Variant report

Variant	rs11714869
Chromosome Location	chr3:158194720-158194721
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	chr3:158193823..158196386-chr3:158204544..158206278,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10936133	0.86[JPT][hapmap]
rs10936134	0.86[JPT][hapmap]
rs10936146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1095642	0.86[JPT][hapmap];0.95[YRI][hapmap]
rs11709804	0.86[JPT][hapmap]
rs11714821	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717725	0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs11719037	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1193509	0.86[JPT][hapmap]
rs1193510	0.86[JPT][hapmap]
rs12107103	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs12107104	0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs12494098	0.86[JPT][hapmap]
rs12496767	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]
rs12629125	0.81[JPT][hapmap]
rs12629587	0.85[JPT][hapmap]
rs12632998	0.85[JPT][hapmap]
rs12633594	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs12637678	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12638438	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13066362	0.86[JPT][hapmap]
rs1369562	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1595028	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs1595029	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1595030	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714518	0.88[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730007	0.81[JPT][hapmap]
rs1730020	0.86[JPT][hapmap]
rs1730040	0.86[JPT][hapmap]
rs1978779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978781	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2222326	0.86[JPT][hapmap]
rs2362965	0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2362969	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs2362972	0.81[ASN][1000 genomes]
rs2682406	0.86[JPT][hapmap]
rs2693542	0.86[JPT][hapmap]
rs2731112	0.81[CHB][hapmap]
rs3845981	0.86[JPT][hapmap]
rs4289388	0.81[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4309677	0.86[JPT][hapmap]
rs4431160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4510417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680431	0.84[JPT][hapmap]
rs4680433	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs4680436	0.81[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs4680437	0.81[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4680439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441188	0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs6441195	0.81[CEU][hapmap]
rs6441198	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6441201	0.82[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441206	0.96[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6762860	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6767008	0.85[JPT][hapmap]
rs6774461	0.86[JPT][hapmap]
rs6778202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778370	0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6780896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6788703	0.86[JPT][hapmap]
rs6791431	0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6795376	0.96[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6800887	0.81[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7430565	0.80[JPT][hapmap]
rs7610691	0.84[CEU][hapmap]
rs7610713	0.91[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7620927	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7623732	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630443	0.85[CEU][hapmap]
rs7632059	0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap]
rs7639678	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7639867	0.91[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs7641954	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7648196	0.86[JPT][hapmap]
rs7648618	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827099	0.86[JPT][hapmap]
rs827106	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	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs827164	0.86[JPT][hapmap]
rs864332	0.86[JPT][hapmap]
rs939114	0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs939117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809952	0.83[JPT][hapmap]
rs9810114	0.96[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9810887	0.96[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9811217	0.81[JPT][hapmap]
rs9812624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819134	0.96[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823076	0.87[CEU][hapmap]
rs9827781	0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs9835244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857535	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858318	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9859129	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9865460	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9867617	0.89[JPT][hapmap]
rs9870802	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9872889	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876322	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs9880806	0.85[JPT][hapmap]
rs9882274	0.81[JPT][hapmap]
rs9883657	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	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
3	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
4	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
5	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
6	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11714869	RARRES1	cis	cerebellum	SCAN
rs11714869	RP11-538P18.2	cis	Artery Tibial	GTEx
rs11714869	LXN	cis	parietal	SCAN
rs11714869	LXN	cis	cerebellum	SCAN
rs11714869	GFM1	cis	cerebellum	SCAN
rs11714869	RSRC1	cis	cerebellum	SCAN
rs11714869	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158190200-158201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:158190600-158195600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:158194000-158203800	Weak transcription	Fetal Heart	heart

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