Variant Annotations
PharmGKB variant annotations provide information about variant-drug pairs based on individual PubMed publications. Each annotation represents information from a single paper and the goal is to report the information that the author states, not an interpretation of the paper. The PMID for supporting PubMed publications is found in the "Evidence" field.
Information presented, including study size, allele frequencies and statistics is taken directly from the publication. However, if the author does not correct p-values in cases of multiple hypotheses, curators may apply a Bonferroni correction. Curators attempt to report study size based on the actual number of participants used for the calculation of the association statistics, so the number may vary slightly from what is reported in the abstract of the paper. OMB Race Category information is derived from the paper and mapped to standardized categories. Category definitions may be found by clicking on the "OMB Race Category" link.
There are 2 disease-related annotations for this variant. Register or sign in to see them.
VIP Variant in PTGS2
The rs689466 variant is found in the promoter of PTGS2. The A variant creates a MYB binding site in the promoter that increases transcription [Article:16083713]. This variant has also been described as -1329A>G in the literature [Article:18085997].
The A variant had a frequency of 0.65 in Pima Indians [Article:12920574], 0.51 in Chinese Asians [Article:16083713], 0.84 in German Caucasians [Article:18085997] and 0.79 in Australian Caucasians [Article:18489027] . This variant has been shown to be part of a haplotype with rs20417 in Pima Indians [Article:12920574], Chinese Asians [Article:16083713] and Australian Caucasians [Article:18489027].
The A variant was associated with asthma in Australian Caucasians [Article:18489027]. (Note: the abstract of PMID:18489027 has a typographical error in which the rs# for -1195G>A and -1290A>G are switched.)
The A variant has been associated with esophageal cancer [Article:16083713] and pancreatic cancer [Article:19422084].
The minor allele (likely G but not described) was associated with risk for hypertension in Japanese Asian men [Article:15167446]. Given the side effects of some NSAIDs include elevation of blood pressure, this could be an interesting variant to study in that context. No report of such a study was found to date.
Note: The PTGS2 gene is found on the minus chromosomal strand. Please note that for standardization, the PharmGKB presents all allele base pairs on the positive chromosomal strand, therefore the alleles within our variant annotations will differ (in a complementary manner) from those in this VIP summary that are given on the minus strand as reported in the literature.
| Key Publications: | |
|---|---|
| Diseases | Asthma Esophageal Neoplasms Hypertension Pancreatic Neoplasms |
Appendix
3. PTGS2: (-1195)G>A (rs689466)
| Genomic Variant & GenBank ID: | 798A>G on AY382629.1 |
|---|---|
| mRNA Variant & GenBank ID: | NA |
| Protein Variant & GenBank ID: | NA |
| GoldenPath Position: | chr1:184917374 (hg18) |
| DNA Source Containing Homozygous Reference Allele(Coriell Lines): | NA17105 G/G |
| DNA Source Containing Heterozygous Reference Allele(Coriell Lines): | NA17102 |
| DNA Source Containing Homozygous Minor Allele(Coriell Lines): | NA17101 |
Connected Diseases
| Evidence | Disease |
|---|---|
| Asthma | |
| Esophageal Neoplasms | |
| Hypertension | |
| Pancreatic Neoplasms |
Publications related to rs689466 at chr1:186650751: 6
Cross-References
- UCSC Golden Path:
- chr1:186650751
- dbSNP:
- rs689466
- ALFRED:
- SI517365B
- HapMap:
- rs689466
- Seattle SNP:
- PTGS2-000798
Platform Availability
- Affymetrix
- Illumina