How common is it for a red head to have dark brown eyes?
I know that being red headed itself is a mutation of the MC1R gene on the 16th chromosome, and unlike being blonde with blue eyes, eye color and hair color (in the case of red hair) are not linked. Blonde hair and blue eyes are both on the 15th chromosome which is why they are linked. Being a red head, I know several with blue eyes, one with green, and tons with hazel eyes. But I am the only one I've ever met with dark brown eyes. They're so dark they show up almost black in pictures. No one on either side of my family has brown eyes. So what gives?
It sounds like you've done some research on chromosomes and genetic expression, so you probably know more than I do. A quick google brings up this wiki page: http://en.wikipedia.org/wiki/Eye_color# … _eye_color
This page tells us that eye color is determined by many different genes and is quite complicated. Brown eyes are the most common color so having brown eyes, irregardless of your hair color, is not surprising. The actual darkness of your brown eyes is just the amount of pigment, or eumelanin, produced by the epithelial cells in your iris.
I imagine that there is no real answer to your question. It's just a trick of your unique genetic code!
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