For genetic ancestry-dependent cis-eQTL mapping, we used the confounders generated from the main effect analysis but removed variables associated with population stratification (SNP principal components 1–5). To identify genetic ancestry-dependent cis-eQTL, we implemented nominal mapping, adjusting for covariates with a mapping window within 0.5 Mb of the transcription start site of each feature and an MAF ≥ 0.05. To generate a subset of strong signals for downstream mash modeling, we performed eigenMT97 by setting run_eigenmt to True. This resulted in a file with the top variant for each feature.
