rs2240032 — RAD50 RAD50 RHS7 TH2-LCR Variant

Intronic RAD50 variant in the Th2 locus control region (RHS7); T allele alters SMAD3 and SP1 transcription factor binding, shifts DNA methylation at the IL13 promoter in cord blood, and is associated with elevated total IgE levels and atopic disease risk.

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RAD50 RHS7 — A Regulatory Switch That Shapes Your Th2 Immune Response Before Birth

Most people are surprised to learn that the gene controlling their allergic immune tone is partly located inside a DNA repair enzyme. The RAD50 gene11 RAD50 gene
A component of the MRN (MRE11-RAD50-NBS1) complex involved in double-strand DNA break sensing and repair; its introns happen to host the Th2 cytokine locus control region, an evolutionary repurposing of non-coding DNA spans a stretch of chromosome 5q31 that also functions as the master volume control for three of the most important allergy cytokines in the human body: IL-4, IL-13, and IL-5. Nested within the final introns of RAD50 is a series of DNase I hypersensitive sites22 DNase I hypersensitive sites
Regions of chromatin that are unusually accessible to DNase I enzyme, indicating open, active regulatory DNA; they mark enhancers and locus control regions (RHS4–7) that form the Th2 locus control region (TH2-LCR). Hypersensitive site 7 (RHS7) is the most distal of these elements and is critical: deleting it in mice dramatically reduces IL-4, IL-13, and IL-5 production and collapses the long-range chromosomal architecture that allows the LCR to communicate with cytokine gene promoters over distances of tens of kilobases.

rs2240032 sits at position 132,641,435 on chromosome 5 (GRCh38), within RHS7 in intron 24 of RAD50. It is one of the most consistently replicated functional variants at this locus — not merely a statistical proxy, but a variant with documented effects on transcription factor binding, DNA methylation, and gene expression.

The Mechanism

The T allele of rs2240032 alters the binding affinity of SMAD333 SMAD3
A transcription factor downstream of TGF-β signalling that, paradoxically, is also recruited to Th2 regulatory elements and modulates their activity and SP144 SP1
Specificity protein 1, a zinc-finger transcription factor that binds GC-rich motifs and influences chromatin accessibility at regulatory elements at the RHS7 element, as shown by electrophoretic mobility shift assays (EMSA) combined with mass spectrometry proteomics. The RHS7 region itself possesses repressor activity in reporter assays, suggesting that variant-driven changes in SMAD3/SP1 occupancy fine-tune the repressive tone of the LCR rather than acting as a simple activator.

The consequence of this altered occupancy is epigenetic: the T allele is associated with changes in DNA methylation55 DNA methylation
Addition of a methyl group to cytosine in CpG dinucleotides; hypermethylation of a gene's promoter typically silences it, hypomethylation activates it at the IL13 promoter, detectable already in cord blood — meaning the epigenetic programming is established in utero, before any environmental allergen exposure.

The Evidence

The functional characterisation was carried out by Kretschmer et al. (Allergy 2014)66 Kretschmer et al. (Allergy 2014), who used Jurkat T-cell nuclear extracts and LC-MS/MS proteomics to demonstrate that rs2240032 drives allele-specific assembly of SMAD3, SP1, and associated protein complexes at RHS7. The same element showed repressor activity in luciferase reporter assays in both Jurkat and HeLa cells.

The clinical link was established by Schieck et al. (Allergy 2014)77 Schieck et al. (Allergy 2014) using the PASTURE birth cohort: IL13 promoter methylation was significantly different by rs2240032 genotype in cord blood (p=0.003) and at age 4.5 years (p=0.032), demonstrating epigenetic persistence from birth into early childhood. In a larger MAGICS/ISAAC II sample of 1,145 children, the T allele was also associated with elevated total serum IgE levels (p=0.023) and altered RAD50 and IL4 gene expression.

The asthma GWAS context was established by Li et al. (2010)88 Li et al. (2010), who identified rs2240032 in the RAD50-IL13 region at P=6.68×10⁻⁶ in 473 severe asthma cases versus 1,892 controls. Fine-mapping by Sharma et al. (Allergy 2014)99 Sharma et al. (Allergy 2014) using 1000 Genomes Project imputation narrowed the 5q31 signal, placing rs2240032 and the nearby rs2214370 among the top associated variants at the RAD50 RHS7 locus.

Practical Actions

The T allele's effect is additive: one copy raises IL13 promoter methylation modestly; two copies compound this. Because the epigenetic imprint is set prenatally, the strategic window is early — optimising the early-life environment and monitoring for atopic sensitisation in infancy can meaningfully shift outcomes for T allele carriers. Elevated IgE is the cardinal biomarker: tracking total and specific IgE levels gives carriers an objective measure of their Th2 tone and a target for clinical intervention with allergen immunotherapy if sensitisation occurs.

Interactions

rs2240032 operates within a dense haplotype block spanning the RAD50-IL13 locus. The nearby rs2244012 (RAD50 intron 2) and the IL13 coding variant rs20541 (R130Q) have independent effects on the same Th2 axis. Fine-mapping data from Sharma et al. suggest that multi-locus haplotypes combining RHS7 variants with IL13 promoter and coding variants confer risks up to fourfold higher for elevated IgE than single variants alone. Interaction analysis combining rs2240032 with rs2244012 and rs1800925 (IL13 promoter) would be informative in clinically complex allergy cases.

Genotype Interpretations

What each possible genotype means for this variant.

CC Normal

Standard Th2 regulatory tone

You carry two copies of the common C allele at this regulatory element inside the RAD50 gene. RHS7 shows normal SMAD3 and SP1 binding at this position, and IL13 promoter methylation is in the typical range from birth onward. About 68% of people carry this genotype globally, rising to roughly 64% in Europeans. Standard allergy vigilance applies, but your Th2 locus control region does not carry the variant associated with elevated IgE or altered epigenetic programming at the IL13 gene.

CT Intermediate

One copy of the Th2-LCR risk variant — modestly elevated IgE tendency

The single-copy effect is additive: one T allele produces intermediate methylation changes at the IL13 promoter compared to either CC or TT. Because this epigenetic pattern is established in utero, it represents a preset Th2 sensitivity that environmental exposures during infancy and early childhood can either amplify or partially offset. If you have clinical atopic symptoms (eczema, allergic rhinitis, asthma), periodic IgE monitoring gives a useful quantitative picture of your Th2 tone and whether allergen immunotherapy is achieving its intended effect of downregulating IgE-mediated sensitisation.

TT High Risk

Two copies of the Th2-LCR risk variant — elevated IgE tendency and compounded epigenetic programming

With both alleles carrying the T variant, SMAD3 and SP1 binding at RHS7 is shifted on both chromosomes, amplifying the regulatory perturbation. The epigenetic programming at the IL13 promoter is established in utero, so the altered methylation pattern is present before birth. This does not guarantee clinical allergy — environmental and other genetic factors play major roles — but it establishes a higher baseline Th2 sensitivity. Total IgE monitoring, proactive identification of sensitisation, and early intervention with allergen immunotherapy where appropriate are the evidence- supported management levers at this locus.