Chimps to humans: What's the difference?

Scientists completed the mapping of Chimpanzee DNA. There's not much difference to humans, either:

"All told, the two sequences differ by 4 percent. But three-quarters of the differences seem to be in non-functional parts of the genome, suggesting that a mere 1 percent variation makes all the difference."

But, 1% makes a difference. Plus, who knows about the that other 3%. What's more, who can say how that difference effects and interacts with the other parts of the genome. Nonetheless this is a step forward.