Joint and conditional analysis of TWAS results was performed using the summary statistic-based method described in Yang et al.41, which we applied to genes instead of SNPs. We used TWAS statistics from the main results and a correlation matrix to evaluate the joint/conditional model. The correlation matrix was estimated by predicting the cis-genetic component of expression for each TWAS gene and computing Pearson correlations across all pairs of genes. We used FUSION tool to perform the joint/conditional analysis, generate conditional outputs, and generate plots.
