Genomics has provided unprecedented opportunities for understanding the genetic architecture and evolutionary history of human traits. Unfortunately, human genomics has been persistently biased toward the study of populations of European-derived ancestry, limiting our understanding. The study of diverse and non-European populations can identify novel genetic loci underlying trait variation, give a clearer picture of human demographic history inside and outside of Africa, and identify how humans have adapted to their environment. In this thesis I present work from two studies; the first aims to identify genetic variants, genes, and molecular pathways contributing to skin pigmentation variation in sub-Saharan Africa, as well as the evolutionary history of this genetic variation. To this end, I combine genome-wide association data with functional genomic data and tools, identifying candidate causal genes and variants, along with their predicted regulatory effects. With the addition of scans of selection and global frequency data, we identify the genes targeted by selection on pigmentation, and how that variation is shared across populations. In the second study, I combine genotype data from a cohort of East Africans with whole blood gene expression data to identify genetic variants underlying gene regulatory variation. I compare these associations with findings from other studies to evaluate the extent of sharing of gene regulatory architecture across populations and compare ability to fine-map QTL signals, finding overall strong replication of QTLs and improved fine-mapping in Africans compared with European-Americans. Finally, the integration of QTL data with signatures of selection identifies genes targeted by selection in specific populations, including a gene which may underly skin pigmentation variation and is under selection in Nilo-Saharan speaking populations.