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Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.

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Table S1. Settings for simulation I.

Table S1.1. Settings for single locus effect.

Table S1.2. Settings for two-way multiplicative interaction.

Table S1.3. Settings for two-way threshold interaction.

Table S1.4. Settings for three-way interaction.

Table S2. Settings for simulation II.

Table S2.1. Settings for two-way multiplicative effect model.

Table S2.2. Settings for two-way no-marginal-effect interaction.

Table S2.3. Settings for two-way one-marginal-effect interaction.

Table S3. Analysis for the 29 previously reported SNPs.

Table S4. Analysis for CD GWAS data.

Figure S1. Standard Z converges as the number of trees increases in the genome-wide joint association analysis.

Figure S2. Q-Q plots of P-values generated under null hypothesis (i.e., no association) in simulation I.

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