To summarize the information obtained from the single-SNP and GCTA analyses, the 105 SNPs selected from the uni-variate analysis and the 115 SNPs selected from the GCTA model selection analysis were combined into a single list of signals independently associated with age at menarche (Supplementary Table 2), using the following selection process (Extended Data Figure 1). For loci with no evidence of allelic heterogeneity, if the uni-variate signal was genome-wide significant, the lead uni-variate SNP was selected (94 independent association signals follow this criterion); otherwise the lead GCTA SNP was selected instead (one independent signal). For loci where evidence for allelic heterogeneity was found, all signals identified in the GCTA joint model were selected if GCTA selected the uni-variate index SNP (21 independent signals at 8 loci) or a very good proxy (r2>0.8) (7 independent signals at 3 loci). When instead GCTA selected a SNP independent from the uni-variate index SNP, both the lead uni-variate SNP and all signals identified in the GCTA joint model were selected (0 independent signals).
