Variant report

Variant	rs12488700
Chromosome Location	chr3:51019129-51019130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12485524	0.86[ASN][1000 genomes]
rs12486828	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487821	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12488831	0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12488948	0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12490502	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490519	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491206	0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491402	0.84[ASN][1000 genomes]
rs12492367	0.81[ASN][1000 genomes]
rs12492615	0.93[JPT][hapmap]
rs12492850	0.93[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12493359	0.89[EUR][1000 genomes]
rs12494214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494776	0.81[ASN][1000 genomes]
rs12496621	0.93[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497067	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17051468	0.93[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2125368	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078296	0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4130473	0.93[JPT][hapmap]
rs4323036	0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs4346580	0.93[JPT][hapmap]
rs4688697	0.92[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	0.93[JPT][hapmap];0.91[YRI][hapmap]
rs4927975	0.91[YRI][hapmap]
rs56844171	0.84[ASN][1000 genomes]
rs58356214	0.84[ASN][1000 genomes]
rs58720544	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58747991	0.83[ASN][1000 genomes]
rs60184902	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60602904	0.82[ASN][1000 genomes]
rs60882641	0.92[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];0.83[ASN][1000 genomes]
rs61627377	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61676409	0.89[EUR][1000 genomes]
rs6446239	0.81[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
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	0.92[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72942567	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72943130	0.89[EUR][1000 genomes]
rs72943137	0.89[EUR][1000 genomes]
rs7372342	0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7426964	0.83[AFR][1000 genomes]
rs7427526	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7427615	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv1004881	chr3:50900793-51032918	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536568	chr3:50900793-51032918	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12488700	HEMK1	cis	multi-tissue	Pritchard
rs12488700	HEMK	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51016600-51019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:51017000-51020800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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