Variant report

Variant	nsv581509
Chromosome Location	chr2:40835285-40857899
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	CEBPB	chr2:40853015-40853457	IMR90	lung:	n/a	n/a
2	CTCF	chr2:40835900-40836050	NHEK	skin:	n/a	n/a
3	CTCF	chr2:40843055-40843124	Kidney_OC	kidney:	n/a	n/a
4	E2F4	chr2:40835780-40835952	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr2:40853241-40853243	GM12878	blood:	n/a	n/a
6	EP300	chr2:40843652-40844316	SK-N-SH	brain:	n/a	n/a
7	FOS	chr2:40853013-40853377	MCF10A-Er-Src	breast:	n/a	chr2:40853169-40853180 chr2:40853215-40853227 chr2:40853217-40853225
8	FOS	chr2:40852992-40853476	MCF10A-Er-Src	breast:	n/a	chr2:40853169-40853180 chr2:40853215-40853227 chr2:40853217-40853225
9	FOS	chr2:40853018-40853306	HUVEC	blood vessel:	n/a	chr2:40853169-40853180 chr2:40853215-40853227 chr2:40853217-40853225
10	FOS	chr2:40852992-40853412	MCF10A-Er-Src	breast:	n/a	chr2:40853169-40853180 chr2:40853215-40853227 chr2:40853217-40853225
11	FOS	chr2:40852959-40853404	MCF10A-Er-Src	breast:	n/a	chr2:40853169-40853180 chr2:40853215-40853227 chr2:40853217-40853225
12	GATA2	chr2:40843913-40844188	SH-SY5Y	brain:	n/a	n/a
13	GATA3	chr2:40843791-40844144	SH-SY5Y	brain:	n/a	chr2:40843893-40843902 chr2:40843892-40843902 chr2:40843893-40843900 chr2:40843893-40843900 chr2:40843886-40843907 chr2:40843893-40843900
14	GATA3	chr2:40855903-40856186	SH-SY5Y	brain:	n/a	n/a
15	GATA3	chr2:40843288-40843369	SH-SY5Y	brain:	n/a	n/a
16	GATA3	chr2:40849087-40849399	SH-SY5Y	brain:	n/a	n/a
17	MAFF	chr2:40850298-40850584	HepG2	liver:	n/a	chr2:40850431-40850449
18	MAFF	chr2:40850367-40850522	K562	blood:	n/a	chr2:40850431-40850449
19	MAFF	chr2:40857232-40857538	HepG2	liver:	n/a	chr2:40857368-40857386
20	MAFK	chr2:40850300-40850592	HepG2	liver:	n/a	chr2:40850432-40850447
21	MAFK	chr2:40857233-40857501	HepG2	liver:	n/a	chr2:40857369-40857384
22	MAFK	chr2:40853083-40853339	IMR90	lung:	n/a	n/a
23	MAFK	chr2:40850320-40850506	HepG2	liver:	n/a	chr2:40850432-40850447
24	MAFK	chr2:40857196-40857550	HepG2	liver:	n/a	chr2:40857369-40857384
25	MAFK	chr2:40857235-40857477	IMR90	lung:	n/a	chr2:40857369-40857384
26	MAFK	chr2:40855394-40855478	HepG2	liver:	n/a	n/a
27	MYC	chr2:40852824-40853424	MCF10A-Er-Src	breast:	n/a	chr2:40853217-40853226
28	MYC	chr2:40842938-40842996	H1-hESC	embryonic stem cell:	n/a	n/a
29	MYC	chr2:40853101-40853309	MCF10A-Er-Src	breast:	n/a	chr2:40853217-40853226
30	NFYA	chr2:40850874-40850945	GM12878	blood:	n/a	n/a
31	NFYA	chr2:40847808-40847936	GM12878	blood:	n/a	n/a
32	NRF1	chr2:40843410-40843451	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:40852667-40852867	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr2:40842703-40842896	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr2:40847988-40847989	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr2:40852957-40853358	U87	brain:	n/a	n/a
37	POLR2A	chr2:40837335-40837416	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr2:40853117-40853222	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr2:40842374-40842574	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr2:40839488-40839640	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr2:40857499-40857555	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr2:40847238-40847261	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr2:40855450-40855924	MCF10A-Er-Src	breast:	n/a	n/a
44	STAT3	chr2:40853024-40853363	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr2:40853010-40853378	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr2:40852999-40853398	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr2:40854990-40855190	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr2:40850304-40850685	MCF10A-Er-Src	breast:	n/a	n/a
49	TCF7L2	chr2:40847873-40848195	HepG2	liver:	n/a	n/a
50	USF1	chr2:40846788-40847143	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:40845989-40846039	BJ	skin:	n/a
2	chr2:40845989-40846039	AG04450	lung:	fetal
3	chr2:40845989-40846039	CMK	blood:	n/a
4	chr2:40845989-40846039	ECC-1	luminal epithelium:	n/a
5	chr2:40845989-40846039	SK-N-MC	brain:	n/a
6	chr2:40845989-40846039	HRE	kidney:	n/a
7	chr2:40845989-40846039	BE2_C	brain:	n/a
8	chr2:40845989-40846039	NHBE	bronchial:	n/a
9	chr2:40845989-40846039	Jurkat	blood:	n/a
10	chr2:40845989-40846039	AG09309	skin:	n/a
11	chr2:40845989-40846039	NB4	blood:	n/a
12	chr2:40845989-40846039	GM12891	blood:	n/a
13	chr2:40845989-40846039	SK-N-SH	brain:	n/a
14	chr2:40845989-40846039	HRCEpiC	kidney:	n/a
15	chr2:40845989-40846039	Caco-2	colon:	n/a
16	chr2:40845989-40846039	A549	lung:	n/a
17	chr2:40845989-40846039	SKMC	muscle:	n/a
18	chr2:40845989-40846039	AoSMC	blood vessel:	n/a
19	chr2:40845989-40846039	AG04449	skin:	fetal
20	chr2:40845989-40846039	HPAEpiC	pulmonary alveolar:	n/a
21	chr2:40845989-40846039	HRPEpiC	eye:	n/a
22	chr2:40845989-40846039	K562	blood:	n/a
23	chr2:40845989-40846039	SAEC	small airway:	n/a
24	chr2:40845989-40846039	GM06990	blood:	n/a
25	chr2:40845989-40846039	PFSK-1	brain:	n/a
26	chr2:40845989-40846039	H1-hESC	embryonic stem cell:	embryo
27	chr2:40845989-40846039	HepG2	liver:	n/a
28	chr2:40845989-40846039	AG10803	skin:	n/a
29	chr2:40845989-40846039	GM12878	blood:	n/a
30	chr2:40845989-40846039	GM12892	blood:	n/a
31	chr2:40845989-40846039	RPTEC	kidney:	n/a
32	chr2:40845989-40846039	NH-A	brain:	n/a
33	chr2:40845989-40846039	IMR90	lung:	fetal
34	chr2:40845989-40846039	HIPEpiC	eye:	n/a
35	chr2:40845989-40846039	HNPCEpiC	eye:	n/a
36	chr2:40845989-40846039	Hepatocyte	liver:	n/a
37	chr2:40845989-40846039	HCT-116	colon:	n/a
38	chr2:40845989-40846039	ovcar-3	ovarian:	n/a
39	chr2:40845989-40846039	HUVEC	blood vessel:	n/a
40	chr2:40845989-40846039	U87	brain:	n/a
41	chr2:40845989-40846039	HCF	heart:	n/a
42	chr2:40845989-40846039	Hela-S3	cervix:	n/a
43	chr2:40845989-40846039	HEK293	kidney:	embryo
44	chr2:40845989-40846039	HL-60	blood:	n/a
45	chr2:40845989-40846039	MCF-7	breast:	n/a
46	chr2:40845989-40846039	GM19239	blood:	n/a
47	chr2:40845989-40846039	HCM	heart:	n/a
48	chr2:40845989-40846039	HAEpiC	amniotic membrane:	n/a
49	chr2:40845989-40846039	MCF10A-Er-Src	breast:	n/a
50	chr2:40845989-40846039	T-47D	breast:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-7	chr2:40847860-40848096	NONHSAT070282
2	lnc-TMEM178-7	chr2:40838265-40838463	l_1815_chr2:40835264-40838463_testes
3	lnc-TMEM178-7	chr2:40835782-40835863	NONHSAT070282
4	lnc-TMEM178-7	chr2:40835782-40835863	l_1815_chr2:40835264-40838463_testes

Variant related genes	Relation type
SLC8A1	TF binding region
SLC8A1	CpG island

Extended variants
information (count: 501 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:501 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201863823	chr2:40835805-40835806	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs13420501	chr2:40835808-40835809	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs558628579	chr2:40835816-40835817	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs558939175	chr2:40835840-40835841	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs42806	chr2:40835848-40835849	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs537714057	chr2:40835857-40835858	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs531228526	chr2:40836206-40836207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs147062725	chr2:40836235-40836236	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs191832140	chr2:40836265-40836266	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs530307491	chr2:40836290-40836291	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs548848102	chr2:40836306-40836307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs566831131	chr2:40836316-40836317	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs527821202	chr2:40836335-40836336	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs528691468	chr2:40836344-40836345	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs552406524	chr2:40836397-40836398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs570799560	chr2:40836402-40836403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs182585650	chr2:40836458-40836459	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs115004047	chr2:40836465-40836466	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs377320385	chr2:40836509-40836510	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs148026400	chr2:40836545-40836546	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs535247519	chr2:40836552-40836553	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs187278480	chr2:40836568-40836569	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs78715253	chr2:40836578-40836579	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs147053171	chr2:40838336-40838337	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs80045429	chr2:40838363-40838364	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs114220009	chr2:40838378-40838379	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs528212281	chr2:40838401-40838402	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs201111721	chr2:40838418-40838419	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs546694262	chr2:40838419-40838420	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs138234660	chr2:40838446-40838447	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs538635445	chr2:40838451-40838452	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs149509357	chr2:40838459-40838460	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs550276479	chr2:40839495-40839496	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs146280126	chr2:40839535-40839536	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs115026992	chr2:40839572-40839573	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs139060705	chr2:40839581-40839582	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs567991200	chr2:40839616-40839617	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs184147605	chr2:40841699-40841700	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs560793977	chr2:40841705-40841706	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs527822373	chr2:40841718-40841719	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs545901514	chr2:40841736-40841737	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs375657712	chr2:40841776-40841777	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs7593990	chr2:40841777-40841778	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs576172457	chr2:40842390-40842391	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs372454097	chr2:40842399-40842400	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs561888595	chr2:40842408-40842409	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs148195593	chr2:40842441-40842442	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs540935666	chr2:40842462-40842463	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs574219875	chr2:40842487-40842488	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs186270364	chr2:40842491-40842492	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40836200-40836600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr2:40843800-40844400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:40844400-40853000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:40852200-40853800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:40852400-40853200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:40852400-40853200	Enhancers	NHDF-Ad	bronchial
7	chr2:40852400-40854000	Enhancers	NHEK	skin
8	chr2:40852600-40853400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:40852600-40853400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:40852800-40853600	Enhancers	Osteobl	bone
11	chr2:40853000-40854200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:40856800-40857200	Enhancers	Colon Smooth Muscle	Colon

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