Although GWAS are a technological breakthrough in the density of markers that are tested across the genome, the genome is not completely represented by the SNP arrays used in the GWAS studies. For example, the Affymetrix Genome-Wide Human SNP Array 6.0 genotypes 906,600 SNPs out of an estimated 10,000,000 SNPs in the human genome (approximately 2,000,000 of which are known). The dense coverage in GWAS studies, although an improvement compared with previous methodology, is still not dense enough to ensure that associations are found. Nonetheless, a SNP reaching genome-wide association significance indicates that functional variation is likely to occur through this SNP or 1 of the correlated, untested SNPs.
