Variant report

Variant	rs562441
Chromosome Location	chr11:104924786-104924787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10895769	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1503399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1503400	0.95[EUR][1000 genomes]
rs1623342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1628434	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1630085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1699073	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1699078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1699080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1699081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1699082	0.91[EUR][1000 genomes]
rs1699084	0.92[EUR][1000 genomes]
rs1699086	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1699087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1699088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs1785864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1785871	0.96[ASN][1000 genomes]
rs1785872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1785873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1785876	0.94[ASN][1000 genomes]
rs1785878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1785882	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1792752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1792755	0.94[ASN][1000 genomes]
rs1792756	0.94[ASN][1000 genomes]
rs1792763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1792764	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1792765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs1792766	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792771	0.85[EUR][1000 genomes]
rs1792773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792777	0.94[ASN][1000 genomes]
rs2062806	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2852987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4534547	0.88[EUR][1000 genomes]
rs4638280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472886	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs484345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489753	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs508337	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs529809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531589	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs572717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7932543	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7934144	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv517089	chr11:104915563-104930676	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
11	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
12	nsv8870	chr11:104920350-104932482	Weak transcription Enhancers Active TSS Strong transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
13	nsv972954	chr11:104920429-104931448	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
14	esv2760182	chr11:104922670-104931988	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	n/a
15	esv3465930	chr11:104923228-104931503	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
16	esv3465953	chr11:104923253-104931477	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
17	esv3465941	chr11:104923281-104931434	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
18	esv3465919	chr11:104923329-104931465	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
19	esv3465964	chr11:104923350-104931394	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
20	esv20753	chr11:104923420-104931406	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
21	esv2421755	chr11:104923862-104931233	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
22	nsv442626	chr11:104923862-104931233	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
23	esv3693099	chr11:104923951-104930676	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
24	nsv818862	chr11:104924246-104930676	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
25	nsv514588	chr11:104924726-104931102	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs562441	CARD17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104918200-104925200	Weak transcription	Ovary	ovary
2	chr11:104924600-104927000	Weak transcription	HepG2	liver

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