rs11588172 (LINC02793): RHCE expression variant

Key takeaways

• rs11588172 sits near LINC02793 (a long intergenic non-coding RNA gene) and IFITM3P7 (a pseudogene in the interferon-induced transmembrane protein family)
• GTEx data from 953 donors link this variant to reduced RHCE expression in both breast mammary tissue and skeletal muscle
• The same direction of effect appears in two independent tissue types, supporting a consistent regulatory signal
• Clinical disease associations at this locus have not been established from the available study data

What the research says GTEx v11 eQTL analysis (an eQTL, or expression quantitative trait locus, is a variant associated with changes in nearby gene expression levels) identifies rs11588172 as linked to reduced RHCE expression in breast mammary tissue (slope -0.22, meaning the alternate allele is associated with a 0.22-unit decrease in log2-normalized expression, p=2.8e-5) and skeletal muscle (slope -0.18, p=8.7e-6), based on 953 donors with FDR (false discovery rate) correction applied GTEx Portal. This locus also falls within a genomic region studied in a multi-trait genome-wide analysis of shared genetic architecture between Alzheimer's disease and cardiovascular traits including coronary artery disease, atrial fibrillation, and blood pressure, though specific quantified associations for rs11588172 in clinical disease outcomes were not reported in the provided study data.

Reported associations

• RHCE expression in breast mammary tissue: reduced expression in carriers of the alternate allele (slope -0.22, p=2.8e-5, GTEx v11 n=953) GTEx Portal
• RHCE expression in skeletal muscle: reduced expression in carriers of the alternate allele (slope -0.18, p=8.7e-6, GTEx v11 n=953) GTEx Portal

Evidence quality Both eQTL associations come from GTEx v11 (953 donors), a large standardized tissue expression reference with FDR correction applied at FDR<0.05; p-values are 2.8e-5 and 8.7e-6 for breast mammary tissue and skeletal muscle respectively. Effect sizes (slopes of -0.22 and -0.18 on a log2-normalized expression scale) both point toward reduced RHCE expression in alternate allele carriers, with concordant direction across both tissues. A multi-trait genome-wide association study (Koskeridis et al., Nature Communications, 2024) investigated shared genetic loci between Alzheimer's disease and cardiovascular diseases in the broader genomic region containing this locus, but the provided study data did not include a direct quantified association for rs11588172 at the disease-trait level, so disease-level evidence is absent from the available sources.

Tissue-specific expression effects

• RHCE: reduced expression in both breast mammary tissue and skeletal muscle in carriers of the alternate allele; the effect is slightly larger in breast mammary tissue (slope -0.22) than in skeletal muscle (slope -0.18) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.