Variant report

Variant	rs6079035
Chromosome Location	chr20:13368741-13368742
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1012242	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1151919	0.85[ASN][1000 genomes]
rs1474954	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1474955	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1474956	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474957	0.82[ASN][1000 genomes]
rs2001178	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2057256	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2070306	0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs2273477	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs2876344	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761890	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap]
rs3803973	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs3827702	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3827703	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4813126	0.97[ASN][1000 genomes]
rs4813132	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4813134	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4813135	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs4814233	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4814234	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4814246	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs518981	0.95[ASN][1000 genomes]
rs527865	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs529646	0.96[ASN][1000 genomes]
rs591089	0.95[ASN][1000 genomes]
rs593846	0.92[ASN][1000 genomes]
rs6033685	0.93[ASN][1000 genomes]
rs6033686	0.86[ASN][1000 genomes]
rs6033687	0.91[ASN][1000 genomes]
rs6033688	0.91[ASN][1000 genomes]
rs6033705	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs6033749	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs6033756	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs6042059	0.86[ASN][1000 genomes]
rs6042188	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6042192	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs6042218	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs6074604	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6074605	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6074610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079032	0.94[ASN][1000 genomes]
rs6079037	0.82[ASN][1000 genomes]
rs6079042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6079043	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079048	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6079049	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6079062	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6079063	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6079097	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs6079115	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs608239	0.95[ASN][1000 genomes]
rs6105087	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6109847	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109854	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap]
rs6109858	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6109862	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6109935	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6131471	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134862	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134870	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs657719	0.84[ASN][1000 genomes]
rs7265499	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs743183	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs911014	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs932568	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13361800-13369400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:13362400-13370600	Weak transcription	HepG2	liver
3	chr20:13362600-13374000	Weak transcription	Fetal Lung	lung
4	chr20:13362600-13376800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:13362800-13380600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:13363200-13377400	Weak transcription	Fetal Brain Female	brain
7	chr20:13363400-13373200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:13363600-13375800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:13363600-13375800	Weak transcription	HSMMtube	muscle
10	chr20:13363800-13368800	Weak transcription	Fetal Kidney	kidney
11	chr20:13363800-13373400	Weak transcription	Liver	Liver
12	chr20:13363800-13376200	Weak transcription	Fetal Muscle Leg	muscle
13	chr20:13364000-13377400	Weak transcription	Brain Angular Gyrus	brain
14	chr20:13364400-13370800	Weak transcription	Fetal Intestine Small	intestine
15	chr20:13364400-13371000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr20:13364400-13376400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
18	chr20:13364600-13371800	Strong transcription	Primary T cells from cord blood	blood
19	chr20:13364600-13374200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr20:13364600-13379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr20:13364800-13375400	Weak transcription	Colonic Mucosa	Colon
23	chr20:13364800-13377600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr20:13365400-13373000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr20:13365400-13375800	Weak transcription	HSMM	muscle
26	chr20:13365600-13369400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr20:13365600-13370400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:13365600-13376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:13366000-13368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:13366200-13370800	Weak transcription	Lung	lung
31	chr20:13366200-13373600	Weak transcription	Brain Hippocampus Middle	brain
32	chr20:13366200-13373800	Weak transcription	Esophagus	oesophagus
33	chr20:13366600-13370600	Weak transcription	Gastric	stomach
34	chr20:13366600-13375600	Weak transcription	Fetal Intestine Large	intestine
35	chr20:13366800-13370600	Weak transcription	Adipose Nuclei	Adipose
36	chr20:13366800-13375800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:13367000-13368800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:13367000-13370600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr20:13367000-13370800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr20:13367200-13378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:13367400-13369800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr20:13367600-13369600	Strong transcription	Fetal Thymus	thymus
43	chr20:13367600-13372000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr20:13367600-13373800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr20:13368000-13372200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr20:13368000-13376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr20:13368200-13368800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:13368200-13368800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:13368200-13369400	Strong transcription	Primary B cells from cord blood	blood
50	chr20:13368200-13369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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