rs9272346

In this 2007 article, titled "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls," rs9272346 has been reported to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes (AA), the risk is 18.52 (CI 12.69-27.03). The P value is extremely significant at 5.47 × 10-134, considering the threshold for genome-wide significance. NOTE: In previous edits of this page, it has been noted that "the (A) allele of rs9272346 is common in various human populations, and one could consider the (G) allele as protective." However, the authors of seem to disagree. (Of course, other significant genetic and/or environmental factors could be protecting the multitude of individuals with AG). In several other lines of their table, the allele identified as the risk allele is _not_ the minor allele. The authors are aware of the conventions for ODs for risk vs. protection, stating that risk allele ODs will be normally 1-2 and protective ODS are between 0.5-1 (Supplement 1, page 3). In light of this, if they wished to signify the G allele was protective, they would have given a protective allele odds-ratio in the range 0.5-1 to AG. Of course, any OD as large as 5.49 (for AG), much less 18.25 (for AA) is quite a significant risk factor compared to all other ODs on its table. Yet it cannot be a typographical error, since the rs9272346 OD of 5.49 and P values were replicated in their Supplement 1 page 43. Their significant P values were confirmed to some degree in a 2015 study listed on this page. In this 2015 article titled "Association of 32 type 1 diabetes risk loci in Pakistani patients," among 191 Pakistani cases and controls, the P value for rs9272346 was (p = 2.83E − 09). However, no risk allele or odds ratio was mentioned. They cited the 2007 study on this page. They noted that "it has been difficult to determine individual effects of HLA genes [17]." Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci.

A;A

See text at Rs9272346

A;G

See text at Rs9272346

G;G

see text at Rs9272346