Using data from a recent genomic map of Copy Number Variation (CNV)25, we established that none of the 42 known, confirmed or possible novel menarche loci were related to CNVs. Next we explored the 1,052 CNV tagging SNPs for association with age at menarche in our GWAS sample. Only one tag SNP was associated with age at menarche after Bonferroni correction (rs3101336, P=3×10−7; Supplementary Fig. 7). This SNP tags a CNV near to the NEGR1 gene locus, which has been previously associated with body mass index20.
