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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

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

Variant
(Position)
Major/minor allele
Minor allele frequency (MAF) OR
(95% CI)
p-value* IAMDGC (17,832 controls, 16,144 cases) [41]
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)
  1. Frequencies and effect size from the IAMDGC study are also provided
  2. (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)