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rs9272346

From SNPedia
Type-1 diabetes
Orientationplus
Stabilizedplus
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
Chromosome6
Position32636595
GeneHLA-DQA1
is asnp
is mentioned by
dbSNPrs9272346
dbSNP (old)rs9272346
ClinGenrs9272346
ebirs9272346
HLIrs9272346
Exacrs9272346
Gnomadrs9272346
Varsomers9272346
Maprs9272346
PheGenIrs9272346
Biobankrs9272346
1000 genomesrs9272346
hgdprs9272346
ensemblrs9272346
gopubmedrs9272346
geneviewrs9272346
scholarrs9272346
googlers9272346
pharmgkbrs9272346
gwascentralrs9272346
openSNPrs9272346
23andMers9272346
23andMe allrs9272346
SNPshotrs9272346
SNPdbers9272346
MSV3drs9272346
GWAS Ctlgrs9272346
GMAF0.4628
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



[PMID 17660530] Risk alleles for multiple sclerosis identified by a genomewide study.

[PMID 18224312OA-icon.png] Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.

[PMID 20369022OA-icon.png] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.

[PMID 21304891OA-icon.png] A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci.


GET Evidence
rs9272346
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.15
summary



[PMID 22972380OA-icon.png] Investigation of genetic risk factors for chronic adult diseases for association with preterm birth

GWAS snp
PMID [PMID 23181788]
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


[PMID 27291710] Association of human leukocyte antigen DP/DQ gene polymorphisms with chronic hepatitis B in Chinese Han and Uygur populations.