Variant report

Variant	rs12633594
Chromosome Location	chr3:158124944-158124945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158116256..158122460-chr3:158123210..158127846,6	K562	blood:
2	chr3:158120939..158122678-chr3:158123102..158125288,2	MCF-7	breast:

Extended variants
information (count: 153 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10936129	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10936133	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10936134	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1095627	0.86[JPT][hapmap]
rs1095637	0.84[CEU][hapmap]
rs1095641	0.86[JPT][hapmap]
rs1095642	0.86[JPT][hapmap]
rs11709804	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs11714869	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11717725	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719188	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193506	0.86[JPT][hapmap]
rs1193509	0.86[JPT][hapmap]
rs1193510	0.86[JPT][hapmap]
rs1193521	0.86[JPT][hapmap]
rs1210359	0.85[JPT][hapmap]
rs12107103	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1213048	0.86[JPT][hapmap]
rs12494098	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12496767	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629587	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631196	0.83[ASN][1000 genomes]
rs12632998	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12638169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13066362	0.86[JPT][hapmap]
rs1369562	0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs1630304	0.86[JPT][hapmap]
rs1730007	0.82[JPT][hapmap]
rs1730020	0.86[JPT][hapmap]
rs1730040	0.86[JPT][hapmap]
rs1852285	0.86[JPT][hapmap]
rs1978781	0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2176893	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2222326	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2362965	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2362968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2362970	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362972	0.92[ASN][1000 genomes]
rs2682405	0.86[JPT][hapmap]
rs2682406	0.86[JPT][hapmap]
rs2693529	0.86[JPT][hapmap]
rs2693542	0.86[JPT][hapmap]
rs28578723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28813180	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28820925	0.98[ASN][1000 genomes]
rs3845981	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4289388	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4309677	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4510417	0.90[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4561872	0.86[ASN][1000 genomes]
rs4679828	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680426	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4680431	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4680433	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680434	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680436	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680437	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56387731	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57519456	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60336101	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6414388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6414390	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441188	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6441195	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441197	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441198	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441200	0.90[ASN][1000 genomes]
rs6441201	0.89[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67385174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767008	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6772237	0.81[EUR][1000 genomes]
rs6772340	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6773939	0.82[EUR][1000 genomes]
rs6774461	0.86[JPT][hapmap]
rs67761009	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6778370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6783284	0.86[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6785063	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787172	0.81[JPT][hapmap]
rs6788703	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6791431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6797629	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6800887	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806702	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73170315	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73170348	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7426603	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430565	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7610691	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7614259	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630443	0.82[CEU][hapmap]
rs7632059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639867	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7641954	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643792	0.86[JPT][hapmap]
rs7648196	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648618	0.80[TSI][hapmap]
rs827092	0.86[JPT][hapmap]
rs827093	0.86[JPT][hapmap]
rs827094	0.86[JPT][hapmap]
rs827099	0.86[JPT][hapmap]
rs827106	0.86[JPT][hapmap]
rs827108	0.86[JPT][hapmap]
rs827113	0.86[JPT][hapmap]
rs827127	0.86[JPT][hapmap]
rs827129	0.86[JPT][hapmap]
rs827131	0.86[JPT][hapmap]
rs827134	0.86[JPT][hapmap]
rs827135	0.82[JPT][hapmap]
rs827164	0.86[JPT][hapmap]
rs827171	0.86[JPT][hapmap]
rs827176	0.82[JPT][hapmap]
rs827177	0.82[JPT][hapmap]
rs827178	0.82[JPT][hapmap]
rs827179	0.84[JPT][hapmap]
rs864332	0.86[JPT][hapmap]
rs939114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs939117	0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs9809952	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9810345	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9823076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827781	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9843089	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847316	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847460	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850856	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858318	0.80[TSI][hapmap]
rs9859129	0.80[TSI][hapmap]
rs9867152	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9867617	1.00[CEU][hapmap];0.89[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870802	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872089	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872889	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9877909	0.99[ASN][1000 genomes]
rs9879545	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9880806	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs9881630	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9882274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9883657	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1000904	chr3:158094357-158159317	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1004480	chr3:158102068-158129826	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv536776	chr3:158102068-158129826	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12633594	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs12633594	RSRC1	cis	Esophagus Muscularis	GTEx
rs12633594	LXN	cis	parietal	SCAN
rs12633594	RARRES1	cis	cerebellum	SCAN
rs12633594	RSRC1	cis	cerebellum	SCAN
rs12633594	GFM1	cis	cerebellum	SCAN
rs12633594	LXN	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158122400-158126000	Weak transcription	Fetal Heart	heart
2	chr3:158123400-158128000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:158124600-158125000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:158124600-158146600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:158124800-158125200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:158124800-158126600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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