The final predicted parameters to evaluate predictive ability were calculated as the mean of the estimates across 100 replicates, respectively. To explore the impact of imputation on our model, we used both 1KGP WGS data and UKB imputed data as the reference in the simulated data. We used the same approaches, except for the one assuming causal variants were known, to analyse GWAS summary statistics of complex traits and diseases in UKB (Supplementary Note 4). While, 1KGP WGS data were used as the reference panel since most causal variants might not be included in the summary statistics.
