Variant report

Variant	rs12496621
Chromosome Location	chr3:51038910-51038911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11130280	0.84[CHD][hapmap]
rs11917538	0.82[CHD][hapmap]
rs12485524	0.86[ASN][1000 genomes]
rs12486828	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs12488700	0.93[JPT][hapmap];0.91[YRI][hapmap]
rs12488831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12488948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12490502	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490519	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491206	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491402	0.84[ASN][1000 genomes]
rs12492367	0.81[ASN][1000 genomes]
rs12492615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs12492850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12493359	0.89[EUR][1000 genomes]
rs12494214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494776	0.81[ASN][1000 genomes]
rs12497067	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13061003	0.82[CHD][hapmap]
rs13080170	0.82[CHD][hapmap]
rs17051468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2125368	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2262847	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2355707	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4073739	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4130473	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4323036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4346580	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs4356848	0.82[CHD][hapmap]
rs4443210	0.82[CHD][hapmap]
rs4560329	0.84[CHD][hapmap]
rs4688697	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688752	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4927961	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4927975	1.00[YRI][hapmap]
rs56844171	0.84[ASN][1000 genomes]
rs58356214	0.84[ASN][1000 genomes]
rs58720544	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58747991	0.82[ASN][1000 genomes]
rs60184902	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60602904	0.82[ASN][1000 genomes]
rs60882641	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60917457	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61627377	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61676409	0.89[EUR][1000 genomes]
rs6446239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6772197	0.82[CHD][hapmap]
rs6784455	0.81[CHD][hapmap]
rs6787805	0.83[CHD][hapmap]
rs6795573	0.82[CHD][hapmap]
rs72937251	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72937253	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72937262	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72937265	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72937299	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72939228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72942567	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72943130	0.89[EUR][1000 genomes]
rs72943137	0.89[EUR][1000 genomes]
rs7372342	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7427526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7427615	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433217	0.81[CHD][hapmap]
rs7614482	0.82[CHD][hapmap]
rs7627266	0.82[CHD][hapmap]
rs7638082	0.82[CHD][hapmap]
rs9865532	0.82[CHD][hapmap]
rs9869945	0.82[CHD][hapmap]
rs9875961	0.81[CHD][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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12496621	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs12496621	HEMK1	cis	multi-tissue	Pritchard
rs12496621	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51038600-51039000	Flanking Active TSS	Liver	Liver
2	chr3:51038800-51041000	Enhancers	HepG2	liver

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