The key analysis in a GWAS for a disease is logistic regression with the dependent variable case-control status (1=case, 0=control) and a SNP genotype as an independent variable (coded as the number of copies of the minor or less frequent allele, 1 degree of freedom). The output of a logistic regression is identity of the reference allele and an odds ratio with its standard error (or confidence intervals) along with a statistic and p-value that test whether the odds ratio differs from unity.
