The familial correlations estimated by RFGLS for the five phenotypes are reported in Supplemental Table 2. Manhattan (Supplemental figures S1 to S5) and Q-Q plots (Supplemental figures S6 to S10) for the tests for additive effects of the 527,828 autosomal SNPs are included with the supplementary material. In the main effects analysis, the genomic inflation factors ranged from 1.01 (for Behavioral Disinhibition) to 1.03 (for Nicotine), suggesting that there is little evidence for stratification effects in the analysis. In total there were 31 SNPS that were associated with one or more of the phenotypes at p < 10-5: 3 for Alcohol Consumption, 5 for Alcohol Dependence, 12 for Illicit Drugs, 8 for Nicotine, and 4 for Behavioral Disinhibition. In 500K tests for each phenotype, we would expect 5 to be significant at this level by chance. The 31 SNPs along with their estimated regression coefficients and associated p-values for each of the five phenotypes are listed in Supplemental Table 3. Of note is that for each of the 31 SNPs the estimated regression coefficient was in the same direction across
