Small changes in DNA strand lead to big changes in eye color

Blue, green, brown eyes are controlled by a very few base pairs. Given these aren't in a protein encoding, this is a signaling structure? Or perhaps there are regions of DNA in which simple modification/mutation/Mendel'ing genetics play out to bigger consequences in more stable portions? Kind of an overlay-configuration on top of a largely stable base configuration?

I still want to know if the rate of base-pair-change frequency is uniform across the entire genome or is it far more stable in certain areas and very dynamic in others?

BBC NEWS | Science/Nature | Genetics of eye colour unlocked: "'When OCA2 is knocked out, there is a loss of pigmentation. The position of these SNPs right at the start of the gene means it is possible we're looking at a change in the regulation of the gene in people with blue eye colour.'"