This array included up to ~25,000 SNPs, or their proxy markers, that showed sub-genome-wide associations (P<0.0022) with age at menarche in our earlier GWAS4. SNPs were excluded from individual study datasets if they were poorly imputed or were rare (MAF <1%). Test statistics for each study were adjusted using study-specific genomic control inflation factors and where appropriate individual studies performed additional adjustments for relatedness (Supplementary Table 1). Association statistics for each of the 2,441,815 autosomal SNPs that passed QC in at least half of the studies were combined across studies in a fixed effects inverse-variance meta-analysis implemented in METAL32.
