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rs2187668

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 3 Autoimmune disorder risk (lupus, celiac disease) due to 2 HLA-DRB1*0301 alleles
(A;G) 2.1 Somewhat increased autoimmune disorder (lupus, celiac disease) risk; 1 HLA-DRB1*0301 allele
(G;G) 0 average
ReferenceGRCh38 38.1/141
Chromosome6
Position32638107
GeneHLA-DQA1
is asnp
is mentioned by
dbSNPrs2187668
ebirs2187668
HLIrs2187668
Exacrs2187668
Varsomers2187668
Maprs2187668
PheGenIrs2187668
hapmaprs2187668
1000 genomesrs2187668
hgdprs2187668
ensemblrs2187668
gopubmedrs2187668
geneviewrs2187668
scholarrs2187668
googlers2187668
pharmgkbrs2187668
gwascentralrs2187668
openSNPrs2187668
23andMers2187668
23andMe allrs2187668
SNP Nexus

SNPshotrs2187668
SNPdbers2187668
MSV3drs2187668
GWAS Ctlgrs2187668
GMAF0.08356
Max Magnitude3
? (A;A) (A;G) (G;G) 28

In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele.

The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). [PMID 17997607OA-icon.png]

From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients.[PMID 17558408OA-icon.png]

rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac disease in Europeans.[PMID 18509540OA-icon.png]

GWAS snp
PMID [PMID 18204098]
Trait Systemic lupus erythematosus
Title Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX
Risk Allele A
P-val 2.9999999999999999E-21
Odds Ratio NR NR
GWAS snp
PMID [PMID 20190752OA-icon.png]
Trait Celiac disease
Title Multiple common variants for celiac disease influencing immune gene expression
Risk Allele A
P-val 1E-50
Odds Ratio 6.23 [5.95-6.52]
GWAS snp
PMID [PMID 20694011]
Trait
Title Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency
Risk Allele A
P-val 2E-33
Odds Ratio 2.53 [2.17-2.95]
GWAS snp
PMID [PMID 21323541]
Trait
Title Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy
Risk Allele
P-val 8E-93
Odds Ratio 4.3200 [3.73-5.01]
GWAS snp
PMID [PMID 21408207OA-icon.png]
Trait
Title Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti-dsDNA Autoantibody Production
Risk Allele A
P-val 6E-28
Odds Ratio 2.2300 [1.94-2.57]

[PMID 15747258OA-icon.png] A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms.

[PMID 18311140OA-icon.png] Newly identified genetic risk variants for celiac disease related to the immune response.

[PMID 19176549OA-icon.png] Genome-wide association analysis by lasso penalized logistic regression.

[PMID 19455305OA-icon.png] No association of multiple type 2 diabetes loci with type 1 diabetes.

[PMID 19846760OA-icon.png] Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases.

[PMID 21379322OA-icon.png] Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.

[PMID 21383967OA-icon.png] Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.

[PMID 22511809] Association of variants in HLA-DQA1-DQB1, PTPN22, INS, and CTLA4 with GAD autoantibodies and insulin secretion in nondiabetic adults of the Botnia Prospective Study.

Kidney Disease


[PMID 23194743] Development of a high resolution melting method for genotyping of risk HLA-DQA1 and PLA2R1 alleles and ethnic distribution of these risk alleles


[PMID 23961418OA-icon.png] Association of the HLA locus and TNF with type I autoimmune hepatitis susceptibility in New Zealand Caucasians

GWAS snp
PMID [PMID 24768677]
Trait Autoimmune hepatitis type-1
Title Genome-wide association study identifies variants associated with autoimmune hepatitis type 1.
Risk Allele
P-val 2E-78
Odds Ratio 2.90 [2.60-3.40]


[PMID 25187357] PLA2R-associated membranous glomerulopathy is modulated by common variants in PLA2R1 and HLA-DQA1 genes


[PMID 26673907] PLA2R antibodies, glomerular PLA2R deposits and variations in PLA2R1 and HLA-DQA1 genes in primary membranous nephropathy in South Asians.