For the pan-ancestry analysis, a Cochran–Mantel–Haenszel test was performed to generate a combined 2 × 2 × N stratified P value, with N representing up to all four genetic ancestry groups. This was performed for 4,836 binary phenotypes where one of the three non-European ancestries had five or more cases and for all quantitative traits. For the quantitative traits, we used a linear regression model that included the following covariates: categorical ancestry (European, African, East Asian or South Asian), the top five ancestry principal components, age and sex.
