GWAS takes advantage of the LD structure of the genome, which reflects the fact that through recombination we inherit chromosomes from our parents that are mosaics of our grandparent's chromosomes. Recombination creates a correlation among variants within these segments. LD is both a strength and weakness of GWAS. It allows one to efficiently test all common variation within the genome with a few hundred thousand carefully selected markers, but any particular variant significantly associated with a phenotype is far from guaranteed to be a causal variant. Rather, the associated variant implicates a genomic locus, which might span millions of nucleotide bases, thousands of variants, and dozens of genes. A major hurdle lies in figuring out which of these variants are causal, and which are only spuriously associated with the phenotype through LD with causal variants.
