Variant report

Variant	esv3391069
Chromosome Location	chr1:103924964-104004662
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	chr1:104003920-104004070	AG04450	lung:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
2	CTCF	chr1:104003894-104004124	ECC-1	luminal epithelium:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
3	CTCF	chr1:104003940-104004090	NHDF-neo	bronchial:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
4	CTCF	chr1:103959701-103959747	Kidney_OC	kidney:	n/a	n/a
5	CTCF	chr1:104003940-104004090	MCF-7	breast:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
6	CTCF	chr1:104004000-104004150	BE2_C	brain:	n/a	n/a
7	CTCF	chr1:104003920-104004070	GM12870	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
8	CTCF	chr1:103994291-103994351	GM20000	blood:	n/a	n/a
9	CTCF	chr1:104003920-104004070	AG04449	skin:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
10	CTCF	chr1:104003960-104004110	RPTEC	kidney:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
11	CTCF	chr1:104003924-104004070	Lung_OC	lung:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
12	CTCF	chr1:103944126-103944341	GM12892	blood:	n/a	n/a
13	CTCF	chr1:103975680-103975699	Pancreas_OC	pancreas:	n/a	n/a
14	CTCF	chr1:104003680-104004265	SK-N-SH	brain:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
15	CTCF	chr1:104003940-104004090	HA-sp	spinal cord:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
16	CTCF	chr1:104003927-104004117	GM20000	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
17	CTCF	chr1:104003924-104004118	Spleen_OC	spleen:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
18	CTCF	chr1:104003940-104004090	HMF	breast:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
19	CTCF	chr1:104003920-104004070	GM12872	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
20	CTCF	chr1:104003889-104004110	LNCaP	prostate:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
21	CTCF	chr1:103944195-103944259	Spleen_OC	spleen:	n/a	n/a
22	CTCF	chr1:104003960-104004110	GM12801	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
23	CTCF	chr1:104003863-104004078	T-47D	breast:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
24	CTCF	chr1:104003940-104004090	GM12869	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
25	CTCF	chr1:104003940-104004090	HEEpiC	esophagus:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
26	CTCF	chr1:103951669-103951747	GM20000	blood:	n/a	chr1:103951723-103951733 chr1:103951715-103951736
27	CTCF	chr1:104003960-104004110	Hela-S3	cervix:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
28	CTCF	chr1:104003920-104004070	GM12873	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
29	CTCF	chr1:103993051-103993077	LNCaP	prostate:	n/a	n/a
30	CTCF	chr1:104003840-104003990	HFF	foreskin:	n/a	n/a
31	CTCF	chr1:103944167-103944326	GM13976	blood:	n/a	n/a
32	CTCF	chr1:104003960-104004110	SK-N-SH_RA	brain:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
33	CTCF	chr1:104003960-104004110	GM12873	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
34	CTCF	chr1:104003807-104004216	IMR90	lung:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
35	CTCF	chr1:103982472-103982560	GM20000	blood:	n/a	n/a
36	CTCF	chr1:104003900-104004050	SAEC	small airway:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
37	CTCF	chr1:104003980-104004130	HA-sp	spinal cord:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
38	CTCF	chr1:104003840-104003990	AG04450	lung:	n/a	n/a
39	CTCF	chr1:104003960-104004110	GM12878	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
40	CTCF	chr1:104003885-104004163	HUVEC	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
41	CTCF	chr1:104003920-104004070	GM12864	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
42	CTCF	chr1:103944141-103944332	GM19238	blood:	n/a	n/a
43	CTCF	chr1:104003900-104004050	HBMEC	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
44	CTCF	chr1:103944191-103944306	K562	blood:	n/a	n/a
45	CTCF	chr1:103987270-103987341	Medullo	brain:	n/a	n/a
46	CTCF	chr1:104003640-104003790	NHEK	skin:	n/a	n/a
47	CTCF	chr1:104003920-104004070	GM12871	blood:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
48	CTCF	chr1:104003920-104004070	AoAF	blood vessel:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
49	CTCF	chr1:104003980-104004130	HCM	heart:	n/a	chr1:104003995-104004013 chr1:104003990-104004011
50	CTCF	chr1:104003940-104004090	HCPEpiC	choroid plexus:	n/a	chr1:104003995-104004013 chr1:104003990-104004011

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

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

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

Extended variants
information (count: 25 )
Associated
traits (count: 113 )

Variant overlapped rSNPs/rCNVs (count:25 , 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
14	rs571198002	chr1:104004239-104004240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs575940563	chr1:104004309-104004310	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs201582474	chr1:104004486-104004487	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs192174923	chr1:104004512-104004513	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs564309249	chr1:104004569-104004570	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs150009121	chr1:104004602-104004603	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs183949296	chr1:104004603-104004604	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs72692394	chr1:104004621-104004622	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs144083043	chr1:104004624-104004625	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs547010907	chr1:104004629-104004630	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs555158667	chr1:104004647-104004648	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs565313268	chr1:104004653-104004654	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:4 , 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	--
3	chr1:104004600-104005200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:104004600-104005200	Enhancers	HUVEC	blood vessel

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