rs4239702

This is a intron variant variant in the CD40 gene.

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GWAS Catalog Trait Associations (5)

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

lymphocyte count

Orrù V et al. “Complex genetic signatures in immune cells underlie autoimmunity and inform therapy.” Nature Genetics 52(10):1036-1045 (2020)
Allele C
OR 0.28
p 2.0e-27
N 3,656
Large GWAS
European

rheumatoid arthritis

Okada Y et al. “Genetics of rheumatoid arthritis contributes to biology and drug discovery.” Nature 506(7488):376-381 (2014)
Allele C
OR 1.13
p 4.0e-18
N 79,799
Large GWAS
multi-ancestry
Laufer VA et al. “Genetic influences on susceptibility to rheumatoid arthritis in African-Americans.” Human Molecular Genetics 28(5):858-874 (2019)
Allele C
OR 0.09
p 3.0e-14
N 2,308
Large GWAS
multi-ancestry

CD40 measurement

Hillary RF et al. “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Genome Medicine 12(1):60 (2020)
Allele T
OR 0.40
p 7.0e-15
N 982
Small GWAS
European

tumor necrosis factor ligand superfamily member 13B amount

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele C
OR 0.04
p 2.0e-14
N 47,745
Large GWAS
European

low affinity immunoglobulin epsilon Fc receptor measurement

Pietzner M et al. “Mapping the proteo-genomic convergence of human diseases.” Science (new York, N.y.) 374(6569):eabj1541 (2021)
Allele T
OR 0.11
p 2.0e-13
N 10,708
Large GWAS
European
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Research that mentions this SNP (2)

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Reduction of CD83 Expression on B Cells and the Genetic Basis for Rheumatoid Arthritis: Comment on the Article by Thalayasingam et al
FunctionalN=16Yumi Tsuchida et al.(2018)· Arthritis &amp; Rheumatology

This functional study integrates epigenomic datasets (ATAC-seq, Hi-C, ChIP-seq, RNA-seq) from fibroblast-like synoviocytes (FLS) to map the functional relevance of 101 fine-mapped rheumatoid arthritis GWAS associations. FLS regulatory elements account for 24% of RA heritability, and the study assigns putative target genes to RA risk loci, identifying TNFAIP3, IFNAR1, CDK6, RBPJ and others as disease-relevant genes. TNF stimulation reveals dynamic chromatin interactions and differential gene expression at RA-associated regulatory regions.

Traits studied:Rheumatoid arthritis
PubMedDOIMetascience Observatory
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Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B
AssociationN=6,033Jiang DK et al.(2015)· Hepatology

A genome-wide association study of 83 plasma proteins relevant to cardiovascular disease in 3,394 European subjects identified 79 genome-wide significant loci (p<5e-8), with 55 replicating in independent cohorts (n=2,639). Using eQTL analysis and network methods, the authors proposed plausible causal mechanisms for 25 trans-acting loci including post-translational regulation of KITLG by MMP9 and several receptor-ligand pairs. Multiple loci showed evidence of causal association with coronary artery disease risk.

Traits studied:AtherosclerosisCoronary artery diseasePlaque rupturePlasma protein levels (83 cardiovascular disease-related proteins)Thrombosis
PubMedDOIMetascience Observatory

About CD40

This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease pathogenesis. Mutations affecting this gene are the cause of autosomal recessive hyper-IgM immunodeficiency type 3 (HIGM3). Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Nov 2014]

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Gene information from NCBI Gene. Variant classifications from ClinVar.

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