<p>Epigenetic mapping studies across individuals have identified many positions of epigenetic variation across the human genome. However the relationships between these positions, and in particular global patterns that recur in many regions of the genome, remains understudied. In this study, we use a stacked chromatin state model to systematically learn global patterns of epigenetic variation across individuals and annotate the human genome based on them. We apply this framework to histone modification data across individuals in lymphoblastoid cell lines and across autism spectrum disorder cases and controls in prefrontal cortex tissue. We find that global patterns are correlated across multiple histone modifications and with gene expression. We use the global patterns as a framework to predict trans-regulators and study a complex disorder. The frameworks for identifying and analyzing global patterns of epigenetic variation are general and we expect will be useful in other systems.</p>