Forgive the double post but it's late and I'm going to bed and I just couldn't resist.
The thread began with the 'claim' that an unrelated 'junk DNA' SNP, on it's own, caused a specific variance in a physiological characteristic. In response, search Yahoo* for "genetic disease from regulatory regions" or "postgene disease". While I never advocate using the internet to conduct a literature search, it will put to rest your contention that no physiological characteristic can be affected by "junk" DNA.
BTW, news to me: "Junk DNA" is no longer an accepted scientific/biological nomenclature. But I assume it will permeate this board for a long time to come. (By the way, notice how this news aligns with my earlier post regarding the appropriate removal of the name "junk").
*I will compile a summary of the search results in a future post.