It is important to emphasize that although the identification of transcript level associations provides another layer of confidence for disease-associating variants and genes, it is entirely possible that a variant in an LD region encompassing multiple genes, could be marking a functional disease variant in one gene and an expression variant in another gene. Thus, although highly useful in conjunction with disease association studies, eGWAS should be seen as a guide rather than ultimate evidence in disease-mapping efforts. Similarly, absence of eGWAS associations for a disease-associated variant should not be seen as contradictory evidence, but rather raise the possibility of alternative functional mechanisms for that variant.
