eQTL-based strategies provide a straightforward method to link non-protein coding risk alleles discovered through genome wide association studies (GWAS). Understanding the genes and pathways underlying common risk alleles remains a formidable challenge because the majority of trait-associated polymorphisms are outside of known protein coding regions (Hindorff et al., 2009). Many of these loci are thought to be involved in transcriptional regulation (Freedman et al., 2011; Nicolae et al., 2010). Therefore, eQTL-based approaches are well suited to identifying candidate genes acting through these loci. We apply our method to known breast cancer risk alleles discovered through GWAS to link the risk variants with their target genes.
