A standard approach to model the strength of association of genotype to phenotype is through the Z-score. For a continuous phenotype, the trait values are marginally regressed on each SNP and the corresponding Z-score is taken to be the Wald statistic (i.e ), which is distributed under the null. For case-control designs, the Z-score can also be obtained through the standard test statistic for two proportions (assuming equal sample sizes of : , where denotes the frequency of the SNP in the cases (controls) and . We define a fine-mapping locus as a contiguous region of the genome flanking a GWAS “hit” on both sides. Let be a vector of Z-scores from the locus of length . In addition, let be the corresponding LD matrix of pairwise correlation coefficients for locus that can be derived directly from individual level data if available, or approximated using an appropriate reference panel such as the 1000 Genomes. We obtain annotations from external repositories (e.g. ENCODE [18]) and for each SNP , create a -length binary annotation vector , where if the SNP at
