Population-scale molecular reconstruction of human circadian phase from blood biomarkers

Circadian timing influences human physiology and disease risk, yet scalable measures of molecular circadian phase are lacking. Here we infer circadian phase from circulating blood biomarkers in UK Biobank. Among 3,228 plasma biomarkers, 58% exhibit significant diurnal variation, with harmonic modeling identifying acrophase clustering consistent with canonical circadian patterns and independent constant-routine datasets. Machine-learning models trained on plasma proteomics predict sampling time (R²≈0.68) and retain substantial accuracy with ∼60 proteins. We define a novel construct, circadian acceleration (CA), as deviation from the population-average phase; CA is temporally stable, associates with chronotype and shift work, and responds to environmental perturbation. CA is heritable (h² _SNP ≈0.10) and genetically correlated with chronotype and accelerometry-derived sleep traits. These results establish plasma proteomics as a scalable approach for population-level molecular circadian phenotyping.