Variant report

Variant	rs62292500
Chromosome Location	chr3:162412596-162412597
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	chr3:162411048..162413287-chr3:162414403..162417401,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12106918	0.83[ASN][1000 genomes]
rs12485395	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12488027	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12490526	0.96[ASN][1000 genomes]
rs12490594	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12491268	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12492947	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12495930	0.96[ASN][1000 genomes]
rs1390794	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496728	0.83[ASN][1000 genomes]
rs16851286	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16851330	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16852157	0.96[ASN][1000 genomes]
rs16852192	0.96[ASN][1000 genomes]
rs28526612	0.83[ASN][1000 genomes]
rs36031770	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3899597	0.83[ASN][1000 genomes]
rs3912606	0.83[ASN][1000 genomes]
rs62292481	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62292482	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62292483	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62292499	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62292501	0.84[EUR][1000 genomes]
rs62292520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62292522	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62294572	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62294574	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62294576	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62294580	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62393480	0.93[ASN][1000 genomes]
rs62393484	0.96[ASN][1000 genomes]
rs62393487	0.96[ASN][1000 genomes]
rs62393488	0.96[ASN][1000 genomes]
rs62393491	0.83[ASN][1000 genomes]
rs62393493	0.83[ASN][1000 genomes]
rs62393494	0.83[ASN][1000 genomes]
rs67006490	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73165527	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73165528	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73165529	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73165566	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73877805	0.83[ASN][1000 genomes]
rs9681374	0.83[ASN][1000 genomes]
rs9681513	0.83[ASN][1000 genomes]
rs9682116	0.83[ASN][1000 genomes]
rs9757964	0.83[ASN][1000 genomes]
rs9759259	0.83[ASN][1000 genomes]
rs9819222	0.83[ASN][1000 genomes]
rs9824287	0.83[ASN][1000 genomes]
rs9843839	0.83[ASN][1000 genomes]
rs9882760	0.83[ASN][1000 genomes]
rs9917843	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1005142	chr3:162284967-162447818	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv877758	chr3:162287573-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877759	chr3:162303276-162521339	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv877761	chr3:162346392-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv592208	chr3:162369863-162437102	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1005637	chr3:162379324-162635451	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv877762	chr3:162400620-162521339	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162408800-162413800	Weak transcription	Dnd41	blood

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