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From SNPedia

Associated with autoimmune diseases
Geno Mag Summary
Make rs1990760(C;T)
Make rs1990760(T;T)
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
1000 genomesrs1990760
23andMe allrs1990760
SNP Nexus

GWAS Ctlgrs1990760
Max Magnitude
? (C;C) (C;T) (T;T) 28

This SNP is unclear. According to GWAS one study says risk allele is A, another study says risk allele is C. Ambiguous flip ?


associated with type-1 diabetes, organ-specific autoimmune diseases, including Graves' disease. (odds ratio 1.47 (CI: 1.23–1.76, p = 1.9 x 10–5)

This polymorphism may also contribute to several other autoimmune disorders.

[PMID 18026693] A study of 261 Chinese patients with Graves' disease failed to find any association with rs1990760.

[PMID 19156166OA-icon.png] A study of 591 French Caucasian multiple sclerosis trio families found no association between rs1990760 or rs2068330 and the disease, which did not confirm one previously reported study.

GWAS snp
PMID [PMID 17554260OA-icon.png]
Trait Type 1 diabetes
Title Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
Risk Allele A
P-val 1.9999999999999999E-11
Odds Ratio 1.18 [1.11-1.23]
GWAS snp
PMID [PMID 19430480OA-icon.png]
Trait Type 1 diabetes
Title Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
Risk Allele
P-val 7E-9
Odds Ratio NR NR

[PMID 19450885] Multiple sclerosis and polymorphisms of innate pattern recognition receptors TLR1-10, NOD1-2, DDX58, and IFIH1

[PMID 19841890] The interferon-induced helicase IFIH1 Ala946Thr polymorphism is associated with type 1 diabetes in both the high-incidence Finnish and the medium-incidence Hungarian populations

[PMID 19956106OA-icon.png] Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families

[PMID 19951419OA-icon.png] Confirmation of the genetic association of CTLA4 and PTPN22 with ANCA-associated vasculitis

[PMID 20467774] Interferon-induced helicase (IFIH1) polymorphism with systemic lupus erythematosus and dermatomyositis/polymyositis

[PMID 20694011] Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency

[PMID 22110759OA-icon.png] Polymorphisms in the Innate Immune IFIH1 Gene, Frequency of Enterovirus in Monthly Fecal Samples during Infancy, and Islet Autoimmunity
GWAS snp
PMID [PMID 21829393OA-icon.png]
Title Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
Risk Allele C
P-val 2E-14
Odds Ratio 1.2000 [NR]

[PMID 16699517] A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region.

[PMID 17442111OA-icon.png] The interferon induced with helicase domain 1 A946T polymorphism is not associated with rheumatoid arthritis.

[PMID 17535987] Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility.

[PMID 17940599OA-icon.png] Assembly of inflammation-related genes for pathway-focused genetic analysis.

[PMID 18071670] The association between the IFIH1 locus and type 1 diabetes.

[PMID 18285833] IFIH1-GCA-KCNH7 locus: influence on multiple sclerosis risk.

[PMID 18556337OA-icon.png] Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1).

[PMID 18647951OA-icon.png] A human type 1 diabetes susceptibility locus maps to chromosome 21q22.3.

[PMID 18776148OA-icon.png] Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms.

[PMID 18840781OA-icon.png] Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes.

[PMID 18927125OA-icon.png] IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells.

[PMID 18987646OA-icon.png] The expanding genetic overlap between multiple sclerosis and type I diabetes.

[PMID 19073967OA-icon.png] Shared and distinct genetic variants in type 1 diabetes and celiac disease.

[PMID 19251732OA-icon.png] Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage.

[PMID 19264985OA-icon.png] Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes.

[PMID 19359276OA-icon.png] Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.

[PMID 19539001] IFIH1 gene polymorphisms in type 1 diabetes: genetic association analysis and genotype-phenotype correlation in the Belgian population.

[PMID 19732865OA-icon.png] A generalized family-based association test for dichotomous traits.

[PMID 19838195OA-icon.png] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.

[PMID 19956101OA-icon.png] Overview of the Rapid Response data.

[PMID 19956109OA-icon.png] The Type I Diabetes Genetics Consortium 'Rapid Response' family-based candidate gene study: strategy, genes selection, and main outcome.

[PMID 19961590OA-icon.png] The rs1990760 polymorphism within the IFIH1 locus is not associated with Graves' disease, Hashimoto's thyroiditis and Addison's disease.

[PMID 20018022OA-icon.png] Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.

[PMID 20644636OA-icon.png] Study of transcriptional effects in Cis at the IFIH1 locus.

[PMID 21705624OA-icon.png] Autoimmune disease risk variant of IFIH1 is associated with increased sensitivity to IFN-alpha and serologic autoimmunity in lupus patients.

[PMID 22053898] IFIH1 gene polymorphisms in type 1 diabetes: genetic association analysis and genotype-phenotype correlation in Chinese Han population.

[PMID 22152027] Genetic variants in IFIH1 play opposite roles in the pathogenesis of psoriasis and chronic periodontitis.

GET Evidence
aa_change Ala946Thr
aa_change_short A946T
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.458635

[PMID 23144876OA-icon.png] Enterovirus RNA in Peripheral Blood May Be Associated with the Variants of rs1990760, a Common Type 1 Diabetes Associated Polymorphism in IFIH1

[PMID 23441136OA-icon.png] Admixture Mapping in Lupus Identifies Multiple Functional Variants within IFIH1 Associated with Apoptosis, Inflammation, and Autoantibody Production

[PMID 23734776] Association of IFIH1 rs1990760 polymorphism with susceptibility to autoimmune diseases: A meta-analysis

[PMID 22789000] Polymorphisms in the interferon-induced helicase (IFIH1) locus and susceptibility to Addison's disease

[PMID 24386202OA-icon.png] The A Allele of the rs1990760 Polymorphism in the IFIH1 Gene Is Associated with Protection for Arterial Hypertension in Type 1 Diabetic Patients and with Expression of This Gene in Human Mononuclear Cells

[PMID 24621100] A Polymorphism in Melanoma Differentiation-associated Gene 5 May Be a Risk Factor for Enterovirus 71 Infection

[PMID 23108955] Association study of IFIH1 rs1990760 polymorphism with systemic lupus erythematosus in a Chinese population.

[PMID 24960033] Association of innate immune IFIH1 gene polymorphisms with dilated cardiomyopathy in a Chinese population

[PMID 25337792OA-icon.png] Genetic association study of TNFAIP3, IFIH1, IRF5 polymorphisms with polymyositis/dermatomyositis in Chinese Han population

[PMID 25515714] Cumulative effect of IFIH1 variants and increased gene expression associated with type 1 diabetes

[PMID 26074154] Non-HLA gene effects on the disease process of type 1 diabetes: From HLA susceptibility to overt disease.