likelihood of the data relative to these terms as:(1)where the sum is taken across all causal indicator vector sets . We note that in order to keep the enumeration of the causal vector sets combinatorially tractable, we restrict the total number of potential causal variants at each locus to three or less in practice (see Figure S4 for assessment of run time versus number of causal variants considered). We define the annotation effect on the causal probability through a standard logistic model:
