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Variant frequency, effect size and GWAS limitation
Figure below very well explains two important attributes of a variant: population frequency (to avoid confusion, we use "population frequency" instead of "allele frequency".) and effect size. Evolution dictates that variant's population frequency is generally inversely proportional to its effect size. To detect significant association between a variant and specific phenotype, the variant has to meet either one of two prerequisites: The variant has to have at least modest popu
