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Genome wide association studies (GWAS)find variants that are associated with a phenotype. These variants often “tag” (i.e. are correlated with) what is actually causal. While these GWAS variants are often reproducibly found, many of the underlying true causal variants that they tag have not been identified. Work has shown that when looking at haplotypes of genes a small number of common haplotypes (<5) can represent the haplotypes of 90% of the population with a number of very rare haplotype representing the remainder of the population (Haplotype Diversity in 11 Candidate Genes Across Four Populations; T.H. Beaty, et al., 2005). I would like to know if GWAS variants more often tag the rare haplotypes or the common haplotypes. Is the presence of a GWAS variant on a haplotype correlated with the frequency of the haplotype?