Variant report

Variant	rs12653046
Chromosome Location	chr5:57962327-57962328
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10060568	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes]
rs1158196	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12054892	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];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158980	0.89[LWK][hapmap];0.89[YRI][hapmap]
rs158986	0.91[JPT][hapmap]
rs158988	0.86[JPT][hapmap]
rs158992	0.86[JPT][hapmap]
rs158998	0.86[JPT][hapmap]
rs159001	0.86[JPT][hapmap]
rs159004	0.89[LWK][hapmap];0.80[YRI][hapmap]
rs159007	0.89[LWK][hapmap];0.80[YRI][hapmap]
rs159009	0.86[JPT][hapmap]
rs16877131	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1833611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186010	0.89[YRI][hapmap]
rs2279980	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2591913	0.82[JPT][hapmap]
rs2591921	0.86[JPT][hapmap]
rs2591923	0.91[JPT][hapmap]
rs2591924	0.89[YRI][hapmap]
rs2662624	0.91[JPT][hapmap]
rs290573	0.91[JPT][hapmap]
rs292994	0.91[JPT][hapmap]
rs292995	0.91[JPT][hapmap]
rs293004	0.85[JPT][hapmap]
rs293016	0.86[JPT][hapmap]
rs293017	0.86[JPT][hapmap]
rs293030	0.86[JPT][hapmap]
rs293031	0.86[JPT][hapmap]
rs49960	0.85[JPT][hapmap]
rs58662773	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59064450	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72760264	0.90[EUR][1000 genomes]
rs7723730	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9292170	0.89[LWK][hapmap]

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	nsv4845	chr5:57949493-57994156	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12653046	CDC20B	cis	parietal	SCAN
rs12653046	GAPT	cis	parietal	SCAN
rs12653046	MAP3K1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57961800-57963000	Weak transcription	Stomach Mucosa	stomach
2	chr5:57961800-57967400	Enhancers	HUVEC	blood vessel
3	chr5:57962200-57962600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:57962200-57963200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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