Variant report

Variant	rs9389980
Chromosome Location	chr6:142586629-142586630
allele	A/G
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	FOXA1	chr6:142586629-142587121	HepG2	liver:	n/a	n/a
2	HDAC2	chr6:142586567-142587107	HepG2	liver:	n/a	chr6:142587047-142587061 chr6:142587043-142587057
3	TCF7L2	chr6:142586508-142587272	HepG2	liver:	n/a	chr6:142586782-142586792
4	HNF4A	chr6:142586508-142587037	HepG2	liver:	n/a	chr6:142586782-142586797 chr6:142586781-142586796 chr6:142586782-142586797 chr6:142586782-142586797 chr6:142586782-142586797
5	RXRA	chr6:142586613-142587019	HepG2	liver:	n/a	n/a
6	FOXA2	chr6:142585784-142587417	HepG2	liver:	n/a	n/a
7	HNF4A	chr6:142586538-142587041	HepG2	liver:	n/a	chr6:142586782-142586797 chr6:142586781-142586796 chr6:142586782-142586797 chr6:142586782-142586797 chr6:142586782-142586797
8	MBD4	chr6:142586498-142587132	HepG2	liver:	n/a	n/a
9	HDAC2	chr6:142586567-142587117	HepG2	liver:	n/a	chr6:142587047-142587061 chr6:142587043-142587057
10	FOXA1	chr6:142586460-142587193	HepG2	liver:	n/a	n/a
11	EP300	chr6:142586504-142587040	HepG2	liver:	n/a	chr6:142586940-142586954
12	TEAD4	chr6:142586331-142587268	HepG2	liver:	n/a	n/a
13	FOXA2	chr6:142586553-142587066	HepG2	liver:	n/a	n/a
14	EP300	chr6:142586514-142587188	HepG2	liver:	n/a	chr6:142587046-142587060 chr6:142586940-142586954
15	MYBL2	chr6:142586542-142587069	HepG2	liver:	n/a	n/a
16	FOXA1	chr6:142586577-142587132	HepG2	liver:	n/a	n/a
17	HNF4G	chr6:142586523-142587016	HepG2	liver:	n/a	chr6:142586782-142586797 chr6:142586780-142586795 chr6:142586782-142586797 chr6:142586782-142586797 chr6:142586782-142586797
18	SP1	chr6:142586555-142587154	HepG2	liver:	n/a	n/a
19	NFIC	chr6:142586595-142587066	HepG2	liver:	n/a	n/a
20	HNF4G	chr6:142586550-142587059	HepG2	liver:	n/a	chr6:142586782-142586797 chr6:142586780-142586795 chr6:142586782-142586797 chr6:142586782-142586797 chr6:142586782-142586797
21	MYBL2	chr6:142586356-142587462	HepG2	liver:	n/a	n/a
22	FOXA1	chr6:142586495-142587134	HepG2	liver:	n/a	n/a
23	RCOR1	chr6:142586621-142587051	HepG2	liver:	n/a	n/a
24	ARID3A	chr6:142586129-142587104	HepG2	liver:	n/a	n/a
25	NFIC	chr6:142586179-142587152	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000266843	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11757046	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11758623	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs11759498	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17789170	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178783	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225604	0.81[JPT][hapmap]
rs225605	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225606	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225618	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs225620	0.81[JPT][hapmap]
rs225622	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225623	0.83[JPT][hapmap]
rs225624	0.81[JPT][hapmap]
rs225629	0.83[JPT][hapmap]
rs225630	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225631	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225632	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225633	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225634	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225635	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs225639	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225641	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225642	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225643	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225652	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225653	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225654	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225656	0.81[JPT][hapmap]
rs225657	0.81[JPT][hapmap]
rs225658	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225659	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225660	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225662	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225663	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225665	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225666	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225671	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225673	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225674	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225675	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225676	0.91[CHB][hapmap]
rs225677	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs225678	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs225679	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225684	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs225685	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs225686	0.84[CHB][hapmap]
rs225687	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs225688	0.81[JPT][hapmap]
rs225689	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs225695	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225700	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225701	0.89[CHB][hapmap]
rs225702	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs225710	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs56061113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62430517	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62430518	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62430519	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs628311	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs639658	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9321861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389979	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389981	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399397	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403376	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5511	chr6:142550032-142594960	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142583200-142590200	Weak transcription	Aorta	Aorta
2	chr6:142586400-142587600	Flanking Active TSS	HepG2	liver
3	chr6:142586600-142587000	Enhancers	Liver	Liver
4	chr6:142586600-142587600	Enhancers	Fetal Intestine Large	intestine

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