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For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you don't need two knocked out copies of that gene for it to confer susceptibility risk to the individual?

In other words, is my assumption that GWAS is likely uncovering alleles that confer risk in single copy, correct?

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Why would a SNP ID tell you anything about its effects? To my knowledge you couldn't say anything about phenotype from just a SNP, but I'm not professional on this. – Armatus Nov 19 '12 at 22:08
@Armatus, there are plenty of diseases with disease phenotypes from a single SNP (e.g., sickle-cell anemia as a classic example, but there are many others). – user560 Nov 19 '12 at 23:20
@leonardo Of course, I wasn't saying that a SNP can't have an effect; but that you can't predict the phenotype just knowing there's a SNP [unless you investigate its effect] (cf. your answer) – Armatus Nov 19 '12 at 23:48

In short, yes.

If a gwas study links a SNP to a particular phenotype then yes, it is an effect of a single copy. Bear in mind, however, that a SNP is not a knockout or even a knockdown. It can be, but it is not always the case. SNPs can produce a change in the protein sequence or in the regulation of the production of that protein. Both types of variation can result in a phenotypical change.

In any case, SNP information is always about a single allele, I imagine that you can find cases where a cell is homozygous for a particular SNP but is is not necessarily, or even often as far as I know, the case.

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