A major challenge in human evolutionary biology is to pinpoint genetic differences that underlie human-specific traits, such as increased neuron number and differences in cognitive behaviors. We used human-chimpanzee tetraploid cells to distinguish gene expression changes due to cis -acting sequence variants that change local gene regulation, from trans expression changes due to species differences in the cellular environment. In neural progenitor cells, examination of both cis and trans changes – combined with CRISPR inhibition and transcription factor motif analyses – identified cis -acting, species-specific gene regulatory changes, including to TNIK , FOSL2 , and MAZ , with widespread trans effects on neurogenesis-related gene programs. In excitatory neurons, we identified POU3F2 as a key cis -regulated gene with trans effects on synaptic gene expression and neuronal firing. This study identifies cis -acting genomic changes that cause cascading trans gene regulatory effects to contribute to human neural specializations, and provides a general framework for discovering genetic differences underlying human traits. ### Competing Interest Statement C.A.W. is on the SAB of Bioskyrb Genomics (cash, equity) and Mosaica Therapeutics (cash, equity), and is an advisor to Maze Therapeutics (equity), but these have no relevance to this work. The remaining authors declare no competing interests.