Variant report

Variant	rs12662510
Chromosome Location	chr6:55079891-55079892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10498801	0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs10948893	0.81[AMR][1000 genomes]
rs10948894	0.82[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs12526414	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs12663056	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13343017	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3006854	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs3122148	0.91[CHD][hapmap];0.83[JPT][hapmap]
rs3122149	0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs3122151	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs3122153	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3134689	0.87[JPT][hapmap]
rs3134696	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs3134699	0.82[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs3134701	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3134703	0.91[ASN][1000 genomes]
rs3134708	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs4236127	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs55873439	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58828550	0.81[AMR][1000 genomes]
rs59420753	0.81[AMR][1000 genomes]
rs59682791	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6922310	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6937705	0.81[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs6937878	0.82[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs6939376	0.81[AMR][1000 genomes]
rs73434718	0.81[AMR][1000 genomes]
rs73743300	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7775745	0.82[CHB][hapmap]
rs9367622	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9475199	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9475200	0.88[AMR][1000 genomes];0.90[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	nsv1016461	chr6:55038131-55129663	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12662510	GSTA4	cis	cerebellum	SCAN
rs12662510	HCRTR2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55079600-55081200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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