path_id	path_score	path_length	cluster_id	adjacent	deletion	eversion	gene1	gene2	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	inversion	library_name	max_map_count	mean_map_count	min_map_count	num_multi_map	repeat_list1	repeat_list2	repeat_proportion1	repeat_proportion2	repeat_proportion_max	span_count	span_coverage1	span_coverage2	span_coverage_max	span_coverage_min
241	0.00319582	0	14828006	N	N	N	ENSG00000182152	ENSG00000104408	5	8	117142614	109330135	downstream	intron	AC114322.2	EIF3E	117142420	109283149	-	-	0.525885559	116868566	109290101	-	-	Y	N	HCC1954	1	1	1	0	LINE	-	0.358381503	0	0.358381503	7	1.01508141	1.148310845	1.148310845	1.01508141
463	0.0544881	0	10062124	N	N	Y	ENSG00000175203	ENSG00000123297	12	12	56227245	56476784	intron	intron	DCTN2	TSFM	56210361	56462826	-	+	0.594488189	56215032	56465960	-	+	N	N	HCC1954	1	1	1	0	-	"DNA,DNA"	0	1	1	3	0.647114399	0.95798308	0.95798308	0.647114399
388	0.271984	0	11192712	N	N	N	ENSG00000128891	ENSG00000122565	15	7	38644544	26219501	intron	utr5p	C15orf57	CBX3	38632592	26207624	-	+	0.607843137	38641482	26207890	-	-	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	10	0.970671598	0.64077014	0.970671598	0.64077014
141	0.300921	0	10248028	N	N	N	ENSG00000185610	ENSG00000168575	12	8	43731149	42516225	intron	intron	DBX2	SLC20A2	43694806	42393173	-	-	0.62585034	43710507	42468436	-	-	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	5	1.154655103	0.704212728	1.154655103	0.704212728
76	0.498376	0	14837326	N	N	N	ENSG00000113504	ENSG00000208693	5	8	1165172	112016351	intron	upstream	SLC12A7	AC104946.4-4	1103491	112016284	-	-	0.553459119	1134430	112599304	-	-	Y	N	HCC1954	6	2.666666667	1	1	SINE	-	1	0	1	3	1.084868256	0.926261786	1.084868256	0.926261786
470	0.598344	0	10182229	N	N	N	ENSG00000196074	ENSG00000018236	20	12	57942105	39750361	downstream	intron	SYCP2	CNTN1	57872016	39588423	-	+	0.536050157	57868847	39622706	-	+	Y	N	HCC1954	1	1	1	0	LINE	LTR	1	1	1	14	0.932606045	1.084868256	1.084868256	0.932606045
449	0.607786	0	3109782	N	Y	N	ENSG00000176155	ENSG00000211264	17	17	77763978	67836854	coding	downstream	CCDC57	AC005243.1	77652635	67836654	-	+	0.531847134	77752806	67953309	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	9	1.059491221	0.926261786	1.059491221	0.926261786
53	1.00658	0	1256178	N	N	N	ENSG00000182240	ENSG00000183762	21	22	41570378	27893094	upstream	intron	BACE2	KREMEN1	41461598	27799066	+	+	0.71969697	41450663	27865956	+	+	Y	N	HCC1954	1	1	1	0	-	SINE	0	0.595744681	0.595744681	2	0.234737576	0.596360328	0.596360328	0.234737576
220	1.03225	0	8030775	N	Y	N	ENSG00000064999	ENSG00000065060	6	6	35193232	34953265	intron	intron	ANKS1A	UHRF1BP1	34965016	34867772	+	+	0.635964912	35190636	34936535	-	+	N	N	HCC1954	1	1	1	0	"LINE,LINE"	SINE	1	1	1	3	0.913573269	0.526573481	0.913573269	0.526573481
65	1.11453	0	8694288	N	N	N	ENSG00000222792	ENSG00000209951	3	7	199408117	86960	upstream	upstream	U6	AC097646.2-1	199408014	86858	+	-	0.6996997	199375722	119570	+	+	Y	N	HCC1954	25	7.083333333	1	7	"LINE,LINE"	LINE	0.660944206	1	1	12	0.824753645	0.628081622	0.824753645	0.628081622
405	1.47521	0	12076345	N	Y	N	ENSG00000156802	ENSG00000206719	8	8	124477868	115032403	intron	upstream	ATAD2	Y_RNA	124401922	115032291	-	+	0.598958333	124435794	114906363	-	+	N	N	HCC1954	11	5.333333333	1	2	SINE	-	0.328947368	0	0.328947368	3	0.48216367	0.729589763	0.729589763	0.48216367
282	1.61558	0	14786743	N	N	N	ENSG00000164754	ENSG00000170561	8	5	117956182	2804774	intron	downstream	RAD21	IRX2	117927355	2798959	-	-	0	117944025	2620914	-	+	Y	N	HCC1954	1	1	1	0	-	LINE	0	1	1	3	0.570983293	0.780343834	0.780343834	0.570983293
566	1.62267	0	1160702	N	N	N	ENSG00000198862	ENSG00000156299	21	21	29287141	31853161	intron	intron	RNF160	TIAM1	29222337	31412607	-	-	0.556862745	29274251	31517322	-	-	N	Y	HCC1954	1	1	1	0	DNA	-	1	0	1	3	0.710556987	0.900884751	0.900884751	0.710556987
48	1.73211	323	14825658	N	N	N	ENSG00000188818	ENSG00000174429	5	8	904101	107851648	intron	upstream	ZDHHC11	ABRA	848722	107840888	-	-	0.606606607	895815	107902540	-	-	Y	N	HCC1954	2	1.666666667	1	6	LTR	-	0.198019802	0	0.198019802	9	0.831097904	0.824753645	0.831097904	0.824753645
48	1.73211	323	14804524	N	N	N	ENSG00000113269	ENSG00000174429	5	8	179431719	107851648	intron	upstream	RNF130	ABRA	179315111	107840888	-	-	0.541528239	179367656	107902863	-	+	Y	N	HCC1954	1	1	1	0	LINE	-	1	0	1	10	0.869163457	1.034114186	1.034114186	0.869163457
474	1.78937	0	12461579	N	N	Y	ENSG00000174137	ENSG00000168924	4	4	1655516	1827772	intron	intron	FAM53A	LETM1	1611607	1784558	-	-	0	1634890	1820477	-	+	N	N	HCC1954	1	1	1	0	"LINE,DNA"	DNA	0.798882682	0.12568306	0.798882682	5	1.097556774	0.590016069	1.097556774	0.590016069
498	1.79514	0	3104350	N	N	Y	ENSG00000120071	ENSG00000136447	17	17	41625943	42012364	intron	intron	KIAA1267	ARL17P1	41463181	41949797	-	-	0.565088757	41521075	42007117	-	+	N	N	HCC1954	8	2.4	2	15	-	"DNA,SINE,SINE"	0	0.926701571	0.926701571	15	0.926261786	1.211753433	1.211753433	0.926261786
589	1.9477	0	14806930	N	N	N	ENSG00000145723	ENSG00000172167	5	8	102483741	121605056	intron	intron	GIN1	MTBP	102449603	121526847	-	+	0	102463379	121559792	-	+	Y	N	HCC1954	1	1	1	0	DNA	LINE	1	1	1	4	0.526573481	0.558294775	0.558294775	0.526573481
575	2.9574	4324	904011	N	N	N	ENSG00000208525	ENSG00000199315	8	11	130372654	97033792	downstream	upstream	AC103833.2-1	5S_rRNA	130372411	97033674	+	+	0.545801527	130389682	96544732	-	+	Y	N	HCC1954	2	1.333333333	1	1	LINE	SINE	1	0.153846154	1	3	0.74862254	0.90722901	0.90722901	0.74862254
575	2.9574	4324	891078	N	N	N	ENSG00000199315	ENSG00000222501	11	8	97033792	129092039	upstream	upstream	5S_rRNA	U4	97033674	129091912	+	-	0.656126482	96540408	129103678	-	+	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	5	0.609048846	0.989704374	0.989704374	0.609048846
290	2.9811	0	1060568	N	N	N	ENSG00000168876	ENSG00000152503	11	5	93872385	114544142	downstream	downstream	ANKRD49	TRIM36	93866801	114488377	+	-	0.522522523	93875528	114467653	+	+	Y	N	HCC1954	4	2	1	1	"Low_complexity,SINE"	SINE	0.353448276	1	1	3	0.735934022	0.666147175	0.735934022	0.666147175
374	3.23405	0	11951168	N	N	Y	ENSG00000215305	ENSG00000088812	20	20	2795378	3579760	intron	intron	VPS16	ATRN	2769373	3399676	+	+	0.309734513	2776967	3519183	-	+	N	N	HCC1954	1	1	1	0	"SINE,LTR"	DNA	0.905172414	0.467889908	0.905172414	4	0.735934022	0.69152421	0.735934022	0.69152421
590	3.33799	0	14790600	N	N	N	ENSG00000170873	ENSG00000183718	8	5	125809911	180620725	upstream	downstream	MTSS1	TRIM52	125632212	180615994	-	-	0.527851459	125915942	180614515	-	+	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	4	0.894540492	0.90722901	0.90722901	0.894540492
279	3.37031	0	14698873	N	N	Y	ENSG00000079313	ENSG00000104885	19	19	1799452	2181007	downstream	intron	REXO1	DOT1L	1766245	2115148	-	+	0.559139785	1765627	2160140	-	+	N	N	HCC1954	1	1	1	0	-	Low_complexity	0	0.245901639	0.245901639	3	0.989704374	0.773999575	0.989704374	0.773999575
607	3.86243	0	12064999	N	N	N	ENSG00000164830	ENSG00000212993	8	8	107834093	128498621	intron	upstream	OXR1	POU5F1P1	107739270	128497039	+	+	0.641196013	107754512	128196712	+	+	N	Y	HCC1954	6	2.545454545	1	4	"LTR,LTR"	-	0.528497409	0	0.528497409	11	1.22444195	0.678835693	1.22444195	0.678835693
117	3.97072	0	8030856	N	N	Y	ENSG00000111912	ENSG00000066651	6	6	126293949	126402115	intron	intron	ESNA1	TRMT11	126144000	126349269	+	+	0	126240407	126362104	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	1	0.507540705	0.501196446	0.507540705	0.501196446
554	4.00005	0	12484588	N	Y	N	ENSG00000138685	ENSG00000172493	4	4	124038840	88281215	upstream	utr3p	FGF2	AFF1	123967313	88147177	+	+	0	123957737	88280483	-	+	N	N	HCC1954	1	1	1	0	LINE	-	1	0	1	4	0.831097904	0.875507716	0.875507716	0.831097904
512	4.03905	0	2398868	N	Y	N	ENSG00000055044	ENSG00000082146	2	2	202876627	202053819	intron	intron	NOP58	STRADB	202838760	202024637	+	+	0.49689441	202870119	202047578	-	+	N	N	HCC1954	1	1	1	0	Low_complexity	SINE	0.0375	0.35	0.35	1	0.507540705	0.507540705	0.507540705	0.507540705
22	4.15045	0	1501028	N	Y	N	ENSG00000164880	ENSG00000164818	7	7	1510772	795716	coding	intron	INTS1	HEATR2	1476439	732864	-	+	0.666666667	1499959	742217	-	+	N	N	HCC1954	2	1.25	1	1	-	LINE	0	1	1	4	1.110245292	0.577327552	1.110245292	0.577327552
397	4.17426	0	12093450	N	N	N	ENSG00000221261	ENSG00000147697	8	8	129231616	130868316	upstream	intron	hsa-mir-1208	GSDMC	129231544	130829625	+	-	0.589041096	129181197	130842583	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	1	0.228393317	0.228393317	0.228393317	0.228393317
287	4.21238	0	14764418	N	N	N	ENSG00000170549	ENSG00000164761	5	8	3654517	120033564	upstream	downstream	IRX1	TNFRSF11B	3649168	120004978	+	-	0.531855956	3262221	119873851	+	+	Y	N	HCC1954	9	1.576923077	1	5	LTR	SINE	0.94047619	0.442708333	0.94047619	26	1.06583548	1.218097691	1.218097691	1.06583548
370	4.32528	0	12858829	N	N	N	ENSG00000152495	ENSG00000164134	5	4	110848645	140531972	intron	intron	CAMK4	NARG1	110587981	140442126	+	+	0.487654321	110789313	140446313	+	+	Y	N	HCC1954	1	1	1	0	-	SINE	0	1	1	2	0.507540705	0.513884964	0.513884964	0.507540705
226	4.34896	0	14448028	N	N	N	ENSG00000119487	ENSG00000205246	9	19	127509334	23802761	intron	downstream	MAPKAP1	RPSAP8	127239494	23801726	-	+	0.472636816	127378909	23803140	-	+	Y	N	HCC1954	15	5	1	3	Other	LINE	1	0.982608696	1	4	0.539261999	0.729589763	0.729589763	0.539261999
166	4.4797	0	12095677	Y	N	N	ENSG00000182197	ENSG00000177570	8	8	119193119	119703365	intron	downstream	EXT1	SAMD12	118875910	119270880	-	-	0.594444444	119182140	119270524	-	-	N	Y	HCC1954	1	1	1	0	SINE	SINE	0.401869159	0.152777778	0.401869159	2	0.678835693	0.456786634	0.678835693	0.456786634
309	4.62985	0	9164275	N	N	N	ENSG00000214116	ENSG00000185986	3	5	197173943	1646257	intron	downstream	AC024937.21-2	AC091849.2	197171055	1625243	-	-	0.701754386	197172567	1622896	-	+	Y	N	HCC1954	1	1	1	0	-	DNA	0	1	1	1	0.209360541	0.507540705	0.507540705	0.209360541
181	4.74815	186	4209530	N	N	N	ENSG00000155352	ENSG00000162783	2	1	114073079	179326595	intron	downstream	FAM39B	IER5	114058161	179324471	+	+	0.526760563	114063073	179347877	-	+	Y	N	HCC1954	5	4.142857143	2	14	"LINE,SINE"	"LTR,LTR"	0.865591398	0.642857143	0.865591398	14	1.180032139	1.06583548	1.180032139	1.06583548
181	4.74815	186	3860476	N	N	N	ENSG00000162783	ENSG00000149218	1	11	179326595	94505463	downstream	intron	IER5	ENDOD1	179324471	94462665	+	+	0.5917603	179347691	94485944	-	+	Y	N	HCC1954	4	1.8	1	2	"LTR,LTR"	"SINE,LINE,LINE"	0.467889908	0.49044586	0.49044586	5	0.69152421	0.996048633	0.996048633	0.69152421
481	5.15597	0	9296278	N	N	N	ENSG00000183784	ENSG00000219850	9	9	205741	67945195	downstream	intron	C9orf66	RP11-764K9.4	202824	67917681	-	-	0.521472393	191427	67924349	+	+	N	Y	HCC1954	12	3.636363636	1	8	LTR	-	0.752941176	0	0.752941176	11	1.053146962	0.685179951	1.053146962	0.685179951
555	5.24923	0	7572689	N	N	N	ENSG00000090565	ENSG00000114541	16	3	512479	69518120	utr3p	intron	RAB11FIP3	FRMD4B	415669	69301836	+	-	0.780645161	512083	69485510	-	+	Y	N	HCC1954	3	2.333333333	1	2	-	Simple_repeat	0	1	1	3	0.742278281	0.234737576	0.742278281	0.234737576
41	5.35277	0	15259515	N	N	Y	ENSG00000198961	ENSG00000131188	5	5	108773594	176815889	downstream	intron	PJA2	PRR7	108698309	176806400	-	+	0.627507163	108661911	176813817	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	14	0.900884751	1.306917315	1.306917315	0.900884751
286	5.49859	1904	15291007	N	N	N	ENSG00000165671	ENSG00000113269	5	5	176655369	179431719	intron	intron	NSD1	RNF130	176493532	179315111	+	-	0.530927835	176608713	179387421	-	-	N	Y	HCC1954	1	1	1	0	SINE	-	0.491712707	0	0.491712707	11	1.148310845	1.306917315	1.306917315	1.148310845
286	5.49859	1904	15248794	N	N	N	ENSG00000165671	ENSG00000165671	5	5	176655369	176655369	intron	intron	NSD1	NSD1	176493532	176493532	+	+	0.650273224	176587780	176610617	+	+	N	Y	HCC1954	1	1	1	0	DNA	SINE	1	0.848739496	1	3	0.399688305	0.754966798	0.754966798	0.399688305
135	5.60697	0	12085523	N	Y	N	ENSG00000164944	ENSG00000079112	8	8	95634864	95289986	intron	downstream	KIAA1429	CDH17	95569776	95208566	-	-	0.6171875	95585070	95123587	-	+	N	N	HCC1954	1	1	1	0	LINE	-	1	0	1	1	0.507540705	0.298180164	0.507540705	0.298180164
207	5.76162	0	12482051	N	N	Y	ENSG00000145431	ENSG00000109572	4	4	158111996	170878731	intron	coding	PDGFC	CLCN3	157902214	170778297	-	+	0.693548387	158035946	170850043	-	+	N	N	HCC1954	1	1	1	0	SINE	-	0.875	0	0.875	1	0.507540705	0.272803129	0.507540705	0.272803129
541	5.79512	0	12064765	N	N	N	ENSG00000155897	ENSG00000155897	8	8	132123854	132123854	utr5p	upstream	ADCY8	ADCY8	131861736	131861736	-	-	0.528350515	132123337	132471191	+	+	N	Y	HCC1954	1	1	1	0	Low_complexity	-	0.106796117	0	0.106796117	19	1.306917315	1.148310845	1.306917315	1.148310845
152	5.88226	0	12085505	Y	N	Y	ENSG00000221176	ENSG00000221261	8	8	129130666	129231616	downstream	downstream	hsa-mir-1207	hsa-mir-1208	129130580	129231544	+	+	0.566091954	129180694	129248061	-	+	N	N	HCC1954	1	1	1	0	-	SINE	0	0.26	0.26	3	1.059491221	0.951638821	1.059491221	0.951638821
138	5.8892	0	14694782	N	N	Y	ENSG00000197863	ENSG00000204866	19	19	42021124	51356385	upstream	upstream	ZNF790	IGFL2	42000176	51274062	-	+	0.572289157	42026987	51261624	-	+	N	N	HCC1954	1	1	1	0	SINE	LTR	1	0.6	1	2	0.444098117	0.602704587	0.602704587	0.444098117
26	5.94207	0	10909896	N	N	N	ENSG00000129514	ENSG00000129514	14	14	37134240	37134240	intron	upstream	FOXA1	FOXA1	37128947	37128947	-	-	0	37133833	37135084	+	+	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	2	0.513884964	0.53291774	0.53291774	0.513884964
330	6.24336	0	14686519	N	N	N	ENSG00000105738	ENSG00000160570	19	19	43390849	47416115	intron	downstream	SIPA1L3	DEDD2	43089708	47394592	+	-	0.534591195	43131489	47375843	+	+	N	Y	HCC1954	1	1	1	0	LINE	-	1	0	1	8	0.932606045	1.078523998	1.078523998	0.932606045
239	6.28592	0	9904	N	Y	N	ENSG00000109861	ENSG00000162105	11	11	87710586	70536020	intron	intron	CTSC	SHANK2	87666421	69991609	-	-	0	87695260	70355429	-	+	N	N	HCC1954	1	1	1	0	"LINE,LINE"	-	0.944954128	0	0.944954128	2	0.69152421	0.697868469	0.697868469	0.69152421
10	6.58713	0	1244353	N	N	N	ENSG00000188681	ENSG00000217850	Y	21	11830682	30558070	downstream	downstream	AC134878.3-1	RPL8P2	11769481	30557569	-	-	0	11715024	30550161	-	+	Y	N	HCC1954	1	1	1	0	Satellite	LTR	1	1	1	2	0.526573481	0.463130893	0.526573481	0.463130893
503	6.82238	0	5551385	N	N	N	ENSG00000207985	ENSG00000160783	20	1	26136914	154479736	upstream	intron	hsa-mir-663	PMF1	26136822	154449408	-	+	0.660714286	26138516	154453280	+	+	Y	N	HCC1954	1	1	1	0	DNA	Low_complexity	0.983193277	0.101851852	0.983193277	458	0.754966798	1.370359903	1.370359903	0.754966798
278	7.1	0	14783801	N	N	N	ENSG00000155897	ENSG00000160867	8	5	132123854	176457749	intron	downstream	ADCY8	FGFR4	131861736	176446521	-	+	0.559366755	131950752	176458417	-	+	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	30	1.06583548	1.33229435	1.33229435	1.06583548
573	7.11156	0	14807120	N	N	N	ENSG00000087206	ENSG00000212993	5	8	176366358	128498621	intron	upstream	UIMC1	POU5F1P1	176264612	128497039	-	+	0	176274073	128134899	-	+	Y	N	HCC1954	1	1	1	0	LINE	SINE	0.9	0.656804734	0.9	8	1.141966586	1.072179739	1.141966586	1.072179739
355	7.16371	0	1160699	N	N	N	ENSG00000166265	ENSG00000182240	21	21	26867452	41570378	upstream	upstream	CYYR1	BACE2	26760402	41461598	-	+	0.613636364	26906321	41450461	-	-	N	Y	HCC1954	1	1	1	0	-	SINE	0	1	1	2	0.837442163	0.551950516	0.837442163	0.551950516
344	7.16511	0	10074388	N	Y	N	ENSG00000139116	ENSG00000110799	12	12	38123190	6104097	downstream	intron	KIF21A	VWF	37973298	5928301	-	-	0.758928571	37950661	6071923	-	+	N	N	HCC1954	2	2	2	1	LTR	SINE	1	1	1	1	0.196672023	0.507540705	0.507540705	0.196672023
123	7.17639	0	15247036	N	N	N	ENSG00000221436	ENSG00000092421	5	5	109877515	115938529	downstream	upstream	hsa-mir-548f-3	SEMA6A	109877429	115807150	-	-	0.656357388	109720309	115998930	+	+	N	Y	HCC1954	4	1.5	1	1	-	LTR	0	1	1	6	0.672491434	1.167343621	1.167343621	0.672491434
320	7.24429	0	1604089	N	N	N	ENSG00000147974	ENSG00000170260	9	7	33666649	148583619	upstream	intron	AL356489.14-3	ZNF212	33665438	148567675	-	+	0.602941176	33667009	148567877	-	-	Y	N	HCC1954	1	1	1	0	Simple_repeat	-	0.870967742	0	0.870967742	1	0.196672023	0.228393317	0.228393317	0.196672023
252	7.30508	2091	12075424	N	N	Y	ENSG00000155897	ENSG00000129292	8	8	132123854	133930234	upstream	intron	ADCY8	PHF20L1	131861736	133856786	-	+	0.493150685	132512039	133888462	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	1	0.228393317	0.228393317	0.228393317	0.228393317
252	7.30508	2091	12075639	N	N	Y	ENSG00000153310	ENSG00000155897	8	8	131097879	132123854	intron	upstream	FAM49B	ADCY8	130922900	131861736	-	-	0.563888889	130944813	132513176	-	+	N	N	HCC1954	11	3	1	2	SINE	-	0.827586207	0	0.827586207	9	1.287884538	0.989704374	1.287884538	0.989704374
252	7.30508	2091	12065872	N	N	N	ENSG00000177570	ENSG00000153310	8	8	119703365	131097879	intron	intron	SAMD12	FAM49B	119270880	130922900	-	-	0.574879227	119281340	130945767	+	+	N	Y	HCC1954	1	1	1	0	"SINE,LTR"	-	0.666666667	0	0.666666667	3	0.551950516	0.704212728	0.704212728	0.551950516
195	7.32662	0	12083087	N	Y	N	ENSG00000147697	ENSG00000221261	8	8	130868316	129231616	intron	upstream	GSDMC	hsa-mir-1208	130829625	129231544	-	+	0.620155039	130843257	129181155	-	+	N	N	HCC1954	1	1	1	0	-	LINE	0	1	1	1	0.507540705	0.304524423	0.507540705	0.304524423
446	7.40245	0	14703573	N	N	Y	ENSG00000007255	ENSG00000007047	19	19	50373325	50500381	upstream	intron	TRAPPC6A	MARK4	50358027	50446390	-	+	0.5	50380014	50448478	-	+	N	N	HCC1954	1	1	1	0	"SINE,LINE"	SINE	0.82278481	0.125	0.82278481	1	0.501196446	0.507540705	0.507540705	0.501196446
108	7.42619	0	17175	N	Y	N	ENSG00000223269	ENSG00000172818	11	11	98496430	65321259	upstream	intron	7SK	OVOL1	98496116	65311105	+	+	0.18705036	98334158	65311789	-	+	N	N	HCC1954	1	1	1	0	-	Low_complexity	0	0.3625	0.3625	1	0.367967011	0.507540705	0.507540705	0.367967011
265	7.64405	0	3077	N	N	N	ENSG00000205867	ENSG00000204572	11	11	1576056	70957628	upstream	upstream	KRTAP5-2	KRTAP5-10	1575523	70954257	-	+	0.604060914	1576877	70953423	+	+	N	Y	HCC1954	1	1	1	0	LTR	"LTR,LTR"	1	0.731092437	1	2	0.488507928	0.754966798	0.754966798	0.488507928
570	7.73351	0	15292572	N	N	N	ENSG00000112893	ENSG00000171444	5	5	109231328	112852010	intron	intron	MAN2A1	MCC	109053055	112385695	+	-	0.739726027	109061060	112495704	-	-	N	Y	HCC1954	1	1	1	0	DNA	Low_complexity	0.111111111	0.722222222	0.722222222	1	0.228393317	0.228393317	0.228393317	0.228393317
55	7.82755	0	1158381	N	N	Y	ENSG00000209722	ENSG00000160193	21	21	17725836	43172747	upstream	downstream	AP000952.2	WDR4	17725745	43136275	+	-	0.586387435	17661143	43119596	-	+	N	N	HCC1954	3	2.5	2	2	SINE	"LINE,SINE"	0.294871795	0.589285714	0.589285714	2	0.494852187	0.710556987	0.710556987	0.494852187
403	7.83342	0	1259349	N	N	N	ENSG00000182871	ENSG00000183762	21	22	45758062	27893094	intron	intron	COL18A1	KREMEN1	45649480	27799066	+	+	0.625	45682991	27865910	-	+	Y	N	HCC1954	1	1	1	0	-	SINE	0	0.133333333	0.133333333	1	0.279147388	0.475819411	0.475819411	0.279147388
217	8.10543	0	1157587	N	Y	N	ENSG00000157540	ENSG00000215353	21	21	37809550	20054277	downstream	upstream	DYRK1A	AP000568.2	37661749	20053544	+	-	0	37822420	20181457	-	+	N	N	HCC1954	1	1	1	0	-	LTR	0	0.1625	0.1625	1	0.48216367	0.507540705	0.507540705	0.48216367
337	8.20393	0	4528168	N	N	N	ENSG00000179571	ENSG00000219481	1	1	16812569	146862781	utr5p	upstream	NBPF1	NBPF15	16762999	146827614	-	+	0.718181818	16812465	146822858	-	-	N	Y	HCC1954	2	1.333333333	1	1	-	-	0	0	0	3	0.386999787	1.002392892	1.002392892	0.386999787
425	8.27458	0	1159613	N	Y	N	ENSG00000183844	ENSG00000186842	21	21	41651524	32870062	intron	intron	FAM3B	C21orf77	41610526	32866420	+	-	0.528795812	41632355	32868401	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	3	0.64077014	0.564639034	0.64077014	0.564639034
88	8.33806	0	3732035	N	N	Y	ENSG00000100399	ENSG00000100412	22	22	39966881	40254939	coding	intron	CHADL	ACO2	39955485	40195075	-	+	0.736363636	39963905	40245553	-	+	N	N	HCC1954	1	1	1	0	-	SINE	0	1	1	1	0.183983505	0.507540705	0.507540705	0.183983505
391	8.61162	0	136522	N	N	N	ENSG00000203360	ENSG00000211547	11	2	71057232	132755208	downstream	downstream	AP003498.2-1	AC097532.3-1	71056959	132755117	+	-	0.641666667	71059462	132745890	+	+	Y	N	HCC1954	2	1.285714286	1	2	"SINE,Simple_repeat"	"Low_complexity,SINE"	0.823529412	0.519480519	0.823529412	7	0.539261999	0.977015857	0.977015857	0.539261999
591	8.72581	0	2686101	N	N	N	ENSG00000221415	ENSG00000115233	4	2	48895063	161976474	downstream	upstream	AC118282.4-1	PSMD14	48894981	161872795	+	+	0.506369427	49022116	161847435	-	+	Y	N	HCC1954	110	9.4	2	60	LINE	SINE	0.167701863	0.092105263	0.167701863	60	1.021425668	0.964327339	1.021425668	0.964327339
242	8.77589	0	15279313	N	Y	N	ENSG00000134970	ENSG00000080709	5	5	114989757	113860096	intron	intron	TICAM2	KCNN2	114942238	113725565	-	+	0.519379845	114985090	113815269	-	+	N	N	HCC1954	1	1	1	0	-	"Low_complexity,SINE"	0	0.842857143	0.842857143	1	0.367967011	0.444098117	0.444098117	0.367967011
33	8.84783	0	12088793	N	N	Y	ENSG00000104313	ENSG00000169946	8	8	72437021	106885939	intron	intron	EYA1	ZFPM2	72272222	106400323	-	+	0.726027397	72293349	106676002	-	+	N	N	HCC1954	1	1	1	0	-	SINE	0	1	1	1	0.228393317	0.228393317	0.228393317	0.228393317
580	8.94009	0	1159545	N	N	Y	ENSG00000160191	ENSG00000160299	21	21	43068688	46690106	downstream	intron	PDE9A	PCNT	42946931	46568483	+	+	0.622047244	43077758	46588184	-	+	N	N	HCC1954	1	1	1	0	Simple_repeat	"LINE,LINE"	1	1	1	1	0.291835905	0.507540705	0.507540705	0.291835905
508	8.9854	0	1158503	N	Y	N	ENSG00000185658	ENSG00000159267	21	21	39607426	37284373	intron	intron	BRWD1	HLCS	39479274	37045066	-	-	0.5	39504523	37222526	-	+	N	N	HCC1954	1	1	1	0	-	SINE	0	0.625	0.625	3	0.653458657	0.659802916	0.659802916	0.653458657
6	9.04195	461	12083087	N	Y	N	ENSG00000147697	ENSG00000221261	8	8	130868316	129231616	intron	upstream	GSDMC	hsa-mir-1208	130829625	129231544	-	+	0.620155039	130843257	129181155	-	+	N	N	HCC1954	1	1	1	0	-	LINE	0	1	1	1	0.507540705	0.304524423	0.507540705	0.304524423
6	9.04195	461	12085505	Y	N	Y	ENSG00000221176	ENSG00000221261	8	8	129130666	129231616	downstream	downstream	hsa-mir-1207	hsa-mir-1208	129130580	129231544	+	+	0.566091954	129180694	129248061	-	+	N	N	HCC1954	1	1	1	0	-	SINE	0	0.26	0.26	3	1.059491221	0.951638821	1.059491221	0.951638821
249	9.15227	0	1500839	N	N	Y	ENSG00000091073	ENSG00000186704	7	7	75973241	76483049	intron	upstream	DTX2	PMS2L11	75928954	76469431	+	+	0.66	75938447	76456373	-	+	N	N	HCC1954	4	4	4	1	SINE	"LINE,SINE"	1	0.6	1	1	0.437753858	0.507540705	0.507540705	0.437753858
71	9.16428	0	3097148	N	N	N	ENSG00000108344	ENSG00000108344	17	17	35407738	35407738	upstream	intron	PSMD3	PSMD3	35390586	35390586	+	+	0	35389851	35391279	+	+	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	1	0.469475152	0.507540705	0.507540705	0.469475152
298	9.39526	0	3115327	N	N	N	ENSG00000131748	ENSG00000131748	17	17	35073248	35073248	intron	intron	STARD3	STARD3	35046938	35046938	+	+	0.508235294	35069003	35069597	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	22	1.325950091	1.319605832	1.325950091	1.319605832
588	9.57492	0	7714325	N	N	N	ENSG00000207985	ENSG00000207986	20	16	26136914	33869267	upstream	upstream	hsa-mir-663	AC136932.4-2	26136822	33869153	-	+	0.803030303	26137126	33868998	+	+	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	5	0.74862254	0.919917527	0.919917527	0.74862254
276	10.0817	0	15245023	N	N	N	ENSG00000201910	ENSG00000177879	5	5	103462638	115277675	upstream	intron	U1	AP3S1	103462474	115205518	+	+	0.520661157	103211669	115246106	+	+	N	Y	HCC1954	19	5.5	1	1	DNA	LINE	0.728070175	1	1	4	0.723245504	0.805720869	0.805720869	0.723245504
346	10.2249	0	11707866	N	N	N	ENSG00000175676	ENSG00000012061	15	19	20999858	50619017	downstream	upstream	GOLGA8E	ERCC1	20986537	50604712	+	-	0.559782609	21060465	50626848	-	-	Y	N	HCC1954	22	12	2	2	-	SINE	0	1	1	2	0.520229222	0.64077014	0.64077014	0.520229222
400	11.0246	0	207711	N	N	N	ENSG00000048649	ENSG00000206951	11	2	77209528	33024022	intron	downstream	RSF1	Y_RNA	77054923	33023910	-	-	0.559440559	77123911	32995011	-	+	Y	N	HCC1954	1	1	1	0	Low_complexity	Simple_repeat	0.2625	1	1	1	0.507540705	0.393344046	0.507540705	0.393344046
314	11.0358	14410	9562527	N	N	N	ENSG00000161405	ENSG00000110799	17	12	35273967	6104097	intron	intron	IKZF3	VWF	35174724	5928301	-	-	0.53909465	35213696	6040829	+	+	Y	N	HCC1954	1	1	1	0	SINE	SINE	0.054054054	1	1	3	0.704212728	0.831097904	0.831097904	0.704212728
314	11.0358	14410	272480	N	N	N	ENSG00000149089	ENSG00000161405	11	17	34894472	35273967	intron	intron	APIP	IKZF3	34860421	35174724	-	-	0.694915254	34887023	35199286	-	-	Y	N	HCC1954	1	1	1	0	-	"SINE,SINE"	0	0.9	0.9	1	0.234737576	0.507540705	0.507540705	0.234737576
233	11.1564	0	2536878	N	N	N	ENSG00000208885	ENSG00000198526	8	2	101764973	147065027	downstream	intron	AP001205.3-1	PABPCP2	101764892	147061731	+	+	0.590163934	101769094	147064378	-	+	Y	N	HCC1954	72	72	72	1	"LINE,SINE"	SINE	0.833333333	1	1	1	0.152262211	0.228393317	0.228393317	0.152262211
104	11.3593	0	8027264	N	Y	N	ENSG00000178729	ENSG00000096433	6	6	48144384	33772324	intron	intron	C6orf138	ITPR3	47953998	33697139	-	+	0	48053506	33714797	-	+	N	N	HCC1954	1	1	1	0	-	LINE	0	1	1	2	0.450442375	0.507540705	0.507540705	0.450442375
205	11.6558	28	14072468	N	N	N	ENSG00000171813	ENSG00000171813	10	10	134081357	134081357	intron	intron	PWWP2B	PWWP2B	134060662	134060662	+	+	0.52173913	134075351	134076707	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	1	0.228393317	0.203016282	0.228393317	0.203016282
205	11.6558	28	14047535	Y	N	N	ENSG00000171813	ENSG00000068383	10	10	134081357	134446974	intron	intron	PWWP2B	INPP5A	134060662	134201343	+	+	0.761904762	134076735	134280639	+	+	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	2	0.190327764	0.602704587	0.602704587	0.190327764
256	11.6835	0	2543472	N	N	N	ENSG00000219507	ENSG00000206951	8	2	82597221	33024022	upstream	downstream	AC023644.6	Y_RNA	82596349	33023910	-	-	0.493150685	82597237	32995139	-	+	Y	N	HCC1954	4	4	4	1	-	Simple_repeat	0	1	1	1	0.228393317	0.228393317	0.228393317	0.228393317
312	11.8566	5882	15288668	N	N	N	ENSG00000201910	ENSG00000134982	5	5	103462638	112209834	upstream	intron	U1	APC	103462474	112101483	+	+	0	103451895	112183890	-	-	N	Y	HCC1954	1	1	1	0	LTR	SINE	0.214285714	0.159090909	0.214285714	2	0.53291774	0.558294775	0.558294775	0.53291774
312	11.8566	5882	15257301	N	N	N	ENSG00000063438	ENSG00000134982	5	5	491392	112209834	intron	intron	PDCD6	APC	324736	112101483	+	+	0.529411765	340800	112189772	+	+	N	Y	HCC1954	1	1	1	0	-	LINE	0	0.516129032	0.516129032	1	0.228393317	0.196672023	0.228393317	0.196672023
266	11.9069	0	7477495	N	N	N	ENSG00000179889	ENSG00000183458	16	16	15140696	16395300	intron	intron	PDXDC1	AC136619.3-1	14976487	16322811	+	+	0.516216216	15031765	16357221	+	+	N	Y	HCC1954	66	16.28571429	5	7	SINE	-	0.759162304	0	0.759162304	7	1.211753433	0.970671598	1.211753433	0.970671598
520	12.148	0	3109801	N	N	Y	ENSG00000214546	ENSG00000141736	17	17	35032292	35138441	upstream	intron	AC087491.2	ERBB2	35029392	35104766	+	+	0.447204969	35026033	35133913	-	+	N	N	HCC1954	1	1	1	0	SINE	SINE	1	0.075	1	1	0.507540705	0.507540705	0.507540705	0.507540705
149	12.7382	0	4698026	N	N	N	ENSG00000153815	ENSG00000212678	16	1	80302866	560165	downstream	intron	AC099524.5	RP5-857K21.11	80036395	559619	+	+	0.684210526	80331844	559938	-	+	Y	N	HCC1954	2	2	2	1	"SINE,LTR"	-	0.514285714	0	0.514285714	1	0.222049058	0.494852187	0.494852187	0.222049058
390	12.8081	0	14830841	N	N	N	ENSG00000145780	ENSG00000155897	5	8	114908490	132123854	downstream	upstream	FEM1C	ADCY8	114884507	131861736	-	-	0.493150685	114884080	132526487	-	-	Y	N	HCC1954	1	1	1	0	-	LINE	0	1	1	1	0.228393317	0.228393317	0.228393317	0.228393317
483	13.376	20629	12088544	N	N	Y	ENSG00000153310	ENSG00000129292	8	8	131097879	133930234	intron	utr3p	FAM49B	PHF20L1	130922900	133856786	-	+	0	130935333	133899457	-	+	N	N	HCC1954	1	1	1	0	-	-	0	0	0	3	0.520229222	0.58367181	0.58367181	0.520229222
483	13.376	20629	12065626	Y	N	N	ENSG00000153310	ENSG00000153317	8	8	131097879	131483399	intron	intron	FAM49B	ASAP1	130922900	131133535	-	-	0	130941868	131470431	+	+	N	Y	HCC1954	1	1	1	0	-	SINE	0	1	1	3	0.507540705	0.444098117	0.507540705	0.444098117
483	13.376	20629	12073106	Y	Y	N	ENSG00000153317	ENSG00000153310	8	8	131483399	131097879	intron	intron	ASAP1	FAM49B	131133535	130922900	-	-	0.542319749	131461522	130951025	-	+	N	N	HCC1954	1	1	1	0	LTR	-	1	0	1	5	1.040458445	0.919917527	1.040458445	0.919917527
483	13.376	20629	14784199	N	N	N	ENSG00000153310	ENSG00000129596	8	5	131097879	115180304	intron	upstream	FAM49B	CDO1	130922900	115168333	-	-	0.637096774	130950223	115180634	-	+	Y	N	HCC1954	1	1	1	0	-	-	0	0	0	8	0.564639034	1.002392892	1.002392892	0.564639034
483	13.376	20629	14807227	N	N	N	ENSG00000129596	ENSG00000201782	5	8	115180304	129302243	intron	upstream	CDO1	7SK	115168333	129301932	-	+	0.57957958	115177913	129279451	-	+	Y	N	HCC1954	1	1	1	0	-	SINE	0	0.978571429	0.978571429	10	1.167343621	0.888196233	1.167343621	0.888196233
483	13.376	20629	12097328	N	N	N	ENSG00000213707	ENSG00000201782	8	8	108255213	129302243	downstream	upstream	AP000428.3-1	7SK	108254706	129301932	-	+	0.597014925	108129591	129278580	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	1	0.336245717	0.507540705	0.507540705	0.336245717
483	13.376	20629	12073372	N	Y	N	ENSG00000177570	ENSG00000213707	8	8	119703365	108255213	utr3p	downstream	SAMD12	AP000428.3-1	119270880	108254706	-	-	0	119277145	108130382	-	+	N	N	HCC1954	7	1.3	1	1	LINE	DNA	0.47029703	0.04040404	0.47029703	20	1.28154028	1.256163244	1.28154028	1.256163244
59	13.796	0	14512310	N	N	N	ENSG00000130402	ENSG00000206951	19	2	43913010	33024022	coding	downstream	ACTN4	Y_RNA	43830167	33023910	+	-	0	43830253	32994871	-	+	Y	N	HCC1954	4	4	4	1	-	Simple_repeat	0	1	1	1	0.507540705	0.507540705	0.507540705	0.507540705
307	14.0044	0	10194905	N	N	N	ENSG00000185834	ENSG00000151229	20	12	53125086	38786158	downstream	intron	AL121593.10	SLC2A13	53124590	38435090	+	-	0.575438596	53408303	38680026	-	-	Y	N	HCC1954	2	1.666666667	1	2	SINE	"LTR,LTR"	0.619834711	0.601226994	0.619834711	3	0.704212728	0.996048633	0.996048633	0.704212728
56	14.0678	0	7498630	N	N	N	ENSG00000183889	ENSG00000196696	16	16	18374143	68657352	downstream	intron	AC126755.3-2	PDXDC2	18359460	68567713	-	-	0.433673469	18354205	68601811	-	-	N	Y	HCC1954	14	7.666666667	2	3	-	SINE	0	1	1	3	0.653458657	0.58367181	0.653458657	0.58367181
424	14.2913	57723	12064999	N	N	N	ENSG00000164830	ENSG00000212993	8	8	107834093	128498621	intron	upstream	OXR1	POU5F1P1	107739270	128497039	+	+	0.641196013	107754512	128196712	+	+	N	Y	HCC1954	6	2.545454545	1	4	"LTR,LTR"	-	0.528497409	0	0.528497409	11	1.22444195	0.678835693	1.22444195	0.678835693
424	14.2913	57723	12078161	N	Y	N	ENSG00000212993	ENSG00000208693	8	8	128498621	112016351	upstream	upstream	POU5F1P1	AC104946.4-4	128497039	112016284	+	-	0.5	128138989	112528589	-	+	N	N	HCC1954	2	1.5	1	1	LINE	LTR	1	1	1	2	0.501196446	0.507540705	0.507540705	0.501196446
506	15.0412	1778	6735373	N	N	N	ENSG00000133119	ENSG00000172057	13	17	33309642	35337380	upstream	upstream	RFC3	ORMDL3	33290206	35330822	+	-	0.76146789	33095566	35341146	-	+	Y	N	HCC1954	7	7	7	1	LINE	SINE	1	1	1	1	0.177639247	0.507540705	0.507540705	0.177639247
506	15.0412	1778	4640140	N	N	N	ENSG00000219764	ENSG00000133119	1	13	554676	33309642	intron	upstream	RP5-857K21.9	RFC3	554305	33290206	+	+	0.597014925	554327	33097344	-	+	Y	N	HCC1954	2	2	2	1	-	-	0	0	0	1	0.336245717	0.507540705	0.507540705	0.336245717
404	15.1049	0	11581697	N	N	N	ENSG00000200216	ENSG00000130702	15	20	68272737	60375763	downstream	intron	U6	LAMA5	68272629	60317516	+	-	0.779735683	68334196	60341328	+	+	Y	N	HCC1954	10	6	3	3	Simple_repeat	-	0.945454545	0	0.945454545	3	0.348934235	0.900884751	0.900884751	0.348934235
12	15.1376	0	1524657	N	N	Y	ENSG00000091127	ENSG00000146776	7	7	104949921	105310263	intron	intron	PUS7	ATXN7L1	104884194	105032750	-	-	0.680672269	104945519	105150345	-	+	N	N	HCC1954	1	1	1	0	"SINE,SINE"	"SINE,SINE"	0.868421053	0.7375	0.868421053	1	0.241081835	0.507540705	0.507540705	0.241081835
384	15.2077	0	2356805	N	N	N	ENSG00000188681	ENSG00000187984	Y	2	11830682	94886721	intron	upstream	AC134878.3-1	AC097374.3-4	11769481	94874856	-	-	0.847368421	11788413	94887414	-	-	Y	N	HCC1954	5	2.5	1	3	-	-	0	0	0	6	1.141966586	1.078523998	1.141966586	1.078523998
169	15.7803	355	3056599	N	N	N	ENSG00000141736	ENSG00000206951	17	2	35138441	33024022	intron	downstream	ERBB2	Y_RNA	35104766	33023910	+	-	0	35116028	32995194	-	+	Y	N	HCC1954	2	1.5	1	2	-	Simple_repeat	0	1	1	4	0.666147175	1.141966586	1.141966586	0.666147175
169	15.7803	355	2915695	N	N	N	ENSG00000206951	ENSG00000197823	2	5	33024022	171969041	downstream	downstream	Y_RNA	AC027309.3	33023910	171968850	-	-	0	32994839	171897324	-	-	Y	N	HCC1954	1	1	1	0	Simple_repeat	"SINE,LINE"	1	0.9625	1	1	0.507540705	0.507540705	0.507540705	0.507540705
352	16.0273	91459	4436392	N	N	N	ENSG00000199879	ENSG00000219481	1	1	146202531	146862781	upstream	upstream	U1	NBPF15	146202375	146827614	+	+	0.562724014	146197833	146826304	+	+	N	Y	HCC1954	6	1.714285714	1	6	-	"SINE,SINE"	0	1	1	14	0.996048633	0.767655316	0.996048633	0.767655316
352	16.0273	91459	4478476	N	N	Y	ENSG00000203834	ENSG00000202167	1	1	146099052	147413503	upstream	downstream	BX842679.19	U1	146098591	147413338	-	-	0.614840989	146106374	147412042	-	+	N	N	HCC1954	6	4.222222222	2	9	DNA	-	0.057471264	0	0.057471264	9	1.103901033	0.685179951	1.103901033	0.685179951
375	16.1741	32051	3115327	N	N	N	ENSG00000131748	ENSG00000131748	17	17	35073248	35073248	intron	intron	STARD3	STARD3	35046938	35046938	+	+	0.508235294	35069003	35069597	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	22	1.325950091	1.319605832	1.325950091	1.319605832
375	16.1741	32051	3098338	Y	N	N	ENSG00000161395	ENSG00000141736	17	17	35097836	35138441	upstream	upstream	PERLD1	ERBB2	35080902	35104766	-	+	0.448717949	35101054	35101928	+	+	N	Y	HCC1954	1	1	1	0	"LINE,SINE"	SINE	0.826666667	1	1	1	0.475819411	0.507540705	0.507540705	0.475819411
461	16.1917	0	3118498	N	N	N	ENSG00000213330	ENSG00000207064	17	17	41020078	41648314	upstream	upstream	AC126544.5-1	Y_RNA	41019020	41648213	+	-	0.745614035	41007288	41659260	-	-	N	Y	HCC1954	2	2	2	1	-	-	0	0	0	1	0.209360541	0.507540705	0.507540705	0.209360541
534	16.3728	23781	14053430	N	Y	N	ENSG00000204043	ENSG00000204043	10	10	81462701	81462701	downstream	downstream	FAM22C	FAM22C	81453188	81453188	+	+	0.531969309	81495366	81464241	-	+	N	N	HCC1954	25	14.5625	3	16	"LTR,LTR"	-	0.895604396	0	0.895604396	16	1.154655103	1.319605832	1.319605832	1.154655103
534	16.3728	23781	14048442	N	N	N	ENSG00000204043	ENSG00000214562	10	10	81462701	88984892	downstream	downstream	FAM22C	FAM22A	81453188	88975185	+	+	0.561643836	81519147	89041128	+	+	N	Y	HCC1954	16	16	16	1	-	-	0	0	0	1	0.228393317	0.228393317	0.228393317	0.228393317
488	16.5929	33998	7054761	N	N	N	ENSG00000152213	ENSG00000153310	13	8	49106009	131097879	upstream	intron	ARL11	FAM49B	49100436	130922900	+	-	0.534246575	49097265	131026811	+	+	Y	N	HCC1954	1	1	1	0	SINE	-	1	0	1	1	0.228393317	0.228393317	0.228393317	0.228393317
488	16.5929	33998	12090317	Y	N	N	ENSG00000153310	ENSG00000153317	8	8	131097879	131483399	intron	intron	FAM49B	ASAP1	130922900	131133535	-	-	0.612244898	131000148	131457725	-	-	N	Y	HCC1954	1	1	1	0	-	-	0	0	0	8	0.951638821	0.596360328	0.951638821	0.596360328
488	16.5929	33998	12065283	N	N	N	ENSG00000201782	ENSG00000153317	8	8	129302243	131483399	upstream	intron	7SK	ASAP1	129301932	131133535	+	-	0	129281602	131459223	+	+	N	Y	HCC1954	1	1	1	0	-	"LTR,LTR"	0	0.641025641	0.641025641	13	0.938950304	0.989704374	0.989704374	0.938950304
488	16.5929	33998	12091637	N	N	N	ENSG00000201782	ENSG00000184156	8	8	129302243	133561961	upstream	intron	7SK	KCNQ3	129301932	133210438	+	-	0.514018692	129280561	133276510	-	-	N	Y	HCC1954	1	1	1	0	SINE	-	0.380645161	0	0.380645161	6	0.983360116	1.027769927	1.027769927	0.983360116
488	16.5929	33998	14775510	N	N	N	ENSG00000204628	ENSG00000184156	5	8	180603512	133561961	intron	intron	GNB2L1	KCNQ3	180596536	133210438	-	-	0.587030717	180602224	133281306	+	+	Y	N	HCC1954	1	1	1	0	SINE	SINE	0.380952381	1	1	7	0.932606045	0.919917527	0.932606045	0.919917527
382	16.7655	41838	1158381	N	N	Y	ENSG00000209722	ENSG00000160193	21	21	17725836	43172747	upstream	downstream	AP000952.2	WDR4	17725745	43136275	+	-	0.586387435	17661143	43119596	-	+	N	N	HCC1954	3	2.5	2	2	SINE	"LINE,SINE"	0.294871795	0.589285714	0.589285714	2	0.494852187	0.710556987	0.710556987	0.494852187
382	16.7655	41838	1159545	N	N	Y	ENSG00000160191	ENSG00000160299	21	21	43068688	46690106	downstream	intron	PDE9A	PCNT	42946931	46568483	+	+	0.622047244	43077758	46588184	-	+	N	N	HCC1954	1	1	1	0	Simple_repeat	"LINE,LINE"	1	1	1	1	0.291835905	0.507540705	0.507540705	0.291835905
293	16.8972	194	2638975	N	N	N	ENSG00000099917	ENSG00000206951	22	2	19271918	33024022	intron	downstream	MED15	Y_RNA	19191886	33023910	+	-	0	19216532	32995117	-	+	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	1	0.507540705	0.507540705	0.507540705	0.507540705
293	16.8972	194	7375870	N	N	N	ENSG00000131149	ENSG00000206951	16	2	84267311	33024022	intron	downstream	KIAA0182	Y_RNA	84202524	33023910	+	-	0.699029126	84259790	32994923	-	-	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	1	0.456786634	0.190327764	0.456786634	0.190327764
516	16.9018	100	3017181	N	N	N	ENSG00000141736	ENSG00000206951	17	2	35138441	33024022	intron	downstream	ERBB2	Y_RNA	35104766	33023910	+	-	0	35125905	32995141	+	+	Y	N	HCC1954	6	3.166666667	1	4	-	Simple_repeat	0	1	1	6	0.970671598	1.192720656	1.192720656	0.970671598
516	16.9018	100	14505664	N	N	N	ENSG00000206951	ENSG00000080573	2	19	33024022	9982147	downstream	intron	Y_RNA	COL5A3	33023910	9931237	-	-	0.601503759	32995041	9965015	-	+	Y	N	HCC1954	1	1	1	0	Simple_repeat	-	1	0	1	1	0.329901458	0.507540705	0.507540705	0.329901458
328	17.0547	14594	15287982	N	N	N	ENSG00000063438	ENSG00000188002	5	5	491392	1687105	intron	utr3p	PDCD6	AC026412.4	324736	1681814	+	-	0.60989011	332088	1681838	-	-	N	Y	HCC1954	4	2.5	1	1	-	-	0	0	0	2	0.507540705	0.412376823	0.507540705	0.412376823
328	17.0547	14594	15257301	N	N	N	ENSG00000063438	ENSG00000134982	5	5	491392	112209834	intron	intron	PDCD6	APC	324736	112101483	+	+	0.529411765	340800	112189772	+	+	N	Y	HCC1954	1	1	1	0	-	LINE	0	0.516129032	0.516129032	1	0.228393317	0.196672023	0.228393317	0.196672023
328	17.0547	14594	15288668	N	N	N	ENSG00000201910	ENSG00000134982	5	5	103462638	112209834	upstream	intron	U1	APC	103462474	112101483	+	+	0	103451895	112183890	-	-	N	Y	HCC1954	1	1	1	0	LTR	SINE	0.214285714	0.159090909	0.214285714	2	0.53291774	0.558294775	0.558294775	0.53291774
313	17.1696	239	3053907	N	N	N	ENSG00000206951	ENSG00000131748	2	17	33024022	35073248	downstream	intron	Y_RNA	STARD3	33023910	35046938	-	+	0	32994802	35050508	-	+	Y	N	HCC1954	2	2	2	1	Simple_repeat	-	1	0	1	1	0.507540705	0.501196446	0.507540705	0.501196446
313	17.1696	239	3033874	N	N	N	ENSG00000073605	ENSG00000206951	17	2	35328429	33024022	upstream	downstream	GSDMB	Y_RNA	35314374	33023910	-	-	0	35329220	32995041	+	+	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	1	0.507540705	0.507540705	0.507540705	0.507540705
182	17.3857	5752	2686101	N	N	N	ENSG00000221415	ENSG00000115233	4	2	48895063	161976474	downstream	upstream	AC118282.4-1	PSMD14	48894981	161872795	+	+	0.506369427	49022116	161847435	-	+	Y	N	HCC1954	110	9.4	2	60	LINE	SINE	0.167701863	0.092105263	0.167701863	60	1.021425668	0.964327339	1.021425668	0.964327339
182	17.3857	5752	12444767	N	N	N	ENSG00000221415	ENSG00000221415	4	4	48895063	48895063	downstream	downstream	AC118282.4-1	AC118282.4-1	48894981	48894981	+	+	0.525821596	49004183	49027868	+	+	N	Y	HCC1954	32	11.71428571	2	7	"LTR,LTR,LTR"	-	0.90990991	0	0.90990991	7	0.704212728	0.64077014	0.704212728	0.64077014
445	17.6977	39024	4765440	N	N	N	ENSG00000124562	ENSG00000220357	6	1	34849545	45770398	intron	upstream	SNRPC	RP4-697E16.1	34833275	45769186	+	+	0.818181818	34843023	45766679	+	+	Y	N	HCC1954	2	2	2	1	-	LTR	0	1	1	1	0.183983505	0.507540705	0.507540705	0.183983505
445	17.6977	39024	479421	N	N	N	ENSG00000166471	ENSG00000186328	11	6	9292872	34791695	upstream	downstream	TMEM41B	RP11-140K17.2	9258780	34791368	-	+	0.796610169	9304542	34803999	-	-	Y	N	HCC1954	3	3	3	1	LINE	SINE	1	0.72972973	1	1	0.507540705	0.234737576	0.507540705	0.234737576
257	17.9495	0	136429	N	N	N	ENSG00000168000	ENSG00000206951	11	2	62233562	33024022	utr5p	downstream	BSCL2	Y_RNA	62214323	33023910	-	-	0	62230071	32994892	+	+	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	1	0.507540705	0.507540705	0.507540705	0.507540705
450	18.3692	192	2920403	N	N	N	ENSG00000206951	ENSG00000028310	2	5	33024022	945915	downstream	coding	Y_RNA	BRD9	33023910	916856	-	-	0.578947368	32994958	918611	-	-	Y	N	HCC1954	2	2	2	1	Simple_repeat	-	1	0	1	1	0.323557199	0.393344046	0.393344046	0.323557199
450	18.3692	192	11235956	N	N	N	ENSG00000137815	ENSG00000206951	15	2	39563053	33024022	coding	downstream	RTF1	Y_RNA	39496594	33023910	+	-	0.614634146	39496748	32995150	-	+	Y	N	HCC1954	2	1.5	1	1	-	Simple_repeat	0	1	1	2	0.786688092	0.507540705	0.786688092	0.507540705
556	18.6538	3345	261703	N	N	N	ENSG00000167995	ENSG00000167914	11	17	61488981	35387545	upstream	upstream	BEST1	GSDMA	61474403	35372752	+	+	0.757142857	61468282	35366028	-	+	Y	N	HCC1954	20	20	20	1	Simple_repeat	LTR	1	0.727272727	1	1	0.228393317	0.209360541	0.228393317	0.209360541
556	18.6538	3345	3056429	N	N	N	ENSG00000204913	ENSG00000206951	17	2	35354622	33024022	downstream	downstream	AC090844.7	Y_RNA	35353259	33023910	+	-	0.769230769	35362683	32995121	-	+	Y	N	HCC1954	2	1.5	1	1	"Simple_repeat,Simple_repeat"	Simple_repeat	0.504545455	1	1	2	1.01508141	0.412376823	1.01508141	0.412376823
436	18.8518	21	10429567	N	N	N	ENSG00000111785	ENSG00000070193	12	5	105807215	44424623	intron	downstream	RIC8B	FGF10	105692529	44340831	+	-	0.714285714	105796831	44301584	-	+	Y	N	HCC1954	6	6	6	1	-	Simple_repeat	0	0.709677419	0.709677419	1	0.507540705	0.196672023	0.507540705	0.196672023
436	18.8518	21	3589055	N	N	N	ENSG00000070193	ENSG00000141736	5	17	44424623	35138441	downstream	intron	FGF10	ERBB2	44340831	35104766	-	+	0.781818182	44301563	35133959	-	+	Y	N	HCC1954	2	2	2	1	Simple_repeat	SINE	1	0.666666667	1	1	0.196672023	0.494852187	0.494852187	0.196672023
107	19.056	0	917658	N	N	N	ENSG00000212451	ENSG00000110092	8	11	127753081	69178422	downstream	upstream	U11	CCND1	127752949	69165054	+	+	0.709090909	128063325	69160783	-	+	Y	N	HCC1954	1	1	1	0	LINE	-	1	0	1	1	0.48216367	0.209360541	0.48216367	0.209360541
513	19.3357	213	3077138	N	N	N	ENSG00000141736	ENSG00000206951	17	2	35138441	33024022	intron	downstream	ERBB2	Y_RNA	35104766	33023910	+	-	0	35117063	32994935	-	-	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	1	0.501196446	0.494852187	0.501196446	0.494852187
513	19.3357	213	2617571	N	N	N	ENSG00000056487	ENSG00000206951	22	2	43784473	33024022	upstream	downstream	PHF21B	Y_RNA	43655706	33023910	-	-	0	43830840	32995148	+	+	Y	N	HCC1954	1	1	1	0	-	Simple_repeat	0	1	1	2	0.983360116	0.577327552	0.983360116	0.577327552
604	19.3493	3822	515709	N	N	N	ENSG00000217397	ENSG00000089597	X	11	87238882	62170680	upstream	intron	RP3-452M16.1	GANAB	87238053	62148876	-	-	0.723809524	87295365	62165262	-	+	Y	N	HCC1954	9	9	9	1	SINE	SINE	0.821428571	1	1	1	0.177639247	0.48216367	0.48216367	0.177639247
604	19.3493	3822	1848974	N	N	N	ENSG00000217397	ENSG00000206951	X	2	87238882	33024022	upstream	downstream	RP3-452M16.1	Y_RNA	87238053	33023910	-	-	0.490066225	87299187	32995087	+	+	Y	N	HCC1954	4	4	4	1	SINE	Simple_repeat	1	1	1	1	0.507540705	0.444098117	0.507540705	0.444098117
569	19.4271	0	14701333	N	Y	N	ENSG00000221923	ENSG00000130299	19	19	57579923	17314530	upstream	downstream	AC010332.7-1	GTPBP3	57579303	17309379	+	+	0.76146789	57571563	17315052	-	+	N	N	HCC1954	9	9	9	1	"LINE,SINE"	SINE	0.571428571	1	1	1	0.177639247	0.507540705	0.507540705	0.177639247
514	19.5632	1377	3468776	N	N	N	ENSG00000108953	ENSG00000138767	17	4	1250267	78959574	upstream	intron	YWHAE	CNOT6L	1194595	78853565	-	-	0.655172414	1252677	78919259	-	+	Y	N	HCC1954	21	21	21	1	Other	SINE	0.666666667	0.703703704	0.703703704	1	0.190327764	0.171294988	0.190327764	0.171294988
514	19.5632	1377	11302940	N	N	N	ENSG00000069869	ENSG00000108953	15	17	54073345	1250267	intron	upstream	NEDD4	YWHAE	53906423	1194595	-	-	0.712328767	54067931	1254054	-	+	Y	N	HCC1954	220	220	220	1	LINE	Other	1	1	1	1	0.228393317	0.228393317	0.228393317	0.228393317
79	19.6116	275	8174408	N	N	N	ENSG00000210450	ENSG00000170381	6	7	27359916	83116262	upstream	utr3p	AL021808.2-3	SEMA3E	27359843	82831158	+	-	0.804878049	27348338	82831424	+	+	Y	N	HCC1954	20	20	20	1	-	SINE	0	1	1	1	0.26645887	0.507540705	0.507540705	0.26645887
79	19.6116	275	1781081	N	N	N	ENSG00000210450	ENSG00000119041	6	2	27359916	197372628	upstream	downstream	AL021808.2-3	GTF3C3	27359843	197336917	+	-	0.661290323	27348325	197322929	-	-	Y	N	HCC1954	20	20	20	1	-	SINE	0	1	1	1	0.272803129	0.507540705	0.507540705	0.272803129
79	19.6116	275	2525847	N	N	N	ENSG00000119041	ENSG00000212451	2	8	197372628	127753081	downstream	downstream	GTF3C3	U11	197336917	127752949	-	+	0.617021277	197323191	128107306	+	+	Y	N	HCC1954	20	20	20	2	SINE	LTR	1	1	1	2	0.869163457	0.615393105	0.869163457	0.615393105
420	19.7538	22688	5714147	N	N	N	ENSG00000216725	ENSG00000213745	1	8	121012114	99987074	downstream	downstream	AL592494.2	AC016877.11-1	120962666	99986636	+	-	0.6	121184756	99949410	-	-	Y	N	HCC1954	1	1	1	0	Satellite	-	1	0	1	1	0.507540705	0.342589976	0.507540705	0.342589976
420	19.7538	22688	6158548	N	N	N	ENSG00000206077	ENSG00000216725	5	1	809253	121012114	downstream	downstream	AC026740.6-1	AL592494.2	786905	120962666	-	+	0.142857143	774670	121186854	-	+	Y	N	HCC1954	1	1	1	0	-	Satellite	0	1	1	1	0.507540705	0.507540705	0.507540705	0.507540705
420	19.7538	22688	15245013	N	N	N	ENSG00000206077	ENSG00000206077	5	5	809253	809253	downstream	downstream	AC026740.6-1	AC026740.6-1	786905	786905	-	-	0	785359	785527	+	+	N	Y	HCC1954	3	1.357142857	1	4	-	-	0	0	0	14	1.205409174	1.135622327	1.205409174	1.135622327
420	19.7538	22688	14825216	N	N	N	ENSG00000206077	ENSG00000153317	5	8	809253	131483399	downstream	intron	AC026740.6-1	ASAP1	786905	131133535	-	-	0.526717557	785359	131458448	-	-	Y	N	HCC1954	3	1.181818182	1	1	-	LINE	0	0.550724638	0.550724638	11	1.17368788	1.313261574	1.313261574	1.17368788
420	19.7538	22688	12072970	N	N	Y	ENSG00000174429	ENSG00000153317	8	8	107851648	131483399	upstream	intron	ABRA	ASAP1	107840888	131133535	-	-	0.56122449	107905449	131460067	-	+	N	N	HCC1954	1	1	1	0	-	LINE	0	1	1	13	0.812065128	1.046802704	1.046802704	0.812065128
420	19.7538	22688	14804679	N	N	N	ENSG00000113269	ENSG00000174429	5	8	179431719	107851648	intron	upstream	RNF130	ABRA	179315111	107840888	-	-	0.486075949	179368226	107913563	-	+	Y	N	HCC1954	7	1.733333333	1	2	SINE	LTR	1	0.759162304	1	15	1.287884538	1.211753433	1.287884538	1.211753433
584	19.9177	161	514017	N	N	N	ENSG00000220252	ENSG00000149084	X	11	890836	43834736	downstream	downstream	RP11-309M23.2	HSD17B12	889238	43658719	-	+	0.646616541	856664	43846664	-	+	Y	N	HCC1954	17	10.5	4	2	-	SINE	0	1	1	2	0.545606258	0.291835905	0.545606258	0.291835905
584	19.9177	161	14944797	N	N	N	ENSG00000220252	ENSG00000168724	X	5	890836	34994825	downstream	downstream	RP11-309M23.2	DNAJA5	889238	34965455	-	+	0.55	856825	35008593	+	+	Y	N	HCC1954	2	2	2	1	-	SINE	0	1	1	1	0.279147388	0.222049058	0.279147388	0.222049058