Extended Data Figure 9 |. Testing for heterogeneity across ancestry for variants included in common variant and rare variant polygenic scores.

We used a Cochran’s Q test to evaluate heterogeneity across ancestry-level single-variant and gene-level association results. QQ plots are shown for p-values from a, single-variant Q tests for common variants and b-h, gene-level Q tests for different rare variant masks; included in each analysis were the variants (or genes) included in the corresponding polygenic score. Departures above the diagonal red line suggest heterogeneity beyond the null expectation (blue lines indicate 90% confidence intervals for the null expectation), while lambda values indicate the ratio of the median observed chi square statistic to the median of the expected chi square statistic under the null; larger lambda values indicate larger deviations from the null.