Variant report

Variant	rs6138453
Chromosome Location	chr20:24972542-24972543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24972188..24974753-chr20:24992355..24994002,2	K562	blood:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:24972013..24974485-chr20:25388171..25390084,2	MCF-7	breast:
4	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
5	chr20:24972059..24974449-chr20:25176101..25177683,2	MCF-7	breast:
6	chr20:24971946..24973582-chr20:25227704..25229248,2	MCF-7	breast:
7	chr20:24971839..24974533-chr20:25228512..25230139,2	MCF-7	breast:
8	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction
ENSG00000154930	Chromatin interaction
ENSG00000100987	Chromatin interaction
ENSG00000101003	Chromatin interaction
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11087486	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11699285	0.80[EUR][1000 genomes]
rs11700073	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11905625	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11906373	0.88[ASN][1000 genomes]
rs12625319	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13041643	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535042	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2008275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092565	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2103736	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2151462	0.88[ASN][1000 genomes]
rs2151463	0.88[ASN][1000 genomes]
rs2179729	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179730	0.93[ASN][1000 genomes]
rs2179732	1.00[JPT][hapmap]
rs2206891	0.87[ASN][1000 genomes]
rs2225459	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235847	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227613	0.84[ASN][1000 genomes]
rs227614	0.86[ASN][1000 genomes]
rs227615	0.82[ASN][1000 genomes]
rs227616	0.88[ASN][1000 genomes]
rs227618	0.81[ASN][1000 genomes]
rs227619	0.86[ASN][1000 genomes]
rs227620	0.86[ASN][1000 genomes]
rs227621	0.88[ASN][1000 genomes]
rs227622	0.88[ASN][1000 genomes]
rs227623	0.86[ASN][1000 genomes]
rs227624	0.88[ASN][1000 genomes]
rs227625	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs227626	0.86[ASN][1000 genomes]
rs227627	0.86[ASN][1000 genomes]
rs227628	0.86[ASN][1000 genomes]
rs227629	0.88[ASN][1000 genomes]
rs227630	0.88[ASN][1000 genomes]
rs227631	0.88[ASN][1000 genomes]
rs227632	0.88[ASN][1000 genomes]
rs227633	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227634	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227635	0.86[ASN][1000 genomes]
rs227639	0.86[ASN][1000 genomes]
rs227643	0.86[ASN][1000 genomes]
rs227646	0.86[ASN][1000 genomes]
rs227648	0.86[ASN][1000 genomes]
rs227650	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227651	0.88[ASN][1000 genomes]
rs227652	0.86[ASN][1000 genomes]
rs227653	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs227657	0.86[ASN][1000 genomes]
rs227658	0.88[ASN][1000 genomes]
rs227659	0.86[ASN][1000 genomes]
rs2387366	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2387572	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424691	0.88[ASN][1000 genomes]
rs2892279	0.93[ASN][1000 genomes]
rs34419834	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3746330	1.00[JPT][hapmap]
rs4527284	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4539860	0.81[ASN][1000 genomes]
rs45468392	0.86[ASN][1000 genomes]
rs45556041	0.86[ASN][1000 genomes]
rs4594518	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4813541	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813542	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815337	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815339	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4815340	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815341	0.93[ASN][1000 genomes]
rs4815351	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4815355	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4815357	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56312312	0.93[ASN][1000 genomes]
rs57265446	0.88[ASN][1000 genomes]
rs58244398	0.91[ASN][1000 genomes]
rs6050177	0.93[ASN][1000 genomes]
rs6050179	0.93[ASN][1000 genomes]
rs6050181	0.93[ASN][1000 genomes]
rs6050198	1.00[CHB][hapmap]
rs6050201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6050249	1.00[JPT][hapmap]
rs6050255	0.86[JPT][hapmap]
rs6050259	0.86[JPT][hapmap]
rs6050261	0.86[JPT][hapmap]
rs6083684	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083685	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083686	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083688	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083692	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083699	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106975	0.93[ASN][1000 genomes]
rs6106984	0.93[ASN][1000 genomes]
rs6114980	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114981	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114984	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6114988	0.93[ASN][1000 genomes]
rs6114992	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6132773	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132774	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132775	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132777	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132778	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6132783	0.84[ASN][1000 genomes]
rs6132784	1.00[JPT][hapmap]
rs6132789	0.86[JPT][hapmap]
rs6138406	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138417	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138423	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138425	0.81[AFR][1000 genomes]
rs6138426	0.84[AFR][1000 genomes]
rs6138431	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138435	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138437	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138438	0.86[ASN][1000 genomes]
rs6138442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138455	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138456	0.91[ASN][1000 genomes]
rs6138457	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138458	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6138460	0.84[ASN][1000 genomes]
rs6138461	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138466	1.00[JPT][hapmap]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.86[JPT][hapmap]
rs62215110	0.86[ASN][1000 genomes]
rs62215115	0.86[ASN][1000 genomes]
rs62215128	0.91[ASN][1000 genomes]
rs62215131	0.91[ASN][1000 genomes]
rs6707	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7268095	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7269416	0.93[ASN][1000 genomes]
rs735886	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8125909	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8183891	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926661	0.93[ASN][1000 genomes]
rs926662	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24961600-24972600	Weak transcription	Aorta	Aorta
2	chr20:24962200-24972600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:24962800-24972600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:24962800-24972600	Weak transcription	Ovary	ovary
5	chr20:24968400-24972600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:24971000-24972600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr20:24971000-24972800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr20:24971000-24972800	Flanking Active TSS	Dnd41	blood
9	chr20:24971000-24973200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr20:24971000-24974200	Active TSS	Right Atrium	heart
11	chr20:24971200-24973600	Active TSS	Liver	Liver
12	chr20:24971400-24972800	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr20:24971400-24973000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr20:24971600-24972600	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr20:24971600-24972600	Enhancers	Left Ventricle	heart
16	chr20:24971600-24972600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr20:24971600-24972600	Enhancers	Small Intestine	intestine
18	chr20:24971600-24972800	Flanking Active TSS	Hela-S3	cervix
19	chr20:24971600-24973000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr20:24971600-24973200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr20:24971600-24973200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr20:24971600-24973200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr20:24971800-24972600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:24971800-24972600	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr20:24971800-24972600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr20:24971800-24972600	Enhancers	Esophagus	oesophagus
27	chr20:24971800-24972600	Enhancers	Pancreas	Pancrea
28	chr20:24971800-24972600	Enhancers	Stomach Mucosa	stomach
29	chr20:24971800-24972600	Enhancers	Spleen	Spleen
30	chr20:24971800-24972800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr20:24971800-24972800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr20:24971800-24972800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr20:24971800-24972800	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr20:24971800-24972800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr20:24971800-24972800	Flanking Active TSS	Fetal Brain Female	brain
36	chr20:24971800-24972800	Flanking Active TSS	HMEC	breast
37	chr20:24971800-24973000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr20:24971800-24973000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr20:24971800-24973800	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr20:24971800-24974000	Active TSS	H1 Cell Line	embryonic stem cell
41	chr20:24972000-24972600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr20:24972000-24972600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:24972000-24972600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
44	chr20:24972000-24972600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr20:24972000-24972600	Enhancers	Primary B cells from peripheral blood	blood
46	chr20:24972000-24972600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr20:24972000-24972600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:24972000-24972600	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr20:24972000-24972600	Enhancers	Gastric	stomach
50	chr20:24972000-24972600	Flanking Active TSS	A549	lung

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