BACKGROUND: The recent advancement in human genome sequencing and genotyping has 
revealed millions of single nucleotide polymorphisms (SNP) which determine the 
variation among human beings. One of the particular important projects is The 
International HapMap Project which provides the catalogue of human genetic 
variation for disease association studies. In this paper, we analyzed the 
genotype data in HapMap project by using National Institute of Environmental 
Health Sciences Environmental Genome Project (NIEHS EGP) SNPs. We first 
determine whether the HapMap data are transferable to the NIEHS data. Then, we 
study how well the HapMap SNPs capture the untyped SNPs in the region. Finally, 
we provide general guidelines for determining whether the SNPs chosen from 
HapMap may be able to capture most of the untyped SNPs.
RESULTS: Our analysis shows that HapMap data are not robust enough to capture 
the untyped variants for most of the human genes. The performance of SNPs for 
European and Asian samples are marginal in capturing the untyped variants, i.e. 
approximately 55%. Expectedly, the SNPs from HapMap YRI panel can only capture 
approximately 30% of the variants. Although the overall performance is low, 
however, the SNPs for some genes perform very well and are able to capture most 
of the variants along the gene. This is observed in the European and Asian 
panel, but not in African panel. Through observation, we concluded that in order 
to have a well covered SNPs reference panel, the SNPs density and the 
association among reference SNPs are important to estimate the robustness of the 
chosen SNPs.
CONCLUSION: We have analyzed the coverage of HapMap SNPs using NIEHS EGP data. 
The results show that HapMap SNPs are transferable to the NIEHS SNPs. However, 
HapMap SNPs cannot capture some of the untyped SNPs and therefore resequencing 
may be needed to uncover more SNPs in the missing region.