The most likely function is in regulation of genes. The protein coding sequences are so highly conserved it seems unlikely that they account for the species differences. It is much more probably that the enhancers, promoters, and other regulatory sequences are what drives differences in morphology during development.
I remember that old story of the FOXP2 gene and its role in language evolution towards modern humans - see papers of Enard and colleagues (2002) and Krause and colleagues (2007):
http://www.evolution.unibas.ch/teaching/molec_evol/doc/Enard_et_al_2002.pdf
http://isites.harvard.edu/fs/docs/icb.topic226673.files/Language_Gene_C.pdf
Humans interaction with the environment determine the biology, physiology and disease susceptibility of humans. It may provide wide and comparative genome that can be differentiated from that of the activities of Chimpanzee. Many characteristcs of humans are unique in phenotypic traits that forms main genome difference between chimps and humans.
I agree with Bharathi. There are strong correlations between brain centers, sense organs, locomotion, diet & niche etc. We know many differences between humans & chimps, e.g. genes affecting brain growth (incl. speech production) probably evolved faster in humans. Human anatomy & other indications (e.g. see attachment) show that our ancestors did not run over open plains (as is still often believed), but followed coasts & rivers, walking & wading bipedally & diving for waterside & shallow aquatic animal & plant foods. All these changes in the human lineage have a genetic basis, e.g. long, straight legs & wading-walking upright, much larger brain & often different brain centres (e.g. smaller olfactory bulb, larger association centres incl. Broca & Wernicke), adaptations to diving & breathing & speaking, food swallowing & suction (rather than biting-chewing alone), immunological changes (other milieus) etc. - all these probably have different genes in chimps & humans.
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