Variant report

Variant	rs10936077
Chromosome Location	chr3:157020974-157020975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1014855	0.81[JPT][hapmap]
rs10460861	0.85[ASN][1000 genomes]
rs10513508	0.91[CHB][hapmap]
rs10513509	0.87[CHB][hapmap]
rs10513510	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs10513512	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs1074864	0.81[JPT][hapmap]
rs10755111	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804777	0.84[AMR][1000 genomes]
rs10804778	0.87[CHB][hapmap]
rs10936078	0.91[CHB][hapmap]
rs10936079	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10936080	0.91[CHB][hapmap]
rs10936081	0.91[CHB][hapmap]
rs10936083	0.90[CHB][hapmap]
rs10936088	0.81[JPT][hapmap]
rs10936089	0.81[JPT][hapmap]
rs11918974	0.82[CHB][hapmap]
rs12486155	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12486955	0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12490120	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12494423	0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12494465	0.87[CHB][hapmap]
rs12632562	0.84[CHB][hapmap]
rs12633099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12633429	0.86[CHB][hapmap]
rs12634054	0.87[CHB][hapmap]
rs12634689	0.87[CHB][hapmap]
rs12634905	0.84[AMR][1000 genomes]
rs12636252	0.81[EUR][1000 genomes]
rs12637476	0.85[CHB][hapmap]
rs12637932	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs1403105	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1403108	0.81[CHB][hapmap]
rs1403109	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1456104	0.81[JPT][hapmap]
rs1456109	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1474281	0.87[CHB][hapmap]
rs1500918	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1500923	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1500924	0.91[CHB][hapmap]
rs1522392	0.91[CHB][hapmap]
rs1522393	0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1546260	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1566521	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1568611	0.81[CHB][hapmap]
rs1581413	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2047647	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs2047648	0.91[CHB][hapmap]
rs2173824	0.87[CHB][hapmap]
rs2321743	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4679790	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4679791	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4680353	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680354	0.90[CHB][hapmap]
rs55734537	0.85[AMR][1000 genomes]
rs62278583	0.81[ASN][1000 genomes]
rs62281378	0.81[EUR][1000 genomes]
rs6799567	0.91[CHB][hapmap]
rs73156724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156728	0.80[AMR][1000 genomes]
rs73156752	0.81[ASN][1000 genomes]
rs73156753	0.80[ASN][1000 genomes]
rs7631257	0.91[CHB][hapmap]
rs7642909	0.81[EUR][1000 genomes]
rs7649737	0.81[CHB][hapmap]
rs872652	0.81[AMR][1000 genomes]
rs9831686	0.81[JPT][hapmap]
rs9848774	0.81[JPT][hapmap]
rs991083	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10936077	PTX3	cis	cerebellum	SCAN
rs10936077	SSR3	cis	cerebellum	SCAN
rs10936077	SMC4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157004800-157028200	Weak transcription	HUVEC	blood vessel
2	chr3:157013000-157032600	Weak transcription	NH-A	brain
3	chr3:157015600-157048400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:157019000-157029000	Weak transcription	NHLF	lung
5	chr3:157019200-157023000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:157019200-157028200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:157019200-157028400	Weak transcription	Osteobl	bone
8	chr3:157019400-157022000	Weak transcription	NHDF-Ad	bronchial
9	chr3:157019400-157028200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:157019600-157021000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:157020200-157021600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:157020600-157022200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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