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One of the things the HGP revealed is that we have way fewer genes than anyone expected. Given that the amount of data encoded in genes appears to be far too small to account for the sophistication and variability in humans, it strongly implied that large areas of DNA that were previously considered marker/filler DNA were of great epigenetic importance.

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There are also a lot more steps between 'genomic dna' -> 'protein' than was previously appreciated or thought to be of importance. There are a lot of ways to regulate and produce new protiens and variation that is not itself a genomic change.

Alternative splicing, readthrough regulaton, multiple kinds of ribosomes, post-translational regulation, etc. all produce significant variation outside of the dna itself.

It always seemed insanely stupid to me every time I read something about people claiming certain genes being "non-important" or "non-functional"

We have about a 0.0001% comprehension of this whole system, how can you possibly be so arrogant as to think you KNOW that certain parts of the sequence are not important or used in _any_ way? Then again, I'm definitely not qualified to comment on the topic.

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