAS5 ENSG00000234741.3 GAS5 ENSG00000185278.10 799 yes noflip 18.4680109 31.58339249 18.23381569 13.59354855 41.1214408 31.42840635 30.79329639 11.18721189 11.04372502 10.9193741 22.21157903 chr1:173837488..173837526,+ chr1:173837344..173837552,+ p1@ZBTB37 chr1:173837517..173837518,+ protein_coding ZBTB37 ENSG00000185278.10 ZBTB37 ENSG00000234741.3 799 yes noflip 2.979117647 2.255956606 2.940938015 3.692074913 0.967563313 2.338858147 1.149616399 1.890796375 2.307644035 2.493931123 2.226375436 chr1:211556107..211556205,+ chr1:211555971..211556179,+ p1@LINC00467 chr1:211556144..211556145,+ Lincrna LINC00467 ENSG00000153363.8 LINC00467 ENSG00000198570.5 60381 no noflip 13.01804798 34.74173174 36.46763138 37.92767866 13.44913005 21.34208059 12.64578039 7.878318231 10.13715058 11.72821663 20.70196869 chr11:5248294..5248308,- chr11:5248266..5248474,- p1@HBB chr11:5248300..5248301,- control HBB ENSG00000244734.2 HBB ENSG00000224091.1 24353 no noflip 4894.738562 0.451191321 0.784250137 0.503464761 0 0 0 0.078783182 0 0 0.201965489 chr11:65190260..65190277,+ chr11:65190095..65190303,+ p1@NEAT1 chr11:65190268..65190269,+ Lincrna NEAT1 ENSG00000245532.4 NEAT1 ENSG00000162241.8 39074 no noflip 245.2032698 168.7455541 151.164214 191.6522523 346.2909097 466.7483789 295.369299 80.35884595 72.77320295 85.06327234 206.462881 chr11:65265141..65265306,+ chr11:65265059..65265267,+ p4@MALAT1 chr11:65265232..65265233,+ Lincrna MALAT1 ENSG00000251562.3 MALAT1 ENSG00000168056.10 61167 no noflip 18.36141689 18.04765285 18.42987823 24.33413011 4.160522245 4.239180391 5.091158337 6.14508822 5.60427837 6.133722491 10.24284569 chr11:65266507..65266522,+ chr11:65266377..65266585,+ p1@MALAT1 chr11:65266515..65266516,+ Lincrna MALAT1 ENSG00000251562.3 MALAT1 ENSG00000168056.10 61167 no noflip 8474.972737 8356.965652 7838.580122 10486.16404 8714.746003 8666.93122 6931.776307 1506.570795 1415.162704 1613.506033 6170.044764 chr12:54362447..54362462,- chr12:54362420..54362628,- p1@HOTAIR chr12:54362454..54362455,- Antisense HOTAIR ENSG00000228630.1 HOTAIR ENSG00000123388.4 1829 no noflip 0.223954223 0 0 0 0.193512663 0.146178634 0.164230914 0 0 0 0.055991357 chr13:50656312..50656405,+ chr13:50656191..50656399,+ p1@DLEU1 chr13:50656364..50656365,+ Lincrna DLEU1 ENSG00000176124.7 DLEUL1 ENSG00000186047.9 120703 no noflip 10.68588556 34.9673274 35.87944378 26.01234598 21.28639288 23.24240283 20.77521063 17.64743284 14.75243865 15.90723635 23.38558126 chr14:101292448..101292462,+ chr14:101292281..101292489,+ p1@MEG3 chr14:101292454..101292455,+ Antisense MEG3 ENSG00000214548.10 MEG3 ENSG00000267918.1 49789 no noflip 112.8953108 1.353573964 2.352750412 1.510394283 0 0.073089317 0 0 0 0 0.587756442 chr16:54962704..54962812,- chr16:54962763..54962971,- p1@CRNDE chr16:54962797..54962798,- Lincrna CRNDE ENSG00000245694.4 CRNDE ENSG00000176842.10 1674 yes flip 14.83026172 20.75480078 19.4101909 20.80987679 18.48045928 22.43842035 17.98328509 0 0 0 13.31967035 chr16:54964740..54964789,+ chr16:54964603..54964811,+ p1@IRX5 chr16:54964776..54964777,+ protein_coding IRX5 ENSG00000176842.10 IRX5 ENSG00000245694.4 1674 yes noflip 2.440691721 1.353573964 0 0.167821587 1.064319644 1.315607708 0.821154571 0 0 0 0.524719719 chr16:86542455..86542500,- chr16:86542457..86542665,- p1@LOC400550 chr16:86542491..86542492,- Lincrna FENDRR ENSG00000268388.1 FENDRR ENSG00000103241.5 1429 yes flip 2.936521265 0 0 0 4.063765914 3.435197903 3.859426482 0 0 0 1.262043367 chr16:86543302..86543316,+ chr16:86543137..86543345,+ p@chr16:86543302..86543316,+ chr16:86543310..86543311,+ protein_coding FOXF1 ENSG00000103241.5 FOXF1 ENSG00000268388.1 1429 yes noflip 0.456756536 0 0 0 0.77405065 0.803982488 0.739039113 0 0 0 0.257452472 chr20:47895175..47895182,+ chr20:47895005..47895213,+ p1@ZNFX1-AS1 chr20:47895178..47895179,+ Antisense ZFAS1 ENSG00000177410.8 ZFAS1 ENSG00000124201.10 247 yes noflip 284.7880109 186.793207 158.6145903 163.2904041 185.0948618 236.8093874 150.6818637 150.6334446 142.6618509 148.8270248 169.2674038 chr3:169482840..169482855,- chr3:169482812..169483020,- p1@TERC chr3:169482846..169482847,- Lincrna TERC ENSG00000270141.2 TERC ENSG00000085274.11 7772 no noflip 55.49972752 23.91314003 22.35112891 13.76137013 72.56724847 48.38512791 66.26717384 28.83464472 27.5268967 22.04095884 36.18307662 chr3:70048881..70048888,+ chr3:70048710..70048918,+ p1@ENST00000483525,p1@uc003dog.2 chr3:70048883..70048884,+ Lincrna RP11-460N16.1 ENSG00000240405.1 SAMMSON ENSG00000114541.10 456995 no noflip 0.431385706 8.347039443 3.921250686 6.377220305 0 0 0 0 0 0 2.071723382 chr5:90610209..90610226,- chr5:90610184..90610392,- p1@ENST00000513626,p1@uc003kjy.1 chr5:90610218..90610219,- Lincrna LUCAT1 ENSG00000248323.1 LUCAT ENSG00000164199.11 773685 no noflip 20.699509 0.451191321 1.176375206 1.006929522 5.321598221 6.724217172 5.665966537 0.945398188 0.906574442 1.213263789 2.601279378 chr7:130794638..130794690,- chr7:130794622..130794830,- p2@FLJ43663 chr7:130794656..130794657,- Antisense MKLN1-AS1 ENSG00000231721.2 LINC_PINT ENSG00000128585.13 0 yes noflip 3.733925845 0.451191321 1.37243774 0.839107935 3.096202601 3.800644488 4.105772853 0.551482276 1.071406159 0.337017719 1.736140344 chr8:128806753..128806815,+ chr8:128806613..128806821,+ p1@PVT1 chr8:128806786..128806787,+ Antisense PVT1 ENSG00000249859.3 PVT1 ENSG00000256655.1 153811 no noflip 22.05940054 6.091082837 4.509438289 5.873755544 23.70530117 19.44175834 21.35001883 8.114667778 8.241585838 8.155828806 11.72038194 chr9:21994344..21994440,- chr9:21994352..21994560,- p1@CDKN2A chr9:21994386..21994387,- protein_coding CDKN2A ENSG00000147889.12 CDKN2A ENSG00000266446.1 182 no flip 38.91748366 0 0 0 270.2404333 322.9086029 318.9364352 1.812013193 1.236237876 2.156913403 101.9211818 chr9:21994775..21994834,+ chr9:21994622..21994830,+ p1@CDKN2B-AS,p2@MTAP chr9:21994795..21994796,+ Antisense CDKN2B-AS1 ENSG00000240498.2 ANRIL ENSG00000147889.12 522 yes flip 1.808457766 0 0 0 6.579430528 6.504949221 5.255389251 0.078783182 0.082415858 0.134807088 2.070641681 chrX:73164167..73164192,+ chrX:73164003..73164211,+ p1@JPX chrX:73164176..73164177,+ Lincrna JPX ENSG00000225470.2 JPX ENSG00000131263.8 670292 no noflip 28.70556161 18.95003549 28.42906748 17.95690981 52.63544422 54.7438985 44.91715501 23.95008742 21.42812318 24.66969705 31.96449091 chr16:54962704..54962812,- chr16:54962763..54962971,+ p1@CRNDE chr16:54962797..54962798,- Lincrna CRNDE ENSG00000245694.4 CRNDE ENSG00000176842.10 1674 yes flip 14.83026172 20.75480078 19.4101909 20.80987679 18.48045928 22.43842035 17.98328509 0 0 0 13.31967035 chr16:86542455..86542500,- chr16:86542457..86542665,+ p1@LOC400550 chr16:86542491..86542492,- Lincrna FENDRR ENSG00000268388.1 FENDRR ENSG00000103241.5 1429 yes flip 2.936521265 0 0 0 4.063765914 3.435197903 3.859426482 0 0 0 1.262043367 chr9:21994344..21994440,- chr9:21994352..21994560,+ p1@CDKN2A chr9:21994386..21994387,- protein_coding CDKN2A ENSG00000147889.12 CDKN2A ENSG00000266446.1 182 no flip 38.91748366 0 0 0 270.2404333 322.9086029 318.9364352 1.812013193 1.236237876 2.156913403 101.9211818 chr9:21994775..21994834,+ chr9:21994622..21994830,- p1@CDKN2B-AS,p2@MTAP chr9:21994795..21994796,+ Antisense CDKN2B-AS1 ENSG00000240498.2 ANRIL ENSG00000147889.12 522 yes flip 1.808457766 0 0 0 6.579430528 6.504949221 5.255389251 0.078783182 0.082415858 0.134807088 2.070641681