Variant report

Variant	rs6963090
Chromosome Location	chr7:38953087-38953088
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10229055	1.00[CHB][hapmap]
rs10239904	0.81[EUR][1000 genomes]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10254873	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10264217	0.81[EUR][1000 genomes]
rs10266279	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270483	0.81[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs11983387	0.91[EUR][1000 genomes]
rs12701656	1.00[ASN][1000 genomes]
rs12701657	1.00[ASN][1000 genomes]
rs12701661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13224619	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13224857	1.00[ASN][1000 genomes]
rs13229445	1.00[ASN][1000 genomes]
rs13230196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13235997	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2058073	0.89[AMR][1000 genomes]
rs2079546	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2190667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2214667	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286103	1.00[JPT][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[ASN][1000 genomes]
rs34886315	1.00[ASN][1000 genomes]
rs34997080	1.00[ASN][1000 genomes]
rs35220172	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400125	1.00[ASN][1000 genomes]
rs35816439	1.00[ASN][1000 genomes]
rs35843038	1.00[ASN][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723786	1.00[JPT][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4723804	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	0.92[EUR][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6951429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964985	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs6974764	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370730	1.00[ASN][1000 genomes]
rs757685	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784065	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784609	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789864	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7802052	1.00[ASN][1000 genomes]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs976350	1.00[JPT][hapmap]
rs976352	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6963090	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38952200-38953200	Enhancers	Muscle Satellite Cultured Cells	--
2	chr7:38952200-38953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:38952800-38953800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:38953000-38953400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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