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Table 1 Single variant analysis of variants significantly associated with AMD risk

From: Genetic pleiotropy between age-related macular degeneration and 16 complex diseases and traits

  Original study Association with AMD Frequency in  
Variant Chromo some Position [hg19] Phenotype Locus name Locus boundary in 1 M bp [hg19] Effect allelea Effect sizea Odds ratio 95% CIb p value raw p value adjc Q-value raw Q-value adjc Controls Cases Imputation quality
rs7523273 1 207977083 SCZ CD46/CR1L 207.8–208.1 A 1.063 (OR) 1.078 1.042-1.116 1.37E-05 2.51E-05 0.0009 5.91E-05 0.667 0.681 0.972
rs1550094 2 233385396 MYP PRSS56 233.3–233.5 G 1.087 (HR) 1.067 1.030-1.106 0.0003 0.0019 0.0093 0.0021 0.290 0.304 0.867
rs9844666 3 135974216 HGT STAG1 135.5–136.9 G 1.024 (SL) 1.079 1.039-1.120 6.70E-05 0.0002 0.0029 0.0003 0.753 0.768 0.999
rs7432375 3 136288405 SCZ STAG1 135.5–136.9 G 1.073 (OR) 0.942 0.911-0.973 0.0003 0.0004 0.0095 0.0005 0.605 0.593 0.999
rs13091182 3 141133960 MYP ZBTB38 141–141.3 G 1.064 (OR) 0.929 0.898-0.960 1.65E-05 5.65E-06 0.0010 2.26E-05 0.668 0.651 0.996
rs3774959 4 103511114 UC NFKB1 103.3–103.6 A 1.119 (OR) 0.928 0.898-0.959 1.11E-05 4.44E-07 0.0007 7.71E-06 0.357 0.341 0.964
rs2277027 5 156932376 LGF ADAM19 156.8–157.1 A 1.462 (SL) 1.096 1.059-1.133 1.31E-07 2.75E-06 1.50E-05 1.28E-05 0.651 0.667 1.000
rs2814982 6 34546560 TC C6ORF106 34.4–34.9 C 1.045 (SL) 1.118 1.061-1.178 2.67E-05 4.82E-05 0.0014 0.0001 0.889 0.898 0.980
rs2207139 6 50845490 BMI TFAP2B 50.7–51 G 1.046 (SL) 0.921 0.883-0.961 0.0001 0.0004 0.0058 0.0006 0.179 0.165 0.997
rs11776767 8 10683929 TG PINX1 10.5–10.8 C 1.022 (OR) 0.936 0.905-0.967 8.83E-05 0.0089 0.0037 0.0089 0.380 0.370 0.999
rs3217992 9 22003223 CAD CDKN2B 21.9–22.2 T 1.160 (OR) 0.914 0.884-0.945 1.07E-07 1.18E-05 1.35E-05 3.67E-05 0.394 0.375 1.000
rs7865618 9 22031005 ODCA; VCDR CDKN2B 21.9–22.2 A 1.023 (SL) 0.937 0.907-0.968 9.23E-05 6.12E-05 0.0037 0.0001 0.593 0.579 1.000
rs7866783 9 22056359 POAG CDKN2B 21.9–22.2 G 1.451 (OR) 0.936 0.906-0.967 6.67E-05 2.53E-05 0.0029 5.91E-05 0.594 0.579 0.995
rs11191548 10 104846178 BP NT5C2 104.4–105.2 T 2.989 (SL) 0.902 0.853-0.954 0.0003 0.0012 0.0092 0.0014 0.914 0.906 1.000
rs11191560 10 104869038 BMI NT5C2 104.4–105.2 C 1.031 (SL) 1.110 1.049-1.173 0.0003 0.0012 0.0087 0.0014 0.086 0.094 0.996
rs634552 11 75282052 HGT SERPINH1 75.2–75.4 T 1.040 (SL) 1.120 1.069-1.173 2.08E-06 1.47E-05 0.0002 4.11E-05 0.130 0.144 0.999
rs11830103 12 123823546 HGT SBNO1 123.3–124 G 1.036 (SL) 1.082 1.040-1.125 9.13E-05 0.0028 0.0037 0.0029 0.205 0.216 1.000
rs4901977 14 60789176 VCDR SIX6 60.7–61.3 T 1.011 (SL) 0.927 0.895-0.959 1.56E-05 8.40E-06 0.0010 2.94E-05 0.319 0.306 0.996
rs2093210 14 60957279 HGT SIX6 60.7–61.3 C 1.033 (SL) 0.920 0.890-0.950 5.00E-07 1.37E-06 4.34E-05 7.71E-06 0.417 0.401 0.997
rs33912345 14 60976537 POAG SIX6 60.7–61.3 C 1.320 (OR) 0.919 0.889-0.949 3.51E-07 1.19E-06 3.21E-05 7.71E-06 0.413 0.397 1.000
rs10483727 14 61072875 ODCA SIX6 60.7–61.3 T 1.026 (SL) 0.915 0.886-0.946 1.11E-07 1.06E-06 1.35E-05 7.71E-06 0.414 0.396 0.999
rs1555399 14 67984370 PD PLEKHH1 67.9–68.1 T 1.115 (OR) 0.929 0.899-0.959 6.27E-06 0.0002 0.0004 0.0003 0.517 0.502 0.997
rs11627032 14 93104072 BRC RIN3 93–93.2 T 1.060 (OR) 1.070 1.032-1.109 0.0002 0.0014 0.0086 0.0015 0.728 0.739 0.931
rs1378942 15 75077367 BP CSK 74.9–75.3 C 1.846 (SL) 0.918 0.887-0.950 8.52E-07 1.38E-06 7.06E-05 7.71E-06 0.345 0.328 1.000
rs2290400 17 38066240 T1D GSDMB 37.8–38.2 C 1.080 (OR) 1.068 1.034-1.103 5.47E-05 7.29E-05 0.0026 0.0001 0.494 0.508 1.000
rs9303280 17 38074031 ALG GSDMB 37.8–38.2 C 1.070 (SL) 0.941 0.911-0.971 0.0002 0.0001 0.0068 0.0002 0.510 0.497 0.984
rs386000 19 54792761 HDL LILRA3 54.7–54.9 C 1.049 (SL) 1.096 1.053-1.141 6.24E-06 0.0006 0.0004 0.0008 0.199 0.211 0.782
rs1547014 22 29100711 VCDR CHEK 28.5–29.2 C 1.013 (SL) 0.936 0.904-0.969 0.0002 6.78E-05 0.0068 0.0001 0.708 0.695 0.999
  1. aRisk-/trait-increasing allele and effect size in the original study (OR odds ratio, SL slope, HR hazard ratio) (see Additional file 2: Table S1 for further details)
  2. b95% CI = 95% confidence interval of AMD OR estimate
  3. cAssociation of variant adjusted for 52 AMD-associated risk variants