Variant report

Variant	rs12475752
Chromosome Location	chr2:186569882-186569883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:186540633..186542551-chr2:186567883..186570534,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1016410	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10173807	0.88[EUR][1000 genomes]
rs10185794	0.85[ASN][1000 genomes]
rs10192219	0.86[EUR][1000 genomes]
rs10803992	0.89[ASN][1000 genomes]
rs10803993	0.87[ASN][1000 genomes]
rs10931178	0.85[EUR][1000 genomes]
rs10931181	0.88[EUR][1000 genomes]
rs1116941	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11886336	0.83[ASN][1000 genomes]
rs11893024	0.89[EUR][1000 genomes]
rs11896364	0.88[EUR][1000 genomes]
rs11897513	0.85[EUR][1000 genomes]
rs11898011	0.87[EUR][1000 genomes]
rs12464911	0.87[ASN][1000 genomes]
rs12615971	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622188	0.89[EUR][1000 genomes]
rs12988839	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991700	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12992042	0.86[ASN][1000 genomes]
rs12998112	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12999848	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001443	0.85[EUR][1000 genomes]
rs13002387	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13003744	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13003900	0.85[EUR][1000 genomes]
rs13027342	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13028347	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468956	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16826958	0.83[ASN][1000 genomes]
rs1861896	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2255620	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2287608	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2370475	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2887742	0.94[ASN][1000 genomes]
rs35740220	0.88[ASN][1000 genomes]
rs36035600	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36114949	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667051	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58696152	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62199142	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62199145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6434137	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6718246	0.89[EUR][1000 genomes]
rs6725306	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729201	0.81[ASN][1000 genomes]
rs6733946	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6735082	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6749577	0.83[ASN][1000 genomes]
rs6749812	0.84[ASN][1000 genomes]
rs6756632	0.80[ASN][1000 genomes]
rs71407825	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7596200	0.81[EUR][1000 genomes]
rs759686	0.84[ASN][1000 genomes]
rs759687	0.83[ASN][1000 genomes]
rs7602728	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs763330	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs984988	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs988937	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875540	chr2:186345148-186583961	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875541	chr2:186345148-186598526	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv584018	chr2:186352959-186598526	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv2763034	chr2:186473461-186587890	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv584020	chr2:186475590-186661567	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1011628	chr2:186523096-186594343	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1003484	chr2:186524793-186591557	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1003603	chr2:186524793-186594343	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv2751838	chr2:186531835-186591557	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv584022	chr2:186531835-186591557	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv1010456	chr2:186531835-186594343	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	esv3414312	chr2:186564235-186579049	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186565600-186603200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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