We tested for heterogeneity in the SNP association statistics between individual sample GWAS using random-effects meta-analysis. The proportion of SNPs meeting a nominal heterogeneity test p value (<.05) in each pair of samples ranged from 0.0417 to 0.0512, on par with the expected chance proportion of 0.05, and the patterns did not systematically differ between pairs of the same versus different sample types (full results available upon request).
