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Genome-wide association studies (GWAS) have successfully identified many genetic variants associated with complex diseases and traits. However, functional consequence of genetic variants studied in GWAS is not yet fully investigated, which would hinder the application of GWAS. We therefore performed a systematic functional analysis of HapMap SNPs, which have been most commonly used as the reference panel for GWAS. Our study highlights several characteristics of HapMap SNPs and identifies subsets of genetic variants with interesting functional implication. The results show that HapMap SNPs have good coverage within RefSeq genes, especially within known disease-related genes. On the other hand, only a small percentage of SNPs are non-synonymous SNPs while many SNPs are actually located at gene deserts. Moreover, many functionally important variants are not yet still interrogated. A redesigned SNP reference panel with additional functionally important variants would be useful to identify disease-causal variants in the future genome-wide studies. (C) 2012 Elsevier B.V. All rights reserved.