For common variants, in most cases, the disease-associated variant itself is unlikely to be functionally relevant. The whole premise of WGAS is that an association can uncover the effect of a closely linked functional variant that is in LD with the observed associated variant. However, when the OR is near 1, and so the effect of a variant is relatively small, it is likely to be very difficult to establish which of a set of closely linked variants in LD with each other is the one that is most relevant functionally.
