In regions with significant association results, we analyzed imputed SNPs to further evaluate the evidence for association. SNPs were imputed to 1000 Genomes (EUR, August 2010 release) using BEAGLE 3.3.1 (Browning and Browning, 2009) as described in Wang et al (Wang et al., 2013). Secondary analyses were performed for significant SNPs to test whether the observed genetic association could be attributed to dependence on a specific substance. Analyses for ANYDEP were performed using the Mantel-Haenszel Chi-Square test of association assuming an additive genetic model. Analyses for QUANTDEP were performed using analysis of covariance employing substance, genotype, and the substance*genotype interaction to test for differences in genotype by substance. Gender and birth cohort were included as covariates.
