In these analyses, we used a two-stage approach that has been successfully applied in other contexts6. In the first stage, we conducted a meta-analysis of our first-stage “proxy phenotype” and used our clumping procedure to identify the set of approximately independent SNPs at the p-value threshold of 10−4. In the second stage, we tested SNPs identified in stage 1 (or high-LD proxies for them) for association with a second-stage phenotype in an independent (non-overlapping) sample. In our analyses, we used our primary phenotype of subjective well-being as the proxy-phenotype. We conducted one analysis with depressive symptoms as the second-stage phenotype, and one analysis with neuroticism as the second-stage phenotype. In the analyses, we omit cohorts from the first-stage or second-stage as needed to ensure that the samples in the two stages are non-overlapping. Supplementary Table 31 lists the cohort restrictions imposed. These cohort restrictions, as well as the p-value threshold of 10−4, were chosen before the data were analyzed on the basis of statistical power calculations.
