GWAS detected 15 loci significantly associated with chronotype in the subjects with self-reported depression, such as rs12736689 at RNASEL (P = 1.00 × 10− 09), rs509476 at RGS16 (P = 1.58 × 10− 09) and rs1006751 at RFX4 (P = 1.54 × 10− 08). This evidence concerns the gene RNASEL and major depressive disorder.