Variant report

Variant	rs6050255
Chromosome Location	chr20:25007089-25007090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1007881	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[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	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.98[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	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4815351	0.86[JPT][hapmap]
rs4815357	0.86[JPT][hapmap]
rs6037010	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050201	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050249	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6050259	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050263	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6132785	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6132788	0.91[ASN][1000 genomes]
rs6132789	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[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	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6138473	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]
rs6138474	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[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	0.83[AMR][1000 genomes];0.94[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	0.90[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: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	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6050255	PYGB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24983200-25007800	Strong transcription	Primary T cells from cord blood	blood
2	chr20:24983200-25008200	Strong transcription	Primary B cells from cord blood	blood
3	chr20:24985200-25007800	Strong transcription	Fetal Muscle Leg	muscle
4	chr20:24985800-25007600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:24985800-25007800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr20:24986200-25012400	Strong transcription	Dnd41	blood
7	chr20:24986400-25012400	Weak transcription	Fetal Brain Male	brain
8	chr20:24987600-25007800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:24993800-25013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:24994000-25013000	Weak transcription	Small Intestine	intestine
12	chr20:24994800-25013200	Weak transcription	Fetal Brain Female	brain
13	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr20:24996200-25010200	Weak transcription	Colon Smooth Muscle	Colon
15	chr20:24996600-25007800	Genic enhancers	Placenta	Placenta
16	chr20:24997200-25007400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr20:24997400-25007800	Strong transcription	Fetal Stomach	stomach
19	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
20	chr20:24998600-25011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:24998600-25016600	Weak transcription	Liver	Liver
22	chr20:24998800-25010200	Weak transcription	Fetal Lung	lung
23	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr20:25002000-25011000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:25002000-25013800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr20:25002200-25007600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr20:25002200-25008400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:25002200-25011000	Weak transcription	Brain Germinal Matrix	brain
29	chr20:25002400-25010600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr20:25003400-25007200	Genic enhancers	Lung	lung
31	chr20:25003400-25007800	Genic enhancers	Right Ventricle	heart
32	chr20:25003800-25007200	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr20:25003800-25010800	Weak transcription	Aorta	Aorta
34	chr20:25003800-25012600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:25004000-25007600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr20:25004000-25010600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr20:25004000-25012200	Weak transcription	Fetal Heart	heart
38	chr20:25004000-25012600	Weak transcription	Colonic Mucosa	Colon
39	chr20:25004400-25010000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr20:25004600-25013000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr20:25004600-25013000	Weak transcription	Fetal Thymus	thymus
42	chr20:25004800-25007800	Strong transcription	Fetal Intestine Small	intestine
43	chr20:25004800-25008800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr20:25004800-25010800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr20:25004800-25011000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr20:25004800-25016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr20:25005000-25007600	Enhancers	Right Atrium	heart
48	chr20:25005000-25007800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr20:25005000-25010800	Weak transcription	Esophagus	oesophagus
50	chr20:25005000-25011200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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