because this method allows for identification of independent SNPs determined by a selected threshold. We changed the default threshold for LD from r2 = 0.5 to r2 = 0.8 because our LD-tagging SNPs were selected based on r2 ≥ 0.8. Additionally, we did not correct for multiple phenotypes because (i) they reflect reasonable a priori hypotheses and (ii) they are, in some cases, substantially inter-correlated, making it difficult to implement any simple multiple test correction.
