Supporting data for "Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize" (https://doi.org/10.1101/2021.09.03.458856). Computational annotations about single-nucleotide polymorphisms (SNPs) and genes are used to predict nucleotide conservation across angiosperms. Experimental annotations at SNPs and genes (within-species conservation, chromatin accessibility, gene expression and gene ontology enrichment) are used to validate predictions in maize