Color code manhattan plots?

[Chloe Saras Thangavelu]

I'm trying to color code regions in my bed file. I am able to change region colors with the itemRgb column.

but the full genome remains blue.

Is there a way to color code the manhattan, full genome plot?

I was able to get the full genome in the online version but the greener regions I am trying to highlight are hard to see/don't stand out much.

[igv-help]

Its not possible to do this in whole genome view with IGV desktop.   The full genome view is a density plot of the features, not the features themselves, and there is no direct correspondence between the 2.