Protective chromosome 1q32 haplotypes mitigate risk for age-related macular degeneration associated with the CFH-CFHR5 and ARMS2/HTRA1 loci

Table 2 Frequencies of CFH-CFHR5 and ARMS2/HTRA1 variants associated with AMD among individuals from the 1000 Genomes Project phase 3 (1000 G) and controls and cases, with associated effect sizes and p-values

Variant (Position) Major/minor allele	Minor allele frequency (MAF)			OR (95% CI)	p-value*	IAMDGC (17,832 controls, 16,144 cases) [41]
	Minor allele frequency (MAF)					MAF		OR	p-value
	1000 G	Controls	Cases			Controls	Cases
IAMGC Locus # 1.5 rs187328863 (chr1:196380158) C/T (+)	0.028	0.029	0.053	2.12 [1.63; 2.74]	1.29e−08	0.028	0.054	2.27	1.1e−68
*CFH* I62V rs800292 (chr1:196642233) G/A (−)	0.260	0.241	0.142	0.52 [0.46; 0.58]	1.83e−29	n.a	n.a	0.49⁽¹⁾	7.94e−286
*CFH* Y402H IAMGC Locus # 1.2 rs1061170 (chr1:196659237) T/C (+)	0.362	0.369	0.559	2.27 [2.06; 2.49]	1.16e−64	0.37⁽²⁾	0.58⁽²⁾	2.38⁽²⁾	2.0e−590⁽²⁾
IAMGC Locus # 1.1 rs1410996 (chr1:196696933) G/A (−)	0.425	0.418	0.237	0.41 [0.37; 0.45]	1.04e−66	0.43⁽³⁾	0.22⁽³⁾	0.38⁽³⁾	9.6e−618⁽³⁾
*CFHR3/1* Deletion rs12144939 (chr1:196698945) G/T (−)	0.190⁽⁴⁾	0.199	0.108	0.45 [0.39; 0.51]	1.43e−34	0.21⁽⁴⁾	0.11⁽⁴⁾	0.48⁽⁴⁾	2.19e−273⁽⁴⁾
IAMGC Locus # 1.6 rs61818925 (chr1:196815450) G/T (−)	0.422	0.340	0.256	0.65 [0.59; 0.72]	1.68e−17	0.385	0.284	0.60	6.0e−165
*ARMS2/HTRA1* IAMGC Locus # 17 rs10490924 (chr10:124214448) G/T (+)	0.195	0.215	0.381	2.33 [2.10; 2.59]	1.59e−56	0.208⁽⁵⁾	0.436⁽⁵⁾	2.81⁽⁵⁾	6.5e−735⁽⁵⁾

Frequencies and effect size from the IAMDGC study are also provided
⁽¹⁾Estimated using the MAF in the 1000 G project (see Methods). ⁽²⁾Based on the perfect proxy rs570618 (r² = 0.9914, Dʹ = 1.0). ⁽³⁾Based on the perfect proxy rs10922109 (r² = 0.9919, Dʹ = 0.9959). ⁽⁴⁾Based on rs6677604, which is another tag for the CFHR3/1 deletion with minor allele A. ⁽⁵⁾Based on the perfect proxy rs3750846 (r² = 1.0, Dʹ = 1.0). *Bonferroni correction for multiple testing of 7 variants = 0.007 (0.05/7)

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