Variant report

Variant	rs7953494
Chromosome Location	chr12:86665156-86665157
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	chr12:86661669..86664440-chr12:86664812..86667661,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10776953	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10776954	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776958	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10776960	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10776967	0.95[EUR][1000 genomes]
rs10858409	0.90[EUR][1000 genomes]
rs10858411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10858417	0.94[EUR][1000 genomes]
rs10858420	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11103946	0.93[EUR][1000 genomes]
rs12311272	0.88[ASN][1000 genomes]
rs12311407	0.88[ASN][1000 genomes]
rs12311449	0.88[ASN][1000 genomes]
rs1389292	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389295	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463749	1.00[ASN][1000 genomes]
rs1493408	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1493413	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1493416	1.00[ASN][1000 genomes]
rs1493417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493420	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1493421	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1532262	0.85[ASN][1000 genomes]
rs1532263	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1552839	0.88[ASN][1000 genomes]
rs1602850	1.00[ASN][1000 genomes]
rs1994863	0.85[EUR][1000 genomes]
rs2131565	0.88[ASN][1000 genomes]
rs2250915	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2406120	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406121	0.96[EUR][1000 genomes]
rs2452803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452805	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452806	1.00[ASN][1000 genomes]
rs2452808	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2452811	0.88[ASN][1000 genomes]
rs2452815	0.88[ASN][1000 genomes]
rs2465142	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465145	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465146	1.00[ASN][1000 genomes]
rs2465148	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2471561	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2471562	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2471563	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2471567	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329741	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7137308	1.00[ASN][1000 genomes]
rs7303642	0.96[EUR][1000 genomes]
rs7954833	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7963957	0.90[EUR][1000 genomes]
rs7966656	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs839107	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr12:86659000-86667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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