Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures

Identifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and developmental stages remain underexplored. Here we harnessed the potential of heterogeneous differentiating cultures (HDCs), anin vitrosystem in which pluripotent cells asynchronously differentiate into a broad spectrum of cell-types. We generated HDCs for 53 human donors and collected single-cell RNA-sequencing data from over 900,000 cells. We identified expression quantitative trait loci in 29 cell-types and characterized regulatory dynamics across diverse differentiation trajectories.This revealed novel regulatory variants for genes involved in key developmental and disease-related processes while replicating known effects from primary tissues, and dynamic regulatory effects associated with a range of complex traits. We differentiated two replicates of 51 iPSC lines across 17 batches consisting of 4 to 8 lines per batch. Each batch contained at least one line of each sex. In each batch, lines were formed and maintained in parallel. Each replicate represents a separate instance of HDC differentiation and will capture technical effects introduced during formation, maintenance, dissociation, and collection.