Variant report

Variant	rs7925662
Chromosome Location	chr11:101408306-101408307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10791501	0.92[EUR][1000 genomes]
rs10791502	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs11601702	1.00[ASN][1000 genomes]
rs11603508	1.00[ASN][1000 genomes]
rs11603928	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603969	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605037	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605091	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606855	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607633	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17675774	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676029	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743562	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743713	1.00[ASN][1000 genomes]
rs1938838	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938839	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938851	1.00[ASN][1000 genomes]
rs1939446	1.00[ASN][1000 genomes]
rs4254048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457714	1.00[CHB][hapmap]
rs4469857	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474404	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553341	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597037	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754765	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754768	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754769	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829971	1.00[ASN][1000 genomes]
rs60385781	1.00[ASN][1000 genomes]
rs61916052	1.00[ASN][1000 genomes]
rs61916053	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916054	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916055	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916056	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61917405	1.00[ASN][1000 genomes]
rs61918162	1.00[ASN][1000 genomes]
rs61918163	1.00[ASN][1000 genomes]
rs61918373	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918375	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918376	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918413	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6590880	1.00[CHB][hapmap]
rs6590881	1.00[CHB][hapmap]
rs6590882	1.00[CHB][hapmap]
rs6590886	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112255	1.00[CHB][hapmap]
rs7115426	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116268	1.00[ASN][1000 genomes]
rs7116748	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131328	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72976319	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931676	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943559	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv556133	chr11:101398450-101433161	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv556134	chr11:101398450-101436689	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv556135	chr11:101399510-101436689	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv519281	chr11:101404645-101436689	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv468852	chr11:101404645-101436689	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv556136	chr11:101404645-101436689	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv556137	chr11:101405218-101436689	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
11	esv2761703	chr11:101406049-101439667	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7925662	TRPC6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101401200-101425800	Weak transcription	Ovary	ovary

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