In order to establish whether genome-wide significant SNPs with low LD in the same chromosomal region (defined as r2<0.05 in a 750 kb region) were independent loci, we carried out a conditional analysis. Each study performed a genome-wide analysis for age at menarche using linear regression adjusting for the top signal at each of the 42 associated regions to determine whether potential second signals remained significant even after adjusting for these variants. Birth year was also included as a covariate. Results from each individual study were meta-analysed to determine whether these potential second signals were truly independent (i.e. if P<5.0×10−8).
