Variant report

Variant	rs6079042
Chromosome Location	chr20:13378117-13378118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1012242	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1474954	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1474955	0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1474956	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474957	0.87[ASN][1000 genomes]
rs1963182	0.80[ASN][1000 genomes]
rs2001178	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2057256	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2070306	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs2273477	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2876344	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2876357	0.83[ASN][1000 genomes]
rs3761889	0.83[ASN][1000 genomes]
rs3761890	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[ASN][1000 genomes]
rs3803973	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3827702	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3827703	0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4813126	0.83[ASN][1000 genomes]
rs4813132	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4813134	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4813135	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4814233	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4814234	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4814239	0.83[ASN][1000 genomes]
rs4814246	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs518981	0.83[ASN][1000 genomes]
rs527865	0.83[ASN][1000 genomes]
rs529646	0.84[ASN][1000 genomes]
rs591089	0.83[ASN][1000 genomes]
rs593846	0.81[ASN][1000 genomes]
rs6033685	0.81[ASN][1000 genomes]
rs6033686	0.81[ASN][1000 genomes]
rs6033705	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6033722	0.85[ASN][1000 genomes]
rs6033749	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6033756	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042059	0.81[ASN][1000 genomes]
rs6042162	0.84[ASN][1000 genomes]
rs6042188	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042192	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6042195	0.81[ASN][1000 genomes]
rs6042218	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs6074604	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6074605	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074610	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074616	0.83[ASN][1000 genomes]
rs6079032	0.89[ASN][1000 genomes]
rs6079035	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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079048	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079049	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6079062	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079063	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079086	0.82[ASN][1000 genomes]
rs6079097	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6079115	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs608239	0.83[ASN][1000 genomes]
rs6105087	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6105118	0.83[ASN][1000 genomes]
rs6105119	0.83[ASN][1000 genomes]
rs6109847	0.87[ASN][1000 genomes]
rs6109854	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6109858	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6109861	0.82[ASN][1000 genomes]
rs6109862	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109918	0.83[ASN][1000 genomes]
rs6109923	0.83[ASN][1000 genomes]
rs6109935	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6131471	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134862	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134870	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134895	0.83[ASN][1000 genomes]
rs6514411	0.81[ASN][1000 genomes]
rs7265499	0.89[ASN][1000 genomes]
rs743183	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs911014	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs932568	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]

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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13362800-13380600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
3	chr20:13364600-13379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr20:13367200-13378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr20:13368600-13378400	Weak transcription	GM12878-XiMat	blood
7	chr20:13368600-13382400	Weak transcription	HMEC	breast
8	chr20:13368600-13397400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:13368800-13392200	Weak transcription	Aorta	Aorta
10	chr20:13369000-13411200	Strong transcription	Dnd41	blood
11	chr20:13369400-13380200	Weak transcription	Psoas Muscle	Psoas
12	chr20:13369400-13397000	Weak transcription	Primary B cells from cord blood	blood
13	chr20:13369400-13397200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr20:13369600-13397000	Weak transcription	Fetal Thymus	thymus
15	chr20:13370000-13378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:13370000-13382400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:13371400-13413600	Weak transcription	Ovary	ovary
18	chr20:13371800-13397200	Weak transcription	Primary T cells from cord blood	blood
19	chr20:13372000-13382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:13372000-13395800	Weak transcription	HepG2	liver
21	chr20:13372000-13396400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr20:13372000-13397400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr20:13372000-13397400	Weak transcription	Left Ventricle	heart
24	chr20:13372000-13397400	Weak transcription	Thymus	Thymus
25	chr20:13372200-13381400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:13374200-13380600	Weak transcription	Spleen	Spleen
27	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr20:13374400-13380400	Weak transcription	Fetal Lung	lung
29	chr20:13374400-13382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:13374400-13382800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr20:13374400-13384000	Weak transcription	Pancreas	Pancrea
32	chr20:13374400-13410800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr20:13374600-13397400	Weak transcription	Fetal Intestine Small	intestine
34	chr20:13374600-13399400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr20:13374600-13405800	Weak transcription	Fetal Stomach	stomach
36	chr20:13375800-13378800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:13375800-13379200	Enhancers	HSMM	muscle
38	chr20:13375800-13379400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:13376000-13379200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:13376400-13378800	Enhancers	HSMMtube	muscle
41	chr20:13376400-13379000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr20:13376600-13378400	Enhancers	Stomach Smooth Muscle	stomach
43	chr20:13376600-13378600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr20:13376800-13378200	Enhancers	Fetal Heart	heart
45	chr20:13376800-13378600	Enhancers	Osteobl	bone
46	chr20:13376800-13381600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:13377200-13379000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr20:13377400-13379400	Enhancers	Colon Smooth Muscle	Colon
49	chr20:13377600-13378800	Enhancers	Rectal Smooth Muscle	rectum
50	chr20:13377800-13378600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links