Identification of novel loci regulating circulating melatonin and its causal relationship with hypertension

Melatonin exerts pleiotropic physiological functions and diverse disease associations, but its genetic architecture remains largely uncharacterized. Using low-coverage whole-genome sequencing (lcWGS) in 3,605 Han Chinese adults, we identified four independent loci (P < 1 × 10⁻⁷) associated with circulating melatonin (pg/mL)-located within or near LINC01807, PTPRD, EDIL3/NBPF22P, and LMO1/STK33. Conditional analyses indicated that the STAARpipeline single-variant and sliding-window signals were largely driven by these genome-wide association study (GWAS) lead variants, whereas a gene-centric noncoding aggregation signal in the ZSWIM9 promoter region remained independent. These genes showed tissue-specific expression in neural, vascular, and adrenal tissues (GTEx ). The heritability of serum melatonin was estimated at 21.72% (SE = 11.2%, P = 0.029) using GCTA-GREML, with the four independent significant loci collectively explaining 3.40%. Genetic risk score and one-sample Mendelian randomization analyses suggested a protective effect of higher serum melatonin levels on hypertension risk (OR = 0.45, P = 0.015), as well as on systolic (β = - 4.14, P = 0.014) and diastolic blood pressure (β = - 3.10, P = 0.007). Summary-data-based Mendelian Randomization and colocalization analyses suggested that LMO1 and PTPRD may influence hypertension through tissue-specific expression and DNA methylation. These findings reveal novel genetic contributors to melatonin regulation and establish their putative causal relationship with hypertension.