chr18:12809340:A>G Detail (hg19) (PTPN2)

Information

Genome

Assembly Position
hg19 chr18:12,809,340-12,809,340
hg38 chr18:12,809,341-12,809,341 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002828.3:c.858+4862T>C
NM_080422.2:c.858+4862T>C
NM_080423.2:c.858+4862T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.109
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 176887 OMIM
HGNC 9650 HGNC
Ensembl ENSG00000175354 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv59300516 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
0.371 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.020 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.124 Inflammatory Bowel Diseases Host-microbe interactions have shaped the genetic architecture of inflammatory b... GWASCAT 23128233 Detail
0.137 Diabetes Mellitus, Insulin-Dependent Genome-wide association study and meta-analysis find that over 40 loci affect ri... GWASCAT 19430480 Detail
0.269 Crohn Disease Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's diseas... GWASCAT 21102463 Detail
0.002 Diabetes Mellitus, Non-Insulin-Dependent [These results suggest that individuals with increased genetic susceptibility to... GAD 20203524 Detail
0.122 celiac disease Multiple common variants for celiac disease influencing immune gene expression. GWASCAT 20190752 Detail
0.006 Autoimmune Diseases [Meta-analysis of genome-wide association studies in celiac disease and rheumato... GAD 21383967 Detail
0.122 celiac disease [Multiple common variants for celiac disease influencing immune gene expression.... GAD 20190752 Detail
0.137 Diabetes Mellitus, Insulin-Dependent [Genome-wide association study and meta-analysis find that over 40 loci affect r... GAD 19430480 Detail
Annotation

Annotations

DescrptionSourceLinks
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. DisGeNET Detail
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabete... DisGeNET Detail
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loc... DisGeNET Detail
[These results suggest that individuals with increased genetic susceptibility to T2D have decreased ... DisGeNET Detail
Multiple common variants for celiac disease influencing immune gene expression. DisGeNET Detail
[Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identif... DisGeNET Detail
[Multiple common variants for celiac disease influencing immune gene expression.] DisGeNET Detail
[Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabet... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1893217 dbSNP
Genome
hg19
Position
chr18:12,809,340-12,809,340
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs1893217
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1091
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1828
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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