Table 2. Haplotypes and their association with AMD in the familial AMD cohort.

Number of SNPs	SNPs involved in best model	Haplotypes	Frequency	Haplotype p-values	Overall p-value
7	rs3766404 rs529825 rs1061147 rs800292 rs1061170 rs203674 rs2274700	TCACCCC	0.58	0.03
		TCCCTAC	0.12	0.90
		TTCTTAT	0.11	0.10	0.12
6	rs3766404 rs529825 rs1061147 rs800292 rs1061170 rs2274700	TCACC C	0.56	0.02
		TCCCT C	0.18	0.44
		TTCTT T	0.11	0.13
		CCCCT T	0.06	0.09	0.02
5	rs529825 rs1061147 rs800292 rs1061170 rs2274700	CACC C	0.55	0.01
		CCCT C	0.18	0.31
		TCTT T	0.11	0.18
		CCCT T	0.10	0.02	0.006
4	rs1061147 rs800292 rs1061170 rs2274700	ACC C	0.56	0.00
		CCT C	0.18	0.31
		CTT T	0.12	0.07
		CCT T	0.100	0.03	0.0008
3	rs1061147 rs1061170 rs2274700	A C C	0.56	0.0006
		C T T	0.25	0.0003
		C T C	0.17	0.35	0.00008
2	rs1061147 rs1061170	A C	0.56	0.00008
		C T	0.41	0.004	0.0001
1	rs1061170	C	0.58	0.006
		T	0.42	0.006	0.006

The most strongly associated haplotype (shown in red) is derived from SNPs genotyped in the CFH gene locus using backward selection. Emboldened ‘C’ indicates CFH rs1061170 risk allele. ‘Best’ haplotype shown in italics. Overall p value describes association of the haplotype with AMD independent of alleles