Variant report

Variant	rs12054892
Chromosome Location	chr5:57945250-57945251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10060568	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[EUR][1000 genomes]
rs1158196	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13354637	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs158980	0.82[LWK][hapmap]
rs158986	0.86[JPT][hapmap]
rs158988	0.81[JPT][hapmap]
rs158992	0.81[JPT][hapmap]
rs158998	0.81[JPT][hapmap]
rs159004	0.87[LWK][hapmap];0.86[YRI][hapmap]
rs159007	0.87[LWK][hapmap];0.86[YRI][hapmap]
rs159009	0.81[JPT][hapmap]
rs16877131	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1833611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279980	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2591921	0.81[JPT][hapmap]
rs2591923	0.86[JPT][hapmap]
rs2662624	0.86[JPT][hapmap]
rs290573	0.86[JPT][hapmap]
rs292994	0.85[JPT][hapmap]
rs292995	0.86[JPT][hapmap]
rs293004	0.80[JPT][hapmap]
rs293016	0.81[JPT][hapmap]
rs293017	0.81[JPT][hapmap]
rs293030	0.81[JPT][hapmap]
rs293031	0.81[JPT][hapmap]
rs49960	0.80[JPT][hapmap]
rs58662773	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59064450	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72760264	0.91[EUR][1000 genomes]
rs7723730	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9292170	1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020937	chr5:57938969-57959918	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12054892	MAP3K1	cis	parietal	SCAN
rs12054892	GAPT	cis	parietal	SCAN
rs12054892	CDC20B	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57944000-57945800	Enhancers	HUVEC	blood vessel
2	chr5:57944000-57947600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr5:57944200-57946800	Weak transcription	Fetal Brain Male	brain
4	chr5:57945000-57945400	Flanking Active TSS	Fetal Lung	lung
5	chr5:57945000-57945800	Enhancers	Fetal Stomach	stomach

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