Variant report

Variant	nsv1000475
Chromosome Location	chr3:88363069-88403165
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	chr3:88370833-88371190	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr3:88396706-88396908	A549	lung:	n/a	chr3:88396754-88396765
3	CEBPB	chr3:88378808-88379094	IMR90	lung:	n/a	chr3:88378941-88378952
4	CEBPB	chr3:88378823-88378968	HepG2	liver:	n/a	chr3:88378941-88378952
5	CEBPB	chr3:88369030-88369230	A549	lung:	n/a	n/a
6	CEBPB	chr3:88396623-88396919	HepG2	liver:	n/a	chr3:88396754-88396765
7	CEBPB	chr3:88396713-88396914	Hela-S3	cervix:	n/a	chr3:88396754-88396765
8	CTCF	chr3:88372984-88373041	MCF-7	breast:	n/a	n/a
9	CTCF	chr3:88391615-88391656	HepG2	liver:	n/a	n/a
10	CTCF	chr3:88366722-88366803	HepG2	liver:	n/a	n/a
11	CTCF	chr3:88366654-88366767	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:88366679-88366802	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:88366714-88366804	GM19238	blood:	n/a	n/a
14	CTCF	chr3:88366673-88366774	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:88366689-88366822	GM12891	blood:	n/a	n/a
16	CTCF	chr3:88366668-88366851	MCF-7	breast:	n/a	n/a
17	CTCF	chr3:88396440-88396590	RPTEC	kidney:	n/a	n/a
18	CTCF	chr3:88383440-88383590	HCM	heart:	n/a	n/a
19	CTCF	chr3:88383460-88383610	HPAF	blood vessel:	n/a	n/a
20	CTCF	chr3:88366675-88366727	GM12878	blood:	n/a	n/a
21	CTCF	chr3:88366736-88366740	GM12878	blood:	n/a	n/a
22	CTCF	chr3:88366721-88366814	GM13977	blood:	n/a	n/a
23	CTCF	chr3:88366660-88366810	HepG2	liver:	n/a	n/a
24	CTCF	chr3:88366712-88366739	Gliobla	brain:	n/a	n/a
25	CTCF	chr3:88366639-88366827	A549	lung:	n/a	n/a
26	CTCF	chr3:88366706-88366789	ProgFib	skin:	n/a	n/a
27	CTCF	chr3:88366691-88366794	GM12892	blood:	n/a	n/a
28	CTCF	chr3:88366680-88366797	MCF-7	breast:	n/a	n/a
29	CTCF	chr3:88366675-88366780	MCF-7	breast:	n/a	n/a
30	CTCF	chr3:88366691-88366812	HepG2	liver:	n/a	n/a
31	CTCF	chr3:88366726-88366760	Hela-S3	cervix:	n/a	n/a
32	E2F4	chr3:88371620-88371836	MCF10A-Er-Src	breast:	n/a	n/a
33	E2F4	chr3:88396640-88396749	MCF10A-Er-Src	breast:	n/a	n/a
34	E2F4	chr3:88398054-88398133	MCF10A-Er-Src	breast:	n/a	n/a
35	E2F4	chr3:88372170-88372370	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr3:88386331-88386647	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:88383685-88383962	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:88364474-88364507	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr3:88370889-88371094	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr3:88392537-88392768	MCF10A-Er-Src	breast:	n/a	chr3:88392636-88392643 chr3:88392634-88392643 chr3:88392635-88392644 chr3:88392635-88392643
41	FOS	chr3:88383791-88383970	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr3:88392449-88392766	MCF10A-Er-Src	breast:	n/a	chr3:88392636-88392643 chr3:88392634-88392643 chr3:88392635-88392644 chr3:88392635-88392643
43	FOS	chr3:88386322-88386690	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr3:88392546-88392820	MCF10A-Er-Src	breast:	n/a	chr3:88392636-88392643 chr3:88392634-88392643 chr3:88392635-88392644 chr3:88392635-88392643
45	FOS	chr3:88370846-88371132	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr3:88386328-88386635	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr3:88370824-88371125	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr3:88370832-88371125	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr3:88392543-88392730	MCF10A-Er-Src	breast:	n/a	chr3:88392636-88392643 chr3:88392634-88392643 chr3:88392635-88392644 chr3:88392635-88392643
50	FOSL2	chr3:88370693-88371198	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88377277..88378950-chr3:88387834..88390220,2	MCF-7	breast:
2	chr3:88377277..88378950-chr3:88387834..88390220,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf38-2	chr3:88387591-88387793	XLOC_002727
2	lnc-C3orf38-2	chr3:88387573-88387793	XLOC_002727
3	lnc-C3orf38-2	chr3:88392301-88392435	NONHSAT090703
4	lnc-C3orf38-2	chr3:88387572-88387793	NONHSAT090703
5	lnc-C3orf38-2	chr3:88392302-88392435	XLOC_002727
6	lnc-C3orf38-2	chr3:88387573-88387793	XLOC_002727

Variant related genes	Relation type
ABCF2P1	TF binding region
VLDLR	miRNA target sites
E2F8	miRNA target sites
BLCAP	miRNA target sites

Extended variants
information (count: 210 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:210 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563418538	chr3:88363350-88363351	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs13089363	chr3:88363494-88363495	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs528399302	chr3:88363554-88363555	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs375245491	chr3:88363572-88363573	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs546443510	chr3:88363576-88363577	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs367841155	chr3:88363600-88363601	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs552151684	chr3:88363601-88363602	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs144601063	chr3:88364478-88364479	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs528579896	chr3:88365014-88365015	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs6779915	chr3:88365050-88365051	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs184390410	chr3:88365062-88365063	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs147524360	chr3:88365064-88365065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs201987009	chr3:88365094-88365095	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs551221199	chr3:88365116-88365117	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs12497401	chr3:88365122-88365123	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs536876614	chr3:88365131-88365132	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs554859567	chr3:88365215-88365216	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs572640303	chr3:88365245-88365246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs6777497	chr3:88365285-88365286	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs140187802	chr3:88365391-88365392	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs190603571	chr3:88365426-88365427	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs145698089	chr3:88365435-88365436	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs147661654	chr3:88365445-88365446	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs115016737	chr3:88365460-88365461	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs111913995	chr3:88365461-88365462	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs376952823	chr3:88365471-88365472	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs148722790	chr3:88365490-88365491	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs528600757	chr3:88365516-88365517	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs562991453	chr3:88365569-88365570	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs547087421	chr3:88365595-88365596	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs565295621	chr3:88365614-88365615	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs532584557	chr3:88365628-88365629	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs142308351	chr3:88365646-88365647	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs569580263	chr3:88365665-88365666	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs182077980	chr3:88365681-88365682	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs12496773	chr3:88365696-88365697	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs186002213	chr3:88365709-88365710	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs13092417	chr3:88365729-88365730	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs373617840	chr3:88365761-88365762	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs386663257	chr3:88365786-88365787	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs576351478	chr3:88365787-88365788	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs368849072	chr3:88365795-88365796	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs151276314	chr3:88365833-88365834	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs144432361	chr3:88365859-88365860	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs73846835	chr3:88365861-88365862	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs73846836	chr3:88365862-88365863	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs56203094	chr3:88365863-88365864	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs200449050	chr3:88365866-88365867	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs192497880	chr3:88365869-88365870	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs201396427	chr3:88365871-88365872	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22522925	CNVD
Lung cancer	19547694	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88365000-88366000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:88370400-88371200	Enhancers	Hela-S3	cervix
3	chr3:88370600-88370800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:88370800-88371000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:88371000-88371200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:88371200-88371400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:88373800-88374800	Enhancers	HepG2	liver
8	chr3:88374000-88374400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:88374200-88374400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:88383600-88384000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:88399800-88400200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links