What you carry at this position in your DNA and what research says about it.
Autoimmune Disease Risk: 7/10 evidence, 33 publications.
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Sample genotype (not yours): G/G
Significantly Elevated Autoimmune Risk
Carrying two copies of the G allele is associated with a roughly twofold increase in Crohn's disease risk and a 1.6-fold increase in type 1 diabetes risk. This genotype is also linked to a higher susceptibility to other inflammatory conditions.
What this genotype means: Approximately 2x higher risk for Crohn's disease; Approximately 1.6x higher risk for type 1 diabetes; Increased susceptibility to rheumatoid arthritis and ulcerative colitis.
Sample genotype (not yours): G/T
Moderately Elevated Autoimmune Risk
Carrying one copy of the G allele moderately increases the risk of developing Crohn's disease and type 1 diabetes by about 1.3 times. It also slightly raises susceptibility to other chronic inflammatory conditions.
What this genotype means: Approximately 1.3x higher risk for Crohn's disease; Approximately 1.3x higher risk for type 1 diabetes; Slightly increased susceptibility to other autoimmune conditions.
Sample genotype (not yours): T/T
Typical Autoimmune Risk
Carrying two copies of the T allele is the most common genetic profile and is associated with typical baseline risks for Crohn's disease and type 1 diabetes.
What this genotype means: Typical baseline risk for Crohn's disease; Typical baseline risk for type 1 diabetes; Standard regulation of inflammatory pathways.
Gene function and biological role
Gene Function: The PTPN2 gene encodes protein tyrosine phosphatase non-receptor type 2, an enzyme that acts as a critical brake on inflammatory signaling pathways [1]. This enzyme is highly active in immune cells and the intestinal lining, where it helps maintain the delicate balance of the immune system [2]. By dephosphorylating key signaling molecules, it prevents the overactivation of immune responses that can lead to tissue damage [1]. When this gene functions suboptimally, the body struggles to shut down inflammatory cascades, leaving tissues vulnerable to chronic inflammation [2]. Consequently, variations in this gene are heavily implicated in several autoimmune and inflammatory conditions [1].
Variant Impact: The rs2542151 variant is located in an intergenic region downstream of the PTPN2 gene, where it acts as a regulatory modifier of gene expression [3]. The G allele is the minor variant and is associated with reduced control over inflammatory signaling cascades [2]. This genetic change alters how immune cells respond to cytokines, leading to heightened sensitivity and prolonged inflammatory states [2]. Because it affects a fundamental pathway of immune tolerance, this single nucleotide polymorphism is a shared genetic link across multiple distinct autoimmune diseases [3].
Key Insight: This single genetic variant serves as a shared biological bridge between inflammatory bowel diseases and type 1 diabetes, demonstrating how different autoimmune conditions can share identical genetic roots.
Location: PTPN2. Chromosome 18 · 18p11.21 · 12.8 Mb
Estimated prevalence by population
Global 2.9%; European 2.6%; African 4.3%; East Asian 2.8%; South Asian 3.5%; Americas 2.0%; Ashkenazi 0.9%; Finnish 1.9%; Middle Eastern 1.6%; Amish 0.2%.
Estimated GG genotype frequency.
Global 27.9%; European 27.0%; African 32.9%; East Asian 28.0%; South Asian 30.3%; Americas 24.5%; Ashkenazi 17.0%; Finnish 24.0%; Middle Eastern 22.0%; Amish 8.8%.
Estimated GT genotype frequency.
Global 69.1%; European 70.4%; African 62.8%; East Asian 69.2%; South Asian 66.2%; Americas 73.5%; Ashkenazi 82.1%; Finnish 74.0%; Middle Eastern 76.4%; Amish 91.0%.
Estimated TT genotype frequency.
Showing effects for G/G genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 7/10. Source: PMID 17554261. ~2x Elevated Risk.
Ulcerative Colitis. Evidence: 4/10. Source: PMID 18438406. Elevated Risk.
Autoimmune Diseases
Rheumatoid Arthritis. Evidence: 3/10. Source: PMID 19359276. Elevated Risk.
Juvenile Arthritis. Evidence: 3/10. Source: PMID 19565500. Elevated Risk.
Cardiovascular & Metabolic
Diabetes & Glycemic Traits
Type 1 Diabetes. Evidence: 6/10. Source: PMID 17554260. ~1.6x Elevated Risk.
Showing effects for G/T genotype
Crohn's Disease. Evidence: 7/10. Source: PMID 17554261. ~1.3x Elevated Risk.
Ulcerative Colitis. Evidence: 4/10. Source: PMID 18438406. Slightly Elevated Risk.
Rheumatoid Arthritis. Evidence: 3/10. Source: PMID 19359276. Slightly Elevated Risk.
Juvenile Arthritis. Evidence: 3/10. Source: PMID 19565500. Slightly Elevated Risk.
Type 1 Diabetes. Evidence: 6/10. Source: PMID 17554260. ~1.3x Elevated Risk.
Showing effects for T/T genotype
Crohn's Disease. Evidence: 7/10. Source: PMID 17554261. Typical Risk.
Ulcerative Colitis. Evidence: 4/10. Source: PMID 18438406. Typical Risk.
Rheumatoid Arthritis. Evidence: 3/10. Source: PMID 19359276. Typical Risk.
Juvenile Arthritis. Evidence: 3/10. Source: PMID 19565500. Typical Risk.
Type 1 Diabetes. Evidence: 6/10. Source: PMID 17554260. Typical Risk.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Inheriting two copies of the G allele significantly impacts the regulation of the body's inflammatory responses [1]. Large-scale genetic studies have demonstrated that this genotype doubles the risk of developing Crohn's disease compared to the typical population [2]. Additionally, it elevates the risk of type 1 diabetes by approximately 1.6 times [3]. The underlying biological mechanism involves a reduced ability of the PTPN2 enzyme to shut down active immune signals, leading to persistent inflammation in the gut and pancreas [1]. This lack of immune braking also increases susceptibility to other autoimmune conditions, such as ulcerative colitis and rheumatoid arthritis [4]. Individuals with this genotype may also experience an earlier onset of type 1 diabetes if the disease develops [5].
Approximately 2x higher risk for Crohn's disease; Approximately 1.6x higher risk for type 1 diabetes; Increased susceptibility to rheumatoid arthritis and ulcerative colitis.
Sample genotype: GT (Heterozygous)
Possessing one copy of the G allele results in a moderate increase in susceptibility to several autoimmune disorders [1]. Research indicates that this heterozygous genotype elevates the risk of both Crohn's disease and type 1 diabetes by approximately 1.3 times [2]. Because only one copy of the risk allele is present, the cellular impact is typically intermediate compared to those with two copies of the risk allele [1]. The PTPN2 enzyme still functions but may not control inflammatory signaling cascades as efficiently as the typical genotype [3]. This slight reduction in immune regulation also contributes to a marginally higher risk for ulcerative colitis and rheumatoid arthritis [4]. Understanding this genetic predisposition can highlight the importance of monitoring for early symptoms of digestive or metabolic inflammation [2].
Approximately 1.3x higher risk for Crohn's disease; Approximately 1.3x higher risk for type 1 diabetes; Slightly increased susceptibility to other autoimmune conditions.
Sample genotype: TT (Homozygous)
Having two copies of the T allele represents the standard genetic baseline for the majority of the global population [1]. This genotype is associated with normal, typical levels of PTPN2 enzyme activity, which helps maintain proper immune tolerance and gut barrier function [2]. Consequently, there is no genetically elevated risk for Crohn's disease or type 1 diabetes from this specific variant [3]. The immune system is generally able to regulate inflammatory signals effectively, preventing the chronic overactivation seen in risk-allele carriers [2]. While autoimmune diseases can still develop due to other genetic and environmental factors, this particular locus does not contribute to an increased susceptibility [1].
Typical baseline risk for Crohn's disease; Typical baseline risk for type 1 diabetes; Standard regulation of inflammatory pathways.
Variants with shared genetic architecture
rs1893217 · PTPN2 Gene · Chr 18 · Autoimmune Disease Risk
rs7234029 · PTPN2 Gene · Chr 18 · Crohn's Disease Risk
rs35667974 · IFIH1 Gene · Chr 2 · Autoimmune Disease Risk
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
A polymorphism in PTPN2 gene is associated with an earlier onset of type 1 diabetes.
Content updated August 2026.
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