rs7927997 — EMSY EMSY/C11orf30 Atopy Regulatory Variant

Regulatory variant near C11orf30 (EMSY) on chromosome 11q13.5

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EMSY and the Epigenetic Gateway to Atopic Disease

The C11orf30 gene — commonly known by its protein product name EMSY — sits at one of the most replicated and broadly acting loci in allergy genetics. Variants at this chromosome 11q13.5 locus have been found to influence risk for atopic dermatitis, asthma, hay fever, food allergy, poly-sensitization to multiple allergens, eosinophilic esophagitis, and inflammatory bowel disease. The rs7927997 variant is an expression quantitative trait locus (eQTL) that modulates EMSY transcript levels.

The Mechanism

The rs7927997 T allele is intergenic, sitting in a regulatory region between C11orf30 and LRRC32 (which encodes GARP, a cell-surface docking molecule for TGF-β on regulatory T cells and platelets). Two independent functional signals have been identified at this locus: one regulating EMSY and one regulating LRRC32 expression, suggesting the region operates as a multi-gene regulatory hub for immune and barrier homeostasis.

The Evidence

rs7927997 was identified in a landmark Crohn's disease GWAS meta-analysis of 6,333 cases and 15,056 controls11 Crohn's disease GWAS meta-analysis of 6,333 cases and 15,056 controls
Franke et al. Nature Genetics 2010 — increased Crohn's disease susceptibility loci to 71; rs7927997 T allele OR 1.17, p=5.62×10⁻¹³.

The eQTL function of rs7927997 was directly demonstrated by Di Narzo et al. 201622 Di Narzo et al. 2016
Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort, confirming that the T allele reduces EMSY transcript levels.

Genotype Interpretations

What each possible genotype means for this variant.

CC Common Genotype Normal

Full EMSY expression — baseline atopic risk at this chromosome 11q13.5 locus

You carry two copies of the C allele at rs7927997. This is the most common genotype, found in approximately 44% of people globally and slightly more prevalent in East Asian populations. At this locus you carry no copies of the T allele that is associated with elevated susceptibility to inflammatory bowel disease.

This genotype does not eliminate all atopic risk — genetic influences on allergy and atopy are highly polygenic — but it means you do not carry additional inflammatory burden from this particular regulatory variant.

CT Heterozygous Intermediate

One T allele — modestly elevated atopic susceptibility via reduced EMSY repressor activity

The C11orf30/EMSY locus is one of the most replicated allergy genetics findings: independently associated with eczema, asthma, hay fever, food allergy, eosinophilic esophagitis, and inflammatory bowel disease in GWAS spanning multiple ancestries. The T allele reduces EMSY expression. rs7927997 T allele carriers show ~37% T allele frequency in Europeans, making it a common risk variant, not a rare one.

The eQTL evidence (Di Narzo et al. 2016, PMID 27336838) is mechanistically precise: rs7927997 directly governs C11orf30 expression.

TT Homozygous Risk High Risk

Two T alleles — greatest reduction of EMSY repressor activity and highest atopic susceptibility at this locus

TT homozygotes at this C11orf30 locus carry additive risk relative to CT heterozygotes under the dose-response model established by Franke et al. 2010 (PMID 21102463) for Crohn's disease (OR 1.17 per allele → OR ~1.37 for TT vs CC).

The mechanistic link is precise: the T allele is an eQTL that reduces EMSY expression in blood (Di Narzo et al. 2016, PMID 27336838).