We used two statistics to evaluate whether an EUR LD reference could approximate well enough the LD structure in our trans-ancestry GWAS meta-analysis. The first statistic that we used is the Wright fixation index57, which measures allele frequency divergence between two populations. We used the Hudson’s estimator of FST58 as previously recommended59 to compare allele frequencies from our METAFE with that from our EUR GWAS meta-analysis and an independent replication sample from the EBB. The other statistic that we used is the attenuation ratio statistic from the LD score regression methodology. These LD score regression analyses were performed using version 1.0 of the LDSC software and using LD scores calculated from EUR participants in the 1KGP (see ‘URLs’ section). Moreover, we performed a stratified LD score regression analysis to quantify the enrichment of height heritability in 97 genomic annotations curated and described previously40. as the baseline-LD model. Annotation-weighted LD scores used for those analyses were also calculated using data from 1KGP (see ‘URLs’ section).
