Variant report

Variant	rs6138431
Chromosome Location	chr20:24933362-24933363
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24932720..24935500-chr20:24938353..24940512,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1056033	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056036	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs11087486	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11699285	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11700073	0.82[ASN][1000 genomes]
rs11905625	0.82[ASN][1000 genomes]
rs11906373	0.87[ASN][1000 genomes]
rs12625319	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13041643	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535042	0.80[ASN][1000 genomes]
rs2008275	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2092565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2151462	0.87[ASN][1000 genomes]
rs2151463	0.87[ASN][1000 genomes]
rs2179729	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2179730	0.91[ASN][1000 genomes]
rs2206891	0.85[ASN][1000 genomes]
rs2225459	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2235847	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs227613	0.82[ASN][1000 genomes]
rs227614	0.85[ASN][1000 genomes]
rs227615	0.80[ASN][1000 genomes]
rs227616	0.87[ASN][1000 genomes]
rs227618	0.80[ASN][1000 genomes]
rs227619	0.85[ASN][1000 genomes]
rs227620	0.85[ASN][1000 genomes]
rs227621	0.87[ASN][1000 genomes]
rs227622	0.87[ASN][1000 genomes]
rs227623	0.85[ASN][1000 genomes]
rs227624	0.87[ASN][1000 genomes]
rs227625	0.87[ASN][1000 genomes]
rs227626	0.85[ASN][1000 genomes]
rs227627	0.85[ASN][1000 genomes]
rs227628	0.85[ASN][1000 genomes]
rs227629	0.87[ASN][1000 genomes]
rs227630	0.87[ASN][1000 genomes]
rs227631	0.87[ASN][1000 genomes]
rs227632	0.87[ASN][1000 genomes]
rs227633	0.85[ASN][1000 genomes]
rs227634	0.85[ASN][1000 genomes]
rs227635	0.85[ASN][1000 genomes]
rs227639	0.85[ASN][1000 genomes]
rs227643	0.85[ASN][1000 genomes]
rs227646	0.85[ASN][1000 genomes]
rs227648	0.85[ASN][1000 genomes]
rs227650	0.85[ASN][1000 genomes]
rs227651	0.87[ASN][1000 genomes]
rs227652	0.85[ASN][1000 genomes]
rs227653	0.85[ASN][1000 genomes]
rs227657	0.85[ASN][1000 genomes]
rs227658	0.87[ASN][1000 genomes]
rs227659	0.85[ASN][1000 genomes]
rs2387366	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2387572	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424691	0.87[ASN][1000 genomes]
rs2892279	0.91[ASN][1000 genomes]
rs34419834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4527284	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4539860	0.80[ASN][1000 genomes]
rs45468392	0.85[ASN][1000 genomes]
rs45556041	0.85[ASN][1000 genomes]
rs4594518	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4813541	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4813542	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815337	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815339	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4815340	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815341	0.91[ASN][1000 genomes]
rs4815351	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4815355	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815357	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56312312	0.82[ASN][1000 genomes]
rs58244398	0.80[ASN][1000 genomes]
rs6050177	0.91[ASN][1000 genomes]
rs6050179	0.91[ASN][1000 genomes]
rs6050181	0.91[ASN][1000 genomes]
rs6050198	0.86[CHB][hapmap]
rs6050201	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs6050249	0.86[JPT][hapmap]
rs6076304	0.83[AMR][1000 genomes]
rs6083684	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083685	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083686	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083688	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083692	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083699	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083709	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6106975	0.91[ASN][1000 genomes]
rs6106984	0.82[ASN][1000 genomes]
rs6114980	0.82[ASN][1000 genomes]
rs6114981	0.82[ASN][1000 genomes]
rs6114984	0.82[ASN][1000 genomes]
rs6114988	0.82[ASN][1000 genomes]
rs6114992	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132774	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132775	0.85[ASN][1000 genomes]
rs6132777	0.85[ASN][1000 genomes]
rs6132778	0.85[ASN][1000 genomes]
rs6138406	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6138417	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138423	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138425	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6138426	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6138427	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6138435	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138437	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138438	0.85[ASN][1000 genomes]
rs6138442	0.80[ASN][1000 genomes]
rs6138453	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138455	0.80[ASN][1000 genomes]
rs6138456	0.80[ASN][1000 genomes]
rs6138457	0.80[ASN][1000 genomes]
rs6138458	0.82[ASN][1000 genomes]
rs6138461	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62215110	0.85[ASN][1000 genomes]
rs62215115	0.85[ASN][1000 genomes]
rs62215128	0.80[ASN][1000 genomes]
rs62215131	0.80[ASN][1000 genomes]
rs6707	0.85[ASN][1000 genomes]
rs7268095	0.82[ASN][1000 genomes]
rs7269416	0.82[ASN][1000 genomes]
rs735886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8125909	0.80[ASN][1000 genomes]
rs8183730	0.82[EUR][1000 genomes]
rs8183891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8184888	0.82[EUR][1000 genomes]
rs926661	0.91[ASN][1000 genomes]
rs926662	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138431	APMAP	cis	Whole Blood	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24928600-24940400	Weak transcription	Right Atrium	heart
2	chr20:24929400-24933800	Active TSS	Primary B cells from cord blood	blood
3	chr20:24929600-24936400	Weak transcription	Fetal Intestine Small	intestine
4	chr20:24930000-24934800	Weak transcription	GM12878-XiMat	blood
5	chr20:24930000-24936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:24930200-24936800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr20:24930200-24939400	Weak transcription	Right Ventricle	heart
8	chr20:24930400-24933600	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr20:24930400-24934200	Weak transcription	Pancreas	Pancrea
10	chr20:24930400-24934400	Weak transcription	Lung	lung
11	chr20:24930400-24935000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr20:24930400-24939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:24930600-24935600	Weak transcription	Primary T cells from cord blood	blood
14	chr20:24930600-24943000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:24930800-24933400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:24930800-24933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:24930800-24933800	Enhancers	Placenta	Placenta
18	chr20:24930800-24934400	Weak transcription	Dnd41	blood
19	chr20:24930800-24935000	Weak transcription	Thymus	Thymus
20	chr20:24930800-24938200	Weak transcription	Colonic Mucosa	Colon
21	chr20:24931000-24933600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr20:24931000-24933600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr20:24931000-24933800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr20:24931000-24938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:24931200-24935000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:24931200-24936400	Weak transcription	Esophagus	oesophagus
27	chr20:24931200-24936400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr20:24931400-24934000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr20:24931400-24939600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr20:24931600-24933800	Enhancers	Fetal Muscle Leg	muscle
31	chr20:24931600-24934400	Weak transcription	Gastric	stomach
32	chr20:24931600-24938000	Weak transcription	NHLF	lung
33	chr20:24931600-24938600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:24931800-24934400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr20:24931800-24934600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr20:24931800-24936400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr20:24932000-24933800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr20:24932000-24934600	Enhancers	Adipose Nuclei	Adipose
39	chr20:24932000-24943000	Weak transcription	HSMM	muscle
40	chr20:24932000-24943400	Weak transcription	HSMMtube	muscle
41	chr20:24932200-24933800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr20:24932200-24934600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr20:24932200-24941000	Weak transcription	A549	lung
44	chr20:24932400-24936000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr20:24932400-24936000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr20:24932600-24933800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr20:24932600-24934600	Enhancers	Liver	Liver
48	chr20:24932600-24934800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
49	chr20:24932600-24938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr20:24932600-24938200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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