Variant report

Variant	rs10513512
Chromosome Location	chr3:157076854-157076855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10460861	0.95[ASN][1000 genomes]
rs10513508	0.86[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10513509	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10513510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755111	0.81[CHB][hapmap]
rs10804778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10936077	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs10936078	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs10936080	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10936081	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs10936083	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10936088	0.86[CHB][hapmap]
rs10936089	0.86[CHB][hapmap]
rs11918974	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12486155	0.81[ASN][1000 genomes]
rs12490120	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12490192	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12494465	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12496269	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12633429	0.81[CHB][hapmap]
rs12634054	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12634689	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12635316	0.80[ASN][1000 genomes]
rs12637476	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1403105	0.81[CHB][hapmap]
rs1403108	0.84[JPT][hapmap]
rs1403109	0.86[CHB][hapmap]
rs1456109	0.85[CHB][hapmap]
rs1474281	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1500917	0.82[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1500918	0.90[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1500922	0.95[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1500924	0.86[CHB][hapmap]
rs1522392	0.86[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs1546260	0.86[CHB][hapmap]
rs1568611	0.82[JPT][hapmap]
rs1587533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16827483	0.80[ASN][1000 genomes]
rs16827516	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16827530	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1875315	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2047648	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs2047650	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2173824	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321743	0.81[CHB][hapmap]
rs4679790	0.81[CHB][hapmap]
rs4679791	0.81[CHB][hapmap]
rs4680353	0.81[CHB][hapmap]
rs4680354	0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs55865575	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56313302	0.80[ASN][1000 genomes]
rs62278575	0.80[ASN][1000 genomes]
rs62278582	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62278583	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278584	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62278585	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62278586	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62278596	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62278597	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62278598	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62278601	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278603	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62281377	0.80[ASN][1000 genomes]
rs62281379	0.80[ASN][1000 genomes]
rs62281383	0.80[ASN][1000 genomes]
rs6799567	0.86[CHB][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs73156724	0.81[ASN][1000 genomes]
rs73156752	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156753	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73156756	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73156757	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73156759	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7631257	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7649737	0.83[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513512	PTX3	cis	cerebellum	SCAN
rs10513512	PTX3	cis	parietal	SCAN
rs10513512	C3orf55	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157066000-157086800	Weak transcription	Pancreas	Pancrea
2	chr3:157066600-157083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:157070400-157077400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:157072400-157077200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:157073000-157077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:157073400-157079800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:157074400-157077400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:157074600-157077200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:157074600-157077400	Enhancers	HUVEC	blood vessel
10	chr3:157075800-157078600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:157075800-157078800	Enhancers	NHEK	skin
12	chr3:157076000-157077200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:157076000-157078800	Enhancers	NH-A	brain
14	chr3:157076200-157077800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:157076400-157077200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:157076400-157079600	Enhancers	Osteobl	bone
17	chr3:157076600-157077000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:157076600-157077400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:157076600-157078800	Enhancers	NHLF	lung
20	chr3:157076600-157079000	Enhancers	Hela-S3	cervix
21	chr3:157076600-157079600	Enhancers	NHDF-Ad	bronchial
22	chr3:157076800-157077200	Enhancers	A549	lung
23	chr3:157076800-157077600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:157076800-157079400	Enhancers	HSMM	muscle

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