Variant report

Variant	rs2892279
Chromosome Location	chr20:24926055-24926056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24912941..24914562-chr20:24924394..24926104,2	MCF-7	breast:

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1056033	0.98[ASN][1000 genomes]
rs1056036	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11087486	0.84[ASN][1000 genomes]
rs11700073	0.86[ASN][1000 genomes]
rs11905625	0.86[ASN][1000 genomes]
rs11906373	0.90[ASN][1000 genomes]
rs12625319	0.95[ASN][1000 genomes]
rs13041643	0.98[ASN][1000 genomes]
rs1331286	0.83[ASN][1000 genomes]
rs1535042	0.88[ASN][1000 genomes]
rs1854849	0.83[ASN][1000 genomes]
rs1977540	0.81[ASN][1000 genomes]
rs2008275	0.93[ASN][1000 genomes]
rs2092565	0.98[ASN][1000 genomes]
rs2103736	0.98[ASN][1000 genomes]
rs2151462	0.90[ASN][1000 genomes]
rs2151463	0.90[ASN][1000 genomes]
rs2179729	0.98[ASN][1000 genomes]
rs2179730	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206891	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2225459	0.98[ASN][1000 genomes]
rs2235847	0.93[ASN][1000 genomes]
rs227590	0.81[ASN][1000 genomes]
rs227598	0.81[ASN][1000 genomes]
rs227613	0.86[ASN][1000 genomes]
rs227614	0.88[ASN][1000 genomes]
rs227615	0.84[ASN][1000 genomes]
rs227616	0.90[ASN][1000 genomes]
rs227618	0.83[ASN][1000 genomes]
rs227619	0.93[ASN][1000 genomes]
rs227620	0.93[ASN][1000 genomes]
rs227621	0.90[ASN][1000 genomes]
rs227622	0.90[ASN][1000 genomes]
rs227623	0.93[ASN][1000 genomes]
rs227624	0.90[ASN][1000 genomes]
rs227625	0.90[ASN][1000 genomes]
rs227626	0.93[ASN][1000 genomes]
rs227627	0.88[ASN][1000 genomes]
rs227628	0.93[ASN][1000 genomes]
rs227629	0.90[ASN][1000 genomes]
rs227630	0.90[ASN][1000 genomes]
rs227631	0.90[ASN][1000 genomes]
rs227632	0.90[ASN][1000 genomes]
rs227633	0.93[ASN][1000 genomes]
rs227634	0.93[ASN][1000 genomes]
rs227635	0.93[ASN][1000 genomes]
rs227639	0.93[ASN][1000 genomes]
rs227643	0.93[ASN][1000 genomes]
rs227646	0.93[ASN][1000 genomes]
rs227648	0.93[ASN][1000 genomes]
rs227649	0.83[ASN][1000 genomes]
rs227650	0.93[ASN][1000 genomes]
rs227651	0.90[ASN][1000 genomes]
rs227652	0.93[ASN][1000 genomes]
rs227653	0.93[ASN][1000 genomes]
rs227657	0.93[ASN][1000 genomes]
rs227658	0.90[ASN][1000 genomes]
rs227659	0.93[ASN][1000 genomes]
rs2387365	0.83[ASN][1000 genomes]
rs2387366	0.98[ASN][1000 genomes]
rs2387572	0.98[ASN][1000 genomes]
rs2424691	0.90[ASN][1000 genomes]
rs34419834	0.98[ASN][1000 genomes]
rs4273288	0.81[ASN][1000 genomes]
rs4527284	0.91[ASN][1000 genomes]
rs4539860	0.88[ASN][1000 genomes]
rs45468392	0.93[ASN][1000 genomes]
rs45556041	0.93[ASN][1000 genomes]
rs4594518	0.88[ASN][1000 genomes]
rs4813541	0.98[ASN][1000 genomes]
rs4813542	0.98[ASN][1000 genomes]
rs4815327	0.81[ASN][1000 genomes]
rs4815337	0.98[ASN][1000 genomes]
rs4815339	0.95[ASN][1000 genomes]
rs4815340	0.98[ASN][1000 genomes]
rs4815341	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815351	0.93[ASN][1000 genomes]
rs4815355	0.98[ASN][1000 genomes]
rs4815357	0.93[ASN][1000 genomes]
rs56312312	0.86[ASN][1000 genomes]
rs57265446	0.86[ASN][1000 genomes]
rs58244398	0.88[ASN][1000 genomes]
rs6036976	0.81[ASN][1000 genomes]
rs6036995	0.82[AFR][1000 genomes]
rs6050134	0.84[ASN][1000 genomes]
rs6050177	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050179	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050181	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050198	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6050201	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083684	0.98[ASN][1000 genomes]
rs6083685	0.98[ASN][1000 genomes]
rs6083686	0.98[ASN][1000 genomes]
rs6083688	0.98[ASN][1000 genomes]
rs6083692	0.95[ASN][1000 genomes]
rs6083699	0.98[ASN][1000 genomes]
rs6083709	0.93[ASN][1000 genomes]
rs6106975	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106984	0.86[ASN][1000 genomes]
rs6114980	0.86[ASN][1000 genomes]
rs6114981	0.86[ASN][1000 genomes]
rs6114984	0.86[ASN][1000 genomes]
rs6114988	0.86[ASN][1000 genomes]
rs6114992	0.82[ASN][1000 genomes]
rs6132773	0.98[ASN][1000 genomes]
rs6132774	0.98[ASN][1000 genomes]
rs6132775	0.93[ASN][1000 genomes]
rs6132777	0.93[ASN][1000 genomes]
rs6132778	0.93[ASN][1000 genomes]
rs6132783	0.82[ASN][1000 genomes]
rs6138406	0.88[ASN][1000 genomes]
rs6138417	0.98[ASN][1000 genomes]
rs6138423	0.98[ASN][1000 genomes]
rs6138431	0.91[ASN][1000 genomes]
rs6138435	0.98[ASN][1000 genomes]
rs6138437	0.98[ASN][1000 genomes]
rs6138438	0.93[ASN][1000 genomes]
rs6138442	0.88[ASN][1000 genomes]
rs6138453	0.93[ASN][1000 genomes]
rs6138455	0.88[ASN][1000 genomes]
rs6138456	0.88[ASN][1000 genomes]
rs6138457	0.88[ASN][1000 genomes]
rs6138458	0.86[ASN][1000 genomes]
rs6138460	0.82[ASN][1000 genomes]
rs6138461	0.87[ASN][1000 genomes]
rs62215110	0.93[ASN][1000 genomes]
rs62215115	0.93[ASN][1000 genomes]
rs62215128	0.88[ASN][1000 genomes]
rs62215131	0.88[ASN][1000 genomes]
rs6707	0.88[ASN][1000 genomes]
rs7268095	0.86[ASN][1000 genomes]
rs7269416	0.86[ASN][1000 genomes]
rs735886	0.98[ASN][1000 genomes]
rs8125909	0.88[ASN][1000 genomes]
rs8183891	0.93[ASN][1000 genomes]
rs914314	0.83[ASN][1000 genomes]
rs926661	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926662	0.98[ASN][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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv524921	chr20:24897355-24932028	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv964444	chr20:24899460-24934649	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2892279	APMAP	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24923600-24930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:24923800-24929800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:24924600-24929800	Weak transcription	Placenta	Placenta

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