Variant report

Variant	rs6109918
Chromosome Location	chr20:13490703-13490704
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1012242	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474954	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474955	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474956	0.90[ASN][1000 genomes]
rs1474957	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1884796	0.89[EUR][1000 genomes]
rs1884797	0.89[EUR][1000 genomes]
rs1963182	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998123	0.91[EUR][1000 genomes]
rs2001178	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057256	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057257	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070306	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273477	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327790	0.93[EUR][1000 genomes]
rs2327791	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2876357	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34590652	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761889	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3761890	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803973	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827702	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827703	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813130	0.90[EUR][1000 genomes]
rs4813134	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813135	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814233	0.89[ASN][1000 genomes]
rs4814234	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4814235	0.88[EUR][1000 genomes]
rs4814239	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814246	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593846	0.81[EUR][1000 genomes]
rs6033705	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033722	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033724	0.90[EUR][1000 genomes]
rs6033749	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6033756	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042135	0.90[EUR][1000 genomes]
rs6042141	0.92[EUR][1000 genomes]
rs6042162	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042188	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042192	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042211	0.90[EUR][1000 genomes]
rs6042218	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074604	0.82[ASN][1000 genomes]
rs6074605	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6074610	0.90[ASN][1000 genomes]
rs6074616	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079042	0.83[ASN][1000 genomes]
rs6079043	0.82[ASN][1000 genomes]
rs6079048	0.87[ASN][1000 genomes]
rs6079049	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079062	0.84[ASN][1000 genomes]
rs6079063	0.84[ASN][1000 genomes]
rs6079086	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079097	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079102	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079115	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6105087	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105119	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109854	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109858	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109861	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6109862	0.88[ASN][1000 genomes]
rs6109923	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109935	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109946	0.90[EUR][1000 genomes]
rs6131471	0.88[ASN][1000 genomes]
rs6134862	0.87[ASN][1000 genomes]
rs6134870	0.84[ASN][1000 genomes]
rs6134895	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514411	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs743183	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911014	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs932568	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13464000-13493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:13473400-13505800	Weak transcription	HSMM	muscle
5	chr20:13474400-13496800	Weak transcription	Pancreas	Pancrea
6	chr20:13478200-13503800	Weak transcription	Gastric	stomach
7	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr20:13483800-13493600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:13483800-13493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:13484000-13493800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:13484000-13493800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:13484000-13493800	Weak transcription	Fetal Thymus	thymus
13	chr20:13484000-13495800	Weak transcription	Thymus	Thymus
14	chr20:13484000-13499000	Weak transcription	Aorta	Aorta
15	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
17	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
18	chr20:13484200-13493600	Weak transcription	Fetal Intestine Small	intestine
19	chr20:13484200-13493800	Weak transcription	Primary B cells from cord blood	blood
20	chr20:13484200-13496800	Weak transcription	Left Ventricle	heart
21	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
23	chr20:13485400-13493800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr20:13485800-13497400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr20:13486200-13493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
28	chr20:13488200-13502600	Weak transcription	Lung	lung
29	chr20:13488200-13502600	Weak transcription	Ovary	ovary
30	chr20:13488600-13494000	Weak transcription	Adipose Nuclei	Adipose
31	chr20:13488600-13496800	Weak transcription	NHEK	skin
32	chr20:13489000-13493800	Weak transcription	A549	lung
33	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
36	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr20:13489400-13493800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr20:13489600-13492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr20:13489600-13497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:13489600-13499000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:13490400-13491600	Strong transcription	Dnd41	blood
42	chr20:13490400-13502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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