Intuitively, it seems obvious that when rare variants are the cause of the associations, there should then be multiple common variants that carry significant independent associations. To evaluate this expectation, we took those genealogies that produced a genome-wide significant association and asked what the strongest association was when the top genome-wide significant association was first incorporated in the model. We found that almost 40% of genealogies with a genome-wide significant variant had secondary, independent associations that also achieved genome-wide significance. We also found that fewer than 10% of genealogies had no further significant associations (at α = 0.05). These results demonstrate a clear tendency of rare variants to create multiple independent signals of synthetic association.
