Variant report

Variant	rs1630085
Chromosome Location	chr11:104939507-104939508
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10895769	0.80[ASN][1000 genomes]
rs10895770	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10895786	0.82[EUR][1000 genomes]
rs1483025	0.84[EUR][1000 genomes]
rs1503399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1623342	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1699073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699074	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1699078	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1699080	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1699081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs1699083	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1699086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699088	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1699095	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1785864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1785871	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1785872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1785873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1785876	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1785878	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1785881	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1785882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792752	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1792753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792755	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792756	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792763	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1792765	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap]
rs1792770	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1792773	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1792777	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1847293	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2174158	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2291269	0.82[CEU][hapmap]
rs2852987	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs3736149	0.82[EUR][1000 genomes]
rs4638280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs472886	0.96[ASN][1000 genomes]
rs484345	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs489753	0.98[ASN][1000 genomes]
rs508337	0.96[ASN][1000 genomes]
rs529809	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs531589	0.80[ASN][1000 genomes]
rs562441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs572717	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7932543	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	esv2757475	chr11:104895876-104979717	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2759863	chr11:104895876-104979717	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv470	chr11:104916361-104961230	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	n/a
11	nsv1042388	chr11:104934347-104988325	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
12	esv2756562	chr11:104937371-104981568	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
13	esv3450730	chr11:104938956-104968986	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	nsv1040275	chr11:104939029-104988325	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1630085	CARD17	cis	Esophagus Mucosa	GTEx
rs1630085	BIRC2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104935200-104941200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:104936200-104939600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:104937600-104939800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:104938200-104941800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:104938600-104939600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:104938600-104939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:104938600-104939600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:104939000-104940600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr11:104939400-104940000	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links