Variant report

Variant	rs613588
Chromosome Location	chr6:80978928-80978929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12176343	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892474	0.84[CEU][hapmap]
rs2256531	0.87[GIH][hapmap]
rs2322635	0.92[GIH][hapmap]
rs2476826	0.92[GIH][hapmap]
rs2490239	0.92[GIH][hapmap]
rs2490241	0.82[CHB][hapmap]
rs2490245	0.92[GIH][hapmap]
rs2490251	0.92[GIH][hapmap]
rs2505930	1.00[CHB][hapmap]
rs3805872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805903	0.80[CHB][hapmap]
rs3805911	0.92[GIH][hapmap]
rs3805913	0.92[GIH][hapmap]
rs3828753	0.92[GIH][hapmap]
rs4446525	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590641	0.80[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs59232999	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs600843	0.91[TSI][hapmap]
rs607130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs615585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs620147	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627240	0.82[MEX][hapmap]
rs660888	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs668329	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs676311	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs682482	0.82[EUR][1000 genomes]
rs684251	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs684283	0.81[CEU][hapmap];0.80[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs688867	0.88[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7747327	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756067	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7770189	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7771593	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs806783	0.92[GIH][hapmap];0.91[TSI][hapmap]
rs806849	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs806851	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs9343977	0.80[CHB][hapmap];0.82[MEX][hapmap]
rs9343980	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352815	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9443742	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9448911	0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80914600-80980400	Weak transcription	Ovary	ovary
2	chr6:80944000-80982800	Weak transcription	Pancreas	Pancrea
3	chr6:80960600-80997400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:80964800-81002600	Weak transcription	Liver	Liver
5	chr6:80968400-81006800	Weak transcription	Psoas Muscle	Psoas
6	chr6:80975200-80985000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:80977000-80983600	Weak transcription	HSMM	muscle
8	chr6:80978400-80979200	Enhancers	Brain Angular Gyrus	brain
9	chr6:80978800-80979000	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr6:80978800-80979000	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr6:80978800-80979200	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:80978800-80979200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:80978800-80979400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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