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Table 2 Candidate approach to search for early AMD association

From: Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

Rs identifier chr:pos [hg19] Locus (Holliday et al.) EA OA Holliday et al. this meta-analysis (excluding ARIC, CHS) P (combined) Known advanced AMD locus (Fritsche et al.)
EAF OR [CI 95%] P EAF OR [CI 95%] P Neff
Experiment-wise significant association (P < 0.05/14)
 rs1967689 1:208039471 CD34,CD46 C G 0.25 0.85 [0.80;0.91] 5.1E-06 0.24 0.93 [0.90;0.96] 2.5E-05 42,119 5.5E-09 no
 rs621313 11:88913663 TYR A G 0.51 0.87 [0.83;0.92] 3.5E-06 0.52 0.95 [0.93;0.98] 6.8E-04 41,661 1.7E-07 no
 rs6857 19:45392254 PVRL2 T C 0.15 0.81 [0.74;0.88] 1.4E-06 0.16 0.92 [0.89;0.96] 7.1E-05 38,938 9.8E-09 yes
 rs2075650 19:45395619 APOE/TOMM40 A G 0.86 1.23 [1.13;1.34] 1.1E-06 0.86 1.08 [1.04;1.13] 2.6E-04 40,405 9.0E-08 yes
No experiment-wise significant association (P ≥ 0.05/14):
 rs16851585 1:177568799 C G 0.92 0.77 [0.69;0.86] 5.0E-06 0.89 1.04 [0.99;1.09] 0.099 42,119 0.74 no
 rs6721654 2:121301911 GLI2,INHBB T C 0.08 1.26 [1.14;1.4] 6.5E-06 0.08 1.01 [0.96;1.07] 0.65 41,718 0.017 no
 rs17586843 4:116924184 T C 0.78 1.18 [1.1;1.27] 1.5E-06 0.78 1.02 [0.98;1.05] 0.31 42,119 0.0048 no
 rs7750345 6:106260128 A G 0.75 1.16 [1.09;1.24] 6.8E-06 0.74 1.02 [0.98;1.05] 0.32 42,119 0.0049 no
 rs2049622 7:42176282 GLI3 A G 0.49 0.87 [0.83;0.93] 8.9E-06 0.52 0.99 [0.96;1.02] 0.41 42,060 0.015 no
 rs11986011 8:127332657 FAM84B T C 0.02 2.5 [1.68;3.71] 5.0E-06   no
 rs6480975 10:54574996 MBL2 C G 0.84 1.21 [1.12;1.32] 2.8E-06 0.85 0.99 [0.95;1.03] 0.63 40,651 0.17 no
 rs4293143 11:82821382 PCF11,RAB30 T G 0.69 0.85 [0.79;0.91] 7.8E-06 0.70 0.99 [0.96;1.02] 0.50 42,119 0.0094 no
 rs9646096 13:38065446 POSTN,TRPC4 A C 0.95 0.74 [0.65;0.84] 6.0E-06 0.96 0.99 [0.92;1.06] 0.76 39,782 0.0087 no
 rs10406174 19:3944240 ITGB1BP3,DAPK3 A G 0.11 1.24 [1.13;1.36] 5.6E-06 0.11 1.00 [0.93;1.07] 0.92 17,936 0.0057 yes
  1. EA effect allele, OA other allele, EAF effect allele frequency, OR odds ratio, CI confidence interval, P P value from Holliday et al. or Double GC corrected early association P value from this meta-analysis, Neff effective sample size
  2. The table shows results for the 14 lead variants reported as suggestive for early AMD by Holliday et al. [12] (effective sample size = 13,631) for their association with early AMD in our non-overlapping data set (P < 0.05/14 = 0.0036, tested at Bonferroni-corrected significance level, effective sample size up to 42,119) and in the combined analysis of the reported and our non-overlapping data (PCombined < 5.0 × 10−8, effective sample size up to 55,750). The ARIC and CHS studies were excluded from our meta-analysis data to avoid overlap with the data by Holliday et al. [12]. The last column indicates whether the locus was identified by Fritsche et al. for advanced AMD [9]