Variant report

Variant	rs2273477
Chromosome Location	chr20:13463749-13463750
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1012242	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474954	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474956	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1474957	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1884796	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1884797	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1963182	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998123	0.95[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2001178	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057256	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057257	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070306	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070334	0.86[YRI][hapmap]
rs2327790	0.90[EUR][1000 genomes]
rs2327791	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2876357	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34590652	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761889	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3761890	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]
rs3789347	0.86[YRI][hapmap]
rs3803973	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827702	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827703	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813130	0.90[EUR][1000 genomes]
rs4813132	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4813134	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813135	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814233	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4814234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4814235	0.91[EUR][1000 genomes]
rs4814239	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814246	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs593846	0.81[EUR][1000 genomes]
rs6033705	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6033722	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033724	0.94[EUR][1000 genomes]
rs6033749	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042106	0.86[YRI][hapmap]
rs6042128	0.86[YRI][hapmap]
rs6042135	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs6042141	0.90[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6042162	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042188	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042192	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042195	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042211	0.90[CEU][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs6042218	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6042224	0.81[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap]
rs6074604	0.85[ASN][1000 genomes]
rs6074605	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6074610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6074616	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079035	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs6079042	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079043	0.85[ASN][1000 genomes]
rs6079048	0.88[ASN][1000 genomes]
rs6079049	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079062	0.87[ASN][1000 genomes]
rs6079063	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6079074	0.86[YRI][hapmap]
rs6079086	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079097	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079102	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079115	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6105087	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105118	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6105119	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109854	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]
rs6109858	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109861	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6109862	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6109918	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109923	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109935	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109946	0.86[EUR][1000 genomes]
rs6131471	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6134862	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6134870	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6134895	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6514411	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911014	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs932568	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13395600-13477800	Weak transcription	Gastric	stomach
2	chr20:13430000-13467800	Weak transcription	Ovary	ovary
3	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
4	chr20:13442600-13471600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr20:13442800-13467800	Weak transcription	Aorta	Aorta
6	chr20:13445400-13467800	Weak transcription	Fetal Stomach	stomach
7	chr20:13451600-13464200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr20:13454400-13471200	Weak transcription	Small Intestine	intestine
9	chr20:13455400-13463800	Strong transcription	Dnd41	blood
10	chr20:13457000-13471400	Weak transcription	Hela-S3	cervix
11	chr20:13457800-13466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr20:13458000-13470600	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:13458000-13471600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:13458600-13472600	Weak transcription	Psoas Muscle	Psoas
15	chr20:13458800-13464200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:13459400-13472000	Weak transcription	HSMMtube	muscle
17	chr20:13459600-13469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr20:13459600-13472600	Weak transcription	NH-A	brain
19	chr20:13459800-13465800	Weak transcription	Spleen	Spleen
20	chr20:13460200-13464000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:13460200-13471600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr20:13460400-13464000	Strong transcription	Liver	Liver
23	chr20:13460400-13464000	Strong transcription	Fetal Lung	lung
24	chr20:13460400-13464200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:13460400-13464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:13460400-13464200	Strong transcription	Fetal Thymus	thymus
27	chr20:13460600-13464200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr20:13460600-13464200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:13460600-13469800	Weak transcription	Fetal Brain Female	brain
30	chr20:13460600-13472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr20:13460800-13464000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr20:13460800-13464200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr20:13460800-13464200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr20:13460800-13464200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:13460800-13472000	Weak transcription	Brain Hippocampus Middle	brain
36	chr20:13460800-13472000	Weak transcription	NHEK	skin
37	chr20:13461000-13463800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr20:13461000-13463800	Strong transcription	HepG2	liver
39	chr20:13461000-13464000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr20:13461000-13464200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr20:13461000-13465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr20:13461200-13463800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr20:13461200-13463800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr20:13461200-13464000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr20:13461200-13464000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr20:13461200-13464000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr20:13461200-13464200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr20:13461200-13464200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr20:13461400-13463800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr20:13461400-13464000	Strong transcription	Fetal Kidney	kidney

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