Variant report

Variant	rs2423750
Chromosome Location	chr20:13794566-13794567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13039364	0.90[CEU][hapmap];0.88[CHB][hapmap]
rs13042637	0.91[ASN][1000 genomes]
rs1547920	0.88[ASN][1000 genomes]
rs1999112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2031933	0.86[ASN][1000 genomes]
rs2209993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2209994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2327797	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs2423745	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2423753	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3180370	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs34449907	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34806363	0.86[ASN][1000 genomes]
rs4813139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4813142	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4814258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6033809	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6033816	0.86[ASN][1000 genomes]
rs6033819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6033821	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs6042324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6042336	0.88[CHB][hapmap]
rs6042357	0.85[ASN][1000 genomes]
rs6042362	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6074643	0.95[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6074644	0.95[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079154	0.88[CHB][hapmap]
rs6079156	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs6079158	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs6079162	0.88[CHB][hapmap]
rs6079165	0.81[ASN][1000 genomes]
rs6079166	0.94[CEU][hapmap];0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs6079176	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079178	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079181	0.94[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079182	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6105162	0.82[ASN][1000 genomes]
rs6110026	0.88[CHB][hapmap]
rs6110035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs62209178	0.81[ASN][1000 genomes]
rs62209207	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68012295	0.88[ASN][1000 genomes]
rs7265467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs754796	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13766400-13796800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:13767600-13799600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:13767800-13799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:13767800-13800600	Weak transcription	Stomach Mucosa	stomach
5	chr20:13768000-13794800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr20:13768000-13799800	Strong transcription	Fetal Thymus	thymus
7	chr20:13768200-13799800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr20:13768200-13799800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr20:13768400-13799600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr20:13768600-13799600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr20:13768800-13799600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:13769000-13799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:13769200-13799600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr20:13769400-13799400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr20:13769400-13802000	Strong transcription	A549	lung
16	chr20:13769600-13799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr20:13770200-13799600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr20:13770600-13799400	Strong transcription	Primary T cells from cord blood	blood
19	chr20:13773600-13799400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:13779200-13799600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr20:13780800-13800800	Strong transcription	Placenta	Placenta
22	chr20:13781600-13800000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr20:13781800-13798200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr20:13781800-13799000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr20:13781800-13799400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr20:13781800-13799400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr20:13782000-13799400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:13782200-13799600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr20:13783000-13799400	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr20:13783600-13802000	Strong transcription	Dnd41	blood
31	chr20:13784400-13799600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr20:13785400-13799400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr20:13785400-13799600	Strong transcription	Left Ventricle	heart
34	chr20:13786200-13797400	Strong transcription	Fetal Stomach	stomach
35	chr20:13786200-13799600	Strong transcription	Thymus	Thymus
36	chr20:13786800-13797200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr20:13786800-13799400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:13786800-13799400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:13787400-13796000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr20:13787400-13799400	Strong transcription	Lung	lung
41	chr20:13787400-13799600	Strong transcription	GM12878-XiMat	blood
42	chr20:13787600-13798600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr20:13787600-13799800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:13787800-13799000	Strong transcription	HSMM	muscle
45	chr20:13787800-13799600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr20:13788000-13794800	Strong transcription	Fetal Intestine Large	intestine
47	chr20:13788000-13799400	Strong transcription	HSMMtube	muscle
48	chr20:13788200-13797000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:13788400-13796400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr20:13788400-13797000	Strong transcription	Muscle Satellite Cultured Cells	--

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