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Figure S1. Prior, normalized likelihood and posterior log odds ratio for the model with fixed π = 0.001

Figure S2. Prior, normalized likelihood and posterior log odds ratio for the model with uncertainty in π

Figure S3. The ranks of the 50 regions rated most highly in the full meta-analysis (Final rank) compared with the ranks according to the P-value in the discovery sample of 9,434 subjects and the Association Probability (AP) for the same discovery sample.

Table S1. Number of SNPs falling in each category of rank comparing P-value alone and association probability of a discovery sample of 9,434 subjects, against the same SNPs in a meta-analysis of 67,093 subjects (final rank).

Table S2. Number of regions falling in each category of rank comparing P-value alone and association probability of a discovery sample of 3,610 subjects, against the same regions in a meta-analysis of 67,093 subjects (final rank)

Table S3. Number of regions falling in each category of rank comparing P-value alone and association probability of a discovery sample of 21,640 subjects, against the same regions in a meta-analysis of 67,093 subjects (final rank)

Table S4. Tabulation corresponding to Table III in the main paper when the SNP characteristics are combined using independent empirical relative probabilities rather than conditional values

Table S5. Tabulation corresponding to Table III in the main paper when the SNP characteristics are combined using independent experts’ relative probabilities rather than conditional values

Table S6. Tabulation corresponding to Table III in the main paper when the SNP characteristics are combined using weights derived from a stepwise analysis of the 14 characteristics that identified the 7 most important (see main paper Table 2)

Table S7. Tabulation by rank in the discovery and the final analysis when the association probabilities are calculated under different prior assumptions.

Table S8. Bayesian association probabilities for a range of P-values and prior probabilities calculated using OpenBUGS under the same assumptions as used in Table I of the main paper.

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