Variant report

Variant	esv3321972
Chromosome Location	chr1:103925464-104004162
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:103981441-103981516	GM13976	blood:	n/a	n/a
2	CTCF	chr1:104003956-104004087	HepG2	liver:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
3	CTCF	chr1:103944139-103944293	Fibrobl	skin:	n/a	n/a
4	CTCF	chr1:103931414-103931485	GM10248	blood:	n/a	n/a
5	CTCF	chr1:104003900-104004050	Caco-2	colon:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
6	CTCF	chr1:104003880-104004030	SAEC	small airway:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
7	CTCF	chr1:104003940-104004090	HepG2	liver:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
8	CTCF	chr1:104003900-104004050	GM12874	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
9	CTCF	chr1:103944191-103944306	K562	blood:	n/a	n/a
10	CTCF	chr1:103944156-103944302	LNCaP	prostate:	n/a	n/a
11	CTCF	chr1:103984650-103984709	GM20000	blood:	n/a	n/a
12	CTCF	chr1:104003889-104004110	LNCaP	prostate:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
13	CTCF	chr1:104003920-104004070	Caco-2	colon:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
14	CTCF	chr1:104003920-104004070	HAc	cerebellar:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
15	CTCF	chr1:104003918-104004115	LNCaP	prostate:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
16	CTCF	chr1:104003929-104004094	Kidney_OC	kidney:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
17	CTCF	chr1:104003900-104004050	GM12866	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
18	CTCF	chr1:104003807-104004216	IMR90	lung:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
19	CTCF	chr1:103944157-103944329	GM13977	blood:	n/a	n/a
20	CTCF	chr1:104003900-104004050	HBMEC	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
21	CTCF	chr1:104003940-104004090	HRPEpiC	eye:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
22	CTCF	chr1:104003893-104004121	GM13977	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
23	CTCF	chr1:104003960-104004110	HPAF	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
24	CTCF	chr1:104003940-104004090	AoAF	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
25	CTCF	chr1:104003940-104004090	NHEK	skin:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
26	CTCF	chr1:103959701-103959747	Kidney_OC	kidney:	n/a	n/a
27	CTCF	chr1:103996811-103996837	GM20000	blood:	n/a	n/a
28	CTCF	chr1:104003960-104004110	K562	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
29	CTCF	chr1:104003940-104004090	AG09319	gingival:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
30	CTCF	chr1:104003927-104004117	GM20000	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
31	CTCF	chr1:104003920-104004070	AG09319	gingival:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
32	CTCF	chr1:103951669-103951747	GM20000	blood:	n/a	chr1:103951723-103951733 chr1:103951715-103951736
33	CTCF	chr1:104003822-104004089	H1-hESC	embryonic stem cell:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
34	CTCF	chr1:104003875-104004134	A549	lung:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
35	CTCF	chr1:104003815-104004176	K562	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
36	CTCF	chr1:104003940-104004090	HL-60	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
37	CTCF	chr1:103931773-103931808	Pancreas_OC	pancreas:	n/a	n/a
38	CTCF	chr1:104003921-104004113	Pancreas_OC	pancreas:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
39	CTCF	chr1:104003960-104004110	GM12873	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
40	CTCF	chr1:103944167-103944326	GM13976	blood:	n/a	n/a
41	CTCF	chr1:104003940-104004090	MCF-7	breast:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
42	CTCF	chr1:104003906-104004120	Hela-S3	cervix:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
43	CTCF	chr1:104003851-104004097	SK-N-SH_RA	brain:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
44	CTCF	chr1:104003940-104004090	GM12869	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
45	CTCF	chr1:104003920-104004070	GM12871	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
46	CTCF	chr1:104003873-104004186	HCT-116	colon:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
47	CTCF	chr1:104003868-104004152	Medullo	brain:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
48	CTCF	chr1:104003960-104004110	GM12864	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
49	CTCF	chr1:103994291-103994351	GM20000	blood:	n/a	n/a
50	CTCF	chr1:104003920-104004070	GM12873	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:103571462..103572103-chr1:104003560..104004261,2	MCF-7	breast:
2	chr1:103571876..103572435-chr1:104003675..104004308,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNPC3-1	chr1:103957501-103957557	XLOC_000325
2	lnc-AMY1B-1	chr1:103975513-103975718	XLOC_000945
3	lnc-AMY1B-1	chr1:103960701-103960846	XLOC_000945
4	lnc-AMY1B-1	chr1:103975600-103975718	XLOC_000945
5	lnc-AMY1B-1	chr1:103971909-103971995	XLOC_000945
6	lnc-AMY1B-1	chr1:103961376-103961437	XLOC_000945
7	lnc-AMY1B-1	chr1:103961376-103961437	ENSG00000224613.2
8	lnc-AMY1B-1	chr1:103975513-103975718	XLOC_000945
9	lnc-AMY1B-1	chr1:103971909-103971995	XLOC_000945
10	lnc-AMY1B-1	chr1:103971909-103971995	XLOC_000945
11	lnc-AMY1B-1	chr1:103971909-103971995	ENSG00000224613.2
12	lnc-AMY1B-1	chr1:103975513-103975718	XLOC_000945
13	lnc-RNPC3-1	chr1:103967727-103968087	XLOC_000325
14	lnc-AMY1B-1	chr1:103971909-103971995	XLOC_000945
15	lnc-AMY1B-1	chr1:103961391-103961437	XLOC_000945
16	lnc-AMY1B-1	chr1:103975513-103975718	ENSG00000224613.2
17	lnc-AMY1B-1	chr1:103975513-103975718	XLOC_000945

Variant related genes	Relation type
ENSG00000230759	TF binding region
TOM1L2	miRNA target sites
TOMM34	miRNA target sites
TOMM20	miRNA target sites

Extended variants
information (count: 13 )
Associated
traits (count: 113 )

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs146522653	chr1:103975711-103975712	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs539117729	chr1:104003604-104003605	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs557958130	chr1:104003605-104003606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs571313489	chr1:104003606-104003607	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs77892914	chr1:104003669-104003670	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs114493807	chr1:104003780-104003781	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs537786628	chr1:104003868-104003869	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs557223791	chr1:104003901-104003902	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs555778602	chr1:104003902-104003903	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs190260102	chr1:104004012-104004013	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs182767931	chr1:104004018-104004019	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs12126785	chr1:104004031-104004032	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs187689700	chr1:104004105-104004106	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:113)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Medulloblastoma	21979893	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21720365	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	22429812	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Esophageal adenocarcinoma	18820669	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Glioblastoma multiforme	21922591	CNVD
Autism	17483303	CNVD
Intestinal disease	21956041	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Schizophrenia	17879154	CNVD
Mental retardation	17124404	CNVD
Intestinal disease	17828263	CNVD
lymphocytic leukemia	21291569	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Immune disease	21076436	CNVD
Immune disease	21042300	CNVD
Lung cancer	17086460	CNVD
Gastric cancer	16891809	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Multiple myeloma	17550852	CNVD
Hypoplastic left heart syndrome	22349727	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Schizophrenia	20967226	CNVD
Non-syndromic sensorineural hearing loss	19812545	CNVD
early-passage human iPS cells	21368824	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Autism	19287141	CNVD
Breast cancer	22522925	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:104003600-104005400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:104003800-104005400	Enhancers	Muscle Satellite Cultured Cells	--

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