Cellular processes mediated through nuclear DNA must contend with chromatin. 
Chromatin structural assays can efficiently integrate information across diverse 
regulatory elements, revealing the functional noncoding genome. In this study, 
we use a differential nuclease sensitivity assay based on micrococcal nuclease 
(MNase) digestion to discover open chromatin regions in the maize genome. We 
find that maize MNase-hypersensitive (MNase HS) regions localize around active 
genes and within recombination hotspots, focusing biased gene conversion at 
their flanks. Although MNase HS regions map to less than 1% of the genome, they 
consistently explain a remarkably large amount (∼40%) of heritable phenotypic 
variance in diverse complex traits. MNase HS regions are therefore on par with 
coding sequences as annotations that demarcate the functional parts of the maize 
genome. These results imply that less than 3% of the maize genome (coding and 
MNase HS regions) may give rise to the overwhelming majority of phenotypic 
variation, greatly narrowing the scope of the functional genome.