Variant report

Variant	rs2876344
Chromosome Location	chr20:13367308-13367309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1012242	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1151919	0.82[ASN][1000 genomes]
rs1474954	0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs1474955	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1474956	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2001178	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2057256	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2070306	0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs2273477	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs3761890	0.87[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap]
rs3803973	0.81[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs3827702	0.95[CHB][hapmap]
rs3827703	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4813126	0.93[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];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4814233	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4814234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4814246	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs518981	0.91[ASN][1000 genomes]
rs527865	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs529646	0.92[ASN][1000 genomes]
rs591089	0.91[ASN][1000 genomes]
rs593846	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033685	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6033686	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6033687	0.87[ASN][1000 genomes]
rs6033688	0.86[ASN][1000 genomes]
rs6033705	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6033749	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap]
rs6033756	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap]
rs6042059	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042188	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs6042192	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs6042218	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs6074604	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074605	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs6074610	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6079032	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6079035	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079037	0.86[ASN][1000 genomes]
rs6079042	0.93[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079043	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079048	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6079049	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6079062	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6079063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6079097	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs6079115	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs608239	0.91[ASN][1000 genomes]
rs6105087	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs6109847	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109854	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6109858	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6109862	0.93[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6109935	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs6131471	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134862	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134870	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657719	0.80[ASN][1000 genomes]
rs7265499	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743183	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs911014	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs932568	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.82[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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13360200-13368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:13361800-13369400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr20:13362400-13368200	Weak transcription	Primary B cells from cord blood	blood
4	chr20:13362400-13370600	Weak transcription	HepG2	liver
5	chr20:13362600-13374000	Weak transcription	Fetal Lung	lung
6	chr20:13362600-13376800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:13362800-13368000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:13362800-13368200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:13362800-13368400	Weak transcription	A549	lung
10	chr20:13362800-13368400	Weak transcription	NHEK	skin
11	chr20:13362800-13380600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:13363200-13377400	Weak transcription	Fetal Brain Female	brain
13	chr20:13363400-13373200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr20:13363600-13375800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:13363600-13375800	Weak transcription	HSMMtube	muscle
16	chr20:13363800-13368000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr20:13363800-13368800	Weak transcription	Fetal Kidney	kidney
18	chr20:13363800-13373400	Weak transcription	Liver	Liver
19	chr20:13363800-13376200	Weak transcription	Fetal Muscle Leg	muscle
20	chr20:13364000-13368000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr20:13364000-13368200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:13364000-13377400	Weak transcription	Brain Angular Gyrus	brain
23	chr20:13364200-13368400	Weak transcription	HMEC	breast
24	chr20:13364400-13368600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr20:13364400-13370800	Weak transcription	Fetal Intestine Small	intestine
26	chr20:13364400-13371000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr20:13364400-13376400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
29	chr20:13364600-13367600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:13364600-13368200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:13364600-13368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr20:13364600-13368600	Strong transcription	Dnd41	blood
33	chr20:13364600-13371800	Strong transcription	Primary T cells from cord blood	blood
34	chr20:13364600-13374200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:13364600-13379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr20:13364800-13368400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr20:13364800-13375400	Weak transcription	Colonic Mucosa	Colon
39	chr20:13364800-13377600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr20:13365200-13367600	Weak transcription	Fetal Thymus	thymus
41	chr20:13365400-13367400	Strong transcription	Pancreas	Pancrea
42	chr20:13365400-13368400	Weak transcription	GM12878-XiMat	blood
43	chr20:13365400-13373000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr20:13365400-13375800	Weak transcription	HSMM	muscle
45	chr20:13365600-13367600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:13365600-13368200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr20:13365600-13369400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr20:13365600-13370400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:13365600-13376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:13365800-13367400	Weak transcription	Primary T cells fromperipheralblood	blood

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