Our mismatched reference LD simulations differed from our main simulations in several ways: (i) we generated summary statistics using up to N=44K unrelated (or related) European-ancestry (British or non-British) UK Biobank target samples in most experiments, compared with N=320K in our main simulations, because the UK Biobank includes only 44K unrelated UK Biobank individuals of non-British European ancestry (we used N=293K unrelated British-ancestry UK Biobank target samples in a subset of experiments to more closely match our main simulations); (ii) we computed summary LD information using either N=400, N=4,000, or N=44K unrelated British-ancestry UK Biobank reference samples (either non-overlapping or overlapping with the target samples), or using N=3,567 reference samples from the UK10K cohort61 (compared with in-sample LD based on the target samples in the main simulations); (iii) we generated summary statistics using individual level genotypes rather than summary LD information (as required when the target sample and the LD reference panel are not the same); (iv) we simulated 3 causal SNPs per locus that jointly explain 0.5% of trait variance, compared with 10 causal SNPs that jointly explain 0.05%
