Supplementary Material, Figures S2 and S3 show LocusZoom plots of regression analyses for ‘age at first tooth’ and ‘number of teeth’, respectively, at each genome-wide significant locus after meta-analysis (9). For most loci, there appeared to be evidence of secondary signals independent of the lead SNP at the locus. To quantify the evidence for independent secondary signals, we first calculated the effective number of statistical tests in each region using Nyholt's procedure (10). For each locus, we estimated the threshold for a family-wise error rate of 5% by dividing alpha = 0.05 by the corresponding number of effective tests in that region, and used this threshold for declaring a secondary signal as significant. These thresholds as well as the strongest P-value in each region after conditioning on the lead SNP are presented in Supplementary Material, Table S3. These analyses showed that there were likely to be independent secondary signals at rs11077486 (KCNJ2 KCNJ160), rs2520397 (FAM155E–EDA), rs1951867 (BMP4), rs1472259 (HMGA2) and rs8069452 (IGF2BP1) for ‘age at first tooth’ and rs9788982 (KCNJ2 KCNJ160), rs2804391 (FAM155E–EDA), rs1458991 (BMP4), rs9894411 (IGF2BP1), rs1976274 (MSRB3) and rs1472259 (HMGA2) for ‘number of teeth’ (Supplementary Material, Table S3).
