Variant report

Variant	rs2182708
Chromosome Location	chr20:13489317-13489318
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13039162	0.93[ASN][1000 genomes]
rs13042843	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057258	0.84[ASN][1000 genomes]
rs2070305	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070334	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073324	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2103972	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2208207	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2208208	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273480	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747931	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789342	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789347	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789348	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789349	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813131	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814236	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814238	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814242	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57218913	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042106	0.88[ASN][1000 genomes]
rs6042128	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042153	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042225	0.81[AFR][1000 genomes]
rs6074611	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074612	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074613	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074627	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6079066	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079072	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079074	0.94[ASN][1000 genomes]
rs6079075	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6079077	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079085	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079095	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079106	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6105096	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6105098	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105103	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6105113	0.92[ASN][1000 genomes]
rs6109887	0.91[ASN][1000 genomes]
rs6109891	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109903	0.88[ASN][1000 genomes]
rs6109905	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109958	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6131483	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131485	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131488	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6134879	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134912	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73086013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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:40 , 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	chr20:13480000-13490400	ZNF genes & repeats	Dnd41	blood
8	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr20:13483800-13493600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:13483800-13493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:13484000-13493800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:13484000-13493800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr20:13484000-13493800	Weak transcription	Fetal Thymus	thymus
14	chr20:13484000-13495800	Weak transcription	Thymus	Thymus
15	chr20:13484000-13499000	Weak transcription	Aorta	Aorta
16	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
18	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
19	chr20:13484200-13493600	Weak transcription	Fetal Intestine Small	intestine
20	chr20:13484200-13493800	Weak transcription	Primary B cells from cord blood	blood
21	chr20:13484200-13496800	Weak transcription	Left Ventricle	heart
22	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
24	chr20:13485400-13493800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr20:13485800-13497400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:13486200-13493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr20:13487600-13489600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
30	chr20:13488000-13489600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr20:13488200-13502600	Weak transcription	Lung	lung
32	chr20:13488200-13502600	Weak transcription	Ovary	ovary
33	chr20:13488600-13494000	Weak transcription	Adipose Nuclei	Adipose
34	chr20:13488600-13496800	Weak transcription	NHEK	skin
35	chr20:13489000-13489600	Weak transcription	Fetal Lung	lung
36	chr20:13489000-13493800	Weak transcription	A549	lung
37	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
40	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain

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