Dan MacArthur's post, Can't find your disease gene? Just sequence them all..., is worth a read. He concludes:
But sequencing won't be enough: we need much better methods for sifting out the truly function-altering genetic variants from the biological noise. This is already difficult enough for protein-coding regions (as this study demonstrates); we currently have virtually no way of picking out disease-causing variants in the remaining 98% of the genome. There's a clear need for developing highly accurate and comprehensive maps of the functional importance of each and every base in the human genome, using all of the tools at our disposal - something that will keep us geneticists busy long after we've run out of genomes to sequence.