Variant report

Variant	rs531589
Chromosome Location	chr11:104952283-104952284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10895769	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895770	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1483025	0.86[ASN][1000 genomes]
rs1503399	0.94[ASN][1000 genomes]
rs1503400	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1623342	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1628434	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630085	0.80[ASN][1000 genomes]
rs1699080	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699082	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1699083	0.93[ASN][1000 genomes]
rs1699084	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1699088	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699095	0.96[ASN][1000 genomes]
rs1785864	0.98[ASN][1000 genomes]
rs1785872	0.92[ASN][1000 genomes]
rs1785873	0.94[ASN][1000 genomes]
rs1785876	0.81[ASN][1000 genomes]
rs1785878	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792752	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792755	0.81[ASN][1000 genomes]
rs1792756	0.81[ASN][1000 genomes]
rs1792757	0.99[ASN][1000 genomes]
rs1792764	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792765	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792766	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792770	0.94[ASN][1000 genomes]
rs1792771	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792773	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792777	0.81[ASN][1000 genomes]
rs1847293	0.90[ASN][1000 genomes]
rs2062806	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2174158	0.92[ASN][1000 genomes]
rs2852987	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736149	0.86[ASN][1000 genomes]
rs4534547	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4638280	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs472886	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs484345	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489753	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508337	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs529809	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs562441	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs572717	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7932543	0.94[ASN][1000 genomes]
rs7934144	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
15	nsv818863	chr11:104940204-104960997	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
16	nsv8871	chr11:104941750-104973508	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
17	esv33277	chr11:104944762-104969485	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
18	nsv1054109	chr11:104948117-104976058	Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
19	nsv949337	chr11:104950007-105510193	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv1049355	chr11:104950412-104972518	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
21	nsv442241	chr11:104950424-104972558	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
22	esv2762941	chr11:104952282-104972558	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs531589	CARD17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104948000-104953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:104950200-104953400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr11:104950600-104952400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr11:104950600-104953800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr11:104950800-104953000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr11:104951000-104953600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:104951200-104952400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr11:104951600-104953000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr11:104951800-104953200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:104952000-104952600	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr11:104952000-104953000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr11:104952000-104953000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:104952000-104953000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:104952000-104953000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:104952000-104953200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:104952200-104952600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:104952200-104956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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