Genome-wide association (GWA) studies have provided novel insights into human traits by identifying single nucleotide polymorphisms (SNPs) associated with disease, including type 1 diabetes, coronary artery disease, HIV-1 infection and type 2 diabetes (Fellay et al., 2007, Preuss et al., 2010, Scott et al., 2007, Sladek et al., 2007, Steinthorsdottir et al., 2007, Todd et al., 2007, Yang et al., 2010, Zeggini et al., 2008), or other phenotypes. Because GWAS identify loci rather than functional variants, most GWAS have provided limited insights into underlying mechanisms (Hindorff et al., 2009). Therefore, annotating the possible functional effects of genetic risk variants is important in understanding genomic data.
