I would like to have an intuitive answer on why the Armitage trend test, commonly used for doing association analysis for a SNP with a trait, is equivalent to a chi square with 1 degree of freedom.
If the trend test usually uses a 2x3 contingency table isn't it more similar to a chi square with 2 degrees of freedom? What is the intuition there? Is it because you can also think of the Armitage trend test as similar to the allele count test where you are counting alleles and not genotypes? So it's actually a 2x2 table?