Variant report

Variant	rs6462976
Chromosome Location	chr7:40396300-40396301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10234636	0.80[JPT][hapmap]
rs10250287	0.92[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10256791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10278208	0.88[EUR][1000 genomes]
rs10280188	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10281352	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10951634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10951635	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11770113	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772069	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12234460	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs12532479	0.85[CHD][hapmap]
rs12533531	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs12669577	0.85[JPT][hapmap]
rs12673516	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs12701818	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12701819	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12701822	0.92[CEU][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs1319467	0.85[JPT][hapmap]
rs16880229	0.92[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs17171680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17171683	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17171686	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17171687	0.90[ASN][1000 genomes]
rs17171693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17171694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17171696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17171703	0.93[CHD][hapmap];0.80[JPT][hapmap]
rs17171704	0.89[ASW][hapmap];0.92[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17171705	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs17171710	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs2190261	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs2329772	0.92[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap]
rs3890819	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs4143205	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4379368	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4421260	0.92[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs4434532	0.84[JPT][hapmap]
rs4452702	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4526265	0.85[JPT][hapmap]
rs4598149	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4612243	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642532	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4723954	0.85[JPT][hapmap]
rs6462972	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6945101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs6965764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73322422	0.93[ASN][1000 genomes]
rs7807217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs9690724	0.92[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1033564	chr7:40273845-40417886	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817404	chr7:40295934-40573605	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv887986	chr7:40311382-40425140	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv949540	chr7:40321357-40528147	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv520748	chr7:40332518-40425140	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1017909	chr7:40337109-40427634	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv520374	chr7:40372593-40427000	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv606712	chr7:40372593-40427000	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv606713	chr7:40372593-40428402	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv34484	chr7:40383159-40489083	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv2757223	chr7:40384030-40497278	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv2759526	chr7:40384030-40497278	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv8081	chr7:40393228-40486239	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6462976	EPDR1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40393800-40397600	Enhancers	Fetal Lung	lung
2	chr7:40395600-40397200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:40395600-40397200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:40395600-40397200	Enhancers	HSMMtube	muscle
5	chr7:40395800-40396800	Weak transcription	Adipose Nuclei	Adipose
6	chr7:40395800-40396800	Enhancers	HSMM	muscle
7	chr7:40395800-40397200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr7:40395800-40397200	Enhancers	Osteobl	bone
9	chr7:40395800-40397400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:40395800-40397600	Enhancers	NHDF-Ad	bronchial
11	chr7:40396000-40396600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:40396200-40397200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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