What you carry at this position in your DNA and what research says about it.
Autoimmune Disease Risk: 10/10 evidence, 39 publications.
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Sample genotype (not yours): C/C
Typical Autoimmune Risk
Baseline risk levels for most autoimmune conditions characterize this genetic profile, though a very slight increase in Crohn's disease susceptibility exists.
What this genotype means: Typical baseline risk for rheumatoid arthritis; Typical baseline risk for type 1 diabetes; Slightly increased risk for Crohn's disease.
Sample genotype (not yours): A/A
Significantly Elevated Autoimmune Risk
Significant elevation in the risk of developing type 1 diabetes, rheumatoid arthritis, and other autoimmune conditions is linked to this genetic profile.
What this genotype means: Significantly increased risk of type 1 diabetes; Significantly increased risk of rheumatoid arthritis; Reduced risk of Crohn's disease.
Sample genotype (not yours): C/A
Increased Autoimmune Risk
Moderate elevation in the odds of developing several autoimmune conditions, such as type 1 diabetes and rheumatoid arthritis, is associated with this genetic profile.
What this genotype means: Moderately increased risk of type 1 diabetes; Moderately increased risk of rheumatoid arthritis; Slightly reduced risk of Crohn's disease.
Gene function and biological role
Gene Function: The PHTF1 gene region on chromosome 1 is closely linked to the neighboring PTPN22 gene, which encodes lymphoid tyrosine phosphatase [1]. This phosphatase acts as a critical gatekeeper in the immune system, regulating the activation of T-cells and B-cells to prevent them from attacking the body's own tissues [2]. Genetic variations in this chromosomal region are heavily implicated in a wide spectrum of pediatric and adult autoimmune conditions [3]. These conditions arise when the immune system's regulatory checkpoints fail, leading to chronic inflammation and tissue damage [2].
Variant Impact: The variant rs6679677 is an upstream genetic marker located near the PHTF1 and PTPN22 genes. This variant is in near-perfect linkage disequilibrium with the well-known functional missense mutation rs2476601 in PTPN22, meaning they are almost always inherited together [1]. The change from a cytosine (C) to an adenine (A) at this locus serves as a strong proxy for altered immune cell signaling [1]. This genetic alteration is strongly associated with an increased susceptibility to multiple autoimmune disorders, including type 1 diabetes and rheumatoid arthritis [4]. Conversely, the same variant has been shown to have a slightly protective effect against certain inflammatory bowel conditions like Crohn's disease [3].
Key Insight: This variant acts as a genetic mirror for a functional mutation in the PTPN22 gene, making it one of the strongest non-HLA genetic predictors of autoimmune susceptibility. While the risk allele increases the likelihood of several autoimmune conditions, it simultaneously offers protection against Crohn's disease.
Location: PTPN22. Chromosome 1 · 1p13.2 · 113.8 Mb
Estimated prevalence by population
Global 87.5%; European 80.9%; African 97.0%; East Asian 99.9%; South Asian 97.5%; Americas 92.5%; Ashkenazi 90.2%; Finnish 72.8%; Middle Eastern 98.6%; Amish 92.3%.
Estimated CC genotype frequency.
Global 11.8%; European 18.1%; African 3.0%; East Asian 0.1%; South Asian 2.4%; Americas 7.3%; Ashkenazi 9.5%; Finnish 25.0%; Middle Eastern 1.4%; Amish 7.6%.
Estimated CA genotype frequency.
Global 0.6%; European 1.0%; African < 0.1%; East Asian < 0.1%; South Asian < 0.1%; Americas 0.1%; Ashkenazi 0.3%; Finnish 2.2%; Middle Eastern < 0.1%; Amish 0.2%.
Estimated AA genotype frequency.
Showing effects for C/C genotype
Immunity & Inflammation
Autoimmune Diseases
Rheumatoid Arthritis. Evidence: 10/10. Source: PMID 17554300. Typical Risk.
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 6/10. Source: PMID 23128233. ~1.2x Increased Risk.
Cardiovascular & Metabolic
Diabetes & Glycemic Traits
Type 1 Diabetes. Evidence: 10/10. Source: PMID 17554260. Typical Risk.
Endocrine & Reproductive
Hormone Levels & Endocrine Regulation
Hypothyroidism. Evidence: 9/10. Source: PMID 22493691. Typical Risk.
Showing effects for A/A genotype
Rheumatoid Arthritis. Evidence: 10/10. Source: PMID 17554300. ~3.3x Increased Risk.
Crohn's Disease. Evidence: 6/10. Source: PMID 23128233. Reduced Risk.
Type 1 Diabetes. Evidence: 10/10. Source: PMID 17554260. ~5.2x Increased Risk.
Hypothyroidism. Evidence: 9/10. Source: PMID 22493691. ~1.36x Increased Risk.
Showing effects for C/A genotype
Rheumatoid Arthritis. Evidence: 10/10. Source: PMID 17554300. ~2x Increased Risk.
Crohn's Disease. Evidence: 6/10. Source: PMID 23128233. Typical Risk.
Type 1 Diabetes. Evidence: 10/10. Source: PMID 17554260. ~1.8x Increased Risk.
Hypothyroidism. Evidence: 9/10. Source: PMID 22493691. Increased Risk.
What this genotype means for the people who carry it
Sample genotype: CC (Homozygous)
Inheriting two copies of the common C allele means you do not inherit the high-risk autoimmune variant linked to PTPN22 [1]. Large-scale genetic studies show that this genetic profile is associated with typical baseline risks for rheumatoid arthritis and type 1 diabetes [2]. However, research indicates a slight trade-off, as the C allele is associated with a minor increase in susceptibility to Crohn's disease [3]. For most individuals, this genetic profile represents the standard genetic background found in the vast majority of the global population. It does not warrant any special clinical concern or lifestyle modifications beyond standard healthy habits.
Typical baseline risk for rheumatoid arthritis; Typical baseline risk for type 1 diabetes; Slightly increased risk for Crohn's disease.
Sample genotype: AA (Homozygous)
Possessing two copies of the A allele represents the highest genetic risk category for several major autoimmune diseases at this locus [1]. Research indicates that this genetic profile is associated with an estimated 5.2-fold increase in the risk of type 1 diabetes and a 3.3-fold increase in the risk of rheumatoid arthritis [2]. The elevated risk extends to other autoimmune conditions, including juvenile idiopathic arthritis and hypothyroidism [3]. On the positive side, this genetic profile is associated with a reduced risk of developing Crohn's disease [1]. While genes are only one part of the puzzle, sharing these findings with your doctor can assist in personalized wellness planning and early detection strategies.
Significantly increased risk of type 1 diabetes; Significantly increased risk of rheumatoid arthritis; Reduced risk of Crohn's disease.
Sample genotype: CA (Heterozygous)
Inheriting one copy of the A allele moderately elevates your genetic susceptibility to multiple autoimmune disorders [1]. According to clinical studies, carriers of this genetic profile have approximately a 1.8-fold increased risk of developing type 1 diabetes and a 2-fold increased risk of rheumatoid arthritis [2]. The variant is also linked to higher susceptibility for other conditions like systemic lupus erythematosus and hypothyroidism [3]. Interestingly, this same genetic profile offers a slight protective effect against Crohn's disease [1]. Knowing this status can help you and your healthcare provider stay vigilant for early signs of joint pain, thyroid dysfunction, or blood sugar changes.
Moderately increased risk of type 1 diabetes; Moderately increased risk of rheumatoid arthritis; Slightly reduced risk of Crohn's disease.
Variants with shared genetic architecture
rs2476601 · PTPN22 Gene · Chr 1 · Autoimmune Disease Risk
rs8043085 · RASGRP1 Gene · Chr 15 · Type 2 Diabetes Risk
rs11889341 · STAT4 Gene · Chr 2 · Autoimmune Disease Risk
Novel associations for hypothyroidism include known autoimmune risk loci.
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
Content updated August 2026.
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