Variant report

Variant	rs10051529
Chromosome Location	chr5:49598937-49598938
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	chr5:49597764..49600386-chr5:49604629..49608751,3	MCF-7	breast:

Extended variants
information (count: 131 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10037889	0.91[EUR][1000 genomes]
rs10038023	0.93[EUR][1000 genomes]
rs10041903	0.95[EUR][1000 genomes]
rs10042504	0.87[EUR][1000 genomes]
rs10042601	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10043101	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10056605	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10060219	0.81[EUR][1000 genomes]
rs10062032	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10066635	0.87[ASN][1000 genomes]
rs10071725	0.90[EUR][1000 genomes]
rs10072182	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10073530	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10074359	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10079493	0.89[EUR][1000 genomes]
rs1010676	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1039798	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10461390	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10461391	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461519	0.89[EUR][1000 genomes]
rs10939999	0.84[EUR][1000 genomes]
rs11959569	0.90[EUR][1000 genomes]
rs12109228	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12188175	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513730	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12519021	0.86[EUR][1000 genomes]
rs12659303	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12697055	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13157992	1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs13173678	0.90[JPT][hapmap]
rs13174293	0.93[EUR][1000 genomes]
rs13180579	0.86[EUR][1000 genomes]
rs13180767	0.85[EUR][1000 genomes]
rs13182357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs13184466	0.83[EUR][1000 genomes]
rs13357429	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1344339	0.96[EUR][1000 genomes]
rs1511737	0.98[EUR][1000 genomes]
rs1511738	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1606224	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1811742	1.00[CEU][hapmap]
rs1812936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2005573	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2011539	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2011540	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2036901	0.80[CHD][hapmap];0.89[JPT][hapmap]
rs2036902	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2137129	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2137134	0.93[EUR][1000 genomes]
rs2199090	0.82[EUR][1000 genomes]
rs2199092	0.89[EUR][1000 genomes]
rs2271236	0.89[JPT][hapmap]
rs2352789	0.86[EUR][1000 genomes]
rs2668024	0.90[JPT][hapmap]
rs28445612	0.90[JPT][hapmap]
rs2883164	0.89[JPT][hapmap]
rs303219	0.90[JPT][hapmap]
rs34185098	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34601168	0.93[EUR][1000 genomes]
rs34741488	0.89[EUR][1000 genomes]
rs34749302	0.82[EUR][1000 genomes]
rs35740733	0.95[EUR][1000 genomes]
rs35858778	0.83[EUR][1000 genomes]
rs3849669	0.90[EUR][1000 genomes]
rs3860731	0.85[EUR][1000 genomes]
rs3860732	0.88[EUR][1000 genomes]
rs3933097	0.85[EUR][1000 genomes]
rs4030571	0.88[EUR][1000 genomes]
rs4031137	0.89[EUR][1000 genomes]
rs4321782	0.90[EUR][1000 genomes]
rs4331898	0.91[EUR][1000 genomes]
rs4337857	0.95[EUR][1000 genomes]
rs4385208	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4398636	0.87[EUR][1000 genomes]
rs4495185	0.81[EUR][1000 genomes]
rs4605784	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637546	0.93[EUR][1000 genomes]
rs471455	0.94[EUR][1000 genomes]
rs481222	0.91[EUR][1000 genomes]
rs4865519	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865698	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4865699	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4865700	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs494540	0.94[EUR][1000 genomes]
rs5011669	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs535100	0.83[EUR][1000 genomes]
rs535113	0.84[EUR][1000 genomes]
rs552892	0.95[EUR][1000 genomes]
rs56104926	0.82[EUR][1000 genomes]
rs57137858	0.90[EUR][1000 genomes]
rs58178891	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58386948	0.89[EUR][1000 genomes]
rs62386175	0.89[EUR][1000 genomes]
rs6449961	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6450056	0.92[EUR][1000 genomes]
rs6450063	0.89[EUR][1000 genomes]
rs6863840	0.96[EUR][1000 genomes]
rs6868380	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868677	0.84[EUR][1000 genomes]
rs6868721	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap]
rs6871761	0.96[EUR][1000 genomes]
rs6876902	0.97[EUR][1000 genomes]
rs6877713	0.96[EUR][1000 genomes]
rs6897412	0.95[EUR][1000 genomes]
rs7341010	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7442762	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7446951	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7447926	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7712849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7717982	0.87[EUR][1000 genomes]
rs7722742	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7732000	0.84[EUR][1000 genomes]
rs9291925	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9292005	1.00[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1021477	chr5:49455624-49624358	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1020912	chr5:49542837-49624358	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv3329361	chr5:49598845-49603343	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10051529	EMB	cis	Thyroid	GTEx
rs10051529	EMB	cis	parietal	SCAN
rs10051529	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs10051529	ARL15	cis	parietal	SCAN
rs10051529	EMB	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49596400-49599400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:49596400-49599400	Enhancers	HMEC	breast
3	chr5:49596600-49599800	Enhancers	NHEK	skin
4	chr5:49598200-49599400	Enhancers	Osteobl	bone
5	chr5:49598200-49599600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:49598400-49599000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:49598600-49599000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr5:49598600-49599400	Enhancers	HSMM	muscle
9	chr5:49598800-49599200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:49598800-49599400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:49598800-49599400	Active TSS	A549	lung

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