Variant report

Variant	rs9564317
Chromosome Location	chr13:67045389-67045390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10507739	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs12859352	0.84[ASN][1000 genomes]
rs12866298	0.95[ASN][1000 genomes]
rs12867615	0.89[ASN][1000 genomes]
rs12868791	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs12868964	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12869171	0.81[ASN][1000 genomes]
rs12870336	0.87[ASN][1000 genomes]
rs12877241	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1470370	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17081420	0.89[ASN][1000 genomes]
rs17081458	0.81[ASN][1000 genomes]
rs17081462	0.81[ASN][1000 genomes]
rs17081473	0.81[ASN][1000 genomes]
rs1932881	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1932883	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1932886	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2324915	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs34979741	0.81[ASN][1000 genomes]
rs3843947	0.80[CHD][hapmap]
rs4144493	0.87[ASN][1000 genomes]
rs4379952	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4516088	0.81[ASN][1000 genomes]
rs4883779	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4883780	0.82[ASN][1000 genomes]
rs4884677	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4884678	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs61955971	0.81[ASN][1000 genomes]
rs67609817	0.81[ASN][1000 genomes]
rs9317591	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs9317595	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9529073	0.97[ASN][1000 genomes]
rs9529076	0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs9529077	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9529079	0.90[ASN][1000 genomes]
rs9529081	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9529083	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9529084	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9529086	0.81[ASN][1000 genomes]
rs9529087	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9540772	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs9540776	0.92[ASN][1000 genomes]
rs9540784	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs9540785	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9540786	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9540787	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9540788	0.88[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs9540789	0.87[ASN][1000 genomes]
rs9540790	0.87[ASN][1000 genomes]
rs9540791	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9540792	0.83[ASN][1000 genomes]
rs9540793	0.83[ASN][1000 genomes]
rs9540794	0.81[ASN][1000 genomes]
rs9540795	0.81[ASN][1000 genomes]
rs9540796	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9540799	0.83[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs9540800	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540803	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540804	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540809	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9540812	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540813	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540817	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9564319	0.92[ASN][1000 genomes]
rs9564320	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9564321	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs9564322	0.81[ASN][1000 genomes]
rs9571587	0.98[ASN][1000 genomes]
rs9571588	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs9571595	0.84[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs9571596	0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][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	nsv530416	chr13:66198235-67126195	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1053763	chr13:66210166-67184972	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541811	chr13:66210166-67184972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv932195	chr13:66215786-67215733	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv530723	chr13:66219650-67200316	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1052017	chr13:66232288-67213033	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv534503	chr13:66287963-67126195	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv915828	chr13:66544825-67212201	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv1051051	chr13:66948744-67126296	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv900390	chr13:66990736-67094634	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2757538	chr13:67005812-67119200	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2759943	chr13:67005812-67119200	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv2422196	chr13:67041890-67295480	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9564317	GJC2	trans	cerebellum	SCAN
rs9564317	SERPINB12	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67045000-67045400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:67045000-67045400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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