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Table 1 Disease-associated alleles vs. null expectations

From: Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations

  Mean frequency of a randomly chosen allele Proportion ancestral
Null expectations   
   HapMap data (n = 1000, unweighted) 0.721 0.623
   HapMap data (n = 1000, weighted) 0.610 0.568
   Theoretical (neutral, unweighted) 0.741 0.741
   Theoretical (neutral, weighted) 0.650 0.650
Disease-associated alleles   
   Cancer (n = 112) 0.362** 0.446*
   Cardiovascular (n = 145) 0.364** 0.379**
   Metabolism (n = 160) 0.365** 0.456*
   Miscellaneous disease (n = 290) 0.413** 0.434**
   Morphological (n = 276) 0.409** 0.467*
   Neurological (n = 135) 0.429** 0.430*
   Multiple phenotypic classes (n = 25) 0.312* 0.320*
   All GWAS alleles (n = 1143) 0.394** 0.437**
   All replicated GWAS alleles (n = 142) 0.396** 0.437**
  1. Unweighted values do not incorporate the probability of detection, and weighted values incoporate the probability of detection in a GWAS. Neutral expectations use a polymorphism threshold (d) of 0.025 and Equations 5 and 10. Relative magnitudes of disease-associated and control allele frequencies were compared via Mann-Whitney U tests, and proportions of ancestral alleles were compared via binomial tests. * indicates significant differences from HapMap and neutral scenarios (p-value < 0.05), and ** indicates highly significant differences from HapMap and neutral scenarios (p-value < 0.0001). Totals for GWAS alleles are labeled in boldface type. Replicated alleles are those alleles that have been implicated in multiple studies.