One of the goals of the International HapMap Project is the identification of 
common haplotypes in genes. However, HapMap uses an incomplete catalogue of 
single nucleotide polymorphisms (SNPs) and might miss some common haplotypes. We 
examined this issue using data from the Environmental Genome Project (EGP) which 
resequenced 335 genes in 90 people, and thus, has a nearly complete catalogue of 
gene SNPs. The EGP identified a total of 45,243 SNPs, of which 10,780 were 
common SNPs (minor allele frequency >or=0.1). Using EGP common SNP genotype 
data, we identified 1,459 haplotypes with frequency >or=0.05 and we use these as 
"benchmark" haplotypes. HapMap release 16 had genotype information for 1,573 of 
10,780 (15%) EGP common SNPs. Using these SNPs, we identified common HapMap 
haplotypes (frequency >or=0.05) in each of the four HapMap ethnic groups. To 
compare common HapMap haplotypes to EGP benchmark haplotypes, we collapsed 
benchmark haplotypes to the set of 1,573 SNPs. Ninety-eight percent of the 
collapsed benchmark haplotypes could be found as common HapMap haplotypes in one 
or more of the four HapMap ethnic groups. However, collapsing benchmark 
haplotypes to the set of SNPs available in HapMap resulted in a loss of 
haplotype information: 545 of 1,459 (37%) benchmark haplotypes were uniquely 
identified, and only 25% of genes had all their benchmark haplotypes uniquely 
identified. We resampled the EGP data to examine the effect of increasing the 
number of HapMap SNPs to 5 million, and estimate that approximately 40% of 
common SNPs in genes will be sampled and that half of the genes will have 
sufficient SNPs to identify all common haplotypes. This inability to distinguish 
common haplotypes of genes may result in loss of power when examining 
haplotype-disease association.