deviance explained in model (1), and therefore small p-values, than we would see in similarly powered studies if there no underlying effects (if all βi were 0). In order to test whether there are more non-zero coefficients than we would expect by chance, we permute the phenotype labels to generate many data sets with the same LD structure among the genotypes, but no consistent relation to the AD phenotype, and ask how unusual is it to find as many significant estimated coefficients bi as in fact occur with the true phenotype labels.
