Variant report

Variant	rs6138473
Chromosome Location	chr20:25012155-25012156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1007881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1056036	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs11700073	0.86[JPT][hapmap]
rs11905625	0.86[JPT][hapmap]
rs1535042	0.86[JPT][hapmap]
rs2008275	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2179732	0.88[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs227625	0.86[JPT][hapmap]
rs227633	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs227634	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs227650	0.85[JPT][hapmap]
rs227653	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3746330	0.88[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4815351	0.86[JPT][hapmap]
rs4815357	0.86[JPT][hapmap]
rs6037010	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050201	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050249	0.86[JPT][hapmap]
rs6050255	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050263	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6083699	0.86[JPT][hapmap]
rs6083709	0.86[JPT][hapmap]
rs60849220	0.91[ASN][1000 genomes]
rs6114980	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6114981	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6114984	0.84[JPT][hapmap]
rs6132775	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6132777	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6132778	0.86[JPT][hapmap]
rs6132784	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6132785	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6132788	0.91[ASN][1000 genomes]
rs6132789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132790	0.87[ASN][1000 genomes]
rs6138437	0.86[JPT][hapmap]
rs6138442	0.86[JPT][hapmap]
rs6138453	0.86[JPT][hapmap]
rs6138455	0.86[JPT][hapmap]
rs6138457	0.86[JPT][hapmap]
rs6138458	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138466	0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6138474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138475	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138476	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62217173	0.87[ASN][1000 genomes]
rs62217174	0.87[ASN][1000 genomes]
rs62217175	0.87[ASN][1000 genomes]
rs6707	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs7268095	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs7273518	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8125909	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs8183891	0.86[JPT][hapmap]

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	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6138473	PYGB	cis	parietal	SCAN
rs6138473	CST7	cis	Whole Blood	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24986200-25012400	Strong transcription	Dnd41	blood
2	chr20:24986400-25012400	Weak transcription	Fetal Brain Male	brain
3	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr20:24993800-25013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:24994000-25013000	Weak transcription	Small Intestine	intestine
6	chr20:24994800-25013200	Weak transcription	Fetal Brain Female	brain
7	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
10	chr20:24998600-25016600	Weak transcription	Liver	Liver
11	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr20:25002000-25013800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr20:25003800-25012600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:25004000-25012200	Weak transcription	Fetal Heart	heart
15	chr20:25004000-25012600	Weak transcription	Colonic Mucosa	Colon
16	chr20:25004600-25013000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:25004600-25013000	Weak transcription	Fetal Thymus	thymus
18	chr20:25004800-25016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr20:25005000-25012400	Weak transcription	Stomach Mucosa	stomach
20	chr20:25005000-25012600	Weak transcription	Adipose Nuclei	Adipose
21	chr20:25006400-25012400	Weak transcription	Ovary	ovary
22	chr20:25007200-25012200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr20:25007600-25012600	Weak transcription	Right Atrium	heart
24	chr20:25007600-25014000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:25007800-25013400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr20:25007800-25014800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr20:25008400-25013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:25008600-25012200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:25008600-25013800	Weak transcription	Fetal Kidney	kidney
30	chr20:25009200-25014000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:25009200-25016600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr20:25009400-25012800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr20:25010000-25012600	Enhancers	Brain Angular Gyrus	brain
34	chr20:25010000-25012600	Enhancers	Brain Cingulate Gyrus	brain
35	chr20:25010000-25012600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr20:25010000-25012600	Enhancers	HepG2	liver
37	chr20:25010000-25017800	Weak transcription	NHDF-Ad	bronchial
38	chr20:25010200-25015000	Strong transcription	Primary T cells from cord blood	blood
39	chr20:25010600-25012200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr20:25010600-25012400	Strong transcription	Fetal Stomach	stomach
41	chr20:25010600-25013000	Genic enhancers	Pancreas	Pancrea
42	chr20:25010600-25014800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr20:25010800-25012600	Strong transcription	Primary B cells from cord blood	blood
44	chr20:25010800-25012800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr20:25011000-25012600	Enhancers	Brain Germinal Matrix	brain
46	chr20:25011000-25013000	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr20:25011200-25012800	Enhancers	Brain Substantia Nigra	brain
48	chr20:25011200-25014800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr20:25011200-25015200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr20:25011400-25012600	Weak transcription	Fetal Lung	lung

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