PLINK 1.07 (Purcell, Neale, Todd-Brown et al. 2007) and R 2.7.2 (R Development Core Team 2010) were used for quality control (QC) and the association statistics. SMARTPCA (Patterson, Price & Reich 2006) was used for principal component analysis (PCA). Haploview 4.2 (Barrett, Fry, Maller et al. 2004) was used for linkage disequilibrium (LD) assessment. For the purposes of replication, GWAS datasets were retrieved from the dbGAP database (Mailman, Feolo, Jin et al. 2007). These datasets had been generated within the following studies: (i) ‘Alcohol Research using Australian twins and their families’ (subsequently referred to as OZ-ALC); (ii) ‘CIDR: Collaborative Study on the Genetics of Alcoholism’ (COGA; subsample of European ancestry only); and (iii) ‘Study of Addiction: Genetics and Environment’ (SAGE; subsample of European ancestry only).
