Variant report

Variant	rs4972343
Chromosome Location	chr2:149029008-149029009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10206569	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210377	0.95[ASN][1000 genomes]
rs10928388	0.91[ASN][1000 genomes]
rs10928389	0.94[ASN][1000 genomes]
rs10928390	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1120671	0.96[ASN][1000 genomes]
rs11676308	0.80[ASN][1000 genomes]
rs11685302	0.91[ASN][1000 genomes]
rs11692246	0.80[ASN][1000 genomes]
rs12691780	0.91[ASN][1000 genomes]
rs12691781	0.91[ASN][1000 genomes]
rs13027785	0.94[ASN][1000 genomes]
rs13032996	0.82[ASN][1000 genomes]
rs13392141	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13425594	0.95[ASN][1000 genomes]
rs1449960	0.88[ASN][1000 genomes]
rs1453318	0.83[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs17274896	0.80[ASN][1000 genomes]
rs2044760	0.88[ASN][1000 genomes]
rs2044761	0.88[ASN][1000 genomes]
rs2084954	0.80[ASN][1000 genomes]
rs2167127	0.91[ASN][1000 genomes]
rs2890917	0.96[ASN][1000 genomes]
rs35042809	0.82[ASN][1000 genomes]
rs35749985	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972276	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972338	0.80[ASN][1000 genomes]
rs4972341	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6430305	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6721794	0.91[ASN][1000 genomes]
rs6746932	0.80[ASN][1000 genomes]
rs7565035	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570104	0.91[ASN][1000 genomes]
rs961207	0.98[ASN][1000 genomes]
rs991554	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4972343	ACVR2A	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
2	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:149011600-149030800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:149012600-149043400	Weak transcription	Gastric	stomach
5	chr2:149012800-149030000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:149012800-149030200	Weak transcription	Fetal Kidney	kidney
7	chr2:149012800-149030800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:149014000-149031600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:149015800-149030200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:149016800-149030800	Weak transcription	Ovary	ovary
12	chr2:149017000-149030400	Weak transcription	NHLF	lung
13	chr2:149017000-149030800	Weak transcription	Primary T cells from cord blood	blood
14	chr2:149017000-149031200	Weak transcription	HSMM	muscle
15	chr2:149017200-149038000	Weak transcription	Primary B cells from cord blood	blood
16	chr2:149017400-149030000	Weak transcription	Fetal Intestine Large	intestine
17	chr2:149017400-149033600	Weak transcription	Pancreas	Pancrea
18	chr2:149017400-149037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:149017400-149050600	Weak transcription	Thymus	Thymus
20	chr2:149017400-149062800	Weak transcription	Fetal Lung	lung
21	chr2:149017400-149070600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:149017600-149031000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:149017600-149043400	Weak transcription	Fetal Stomach	stomach
24	chr2:149017600-149049000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:149017600-149060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:149017800-149030800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:149018000-149031000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:149023600-149039200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:149025800-149044600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:149026000-149029400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:149026000-149031000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:149026000-149031000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:149026000-149045000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
35	chr2:149027000-149039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:149027400-149032600	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:149027600-149038000	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links