  The biological significance of genomic features is often context-dependent.
We present CruzDB, a fast and intuitive programmatic interface to the UCSC
genome browser that facilitates integrative analyses of diverse local and
remotely hosted datasets. We showcase the syntax of CruzDB using miRNA-binding
sites as examples, and further demonstrate its utility with 3 novel biological
discoveries. First, we find that while exons replicate early, introns tend to
replicate late, suggesting a complex replication pattern in gene regions.
Second, variants associated with cognitive functions map to lincRNA transcripts
of relevant function. Third, lamina-associated domains are highly enriched in
olfaction-related genes. CruzDB is available at
https://github.com/brentp/cruzdb
