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Table 5 Comparison of the distribution of derived allele frequencies (DAF) for SNPs within several classes.

From: Predicting functionally important SNP classes based on negative selection

class Perlegen population class DAF median ancestral repeats genome
    DAF median p -value DAF median p -value
constrained elements AFR 0.174 0.196 3.6 × 10-5 0.205 < 1 × 10-8
  EUR 0.188 0.208 3.4 × 10-4 0.229 < 1 × 10-8
  CHN 0.174 0.208 8.7 × 10-3 0.217 < 1 × 10-8
constrained elements 1 kb from genes AFR 0.174 0.196 3.2 × 10-3 0.200 < 1 × 10-8
  EUR 0.190 0.208 5.4 × 10-3 0.229 < 1 × 10-8
  CHN 0.188 0.208 6.0 × 10-2 0.217 < 1 × 10-8
constrained elements 100 kb from genes AFR 0.174 0.196 1.1 × 10-2 0.200 1.0 × 10-8
  EUR 0.205 0.208 9.6 × 10-3 0.229 1.1 × 10-6
  CHN 0.188 0.208 8.3 × 10-2 0.217 8.5 × 10-7
constrained elements outside of genes AFR 0.174 0.196 3.0 × 10-3 0.196 < 1 × 10-8
  EUR 0.188 0.208 5.3 × 10-3 0.229 < 1 × 10-8
  CHN 0.188 0.208 6.1 × 10-2 0.217 < 1 × 10-8
H3K79me3 AFR 0.174 0.196 8.0 × 10-3 0.200 < 1 × 10-8
  EUR 0.208 0.208 1.6 × 10-2 0.229 1.7 × 10-7
  CHN 0.188 0.202 1.2 × 10-1 0.217 5.0 × 10-8
  1. Classes presented are 1) constrained elements, 2) constrained elements at least 1 kb from the closest gene, and 3) constrained elements at least 100 kb from the closest gene, 4) constrained elements outside of genes, and 5) H3K79me3 regulatory attributes in comparison with the genome as a whole and ancestral repeats. We perform a Mann-Whitney U-test to compare the DAF distribution for SNPs in constrained elements, constrained elements outside of genes, and H3K79me3 regulatory attributes with that of the genome and that of ancestral repeats. We list the resulting p-values as well as the median DAF for each class.