I'm not from a biology background so please forgive the ignorance. I have just read that a rare variants (MAF < 0.5%) needs a large effect size to be detected by association studies. I don't follow the reasoning behind this. As long as the rare variant is on the DNA chip you are using to detect the genotypes of the individuals in the study, why should the rare variant need to have a larger effect than any other SNP on the chip. Is it just because the biological effect in question might be over-looked and not spotted at all as a biological effect if it is rare in the population? I don't really know what 'symptoms' are measured in these studies to know how it is possible to overlook an effect. In my limited conceptualisation the subjects in the studies either have or don't a detectable illness/trait but i imagine its more subtle than this.
thanks for your help