AA genotype at rs16969968 on other background genotypes at rs578776, and similarly the A-A haplotype is not observed (double heterozygotes being extremely likely to carry A-G and G-A). However, the effect on the observed background is clear from the cells of the first row and first column of Table III, where GG/GG is set as the reference genotype. We see that on the background of the low risk (protective) genotype at rs16969968 (GG), there is significantly increased protection for one and two copies of the A allele at rs578776 along row 1 (OR = 0.68 and 0.60 respectively). On the background of the risk genotype at rs578776 (GG), there is significantly increased risk for two copies of the A allele at rs16969968 along column 1 (OR = 1.49).
