Three loci were associated with PCOS in our cohort (Table 1) at a genome-wide significant threshold after Stage 3: the 8p32.1 GATA4/NEIL2 locus, the 9q22.32 c9orf3/FANCC locus, and 11p14.1 FSHB/ARL14EP locus with sample-size weighted three-strata meta-analyses Pmeta-all=8.0 × 10−10; Pmeta-all=4.6 × 10−13; and Pmeta-all=1.9 × 10−8, respectively (Table 2; Figs 1a and 2a–c; Supplementary Data 1, 2). This evidence concerns the gene NEIL2 and polycystic ovary syndrome.