What you carry at this position in your DNA and what research says about it.
Inflammatory Disease Risk: 6/10 evidence, 57 publications.
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Sample genotype (not yours): T/T
Typical Inflammatory Risk and Better Treatment Response
Balanced cytokine production supports a typical, well-regulated immune response. This genotype is linked to a lower risk of inflammatory bowel issues and a more favorable response to certain anti-inflammatory therapies.
What this genotype means: Typical risk of inflammatory conditions; Better response to TNF-alpha blockers; Typical risk of chemotherapy-induced platelet drops.
Sample genotype (not yours): C/C
Highest Risk of Inflammatory and Autoimmune Conditions
Carrying two copies of the C allele is linked to the highest levels of cytokine production and a significantly elevated risk of inflammatory disorders. This genotype also correlates with a higher susceptibility to adverse drug reactions.
What this genotype means: Highest risk of Crohn's disease; Significantly increased susceptibility to autoimmune conditions; Elevated risk of chemotherapy-induced platelet depletion.
Sample genotype (not yours): T/C
Moderately Increased Risk of Inflammatory and Autoimmune Conditions
Carrying one copy of the C allele is associated with elevated cytokine activity and a moderately higher risk of inflammatory conditions. This genetic profile may also increase susceptibility to specific medication side effects.
What this genotype means: Moderately increased risk of Crohn's disease; Higher susceptibility to autoimmune conditions; Increased risk of specific drug-induced side effects.
Gene function and biological role
Gene Function: Lymphotoxin alpha, encoded by the LTA gene, is a key pro-inflammatory cytokine belonging to the tumor necrosis factor family [1]. It plays a critical role in mediating immune responses, cell survival, and the formation of secondary lymphoid organs [1]. Because of its close physical proximity to the TNF gene on chromosome 6, genetic variations in this region often influence the expression of both cytokines [2]. Dysregulation of lymphotoxin alpha is strongly linked to chronic inflammatory conditions, autoimmune disorders, and tissue damage [3]. Proper regulation of this cytokine is essential for maintaining a balanced immune response and preventing systemic inflammation [4].
Variant Impact: The rs1799964 variant is an upstream genetic change located in the promoter region shared by the LTA and TNF genes [2]. This specific change alters the transcription rate of these powerful pro-inflammatory cytokines [5]. The C allele is associated with significantly higher promoter activity, leading to increased production of tumor necrosis factor alpha [4]. This elevated cytokine production can trigger a more reactive and prolonged inflammatory response [6]. Consequently, this variant serves as a genetic modulator for susceptibility to various autoimmune and inflammatory diseases [3].
Key Insight: This genetic variant sits in a shared promoter region that simultaneously controls the activity of two major inflammatory genes, LTA and TNF. Carrying the C allele can significantly increase the transcription rate of these genes, leading to a highly reactive immune response.
Location: LTA. Chromosome 6 · 6p21.33 · 31.6 Mb
Estimated prevalence by population
Global 64.8%; European 62.5%; African 70.3%; East Asian 65.5%; South Asian 45.7%; Americas 65.1%; Ashkenazi 60.9%; Finnish 67.6%; Middle Eastern 63.3%; Amish 66.5%.
Estimated TT genotype frequency.
Global 31.3%; European 33.1%; African 27.1%; East Asian 30.9%; South Asian 43.8%; Americas 31.2%; Ashkenazi 34.3%; Finnish 29.3%; Middle Eastern 32.5%; Amish 30.1%.
Estimated TC genotype frequency.
Global 3.9%; European 4.4%; African 2.6%; East Asian 3.6%; South Asian 10.5%; Americas 3.7%; Ashkenazi 4.8%; Finnish 3.2%; Middle Eastern 4.2%; Amish 3.4%.
Estimated CC genotype frequency.
Showing effects for T/T genotype
Immunity & Inflammation
Chronic Inflammatory Diseases
Crohn's Disease. Evidence: 5/10. Source: PMID 21102463. Typical Risk.
Autoimmune Diseases
Autoimmune Disease Risk. Evidence: 6/10. Source: PMID 37377963. Typical Risk.
Organ Systems
Respiratory Health
Childhood Asthma. Evidence: 6/10. Source: PMID 31669095. Typical Risk.
Pharmacogenomics
Chemotherapy Response
Chemotherapy Toxicity. Evidence: 5/10. Source: PMID 37898586. Typical Risk.
Antimicrobial & Antiviral Response
Antiviral Neuropathy. Evidence: 5/10. Source: PMID 20887379. Typical Risk.
Showing effects for C/C genotype
Crohn's Disease. Evidence: 5/10. Source: PMID 21102463. ~1.19x Higher Risk.
Autoimmune Disease Risk. Evidence: 6/10. Source: PMID 37377963. Highest Risk.
Childhood Asthma. Evidence: 6/10. Source: PMID 31669095. Highest Risk.
Chemotherapy Toxicity. Evidence: 5/10. Source: PMID 37898586. Increased Risk.
Antiviral Neuropathy. Evidence: 5/10. Source: PMID 20887379. Increased Risk.
Showing effects for T/C genotype
Crohn's Disease. Evidence: 5/10. Source: PMID 21102463. Increased Risk.
Autoimmune Disease Risk. Evidence: 6/10. Source: PMID 37377963. Increased Risk.
Childhood Asthma. Evidence: 6/10. Source: PMID 31669095. Increased Risk.
What this genotype means for the people who carry it
Sample genotype: TT (Homozygous)
Balanced immune signaling is a hallmark of this genotype, which is associated with typical baseline levels of pro-inflammatory cytokines [1]. Research indicates that carrying two copies of the T allele provides a protective effect against Crohn's disease compared to carrying the C allele [2]. Additionally, individuals with this genetic profile show a lower susceptibility to other autoimmune conditions like rheumatoid arthritis and type 1 diabetes [3]. Clinical studies have also observed a significantly better therapeutic response to tumor necrosis factor alpha blockers in patients with this genotype [4]. Furthermore, this genetic makeup is associated with a typical risk of developing sensory neuropathy during certain antiviral treatments [5]. It also correlates with a lower likelihood of experiencing severe platelet drops during specific chemotherapy regimens [6]. Overall, this profile represents a well-balanced inflammatory baseline.
Typical risk of inflammatory conditions; Better response to TNF-alpha blockers; Typical risk of chemotherapy-induced platelet drops.
Sample genotype: CC (Homozygous)
Maximum promoter activity associated with two copies of the C allele results in the highest levels of pro-inflammatory cytokine expression [1]. This pronounced inflammatory response significantly raises the risk of developing Crohn's disease [2]. Strong associations have also been established between this genotype and an increased risk of rheumatoid arthritis and type 1 diabetes [3]. Furthermore, individuals with this genetic profile have a higher susceptibility to childhood-onset asthma and elevated lymphocyte counts [4] [5]. In clinical settings, this genotype is linked to a higher incidence of sensory neuropathy during antiviral therapy with stavudine [6]. It also predicts a greater likelihood of severe platelet depletion during chemotherapy regimens [7]. Proactive anti-inflammatory strategies and close coordination with healthcare providers during treatments are highly relevant for this profile [8].
Highest risk of Crohn's disease; Significantly increased susceptibility to autoimmune conditions; Elevated risk of chemotherapy-induced platelet depletion.
Sample genotype: TC (Heterozygous)
Elevated promoter activity from the single C allele leads to moderately increased production of pro-inflammatory cytokines [1]. This heightened inflammatory state is linked to a moderately increased risk of developing Crohn's disease [2]. Susceptibility to other autoimmune disorders, including rheumatoid arthritis and type 1 diabetes, is also elevated with this genotype [3]. In addition to autoimmune risks, this genetic variation is associated with a higher likelihood of childhood-onset asthma [4]. Pharmacogenomic studies indicate that carrying this allele increases the risk of developing sensory neuropathy when taking specific antiviral medications like stavudine [5]. There is also an increased risk of experiencing low platelet counts during chemotherapy treatments involving cisplatin or docetaxel [6]. Managing systemic inflammation through lifestyle and dietary choices may be particularly beneficial for individuals with this profile [7].
Moderately increased risk of Crohn's disease; Higher susceptibility to autoimmune conditions; Increased risk of specific drug-induced side effects.
Variants with shared genetic architecture
rs2229094 · LTA Gene · Chr 6 · Gastric Cancer Risk
rs1800630 · LTA Gene · Chr 6 · Autoimmune Disease Risk
rs2229092 · LTA Gene · Chr 6 · Psoriasis Risk
Content updated August 2026.
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