Variant report

Variant	rs12490517
Chromosome Location	chr3:162453428-162453429
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52605031..52607219-chr3:162453213..162454978,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10513594	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11918363	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918500	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11918979	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11923774	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11924257	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11927727	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11928655	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491591	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12495037	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496727	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13058972	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13059540	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13060141	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063263	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064537	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067070	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13069996	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13073470	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075806	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13078228	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083194	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13083759	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13084024	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13087013	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13087656	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13088590	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090685	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090953	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13091802	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13092345	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13093528	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13095618	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13097448	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100415	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13100841	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13101227	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17710556	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1874508	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132619	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173064	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220976	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34116551	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478986	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34778164	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35261604	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36057496	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853174	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3853175	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3853176	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3866343	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3866344	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3912604	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3912605	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4007775	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4007776	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289366	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55638495	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56139505	0.84[AMR][1000 genomes]
rs62292527	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62292533	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62292534	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71625443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs903941	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs982541	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs987233	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	nsv869804	chr3:162414099-162776884	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv829776	chr3:162422424-162577578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1001282	chr3:162429561-162513137	Enhancers Weak transcription Active TSS 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
14	nsv999246	chr3:162447248-162625983	Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv592210	chr3:162447818-162633607	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162439800-162459200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:162444200-162453800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:162451400-162453800	Weak transcription	Dnd41	blood
4	chr3:162452000-162453800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:162452000-162454000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:162453400-162453800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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