chr1:113872746:G>C Detail (hg38) (PTPN22, AP4B1-AS1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:114,415,368-114,415,368 View the variant detail on this assembly version. |
| hg38 | chr1:113,872,746-113,872,746 |
HGVS
[No Data.]
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.415 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
Prediction
ClinVar
| Clinical Significance |
risk factor
|
| Review star |  |
| Show details | |
Links
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
risk factor
|
2006-03-15 | no assertion criteria provided | Diabetes mellitus, insulin-dependent, susceptibility to |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.226 | Autoimmune Diseases | Polymorphisms in PTPN22 are associated with many autoimmune diseases; while rs24... | BeFree | 22197427 | Detail |
| 0.475 | Diabetes Mellitus, Insulin-Dependent | Association of the PTPN22 gene (+1858C/T, -1123G/C) polymorphisms with type 1 di... | BeFree | 22572103 | Detail |
| 0.009 | ulcerative colitis | Association of PTPN22 gene (rs2488457) polymorphism with ulcerative colitis and ... | BeFree | 23456301 | Detail |
| 0.019 | Juvenile arthritis | STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C polymorphisms influence the risk of... | BeFree | 25781893 | Detail |
| 0.004 | juvenile rheumatoid arthritis | STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C polymorphisms influence the risk of... | BeFree | 25781893 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_015967.6(PTPN22):c.-1123C>G AND Diabetes mellitus, insulin-dependent, susceptibility to | ClinVar | Detail |
| Polymorphisms in PTPN22 are associated with many autoimmune diseases; while rs2476601 is supposed to... | DisGeNET | Detail |
| Association of the PTPN22 gene (+1858C/T, -1123G/C) polymorphisms with type 1 diabetes mellitus: a s... | DisGeNET | Detail |
| Association of PTPN22 gene (rs2488457) polymorphism with ulcerative colitis and high levels of PTPN2... | DisGeNET | Detail |
| STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C polymorphisms influence the risk of developing juvenile... | DisGeNET | Detail |
| STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C polymorphisms influence the risk of developing juvenile... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs2488457 dbSNP
- Genome
- hg38
- Position
- chr1:113,872,746-113,872,746
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- 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))
- rs2488457
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4148
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6952
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
Genome browser