Variant report

Variant	rs12257540
Chromosome Location	chr10:90574051-90574052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1029024	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1029025	0.94[ASN][1000 genomes]
rs10509555	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509556	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs10509558	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10509559	1.00[EUR][1000 genomes]
rs10509560	1.00[TSI][hapmap]
rs11202885	1.00[EUR][1000 genomes]
rs12242274	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12243282	1.00[EUR][1000 genomes]
rs12243621	1.00[EUR][1000 genomes]
rs12245525	1.00[EUR][1000 genomes]
rs12245668	1.00[EUR][1000 genomes]
rs12254451	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12260572	1.00[EUR][1000 genomes]
rs12263461	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12413277	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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414211	0.96[ASN][1000 genomes]
rs12414648	1.00[ASN][1000 genomes]
rs12414800	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113344	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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113363	0.91[CHB][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113426	0.83[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17113457	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs17113476	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs17113724	1.00[EUR][1000 genomes]
rs17113942	1.00[EUR][1000 genomes]
rs17113959	1.00[EUR][1000 genomes]
rs17114000	1.00[EUR][1000 genomes]
rs17114016	1.00[EUR][1000 genomes]
rs17114020	1.00[EUR][1000 genomes]
rs17114024	1.00[EUR][1000 genomes]
rs17114057	1.00[EUR][1000 genomes]
rs17114116	1.00[TSI][hapmap]
rs17114283	1.00[TSI][hapmap]
rs2231780	1.00[EUR][1000 genomes]
rs2231785	1.00[EUR][1000 genomes]
rs2231786	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2282122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35996190	1.00[EUR][1000 genomes]
rs3781206	1.00[TSI][hapmap]
rs3814691	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816245	1.00[TSI][hapmap]
rs3898173	1.00[EUR][1000 genomes]
rs3898174	1.00[EUR][1000 genomes]
rs56848106	0.97[ASN][1000 genomes]
rs56998609	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58673564	1.00[EUR][1000 genomes]
rs58986570	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59661152	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60040082	1.00[ASN][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077019	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7090604	1.00[EUR][1000 genomes]
rs7098246	1.00[EUR][1000 genomes]
rs73364839	1.00[EUR][1000 genomes]
rs73364841	1.00[EUR][1000 genomes]
rs73364851	1.00[EUR][1000 genomes]
rs7908852	1.00[TSI][hapmap]
rs7913997	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12257540	PPP2R3B	trans	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90570400-90574400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr10:90570600-90574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr10:90570600-90574800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr10:90570600-90575200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:90570600-90575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:90570600-90577400	Weak transcription	Thymus	Thymus
7	chr10:90570600-90584200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr10:90573400-90583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:90574000-90574200	Enhancers	Gastric	stomach
10	chr10:90574000-90577400	Enhancers	Primary T cells from cord blood	blood

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