Supporting data for analyses of hybrid panels in “The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize” (bioRxiv: https://www.biorxiv.org/content/10.1101/745208v1). This study examined within-locus complementation and enrichment of genetic effects by functional classes in maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the United States (1,106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1,640 hybrids). We assayed these hybrids for more than 12 millions SNP markers, and evaluated them for three agronomic traits: days to silking, plant height and grain yield.