I'm familiar with some ways to make Manhattan plots, the easiest and most flexible I've found is Stephen Turner's qqman, from Getting Genetics Done, located here.
Manhattans are useful for showing P-values for individual SNPs, but is there a simple way to include other types of genetic architecture in such a plot? Specifically I am interested in plotting (as bars or in a different color) CNVs that may overlap these SNPs and span 10s to 100s of kb. Best way to do this? Any programs that permit p-values for more than SNPs and yet permit a Manhattan-esque (that is genome-wide) presentation of results?