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Figure S1. Sample P-value versus quantiles of the uniform distribution when the null hypothesis is true (the genotype is not associated with the disease phenotype).

Figure S2. Power comparison between KBAC and WSS, with different numbers of causal variant sites (ND).

Figure S3. Means of the genome-wide rankings of known disease genes in 100 searches.

Figure S4. Distribution of P-values when cases and controls are not equally sampled from subpopulations.

Table S1. The average number of observed disease-causal mutations per individual in simulations.

Table S2. The average number of multisite genotypes in the KBAC-WSS comparison.

Table S3. The improvement of the power of SKAT on LPL dataset after applying variant grouping.

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