Variant report

Variant	rs1925188
Chromosome Location	chr6:56134853-56134854
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10498810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948981	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs10948988	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12525967	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs12526228	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12530020	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap]
rs12665485	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1925158	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1925160	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1925187	0.84[ASN][1000 genomes]
rs2328693	0.82[ASN][1000 genomes]
rs2397210	0.84[ASN][1000 genomes]
rs2397212	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs2397213	0.82[ASN][1000 genomes]
rs3807013	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846927	0.82[ASN][1000 genomes]
rs3846928	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846929	0.82[ASN][1000 genomes]
rs3846931	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4119562	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs4119563	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4236138	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4435945	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4712121	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715602	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs4715603	0.84[ASN][1000 genomes]
rs4715606	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55734123	0.84[ASN][1000 genomes]
rs60619715	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs66796842	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67454631	0.84[ASN][1000 genomes]
rs72645373	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72645374	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745111	0.82[ASN][1000 genomes]
rs7759570	0.84[ASN][1000 genomes]
rs9349807	0.82[ASN][1000 genomes]
rs9349809	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9370494	0.81[EUR][1000 genomes]
rs9370495	0.81[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs9370506	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9370511	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9370513	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9382597	0.84[ASN][1000 genomes]
rs9382598	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9382599	0.84[ASN][1000 genomes]
rs9382600	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382601	0.82[ASN][1000 genomes]
rs9382603	0.82[ASN][1000 genomes]
rs9382604	0.82[ASN][1000 genomes]
rs9382606	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382617	0.83[AMR][1000 genomes]
rs9396185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs994039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs994040	0.81[CHB][hapmap];0.83[JPT][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	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1925188	ICK	cis	parietal	SCAN
rs1925188	COL21A1	cis	cerebellum	SCAN
rs1925188	GSTA5	cis	parietal	SCAN
rs1925188	KLHL31	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56133400-56139000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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