The Impact of Non-coding G-quadruplex Variants on Human Traits and Disease Susceptibility

Non-coding variants are important contributors to human traits and diseases but linking them to molecular mechanisms and phenotypes at scale remains challenging. G-quadruplexes (G4s) are four-stranded structures formed by guanine-rich sequences and have emerged as key functional elements within the non-coding genome. G4s are enriched in regulatory regions and can modulate gene expression at both the DNA and RNA levels, influencing transcription, replication, and RNA processing, positioning them as key mediators linking non-coding variation to complex biological traits. Here, we profile putative G4s across five regulatory regions in 459,449 UK Biobank genomes and perform phenome-wide association analyses spanning 2,941 plasma protein abundances, 13,321 binary traits, and 1,682 quantitative traits. We show that putative G4-modifying variants are depleted under purifying selection despite elevated local mutability and drive large, bidirectional associations with plasma proteins and clinical traits, including associations not captured by coding variants. Using a mechanism-aware collapsing strategy that groups rare non-coding variants by their predicted impact on G4 stability, we achieved stronger gene-level signals than those obtained with standard rare-variant collapsing approaches. Integrating non-coding and protein-truncating variants (PTVs) increases discovery power, revealing 843 significant associations missed by the PTV-only model. Replication in the Alliance for Genomic Discovery cohort demonstrates cross-cohort robustness. Our study suggests G4s as widespread mediators of non-coding regulation and provides a framework for mechanism-informed target discovery and prioritization across the non-coding genome.