Main effects of the one common rs16969968 coding variant, aggregate low frequency variants, and aggregate rare variants were analyzed together in a multivariate model of case-control status (Multivariate Model Set 1). This approach was used to examine the effect of low frequency and rare variants conditioned on the effect of the well-established, common coding risk variant rs16969968. The primary logistic regression model was logit(p)=β0+βG1rs16969968+βG2LowFrequencyTerm+βG3RareTerm+βCC where C is the vector of standard covariates.
