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From SNPedia

Type-1 diabetes
Geno Mag Summary
(A;A) 3 18.5x risk for type-1 diabetes
(A;G) 3 5.49x risk of type-1 diabetes
(G;G) 1.5 No increased risk of Type 1 Diabetes on an important SNP
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
dbSNP (classic)rs9272346
1000 genomesrs9272346
23andMe allrs9272346
GWAS Ctlgrs9272346
Max Magnitude3
? (A;A) (A;G) (G;G) 28

CPMC Logo.png

This SNP has been recognized by the Coriell Personalized Medicine Collaborative ICOB.
Additional information is available here

[PMID 17554300OA-icon.png] 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 [PMID 17554300OA-icon.png] 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.

[PMID 25661663OA-icon.png] 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]."

GWAS snp
PMID [PMID 18978792OA-icon.png]
Trait Type 1 diabetes
Title Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
Risk Allele G
P-val 6E-129
Odds Ratio NR NR

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GWAS snp
PMID [PMID 23181788OA-icon.png]
Trait Asthma
Title HLA-DQ strikes again: genome-wide association study further confirms HLA-DQ in the diagnosis of asthma among adults.
Risk Allele
P-val 2E-8
Odds Ratio NR NR

[PMID 26406233OA-icon.png] Combination Testing Using a Single MSH5 Variant alongside HLA Haplotypes Improves the Sensitivity of Predicting Coeliac Disease Risk in the Polish Population

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