eQTM Atlas maps over 11 million DNA methylation–gene expression associations across 11 tissues and four diseases

A preprint posted to bioRxiv on 10 June 2026 describes the eQTM Atlas, a comprehensive reference resource cataloguing expression quantitative trait methylation (eQTM) associations — statistical links between DNA methylation at specific CpG sites and gene expression levels — across 11 human tissues and four disease contexts. The resource contains over 11 million such associations.

Epigenome-wide association studies (EWAS) regularly identify CpG sites associated with complex traits and diseases, but the functional interpretation of these findings has been hampered by the absence of a systematic resource connecting methylation changes to their downstream effects on gene expression. Current practice typically links EWAS CpGs to nearby genes based on genomic proximity alone, a method that misses distal regulatory relationships and conflates correlation with mechanism.

The eQTM Atlas aims to address this gap by providing a tissue-resolved, disease-contextualised map of methylation-expression relationships that researchers can query when interpreting EWAS findings. The multi-tissue design is particularly valuable given the tissue-specificity of both methylation patterns and gene regulation. The resource is positioned as a community tool for functional genomics, complementing existing eQTL and chromatin accessibility references. The preprint has not yet been peer-reviewed.