GWAS (genome-wide association studies) is not the final answer or ultimate tool in finding out the variations in genes, genomic regions. Still need more to do. Gene gene interactions are quite important as well.
Info for non-science readers:
A genome-wide association study (GWAS), also known as whole genome association study (WGAS), is an examination of all or most of the genes (the genome) of different individuals of a particular species to see how much the genes vary from individual to individual. [Wikipedia]