Tests for excess of rare exonic variants in the YRI population compared to the CEU population.

For each Encode region, we test whether rare exonic variants are overrepresented in the African (YRI) population compared to the central European (CEU) population. To mimic studies of rare variants, five different minor allele frequency (MAF) cut-off values (1%�C5%) are used; all variants with a MAF over the cut-off value are omitted in the analysis. For each set of variants, the number of tested variants is reported along with the number of variants that are only polymorphic in the YRI population (the first number in the parenthesis), and the number of variants that are only polymorphic in the CEU population (the second number in the parenthesis). Below the number of variants, p-values from the investigated methods are reported. It is seen that the proposed test yields lower p-values than the alternative tests in nearly all cases where the rare variants are significantly overrepresented in the YRI population. The only exception is for the ENm010 region with MAF cut-off at 1%; in that case, the weighted-sum method yields a slightly higher p-value than the CMC and CAST methods.