Variant report

Variant	rs3134696
Chromosome Location	chr6:55062101-55062102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54710275..54712638-chr6:55059512..55062485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10498801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948893	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948894	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662510	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs12663056	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13343017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2998995	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006854	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122148	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3122149	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3122151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122152	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3122153	0.94[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3134689	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134690	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3134691	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3134692	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134694	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3134699	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3134700	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3134701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3134703	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3134708	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873439	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58828550	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59420753	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59867521	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60304167	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60550710	0.91[ASN][1000 genomes]
rs62418310	0.91[ASN][1000 genomes]
rs62418311	0.92[ASN][1000 genomes]
rs6922310	0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs6927478	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6937705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6937878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939376	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73434718	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758861	0.88[ASN][1000 genomes]
rs7775741	0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7775745	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs9367622	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9396060	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3134696	GSTA4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55057800-55063200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:55060200-55063200	Weak transcription	Hela-S3	cervix
3	chr6:55062000-55062400	Enhancers	Stomach Mucosa	stomach

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