Variant report

Variant	rs3761890
Chromosome Location	chr20:13509263-13509264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1012242	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474954	0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1474955	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1474956	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1474957	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1963182	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1998123	0.85[TSI][hapmap]
rs2001178	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2057256	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2057257	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070306	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273477	0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327791	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2876357	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34590652	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3761889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803973	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3827702	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827703	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4813132	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4813134	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813135	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4814233	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4814234	0.87[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4814239	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4814246	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6033705	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6033722	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033749	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033756	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042141	0.83[TSI][hapmap]
rs6042162	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6042188	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042192	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042195	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6042211	0.85[TSI][hapmap]
rs6042218	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074604	0.82[ASN][1000 genomes]
rs6074605	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6074610	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6074616	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079035	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap]
rs6079042	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[ASN][1000 genomes]
rs6079043	0.82[ASN][1000 genomes]
rs6079048	0.86[ASN][1000 genomes]
rs6079049	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6079062	0.84[ASN][1000 genomes]
rs6079063	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs6079086	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079097	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079102	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6079115	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6105087	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6105118	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105119	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6109854	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6109858	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6109861	0.80[ASN][1000 genomes]
rs6109862	0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6109918	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109923	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109935	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131471	0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6134862	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6134870	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6134895	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6514411	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743183	0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs910969	0.90[EUR][1000 genomes]
rs911014	0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs932568	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.85[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	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv912687	chr20:13507057-13591596	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
2	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
3	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr20:13493600-13510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr20:13494000-13512400	Weak transcription	Placenta	Placenta
9	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr20:13494200-13516000	Weak transcription	Colonic Mucosa	Colon
11	chr20:13494400-13514800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:13494600-13516400	Weak transcription	Esophagus	oesophagus
13	chr20:13495400-13511000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:13495800-13515000	Weak transcription	Fetal Brain Male	brain
15	chr20:13496000-13520200	Weak transcription	HSMMtube	muscle
16	chr20:13496200-13512400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr20:13496800-13509800	Weak transcription	Brain Substantia Nigra	brain
18	chr20:13497200-13509600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
20	chr20:13499200-13514600	Weak transcription	Brain Angular Gyrus	brain
21	chr20:13499800-13512800	Weak transcription	Colon Smooth Muscle	Colon
22	chr20:13501200-13514600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:13502400-13516400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr20:13502600-13509800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr20:13502600-13509800	Strong transcription	Fetal Thymus	thymus
26	chr20:13502800-13512200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:13502800-13519200	Weak transcription	Lung	lung
28	chr20:13503000-13509800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:13503000-13537600	Weak transcription	Psoas Muscle	Psoas
30	chr20:13503000-13538200	Weak transcription	Ovary	ovary
31	chr20:13503200-13509400	Weak transcription	Fetal Brain Female	brain
32	chr20:13504200-13527000	Strong transcription	Dnd41	blood
33	chr20:13504600-13509600	Weak transcription	K562	blood
34	chr20:13504600-13516200	Weak transcription	Brain Hippocampus Middle	brain
35	chr20:13505800-13509600	Strong transcription	Liver	Liver
36	chr20:13505800-13509600	Weak transcription	Brain Anterior Caudate	brain
37	chr20:13505800-13517000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr20:13506000-13517200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:13506400-13509800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr20:13506400-13510600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:13506400-13516800	Weak transcription	NH-A	brain
42	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr20:13506600-13509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr20:13506600-13514600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr20:13506600-13516000	Weak transcription	HUVEC	blood vessel
46	chr20:13506600-13517800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr20:13506800-13510800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr20:13507000-13509800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr20:13507000-13515800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr20:13507400-13514600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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