To augment this list we performed approximate conditional analysis using GCTA software34, where the LD between variants was estimated from the Northern Finland Birth Cohort (NFBC66) consisting of 5,402 individuals of European ancestry with GWAS data imputed using CEU haplotypes from Hapmap Phase II. Assuming that the LD correlations between SNPs more than 10 Mb away or on different chromosomes are zero, we performed the GCTA model selection to select SNPs independently associated with age at menarche at genome-wide significant P-values. This software selected as independently associated with age at menarche 115 SNPs at 98 loci, 11 of which had two or more signals of association (six loci contained two signals, four loci contained three signals, and one locus contained four signals). Plots of all 106 loci are available at www.reprogen.org. SNPs with A/T or C/G alleles were excluded from this analysis to prevent strand issues leading to false-positive results.
