Variant report

Variant	rs7638625
Chromosome Location	chr3:156558056-156558057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156557512..156559174-chr3:156562252..156564501,2	K562	blood:
2	chr3:156544026..156547043-chr3:156557512..156560526,3	MCF-7	breast:
3	chr3:156537501..156540468-chr3:156557246..156559245,2	K562	blood:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10212230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10936038	0.82[EUR][1000 genomes]
rs10936040	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs10936043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs11707914	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709901	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711674	0.82[EUR][1000 genomes]
rs11712111	0.89[ASN][1000 genomes]
rs12492968	0.84[EUR][1000 genomes]
rs12629380	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634915	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12638253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs13068223	0.84[JPT][hapmap]
rs13070271	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs13086516	0.81[EUR][1000 genomes]
rs13088978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs13097325	0.82[EUR][1000 genomes]
rs1320011	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13322318	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384538	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1430410	0.82[TSI][hapmap]
rs1560415	0.82[EUR][1000 genomes]
rs1560416	0.82[EUR][1000 genomes]
rs1574980	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs17382070	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2321290	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2321292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2874488	0.81[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2874494	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs344073	0.83[JPT][hapmap]
rs344079	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs344080	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs344082	0.88[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs344084	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs344087	0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs34667021	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851992	0.84[ASW][hapmap]
rs3910072	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4098	0.84[ASW][hapmap]
rs416600	0.80[ASN][1000 genomes]
rs4315647	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs453219	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4589888	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680305	0.81[EUR][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4680312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4680317	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs62275765	0.82[ASN][1000 genomes]
rs6762708	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs6765353	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6780427	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7637701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9812895	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap]
rs9818684	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9820830	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9837038	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs9837271	0.82[EUR][1000 genomes]
rs9844054	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9847187	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858158	0.89[ASN][1000 genomes]
rs9858861	0.82[TSI][hapmap]
rs9865905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9866373	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9871817	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9875585	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9875688	0.85[ASN][1000 genomes]
rs9876010	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876148	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs987724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs9878585	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7638625		cis	Lymphoblastoid	GTEx
rs7638625	LINC00886	cis	Nerve Tibial	GTEx
rs7638625	LINC00886	cis	Adipose Subcutaneous	GTEx
rs7638625	LINC00886	cis	Esophagus Muscularis	GTEx
rs7638625	LINC00886	cis	lung	GTEx
rs7638625	SCHIP1	cis	cerebellum	SCAN
rs7638625	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs7638625	LINC00886	cis	Stomach	GTEx
rs7638625	VEPH1	cis	cerebellum	SCAN
rs7638625	LINC00886	cis	Artery Aorta	GTEx
rs7638625	LINC00886	cis	Artery Tibial	GTEx
rs7638625	LINC00886	cis	Muscle Skeletal	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156554000-156558200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:156554400-156558400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:156554400-156561000	Weak transcription	Aorta	Aorta
5	chr3:156555400-156558800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:156555400-156560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:156555400-156560400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:156555400-156560400	Weak transcription	Osteobl	bone
9	chr3:156555400-156560800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:156555600-156560600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:156555600-156560600	Weak transcription	NHDF-Ad	bronchial
12	chr3:156556800-156558200	Weak transcription	HepG2	liver
13	chr3:156557200-156561000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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