Variant report

Variant	rs4972277
Chromosome Location	chr2:149039379-149039380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10196090	0.82[EUR][1000 genomes]
rs10208839	0.80[EUR][1000 genomes]
rs10432369	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11675979	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676308	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11678688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11683219	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11692246	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12053104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470061	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618358	0.89[EUR][1000 genomes]
rs13001946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13022005	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13032996	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1453317	0.91[EUR][1000 genomes]
rs1453318	0.84[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1580063	0.91[ASN][1000 genomes]
rs17274896	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17276501	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2084954	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2167880	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602352	0.90[EUR][1000 genomes]
rs2602358	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2656317	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2656319	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656320	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656324	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656325	0.91[EUR][1000 genomes]
rs2839755	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28831467	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2938705	0.91[EUR][1000 genomes]
rs35042809	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4399670	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4972278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972347	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972355	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972358	0.89[EUR][1000 genomes]
rs6734448	0.89[EUR][1000 genomes]
rs6746932	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7572948	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7592019	0.81[EUR][1000 genomes]
rs869595	0.89[EUR][1000 genomes]
rs949679	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987625	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs987626	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs991554	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012600-149043400	Weak transcription	Gastric	stomach
2	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:149017400-149050600	Weak transcription	Thymus	Thymus
4	chr2:149017400-149062800	Weak transcription	Fetal Lung	lung
5	chr2:149017400-149070600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:149017600-149043400	Weak transcription	Fetal Stomach	stomach
7	chr2:149017600-149049000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:149017600-149060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:149025800-149044600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:149026000-149045000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
12	chr2:149029400-149055400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:149031000-149041400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:149031400-149039400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:149031400-149040400	Weak transcription	Aorta	Aorta
16	chr2:149031400-149042000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
18	chr2:149031600-149046200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:149031600-149055200	Weak transcription	Primary T cells from cord blood	blood
20	chr2:149036600-149047000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:149037200-149039400	Weak transcription	NHDF-Ad	bronchial
22	chr2:149037200-149041200	Weak transcription	HepG2	liver
23	chr2:149038400-149044800	Weak transcription	Primary B cells from cord blood	blood
24	chr2:149038800-149039600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:149039200-149039400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr2:149039200-149039400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:149039200-149039400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:149039200-149039600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:149039200-149040000	Enhancers	HUES48 Cell Line	embryonic stem cell

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