For the conditionally independent variants for AUD or PAU, we also conducted a multitrait analysis conditioning on GSCAN drinks per week [9] using GCTA-mtCOJO [31] to identify variants associated with AUD or PAU, but not drinks per week, i.e., not alcohol consumption alone. Europeans from the 1000 Genomes were used as the LD reference. For variants missing in GSCAN, we used proxy variants (p < 5 × 10−8) in high LD with the locus for analyses. Whereas conditional analyses require the beta (effect size) and standard error, we calculated these using Z-scores (z), allele frequency (p) and sample size (n) from the meta-analyses [53]: beta=z2p(1−p)(n+z2)SE=12p(1−p)(n+z2)
