found it was in LD with the top chromosome 6 signal (rs7759938, r2=0.3). In HapMap the r2 between the two chr 6 SNPs was 0.015, but the D’ was 1.0. To verify the independency of additional loci, we performed a conditional analysis and meta-analysis of all 32 studies using the top SNP at all the 42 genome-wide significant regions as covariates (in addition to birth year). In these conditional analyses the possible second signals on chromosomes 2 and 14 showed strong but sub-genome-wide significant associations with age at menarche (P<7.1×10−6), suggestive of, but not confirming, second independent signals in these two regions (Fig. 1; Supplementary Table 3).
