Variant report

Variant	rs13001946
Chromosome Location	chr2:148994598-148994599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10206569	0.82[ASN][1000 genomes]
rs10210377	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10432369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10928388	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10928389	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10928390	0.82[ASN][1000 genomes]
rs1120671	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11675979	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11676308	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678688	0.84[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11683219	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11685302	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11692246	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12053104	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12470061	0.83[EUR][1000 genomes]
rs12691780	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12691781	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027785	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13032996	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13392141	0.82[ASN][1000 genomes]
rs13425594	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1449960	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1453318	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17274896	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17276501	0.81[EUR][1000 genomes]
rs1869341	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2044760	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2044761	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084954	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2167127	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602358	0.82[EUR][1000 genomes]
rs2656319	0.82[EUR][1000 genomes]
rs2656320	0.82[EUR][1000 genomes]
rs2656324	0.82[EUR][1000 genomes]
rs2839755	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2890917	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35042809	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35749985	0.81[ASN][1000 genomes]
rs4399670	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972276	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs4972277	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4972278	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4972338	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4972341	0.82[ASN][1000 genomes]
rs4972347	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4972355	0.83[EUR][1000 genomes]
rs6430305	0.92[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6721794	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6746932	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7570104	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7572948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949679	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs961207	0.89[EUR][1000 genomes]
rs987625	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs987626	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs991554	0.91[CHB][hapmap]

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	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148981400-148996600	Weak transcription	Psoas Muscle	Psoas
2	chr2:148983600-148996000	Weak transcription	Brain Angular Gyrus	brain
3	chr2:148984400-149011800	Weak transcription	Gastric	stomach
4	chr2:148984800-149011800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:148985400-149011200	Weak transcription	Pancreas	Pancrea
6	chr2:148986000-149002200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:148986800-149011600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:148987600-148996200	Weak transcription	Esophagus	oesophagus
9	chr2:148987600-148997200	Weak transcription	Lung	lung
10	chr2:148987800-148994600	Weak transcription	Thymus	Thymus
11	chr2:148988200-148994600	Weak transcription	HUVEC	blood vessel
12	chr2:148988800-148994800	Weak transcription	Aorta	Aorta
13	chr2:148989000-148997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:148989200-149000200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:148990200-149011400	Weak transcription	Spleen	Spleen
16	chr2:148990400-148997200	Weak transcription	Brain Anterior Caudate	brain
17	chr2:148991000-148994600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:148991800-148994800	Weak transcription	Placenta	Placenta
19	chr2:148992200-148994600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:148992400-148995600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:148992400-148997600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:148992600-149009600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:148992800-148994800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:148993000-148994600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:148993000-148994600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:148993000-148994800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:148993000-148995000	ZNF genes & repeats	NHDF-Ad	bronchial
28	chr2:148993000-148995400	Strong transcription	Fetal Thymus	thymus
29	chr2:148993000-148996400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:148993200-148995000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:148993200-148995000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:148993200-148995200	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr2:148993200-148995400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:148993200-148995400	Strong transcription	Ovary	ovary
35	chr2:148993200-148995400	ZNF genes & repeats	GM12878-XiMat	blood
36	chr2:148993200-148999400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:148993200-148999600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:148993400-148994600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:148993400-148994800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
40	chr2:148993400-148995000	Strong transcription	Left Ventricle	heart
41	chr2:148993400-148995000	ZNF genes & repeats	HSMMtube	muscle
42	chr2:148993400-148995400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:148993400-148995400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:148993400-148995400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr2:148993400-148995400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:148993600-148995000	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr2:148993600-148995200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
48	chr2:148993600-148995400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr2:148993600-148995400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:148993600-148995400	Strong transcription	Rectal Mucosa Donor 29	rectum

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