Variant report

Variant	rs6459154
Chromosome Location	chr6:56207337-56207338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12199257	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12204179	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12204391	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209253	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17224911	0.89[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17224995	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17225023	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225519	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17225591	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17823397	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17823553	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1883600	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3950165	0.89[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60268580	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6903698	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6908736	0.95[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6929337	0.89[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6929994	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6938343	0.81[JPT][hapmap]
rs7452915	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9464380	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9464381	0.81[JPT][hapmap]
rs9475676	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9475677	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475678	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475679	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9475680	0.89[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9475682	0.81[JPT][hapmap]
rs9475687	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9475688	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9986501	0.89[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.89[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6459154	GSTA2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56201000-56210000	Weak transcription	Osteobl	bone
2	chr6:56201200-56207600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:56201400-56207600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:56204200-56211600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:56206400-56208800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:56207200-56207800	Enhancers	Colon Smooth Muscle	Colon

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