If a SNP is associated with a disease, is that referring to the minor allele?

Bioinformatics

It is good to keep in mind that when we are discussing SNPs, we are generally considering them relative to a reference genome.

Reference genomes are useful as a common yardstick that an individual genome can be compared to. The sequence that makes up the reference comes from a few individuals combined in a thoughtful way. It is not guaranteed that the sequence at any given position in the reference reflects 1) the most common allele in the population, 2) the ancestral allele for humans, or 3) the non-disease associated allele.

Because sampling of a few individuals will mostly find common things, it will often, but not always, be the case that a SNP relative to the reference represents the minor allele in the human population.

So you will need to look at the actual genotype and the association with that genotype to draw a conclusion.

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