We then investigated whether any of our genome-wide significant loci exerted pleiotropic actions by looking at their association with height, craniofacial shape and size and permanent tooth eruption. In the case of height, we conducted linear regression of height measured at age 17 (in ALSPAC) and age 31 (in NFBC) on genome-wide significant SNPs from Table 1. For craniofacial shape and size, we looked up genome-wide significant SNPs from the present study in the results from a previous GWAS of the 54 variables characterizing different facial features consisting of facial height, width, convexity and prominence of landmark in respect to facial planes (11) (see Supplementary Material, Fig. S4, for a list of distances examined). To account for multiple testing, empirical levels of significance were determined using permutation analyses, where for each SNP, genotype was permuted with respect to the 54 craniofacial variables. In this way, an adjusted P-value could be calculated for each SNP, which took into account the fact that association had been tested across the 54 correlated variables.
