Another approach is to test putatively functional variants within a locus for association. One expects, for example, that coding variants inducing a nonsense or missense mutation are more likely to have functional effects on gene transcription and, by the same token, larger effects on downstream phenotypes. An excellent example of the power of functional annotation was recently reported for the intronic variants in FTO associated with BMI, as discussed above. While these variants were first discovered over a decade ago, their mechanism of action was unknown until 2015. In the end, FTO is not the relevant gene affecting BMI levels. Instead, the intronic locus harboring the BMI-associated variants is an enhancer—a functional unit in the genome that influences expression of a gene—for nearby genes, IRX3 and IRX5, over 1 million bases away from FTO. The finding was originally suggested by epigenomic annotations (e.g., from ENCODE or NIH Roadmap) indicating that the intronic locus in FTO contained an enhancer for IRX3/IRX5, the phenotypic effects of which were subsequently confirmed through mouse and patient tissue samples (Claussnitzer et al., 2015). Understanding the
