When multiple lines were available for a donor, the mean expression value of lines was used. In the array-based iPSC dataset, which had the largest number of replicate lines available per donor (246 donors with multiple lines), we additionally mapped the eQTLs using two randomly drawn sets of individual lines per donor to assess the replicability of the iPSC eQTLs (Extended Data Fig. 6f-h). In the main RNA-seq based map, we identified both primary and secondary eQTL effects. To identify secondary effects, we repeated the mapping with the genotypes of the lead eQTL variant included as a covariate in the model. Finally, an alternative version of the main eQTL map was generated using a pipeline matched with GTEx V6p eQTLs for quality control purposes (See Supplementary Information).
