chr12:112007756:C>T Detail (hg19) (ATXN2)

Information

Genome

Assembly Position
hg19 chr12:112,007,756-112,007,756
hg38 chr12:111,569,952-111,569,952 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001310123.1:c.-27-15735G>A
NM_001310121.1:c.-64-14033G>A
Ensemble ENST00000672613.1:c.252-14033G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:1.000
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 601517 OMIM
HGNC 10555 HGNC
Ensembl ENSG00000204842 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv47257005 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.125 Systemic arterial pressure [Genome-wide association study identifies six new loci influencing pulse pressur... GAD 21909110 Detail
0.243 coronary artery disease The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed... BeFree 23474010 Detail
0.127 celiac disease Multiple common variants for celiac disease influencing immune gene expression. GWASCAT 20190752 Detail
0.133 celiac disease [Type 1 diabetes and celiac disease share HLA-DQ, IL2-IL21, CCR3 and SH2B3 risk ... GAD 18311140 Detail
<0.001 Coronary Arteriosclerosis The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed... BeFree 23474010 Detail
0.127 celiac disease Newly identified genetic risk variants for celiac disease related to the immune ... GWASCAT 18311140 Detail
0.125 Blood pressure finding [Genome-wide association study identifies six new loci influencing pulse pressur... GAD 21909110 Detail
0.127 celiac disease [Newly identified genetic risk variants for celiac disease related to the immune... GAD 18311140 Detail
0.003 Coronary heart disease The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed... BeFree 23474010 Detail
0.005 Autoimmune Diseases [Meta-analysis of genome-wide association studies in celiac disease and rheumato... GAD 21383967 Detail
0.133 celiac disease One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically s... BeFree 25893417 Detail
0.125 Blood pressure finding Genome-wide association study identifies six new loci influencing pulse pressure... GWASCAT 21909110 Detail
0.120 Peripheral Arterial Diseases The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electro... GWASCAT 25009551 Detail
0.243 coronary artery disease One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically s... BeFree 25893417 Detail
0.125 Blood pressure finding [Genome-wide association study identifies eight loci associated with blood press... GAD 19430483 Detail
0.127 celiac disease [Multiple common variants for celiac disease influencing immune gene expression.... GAD 20190752 Detail
0.120 Chronic Kidney Diseases Follow-up of the 23 new genome-wide-significant loci (P &lt; 5 x 10(-8)) in 22,9... GWASCAT 20383146 Detail
0.133 celiac disease [Multiple common variants for celiac disease influencing immune gene expression.... GAD 20190752 Detail
0.125 Systemic arterial pressure Genome-wide association study identifies six new loci influencing pulse pressure... GWASCAT 21909110 Detail
0.127 celiac disease One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically s... BeFree 25893417 Detail
0.125 Systemic arterial pressure [Genome-wide association study identifies eight loci associated with blood press... GAD 19430483 Detail
<0.001 coronary artery disease One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically s... BeFree 25893417 Detail
<0.001 antiphospholipid syndrome Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs318... BeFree 23844121 Detail
Annotation

Annotations

DescrptionSourceLinks
[Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial ... DisGeNET Detail
The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed direction-consisten... DisGeNET Detail
Multiple common variants for celiac disease influencing immune gene expression. DisGeNET Detail
[Type 1 diabetes and celiac disease share HLA-DQ, IL2-IL21, CCR3 and SH2B3 risk regions.] DisGeNET Detail
The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed direction-consisten... DisGeNET Detail
Newly identified genetic risk variants for celiac disease related to the immune response. DisGeNET Detail
[Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial ... DisGeNET Detail
[Newly identified genetic risk variants for celiac disease related to the immune response.] DisGeNET Detail
The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed direction-consisten... DisGeNET Detail
[Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identif... DisGeNET Detail
One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically significant associati... DisGeNET Detail
Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial p... DisGeNET Detail
The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-b... DisGeNET Detail
One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically significant associati... DisGeNET Detail
[Genome-wide association study identifies eight loci associated with blood pressure.] DisGeNET Detail
[Multiple common variants for celiac disease influencing immune gene expression.] DisGeNET Detail
Follow-up of the 23 new genome-wide-significant loci (P &lt; 5 x 10(-8)) in 22,982 replication sampl... DisGeNET Detail
[Multiple common variants for celiac disease influencing immune gene expression.] DisGeNET Detail
Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial p... DisGeNET Detail
One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically significant associati... DisGeNET Detail
[Genome-wide association study identifies eight loci associated with blood pressure.] DisGeNET Detail
One SNP (rs653178 at the SH2B3/ATXN2 locus) displayed study-wise statistically significant associati... DisGeNET Detail
Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs3184504) and two SNPs i... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs653178 dbSNP
Genome
hg19
Position
chr12:112,007,756-112,007,756
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs653178
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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