rs2239704

This variant is located in the LTA gene.

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GWAS Catalog Trait Associations (5)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

eosinophil count

Xiang R et al. “Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction.” Nature Communications 16(1):4260 (2025)
Allele A
OR 0.02
p 4.0e-21
N 406,469
Large GWAS
European

monocyte count

Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele A
OR 0.02
p 2.0e-12
N 408,112
Large GWAS
European

cervical carcinoma

Leo PJ et al. “Defining the genetic susceptibility to cervical neoplasia-A genome-wide association study.” Plos Genetics 13(8):e1006866 (2017)
Allele A
OR 1.23
p 6.0e-9
N 9,347
Large GWAS
European
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ClinVar annotation

Risk Factor
1 submitter2 publications

Leprosy, early-onset, susceptibility to

View on ClinVar →
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Research that mentions this SNP (2)

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Genetic variation in the TLR and NF‐κB pathways and cervical and vulvar cancer risk: A population‐based case–control study
AssociationN=2,493Clara Bodelon et al.(2014)· International Journal of Cancer

Population-based case-control study of 876 cervical cancer cases, 517 vulvar cancer cases, and 1,100 controls examining genetic variation in TLR and NFκB pathways. The TNF region was significantly associated with cervical cancer (gene-based P=2.0×10⁻⁴) and vulvar cancer (gene-based P=1.0×10⁻⁴) risk. The rare A allele of rs2239704 in the LTA gene 5' UTR was significantly associated with increased cervical cancer risk (OR=1.31, 95% CI: 1.15–1.50) and vulvar cancer risk (OR=1.51, 95% CI: 1.30–1.75).

Traits studied:Cervical cancerVulvar cancer
PubMedDOIMetascience Observatory
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A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 polymorphism in severe malaria susceptibility
AssociationN=2,162Mahamadou Diakite et al.(2009)· Human Genetics

A case-control association study of 2162 Gambian individuals identified a BAT2 polymorphism (rs1046089) significantly associated with severe malaria (G vs A OR=0.73, P<10⁻⁶ for allelic test; recessive model GG vs GA/AA OR=0.48, P<10⁻⁶). Haplotype analysis confirmed BAT2-associated variants conferred ~40% reduced risk. Secondary findings included AIF1 (rs2259571, OR=0.57, P=0.004) and TNF-238 (rs361525, OR=1.33, P=0.04) associations, though only BAT2 remained significant after Bonferroni correction.

Traits studied:Cerebral malariaSevere malariaSevere malarial anaemia
PubMedDOIMetascience Observatory

About LTA

The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

View all LTA variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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