Variant report

Variant	rs3789342
Chromosome Location	chr20:13499041-13499042
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs13039162	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13042843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057258	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2070305	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070334	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2073324	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2103972	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2180569	0.81[JPT][hapmap]
rs2182708	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208207	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2208208	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747931	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789347	0.94[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789348	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3789349	0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4813131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814236	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814238	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814242	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57218913	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042106	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6042128	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042153	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042225	0.84[JPT][hapmap];0.94[YRI][hapmap]
rs6074611	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074612	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074613	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074618	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6074627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6079066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079072	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079074	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079075	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079077	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079095	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6105096	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105098	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6105103	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105113	0.92[ASN][1000 genomes]
rs6109887	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109891	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109903	0.89[ASN][1000 genomes]
rs6109905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6131483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131485	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6134879	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134902	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134912	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6514418	0.85[JPT][hapmap]
rs73086013	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:13473400-13505800	Weak transcription	HSMM	muscle
4	chr20:13478200-13503800	Weak transcription	Gastric	stomach
5	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
8	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
9	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
11	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
13	chr20:13488200-13502600	Weak transcription	Lung	lung
14	chr20:13488200-13502600	Weak transcription	Ovary	ovary
15	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
18	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr20:13490400-13502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr20:13490800-13502800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr20:13491800-13503400	Weak transcription	Liver	Liver
23	chr20:13492200-13499600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:13492200-13503800	Weak transcription	Right Ventricle	heart
25	chr20:13492200-13505600	Weak transcription	Spleen	Spleen
26	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr20:13492600-13502600	Weak transcription	Brain Hippocampus Middle	brain
28	chr20:13493600-13502800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr20:13493600-13505400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr20:13493600-13507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:13493600-13510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr20:13493800-13504000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr20:13494000-13502600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:13494000-13502600	Weak transcription	A549	lung
36	chr20:13494000-13504000	Weak transcription	Fetal Intestine Small	intestine
37	chr20:13494000-13505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:13494000-13507800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:13494000-13512400	Weak transcription	Placenta	Placenta
40	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr20:13494200-13502800	Weak transcription	Fetal Muscle Leg	muscle
42	chr20:13494200-13516000	Weak transcription	Colonic Mucosa	Colon
43	chr20:13494400-13502600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr20:13494400-13506400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr20:13494400-13507600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:13494400-13507600	Weak transcription	GM12878-XiMat	blood
47	chr20:13494400-13514800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:13494600-13502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:13494600-13503800	Weak transcription	Adipose Nuclei	Adipose
50	chr20:13494600-13516400	Weak transcription	Esophagus	oesophagus

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