Variant report

Variant	rs11905625
Chromosome Location	chr20:24977065-24977066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr20:24976760-24977244	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr20:24976696-24977226	SK-N-SH	brain:	n/a	n/a
3	SMC3	chr20:24975183-24977397	SK-N-SH	brain:	n/a	chr20:24976860-24976870 chr20:24976860-24976874 chr20:24976863-24976871
4	MYC	chr20:24976907-24977111	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr20:24976637-24977254	ECC-1	luminal epithelium:	n/a	n/a
6	FOS	chr20:24976891-24977229	MCF10A-Er-Src	breast:	n/a	n/a
7	TCF12	chr20:24976602-24977300	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr20:24976637-24977226	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr20:24976629-24977181	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr20:24976734-24977249	SK-N-SH	brain:	n/a	n/a
11	FOS	chr20:24976823-24977144	MCF10A-Er-Src	breast:	n/a	n/a
12	TCF12	chr20:24976657-24977325	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr20:24976661-24977373	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:24974463..24977428-chr20:25038810..25041777,2	MCF-7	breast:
2	chr20:24975304..24980368-chr20:25042845..25047055,6	MCF-7	breast:
3	chr20:24976100..24978484-chr20:25364511..25366126,2	MCF-7	breast:

Variant related genes	Relation type
APMAP	TF binding region
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.88[ASN][1000 genomes]
rs1056036	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11700073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906373	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12625319	0.86[ASN][1000 genomes]
rs13041643	0.88[ASN][1000 genomes]
rs1331286	0.83[ASN][1000 genomes]
rs1535042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1854849	0.83[ASN][1000 genomes]
rs1977540	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2092565	0.88[ASN][1000 genomes]
rs2103736	0.88[ASN][1000 genomes]
rs2151462	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2151463	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179729	0.88[ASN][1000 genomes]
rs2179730	0.86[ASN][1000 genomes]
rs2179732	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2225459	0.88[ASN][1000 genomes]
rs2235847	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227590	0.85[ASN][1000 genomes]
rs227597	0.83[ASN][1000 genomes]
rs227598	0.80[ASN][1000 genomes]
rs227613	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227614	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227615	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227616	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227618	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227619	0.93[ASN][1000 genomes]
rs227620	0.93[ASN][1000 genomes]
rs227621	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227622	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227623	0.93[ASN][1000 genomes]
rs227624	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227626	0.93[ASN][1000 genomes]
rs227627	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227628	0.93[ASN][1000 genomes]
rs227629	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227630	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227631	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227632	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227634	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227651	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227652	0.93[ASN][1000 genomes]
rs227653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227657	0.93[ASN][1000 genomes]
rs227658	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227659	0.93[ASN][1000 genomes]
rs2387365	0.83[ASN][1000 genomes]
rs2387366	0.88[ASN][1000 genomes]
rs2387572	0.88[ASN][1000 genomes]
rs2424691	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2892279	0.86[ASN][1000 genomes]
rs34419834	0.88[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4273288	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4527284	0.82[ASN][1000 genomes]
rs4539860	0.88[ASN][1000 genomes]
rs45468392	0.93[ASN][1000 genomes]
rs45556041	0.93[ASN][1000 genomes]
rs4813541	0.88[ASN][1000 genomes]
rs4813542	0.88[ASN][1000 genomes]
rs4815325	0.80[EUR][1000 genomes]
rs4815327	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815337	0.88[ASN][1000 genomes]
rs4815339	0.86[ASN][1000 genomes]
rs4815340	0.88[ASN][1000 genomes]
rs4815341	0.86[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4815355	0.88[ASN][1000 genomes]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs56312312	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57265446	0.95[ASN][1000 genomes]
rs58244398	0.97[ASN][1000 genomes]
rs6036976	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050134	0.83[ASN][1000 genomes]
rs6050177	0.86[ASN][1000 genomes]
rs6050179	0.86[ASN][1000 genomes]
rs6050181	0.86[ASN][1000 genomes]
rs6050198	0.85[CHB][hapmap]
rs6050201	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050249	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6050255	0.86[JPT][hapmap]
rs6050259	0.86[JPT][hapmap]
rs6050261	0.86[JPT][hapmap]
rs6083684	0.88[ASN][1000 genomes]
rs6083685	0.88[ASN][1000 genomes]
rs6083686	0.88[ASN][1000 genomes]
rs6083688	0.88[ASN][1000 genomes]
rs6083692	0.86[ASN][1000 genomes]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6106975	0.86[ASN][1000 genomes]
rs6106984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114988	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114992	0.82[ASN][1000 genomes]
rs6132773	0.88[ASN][1000 genomes]
rs6132774	0.88[ASN][1000 genomes]
rs6132775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132783	0.90[ASN][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132785	0.81[ASN][1000 genomes]
rs6132789	0.86[JPT][hapmap]
rs6138417	0.88[ASN][1000 genomes]
rs6138423	0.88[ASN][1000 genomes]
rs6138431	0.82[ASN][1000 genomes]
rs6138435	0.88[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6138438	0.93[ASN][1000 genomes]
rs6138442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6138455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138456	0.97[ASN][1000 genomes]
rs6138457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138460	0.90[ASN][1000 genomes]
rs6138461	0.87[ASN][1000 genomes]
rs6138463	0.85[ASN][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.86[JPT][hapmap]
rs62215110	0.93[ASN][1000 genomes]
rs62215115	0.93[ASN][1000 genomes]
rs62215128	0.97[ASN][1000 genomes]
rs62215131	0.97[ASN][1000 genomes]
rs6707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7268095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7269416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735886	0.88[ASN][1000 genomes]
rs8125909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs914314	0.83[ASN][1000 genomes]
rs926661	0.86[ASN][1000 genomes]
rs926662	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24974000-24977800	Enhancers	Placenta	Placenta
2	chr20:24974000-24979000	Enhancers	Duodenum Mucosa	Duodenum
3	chr20:24974000-24981000	Weak transcription	Psoas Muscle	Psoas
4	chr20:24974000-24985800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:24974000-24985800	Weak transcription	Thymus	Thymus
6	chr20:24974000-24986400	Weak transcription	Aorta	Aorta
7	chr20:24974200-24985200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr20:24974200-24985800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr20:24974200-24988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:24974400-24977600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:24974400-24977800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr20:24974400-24978600	Weak transcription	Small Intestine	intestine
13	chr20:24974400-24981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:24974400-24983200	Weak transcription	Primary T cells from cord blood	blood
15	chr20:24974400-24992000	Weak transcription	GM12878-XiMat	blood
16	chr20:24974600-24977200	Enhancers	Pancreas	Pancrea
17	chr20:24974600-24977200	Enhancers	A549	lung
18	chr20:24974800-24985800	Weak transcription	Spleen	Spleen
19	chr20:24975000-24977800	Enhancers	Left Ventricle	heart
20	chr20:24975200-24977200	Enhancers	Fetal Stomach	stomach
21	chr20:24975200-24978200	Enhancers	Right Ventricle	heart
22	chr20:24975200-24981400	Enhancers	Fetal Intestine Large	intestine
23	chr20:24975400-24978200	Enhancers	Fetal Heart	heart
24	chr20:24975600-24980400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:24975800-24977800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr20:24975800-24983200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr20:24975800-24986400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr20:24976000-24977400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr20:24976000-24977800	Enhancers	NHDF-Ad	bronchial
30	chr20:24976000-24978000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr20:24976000-24983200	Weak transcription	Primary B cells from cord blood	blood
32	chr20:24976000-24983200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr20:24976000-24983200	Weak transcription	Fetal Lung	lung
34	chr20:24976000-24983400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr20:24976000-24985000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr20:24976000-24985000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr20:24976000-24985800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr20:24976000-24985800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:24976000-24986000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr20:24976000-24986000	Weak transcription	Colonic Mucosa	Colon
41	chr20:24976000-24986400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr20:24976000-24986400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr20:24976000-24987600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr20:24976000-24988000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr20:24976200-24977200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr20:24976200-24977200	Enhancers	Brain Cingulate Gyrus	brain
48	chr20:24976200-24977400	Enhancers	Brain Angular Gyrus	brain
49	chr20:24976200-24977400	Enhancers	Brain Anterior Caudate	brain
50	chr20:24976200-24977400	Enhancers	Brain Hippocampus Middle	brain

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