I didn't see your post++ before posting my own revised solution according to the changing requirement specs! I encourage posters to be as clear as possible on the requirements - that makes a big difference! If the code doesn't work and the requirements don't either, then that is a mess!

A very small nit: $data{"$chr$bp"} = $min;, I added a space between the values "$chr $bp" to prevent possible collisions between these two things.

Update: Cristoforo is right about this seldom used hash key idiom with the commas for hash keys. I also wondered about /CHR/.