Variant report

Variant	rs12496767
Chromosome Location	chr3:158179237-158179238
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158177518..158180211-chr3:158180565..158183137,2	MCF-7	breast:

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10936129	0.83[EUR][1000 genomes]
rs10936133	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs10936134	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs10936146	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1095642	0.85[JPT][hapmap];0.95[YRI][hapmap]
rs11709804	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs11710570	0.82[EUR][1000 genomes]
rs11714821	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714869	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717725	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11719037	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719188	0.80[CEU][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1193506	0.85[JPT][hapmap]
rs1193509	0.84[JPT][hapmap]
rs1193510	0.84[JPT][hapmap]
rs1193521	0.85[JPT][hapmap]
rs1210359	0.82[JPT][hapmap]
rs12107103	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12107104	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1213048	0.84[JPT][hapmap]
rs12494098	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs12629125	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629587	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs12631196	0.85[ASN][1000 genomes]
rs12632998	0.81[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs12633594	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12637678	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12638169	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638438	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13066362	0.84[JPT][hapmap]
rs1369562	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1595028	0.92[CEU][hapmap]
rs1595029	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1595030	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1630304	0.85[JPT][hapmap]
rs1714518	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1730020	0.85[JPT][hapmap]
rs1730040	0.85[JPT][hapmap]
rs1852285	0.84[JPT][hapmap]
rs1978779	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1978781	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap]
rs2176893	0.83[EUR][1000 genomes]
rs2222326	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2362965	0.81[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs2362968	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2362969	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[ASN][1000 genomes]
rs2362970	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2362972	0.91[ASN][1000 genomes]
rs2682405	0.84[JPT][hapmap]
rs2682406	0.85[JPT][hapmap]
rs2693542	0.85[JPT][hapmap]
rs28578723	0.83[EUR][1000 genomes]
rs28820925	0.87[ASN][1000 genomes]
rs3845981	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs4289388	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4309677	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs4431160	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4510417	0.96[CEU][hapmap];0.88[CHB][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4561872	0.81[ASN][1000 genomes]
rs4679828	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680426	0.83[EUR][1000 genomes]
rs4680431	0.82[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs4680433	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680434	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680436	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680437	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680439	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56387731	0.83[EUR][1000 genomes]
rs57519456	0.82[EUR][1000 genomes]
rs60336101	0.83[EUR][1000 genomes]
rs6414388	0.83[EUR][1000 genomes]
rs6414390	0.82[EUR][1000 genomes]
rs6441188	0.81[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs6441195	0.89[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441197	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441198	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441200	0.89[ASN][1000 genomes]
rs6441201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441203	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441204	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441206	0.85[CEU][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67385174	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762860	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6767008	0.82[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs6772340	0.82[EUR][1000 genomes]
rs6774461	0.84[JPT][hapmap]
rs67761009	0.83[EUR][1000 genomes]
rs6778202	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778370	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs6780896	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6783284	0.96[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6787172	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs6788703	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6791431	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs6795376	0.92[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6800887	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806702	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170315	0.83[EUR][1000 genomes]
rs73170348	0.82[EUR][1000 genomes]
rs7426603	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7430565	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7610691	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7610713	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7614259	0.82[EUR][1000 genomes]
rs7620927	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623732	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630443	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7632059	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7639678	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7639867	0.83[EUR][1000 genomes]
rs7641954	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7643792	0.84[JPT][hapmap]
rs7648196	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7648618	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7649463	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650256	0.83[EUR][1000 genomes]
rs827092	0.85[JPT][hapmap]
rs827093	0.85[JPT][hapmap]
rs827094	0.85[JPT][hapmap]
rs827099	0.84[JPT][hapmap]
rs827106	0.84[JPT][hapmap]
rs827108	0.84[JPT][hapmap]
rs827113	0.84[JPT][hapmap]
rs827127	0.85[JPT][hapmap]
rs827129	0.84[JPT][hapmap]
rs827131	0.85[JPT][hapmap]
rs827134	0.85[JPT][hapmap]
rs827135	0.95[YRI][hapmap]
rs827164	0.85[JPT][hapmap]
rs864332	0.84[JPT][hapmap]
rs939114	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs939117	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9809952	0.82[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs9810114	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9810345	0.86[ASN][1000 genomes]
rs9810887	0.92[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9811217	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9812624	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9819134	0.92[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9823076	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827781	0.80[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs9835244	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843089	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847045	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847316	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847460	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9850856	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9857535	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9858318	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9859129	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9865460	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9867152	0.83[EUR][1000 genomes]
rs9867617	0.83[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs9870802	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9872089	0.83[EUR][1000 genomes]
rs9872889	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876322	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9877909	0.88[ASN][1000 genomes]
rs9879545	0.82[EUR][1000 genomes]
rs9880806	0.82[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs9881630	0.81[EUR][1000 genomes]
rs9882274	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9883657	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1013046	chr3:158176582-158244606	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1014557	chr3:158176582-158251602	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12496767	RP11-538P18.2	cis	Artery Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158169600-158182400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:158177800-158179600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:158177800-158179600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:158178200-158179600	Enhancers	Adipose Nuclei	Adipose
5	chr3:158179000-158179400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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