Table 3. Replication of best haplotype in (a) case control data and (b) AREDS data.

Case control cohort
Haplotype	Hap Score	Pooled Haplotype Frequency	Control Haplotype Frequency	Case Haplotype Frequency	OR (lower bound–upper bound)	Associated P-value	Overall p value
ACC	−5.85	0.47	0.36	0.57	0.43 (0.29–0.64)	<10−9	<0.00001
CTT	−7.83	0.33	0.48	0.20	3.88 (2.51–6.01)	<10−14
CTC	−1.07	0.20	0.16	0.23	0.62 (0.38–1.03)	0.28

The odds ratios are computed by comparing each haplotype against all other haplotypes pooled. Cases defined as AREDS category 4, advanced AMD. Controls defined as AREDS category 1, unaffected. Overall p value describes association of the haplotype with AMD independent of alleles