For the disease traits, we used the self-reported diagnoses rather than ICD10 diagnoses, as they tend to have larger sample sizes. For depression, we used a more refined definition of cases and controls, where individuals were not counted as cases if they had any history of psychiatric symptoms or diagnoses other than depression or if they were prescribed drugs that are indicative of such diagnoses. Individuals were selected as controls only when there was an absence of any psychiatric symptoms or diagnoses and only when they were not prescribed any drugs that could be indicative of such diagnoses. All 6 traits in the UK Biobank were corrected for age, sex and the first 10 principal components by regressing the phenotype on these covariates and using the residuals from that regression for further analysis. For each trait, the SNPs that went into the analysis were based on the overlap between the GWAS summary statistics, the HapMap3 SNPs, the GERA data set, which was used as an LD reference in the SBLUP analysis, and the imputed SNPs from the UK Biobank. (For details on the QC process and imputation, see URLs.) Depending on the trait, the total number of SNPs ranged from around 660,000 to around 930,000.