No genome-wide significant associations between individual SNPs and lifetime cannabis use were observed (see Manhattan plot, Supplementary Figure 1a). However, the QQ plot (Supplementary Figure 1b) reveals strong enrichment of SNPs with P<10−4. Supplementary Figures 2a–m and 3a–m illustrate the Manhattan and QQ plots for each sample. Table 2 illustrates the top 10 independent (R2<0.1) SNPs associated with lifetime cannabis use. None of these 10 SNPs were replicated in the four independent replication samples (Supplementary Table 3). In a combined meta-analysis of the 10 top SNPs (that is, discovery plus replication samples), none of the SNPs reached genome-wide significance. Local plots of the most strongly associated regions, including neighboring genes, are provided in Supplementary Figures 4a–j. The most statistically significant marker (P-value =4.6 × 10−7) was rs4984460 located on chromosome 15 (see Supplementary Figure 5 for the forest plot). The SNP is located in an intergenic region between LOC400456/LOC145820 and NR2F2 and MIR1469 genes. Supplementary Table 4 includes the 153 SNPs identified with P-values <10−5. Because not all SNPs passed the post-imputation quality control steps in all the samples, this table includes the effective sample size per SNP.
