Variant report

Variant	rs4972344
Chromosome Location	chr2:149032151-149032152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10153599	0.89[AMR][1000 genomes]
rs10168750	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10168759	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10177233	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10188956	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10208949	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10928387	1.00[AMR][1000 genomes]
rs10928392	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11692197	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12472437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12691783	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1377455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470862	1.00[AMR][1000 genomes]
rs1542323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869342	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1992989	1.00[AMR][1000 genomes]
rs2034672	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2123617	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2167881	0.81[AMR][1000 genomes]
rs2167882	1.00[AMR][1000 genomes]
rs2219066	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2656318	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2890919	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4972339	1.00[AMR][1000 genomes]
rs4972340	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972350	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972351	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972352	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972353	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55721902	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6430307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6709521	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6722460	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6725093	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726373	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7424220	1.00[AMR][1000 genomes]
rs7569947	1.00[AMR][1000 genomes]
rs7572485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7573171	1.00[AMR][1000 genomes]
rs7588000	0.89[AMR][1000 genomes]
rs7602337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:32 , 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	chr2:149017200-149038000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:149017400-149033600	Weak transcription	Pancreas	Pancrea
5	chr2:149017400-149037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:149017400-149050600	Weak transcription	Thymus	Thymus
7	chr2:149017400-149062800	Weak transcription	Fetal Lung	lung
8	chr2:149017400-149070600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:149017600-149043400	Weak transcription	Fetal Stomach	stomach
10	chr2:149017600-149049000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:149017600-149060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:149023600-149039200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:149025800-149044600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:149026000-149045000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
16	chr2:149027000-149039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:149027400-149032600	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:149027600-149038000	Weak transcription	GM12878-XiMat	blood
19	chr2:149029400-149055400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:149029600-149036600	Weak transcription	Esophagus	oesophagus
21	chr2:149030200-149039200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:149031000-149041400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:149031200-149032200	Weak transcription	NH-A	brain
24	chr2:149031400-149033200	Weak transcription	Adipose Nuclei	Adipose
25	chr2:149031400-149036400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:149031400-149036800	Weak transcription	HepG2	liver
27	chr2:149031400-149039400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:149031400-149040400	Weak transcription	Aorta	Aorta
29	chr2:149031400-149042000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
31	chr2:149031600-149046200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:149031600-149055200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links