Nine hits from the correlated factors model were in LD across the factors, and one hit was in LD with a QSNP hit. In total, our structured GWAS discovered 152 independent loci that are likely to operate broadly within constellations of phenotypes, 20 of which were novel relative to the univariate traits. We identify nine independent QSNP hits that do not conform to the identified factor structure (Table 2), a third of which appeared to operate through pathways unique to ALCH.
