Variant report

Variant	rs12191165
Chromosome Location	chr6:54160851-54160852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10085239	0.87[GIH][hapmap]
rs10447407	0.82[EUR][1000 genomes]
rs10948810	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150873	1.00[JPT][hapmap]
rs12193042	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198031	0.85[CEU][hapmap]
rs12198070	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs12199953	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201064	1.00[ASN][1000 genomes]
rs12201103	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206200	0.82[EUR][1000 genomes]
rs12208501	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12212689	0.82[EUR][1000 genomes]
rs12212836	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1298143	0.84[CEU][hapmap]
rs1340660	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417390	1.00[JPT][hapmap]
rs16885122	0.85[CEU][hapmap]
rs16885246	1.00[JPT][hapmap]
rs17681477	0.84[CEU][hapmap]
rs1934790	0.85[CEU][hapmap]
rs2136134	0.90[AMR][1000 genomes]
rs2211241	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2297980	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754813	1.00[JPT][hapmap]
rs2792644	1.00[JPT][hapmap]
rs60334573	0.82[EUR][1000 genomes]
rs62396365	0.81[EUR][1000 genomes]
rs6937514	0.84[CEU][hapmap]
rs73442548	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741347	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs7746489	0.82[EUR][1000 genomes]
rs7774316	0.81[EUR][1000 genomes]
rs843827	1.00[JPT][hapmap]
rs9296744	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9349700	0.82[CEU][hapmap]
rs9357793	0.85[CEU][hapmap]
rs9357795	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9367556	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs9370276	0.84[CEU][hapmap]
rs9382311	0.84[CEU][hapmap]
rs9382318	0.82[EUR][1000 genomes]
rs9382319	0.82[EUR][1000 genomes]
rs9395920	0.83[CEU][hapmap]
rs9885789	0.85[CEU][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2762594	chr6:54159146-54168766	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12191165	GSTA3	cis	parietal	SCAN
rs12191165	TINAG	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54157200-54164000	Weak transcription	NHDF-Ad	bronchial
2	chr6:54157600-54162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:54157600-54164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:54160400-54161000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:54160800-54161000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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