Variant report

Variant	rs6109854
Chromosome Location	chr20:13381995-13381996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1012242	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474954	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474955	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474956	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1474957	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1884796	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1884797	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1963182	0.86[EUR][1000 genomes]
rs1998123	0.90[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2001178	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2057256	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2057257	0.82[EUR][1000 genomes]
rs2070306	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2273477	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2327790	0.84[EUR][1000 genomes]
rs2327791	0.84[EUR][1000 genomes]
rs2876344	0.85[ASN][1000 genomes]
rs2876357	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761889	0.81[ASN][1000 genomes]
rs3761890	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3803973	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3827702	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827703	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4813130	0.87[EUR][1000 genomes]
rs4813132	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4813134	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs4813135	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4814233	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4814234	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4814235	0.88[EUR][1000 genomes]
rs4814239	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4814246	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs527865	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs593846	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033705	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033722	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6033724	0.88[EUR][1000 genomes]
rs6033749	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs6033756	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6042135	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6042141	0.85[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6042162	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042188	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6042192	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042195	0.82[EUR][1000 genomes]
rs6042211	0.85[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6042218	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6074604	0.95[ASN][1000 genomes]
rs6074605	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074610	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6074616	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6079032	0.85[ASN][1000 genomes]
rs6079035	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap]
rs6079042	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6079043	0.95[ASN][1000 genomes]
rs6079048	0.88[ASN][1000 genomes]
rs6079049	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079062	0.90[ASN][1000 genomes]
rs6079063	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6079086	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6079097	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6079102	0.81[AMR][1000 genomes]
rs6079115	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6105087	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105118	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6105119	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109847	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6109858	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109861	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6109862	0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6109918	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109923	0.81[ASN][1000 genomes]
rs6109935	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6109946	0.82[EUR][1000 genomes]
rs6131471	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6134862	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6134870	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6134895	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6514411	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7265499	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743183	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs911014	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs932568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
2	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13368600-13382400	Weak transcription	HMEC	breast
4	chr20:13368600-13397400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:13368800-13392200	Weak transcription	Aorta	Aorta
6	chr20:13369000-13411200	Strong transcription	Dnd41	blood
7	chr20:13369400-13397000	Weak transcription	Primary B cells from cord blood	blood
8	chr20:13369400-13397200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:13369600-13397000	Weak transcription	Fetal Thymus	thymus
10	chr20:13370000-13382400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:13371400-13413600	Weak transcription	Ovary	ovary
12	chr20:13371800-13397200	Weak transcription	Primary T cells from cord blood	blood
13	chr20:13372000-13382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:13372000-13395800	Weak transcription	HepG2	liver
15	chr20:13372000-13396400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr20:13372000-13397400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr20:13372000-13397400	Weak transcription	Left Ventricle	heart
18	chr20:13372000-13397400	Weak transcription	Thymus	Thymus
19	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr20:13374400-13382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:13374400-13382800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr20:13374400-13384000	Weak transcription	Pancreas	Pancrea
23	chr20:13374400-13410800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr20:13374600-13397400	Weak transcription	Fetal Intestine Small	intestine
25	chr20:13374600-13399400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:13374600-13405800	Weak transcription	Fetal Stomach	stomach
27	chr20:13377800-13382400	Weak transcription	NHDF-Ad	bronchial
28	chr20:13378600-13382000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr20:13379000-13410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:13379200-13382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:13379200-13463000	Weak transcription	HSMM	muscle
32	chr20:13379400-13382400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr20:13380800-13397600	Weak transcription	Fetal Lung	lung
34	chr20:13381600-13382200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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