chr18:12779948:G>T Detail (hg38)

Information

Genome

Assembly Position
hg19 chr18:12,779,947-12,779,947 View the variant detail on this assembly version.
hg38 chr18:12,779,948-12,779,948

HGVS

[No Data.]
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.894
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
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.234 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.327 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.129 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.033 ulcerative colitis Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and P... BeFree 22457781 Detail
0.003 ankylosing spondylitis Polymorphisms associated in the allele frequencies test with severe BASFI/t in a... BeFree 22984424 Detail
<0.001 ankylosing spondylitis Polymorphisms associated in the allele frequencies test with severe BASFI/t in a... BeFree 22984424 Detail
0.007 Crohn Disease [Genome-wide association study of 14,000 cases of seven common diseases and 3,00... GAD 17554300 Detail
0.007 Diabetes Mellitus, Insulin-Dependent [Meta-analysis of genome-wide association study data identifies additional type ... GAD 18978792 Detail
0.137 Diabetes Mellitus, Insulin-Dependent [Robust associations of four new chromosome regions from genome-wide analyses of... GAD 17554260 Detail
0.137 Diabetes Mellitus, Insulin-Dependent [Meta-analysis of genome-wide association study data identifies additional type ... GAD 18978792 Detail
0.129 ulcerative colitis The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region ... BeFree 22021207 Detail
0.007 Crohn Disease [Sequence variants in the autophagy gene IRGM and multiple other replicating loc... GAD 17554261 Detail
0.248 rheumatoid arthritis The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region ... BeFree 22021207 Detail
0.137 Diabetes Mellitus, Insulin-Dependent The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region ... BeFree 22021207 Detail
0.007 Diabetes Mellitus, Insulin-Dependent [Robust associations of four new chromosome regions from genome-wide analyses of... GAD 17554260 Detail
0.124 Inflammatory Bowel Diseases Genomic DNA from 2131 individuals of Caucasian origin (905 patients with CD, 318... BeFree 22457781 Detail
0.007 Crohn Disease [Genome-wide association defines more than 30 distinct susceptibility loci for C... GAD 18587394 Detail
0.007 Diabetes Mellitus, Insulin-Dependent [Genome-wide association analysis of autoantibody positivity in type 1 diabetes ... GAD 21829393 Detail
Annotation

Annotations

DescrptionSourceLinks
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and PTPN2 SNP rs2542151 (... DisGeNET Detail
Polymorphisms associated in the allele frequencies test with severe BASFI/t in all classifications w... DisGeNET Detail
Polymorphisms associated in the allele frequencies test with severe BASFI/t in all classifications w... DisGeNET Detail
[Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.] DisGeNET Detail
[Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci... DisGeNET Detail
[Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.] DisGeNET Detail
[Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci... DisGeNET Detail
The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region encoding protein tyr... DisGeNET Detail
[Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Croh... DisGeNET Detail
The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region encoding protein tyr... DisGeNET Detail
The single nucleotide polymorphism (SNP) rs2542151 within the gene locus region encoding protein tyr... DisGeNET Detail
[Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.] DisGeNET Detail
Genomic DNA from 2131 individuals of Caucasian origin (905 patients with CD, 318 patients with UC, a... DisGeNET Detail
[Genome-wide association defines more than 30 distinct susceptibility loci for Crohn\'s disease.] DisGeNET Detail
[Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.] DisGeNET Detail
Gene
-
dbSNP
rs2542151 dbSNP
Genome
hg38
Position
chr18:12,779,948-12,779,948
Variant Type
snv
Reference Allele
G
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))
rs2542151
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8937
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14979
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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