Genome-wide association studies (GWAS) have yielded large lists of disease-associated loci. Progress in identifying the causal variants driving these associations, particularly for complex psychiatric disorders such as schizophrenia, has lagged much further behind. Interpreting associated variants and loci is therefore vital to understanding how genetic variation contributes to disease pathology. Expression Quantitative Trait Loci (eQTLs), which are responsible for a substantial proportion of gene expression variance, have been posited as a link between associated loci and disease susceptibility1-5, and have yielded results for a host of complex traits6-9. Consequently, numerous methods to identify and interpret co-localization of eQTLs and GWAS loci have been developed10-13. However, these methods require simplifying assumptions about genetic architecture (i.e., one causal variant per GWAS locus) and/or linkage disequilibrium, may be underpowered or overly conservative, especially in the presence of allelic heterogeneity, and have not yet yielded substantial insights into disease biology.
