AFR). To further assess whether LD in our METAFE could be reasonably approximated by the LD from EUR, we performed an LD score regression16 analysis of our METAFE using LD scores estimated in EUR. In this analysis, we focused on the attenuation ratio statistic (RLDSC-EUR), for which large values can also indicate strong LD inconsistencies between a given reference and GWAS summary statistics. A threshold of RLDSC > 20% was recommended by the authors of the LDSC software as a rule-of-thumb to detect such inconsistencies. Using EUR LD scores in the GWAS of HIS, which is the non-EUR group that is genetically closest to EUR (FST ≈ 0.02), yields an estimated RLDSC-EUR of around 25% (standard error (s.e.) 1.8%), consistent with strong LD differences between HIS and EUR. By contrast, in our METAFE, we found an estimated RLDSC-EUR of around 4.5% (s.e. 0.8%), which is significantly lower than 20% and not statistically different from 3.8% (s.e. 0.8%) in our EUR meta-analysis. Furthermore, we show in Supplementary Note 1 that using a composite LD reference containing samples from various ancestries (with proportions matching that in our METAFE) does not improve signal detection over using an EUR LD reference. Altogether, these analyses
