Mapping of expression quantitative trait loci (eQTL) is one way to demonstrate that a risk variant within a locus has a functional effect on gene expression (Cheung et al., 2005, Morley et al., 2004, Myers et al., 2007, Stranger et al., 2007). eQTL analysis is performed by examining the association of each SNP with expression of mRNA transcripts. In general, eQTL effects are stronger for SNPs and transcripts that are physically close to each other (Gibbs et al., 2010). Trait associated SNPs from GWAS have been proposed to be more likely associated with expression differences than other SNPs (Nicolae et al., 2010). Such studies have generally been performed with transformed cell lines but eQTLs can also be identified in liver (Schadt et al., 2008), kidney (Wheeler et al., 2009), cell lines from asthma patients (Dixon et al., 2007, Moffatt et al., 2007) blood (Nalls et al., 2011a), subcutaneous adipose tissue (Emilsson et al., 2008) and brain (Gibbs et al., 2010, Heinzen et al., 2008, Liu et al., 2010a, Myers et al., 2007, Webster et al., 2009). For at least some
