Table 4.
Re-analysis results of gene variants with genome wide statistical significance (p-value < 5 × 10−8) and borderline statistical significance (5 × 10−8 ≤ p-value < 0.05) in the GWAS datasets included in GWAS meta-analyses (results of FPRP < 0.2 and BFDP < 0.8).
| Author, Year | Trait | Gene(s) | Variant | Comparison | OR (95% CI) | p-Value | Power OR 1.2 | Power OR 1.5 | FPRP Values at Prior Probability | BFDP 0.001 |
BFDP 0.000001 |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR 1.2 | OR 1.5 | |||||||||||||
| 0.001 | 0.000001 | 0.001 | 0.000001 | |||||||||||
| Anney et al., 2012 [34] | ASD (European) | ERBB4 | rs1879532 | A | 2.02 (1.57–2.59) | 1.55 × 10−8 | 0.000 | 0.009 | 0.595 | 0.999 | 0.003 | 0.757 | 0.026 | 0.964 |
| Anney et al., 2012 [34] | Autism (European) | None | rs289932 | A | 0.49 (0.38–0.64) | 5.04 × 10−8 | 0.000 | 0.012 | 0.772 | 1.000 | 0.014 | 0.932 | 0.114 | 0.992 |
| Anney et al., 2012 [34] | ASD | TMEM132B | rs16919315 | A | 0.53 (0.42–0.67) | 5.12 × 10−8 | 0.000 | 0.028 | 0.589 | 0.999 | 0.004 | 0.800 | 0.049 | 0.981 |
| Anney et al., 2012 [34] | Autism (European) | ERBB4 | rs1879532 | A | 1.72 (1.39–2.11) | 1.66 × 10−7 | 0.000 | 0.095 | 0.416 | 0.999 | 0.002 | 0.676 | 0.044 | 0.979 |
| Anney et al., 2010 [30] | Autism | NA | rs6557675 | A (minor allele) | 0.61 (0.51–0.71) | 2.20 × 10−7 | 0.000 | 0.126 | 0.006 | 0.861 | 0.000 | 0.001 | 0.000 | 0.048 |
| Anney et al., 2012 [34] | Autism (European) | None | rs289858 | A | 0.52 (0.40–0.67) | 2.81 × 10−7 | 0.000 | 0.027 | 0.762 | 1.000 | 0.015 | 0.940 | 0.161 | 0.995 |
| Anney et al., 2012 [34] | ASD | SYNE2 | rs2150291 | A | 1.72 (1.40–2.13) | 2.83 × 10−7 | 0.000 | 0.105 | 0.579 | 0.999 | 0.006 | 0.864 | 0.119 | 0.993 |
| Anney et al., 2012 [34] | ASD (European) | RPH3AL | rs7207517 | A | 1.97 (1.51–2.57) | 3.05 × 10−7 | 0.000 | 0.022 | 0.817 | 1.000 | 0.025 | 0.963 | 0.226 | 0.997 |
| Anney et al., 2012 [34] | Autism (European) | None | rs4761371 | A | 0.46 (0.34–0.63) | 3.91 × 10−7 | 0.000 | 0.010 | 0.924 | 1.000 | 0.111 | 0.992 | 0.521 | 0.999 |
| Anney et al., 2012 [34] | ASD (European) | PRAMEF12 | rs1812242 | A | 1.44 (1.25–1.66) | 4.29 × 10−7 | 0.006 | 0.713 | 0.077 | 0.988 | 0.001 | 0.411 | 0.038 | 0.975 |
| Anney et al., 2012 [34] | ASD | None | rs10904487 | G | 0.63 (0.52–0.75) | 4.29 × 10−7 | 0.001 | 0.262 | 0.198 | 0.996 | 0.001 | 0.440 | 0.028 | 0.966 |
| Anney et al., 2012 [34] | Autism (European) | None | rs289932 | A | 0.67 (0.57–0.79) | 5.42 × 10−7 | 0.005 | 0.524 | 0.286 | 0.998 | 0.004 | 0.784 | 0.135 | 0.994 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs4141463 | A (minor allele) | 0.62 (0.52–0.73) | 5.50 × 10−7 | 0.000 | 0.192 | 0.047 | 0.980 | 0.000 | 0.048 | 0.002 | 0.655 |
| Anney et al., 2012 [34] | Autism | None | rs9608521 | A | 1.46 (1.25–1.69) | 7.62 × 10−7 | 0.004 | 0.641 | 0.084 | 0.989 | 0.001 | 0.383 | 0.033 | 0.971 |
| Anney et al., 2012 [34] | ASD | None | rs1408744 | A | 0.65 (0.54–0.77) | 8.06 × 10−7 | 0.002 | 0.385 | 0.235 | 0.997 | 0.002 | 0.618 | 0.062 | 0.985 |
| Anney et al., 2017 [31] | ASD | LINC00535 | chr8_94389815_I | I vs. D | 1.14 (1.09–1.19) | 9.47 × 10−7 | 0.990 | 1.000 | 0.000 | 0.002 | 0.000 | 0.002 | 0.686 | 1.000 |
| Anney et al., 2012 [34] | ASD (European) | PC | rs7122539 | A | 0.60 (0.49–0.74) | 9.64 × 10−7 | 0.001 | 0.162 | 0.628 | 0.999 | 0.011 | 0.917 | 0.213 | 0.996 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs4814324 | A (minor allele) | 1.58 (1.34–1.86) | 9.80 × 10−7 | 0.000 | 0.266 | 0.076 | 0.988 | 0.000 | 0.128 | 0.006 | 0.859 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6079544 | A (minor allele) | 1.57 (1.33–1.84) | 1.20 × 10−6 | 0.000 | 0.287 | 0.053 | 0.982 | 0.000 | 0.081 | 0.004 | 0.797 |
| Anney et al., 2017 [31] | ASD | EXOC4 | rs6467494 | T vs. C | 1.12 (1.07–1.16) | 1.43 × 10−6 | 1.000 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.197 | 0.996 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6079536 | A (minor allele) | 0.64 (0.54–0.75) | 1.60 × 10−6 | 0.001 | 0.307 | 0.059 | 0.984 | 0.000 | 0.102 | 0.005 | 0.837 |
| Anney et al., 2010 [30] | ASD | MYH11 | rs17284809 | A (minor allele) | 0.52 (0.39–0.69) | 1.70 × 10−6 | 0.001 | 0.043 | 0.915 | 1.000 | 0.121 | 0.993 | 0.636 | 0.999 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6079553 | A (minor allele) | 1.55 (1.31–1.82) | 2.10 × 10−6 | 0.001 | 0.344 | 0.090 | 0.990 | 0.000 | 0.204 | 0.011 | 0.920 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6074798 | A (minor allele) | 1.56 (1.32–1.84) | 2.10 × 10−6 | 0.001 | 0.321 | 0.123 | 0.993 | 0.000 | 0.287 | 0.017 | 0.945 |
| Anney et al., 2017 [31] | ASD | OPCML | rs7952100 | C vs.G | 1.14 (1.09–1.19) | 2.49 × 10−6 | 0.990 | 1.000 | 0.000 | 0.002 | 0.000 | 0.002 | 0.686 | 1.000 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs10446030 | G (minor allele) | 1.54 (1.30–1.81) | 3.20 × 10−6 | 0.001 | 0.375 | 0.116 | 0.992 | 0.000 | 0.301 | 0.019 | 0.951 |
| Kuo et al., 2015 [33] | ASD | STYK1 | rs16922945 | C (minor allele) | 1.86 (1.43–2.43) | 3.43 × 10−6 | 0.001 | 0.057 | 0.891 | 1.000 | 0.085 | 0.989 | 0.572 | 0.999 |
| Anney et al., 2010 [30] | ASD | POU5F2 | rs10258862 | G (minor allele) | 1.41 (1.23–1.61) | 3.70 × 10−6 | 0.009 | 0.820 | 0.043 | 0.978 | 0.000 | 0.319 | 0.027 | 0.966 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6079540 | A (minor allele) | 0.65 (0.55–0.77) | 3.70 × 10−6 | 0.002 | 0.385 | 0.235 | 0.997 | 0.002 | 0.618 | 0.062 | 0.985 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6074787 | A (minor allele) | 1.53 (1.30–1.80) | 4.10 × 10−6 | 0.002 | 0.406 | 0.147 | 0.994 | 0.001 | 0.418 | 0.031 | 0.970 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6074798 | A (minor allele) | 1.38 (1.22–1.56) | 4.80 × 10−6 | 0.013 | 0.909 | 0.020 | 0.954 | 0.000 | 0.224 | 0.018 | 0.948 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs980319 | G (minor allele) | 1.52 (1.29–1.79) | 5.10 × 10−6 | 0.002 | 0.437 | 0.184 | 0.996 | 0.001 | 0.543 | 0.050 | 0.981 |
| Anney et al., 2010 [30] | Autism | MACROD2 | rs6079537 | G (minor allele) | 1.52 (1.29–1.79) | 6.00 × 10−6 | 0.002 | 0.437 | 0.184 | 0.996 | 0.001 | 0.543 | 0.050 | 0.981 |
| Kuo et al., 2015 [33] | ASD | NA | rs10966205 | A (minor allele) | 1.52 (1.27–1.83) | 6.25 × 10−6 | 0.006 | 0.444 | 0.609 | 0.999 | 0.022 | 0.957 | 0.426 | 0.999 |
| Kuo et al., 2015 [33] | ASD | OR2M4 | rs10888329 | T (minor allele) | 0.55 (0.43–0.72) | 8.05 × 10−6 | 0.001 | 0.081 | 0.916 | 1.000 | 0.144 | 0.994 | 0.718 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6079536 | A (minor allele) | 0.73 (0.65–0.83) | 8.50 × 10−6 | 0.022 | 0.917 | 0.067 | 0.986 | 0.002 | 0.628 | 0.084 | 0.989 |
| Anney et al., 2010 [30] | ASD | NA | rs6557675 | A (minor allele) | 0.72 (0.63–0.82) | 8.70 × 10−6 | 0.014 | 0.877 | 0.051 | 0.982 | 0.001 | 0.457 | 0.047 | 0.980 |
| Kuo et al., 2015 [33] | ASD | NA | rs7933990 | A (minor allele) | 1.72 (1.35–2.19) | 9.40 × 10−6 | 0.002 | 0.133 | 0.861 | 1.000 | 0.075 | 0.988 | 0.606 | 0.999 |
| Kuo et al., 2015 [33] | ASD | MNT | rs2447097 | A (minor allele) | 1.53 (1.27–1.85) | 9.45 × 10−6 | 0.006 | 0.419 | 0.652 | 0.999 | 0.026 | 0.965 | 0.467 | 0.999 |
| Anney et al., 2010 [30] | ASD | GSG1L | rs205409 | G (minor allele) | 0.72 (0.64–0.82) | 9.60 × 10−6 | 0.014 | 0.877 | 0.051 | 0.982 | 0.001 | 0.457 | 0.047 | 0.980 |
| Kuo et al., 2015 [33] | ASD | OR2M4 | rs6672981 | C (minor allele) | 0.55 (0.42–0.72) | 9.64 × 10−6 | 0.001 | 0.081 | 0.916 | 1.000 | 0.144 | 0.994 | 0.718 | 1.000 |
| Kuo et al., 2015 [33] | ASD | OR2M4 | rs4397683 | C (minor allele) | 0.55 (0.42–0.72) | 9.86 × 10−6 | 0.001 | 0.081 | 0.916 | 1.000 | 0.144 | 0.994 | 0.718 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs980319 | G (minor allele) | 1.36 (1.20–1.54) | 1.00 × 10−5 | 0.024 | 0.939 | 0.049 | 0.981 | 0.001 | 0.570 | 0.068 | 0.987 |
| Kuo et al., 2015 [33] | ASD | BCAS1/CYP24A1 | rs12479663 | G (minor allele) | 1.81 (1.38–2.36) | 1.08 × 10−5 | 0.001 | 0.083 | 0.907 | 1.000 | 0.124 | 0.993 | 0.687 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs4814324 | A (minor allele) | 1.36 (1.20–1.54) | 1.10 × 10−5 | 0.024 | 0.939 | 0.049 | 0.981 | 0.001 | 0.570 | 0.068 | 0.987 |
| Kuo et al., 2015 [33] | ASD | KRR1 | rs3741496 | C (minor allele) | 1.49 (1.24–1.78) | 1.15 × 10−5 | 0.009 | 0.529 | 0.565 | 0.999 | 0.020 | 0.954 | 0.430 | 0.999 |
| Kuo et al., 2015 [33] | ASD | OR2M4 | rs4642918 | C (minor allele) | 0.56 (0.43–0.73) | 1.24 × 10−5 | 0.002 | 0.099 | 0.917 | 1.000 | 0.155 | 0.995 | 0.745 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6079544 | A (minor allele) | 1.35 (1.20–1.53) | 1.30 × 10−5 | 0.033 | 0.951 | 0.074 | 0.988 | 0.003 | 0.733 | 0.124 | 0.993 |
| Kuo et al., 2015 [33] | ASD | NA | rs13211684 | G (minor allele) | 1.56 (1.28–1.91) | 1.36 × 10−5 | 0.006 | 0.352 | 0.750 | 1.000 | 0.045 | 0.979 | 0.572 | 0.999 |
| Kuo et al., 2015 [33] | ASD | MNT | rs2447095 | A (minor allele) | 1.52 (1.26–1.84) | 1.45 × 10−5 | 0.008 | 0.446 | 0.695 | 1.000 | 0.038 | 0.975 | 0.552 | 0.999 |
| Kuo et al., 2015 [33] | ASD | NA | rs12543592 | G (minor allele) | 0.67 (0.56–0.81) | 1.63 × 10−5 | 0.012 | 0.521 | 0.744 | 1.000 | 0.063 | 0.985 | 0.678 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6079553 | A (minor allele) | 1.35 (1.19–1.52) | 1.70 × 10−5 | 0.026 | 0.959 | 0.027 | 0.965 | 0.001 | 0.424 | 0.041 | 0.977 |
| Kuo et al., 2015 [33] | ASD | KRR1 | rs1051446 | C (minor allele) | 1.47 (1.23–1.76) | 1.77 × 10−5 | 0.014 | 0.587 | 0.669 | 1.000 | 0.045 | 0.979 | 0.614 | 0.999 |
| Anney et al., 2010 [30] | ASD | NA | rs4078417 | C (minor allele) | 1.38 (1.21–1.57) | 1.90 × 10−5 | 0.017 | 0.897 | 0.055 | 0.983 | 0.001 | 0.524 | 0.059 | 0.984 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs10446030 | G (minor allele) | 1.34 (1.19–1.52) | 2.20 × 10−5 | 0.043 | 0.960 | 0.110 | 0.992 | 0.006 | 0.847 | 0.210 | 0.996 |
| Kuo et al., 2015 [33] | ASD | GPD2 | rs3916984 | T (minor allele) | 0.62 (0.49–0.77) | 2.25 × 10−5 | 0.004 | 0.256 | 0.804 | 1.000 | 0.056 | 0.984 | 0.595 | 0.999 |
| Kuo et al., 2015 [33] | ASD | NA | rs12366025 | T (minor allele) | 1.67 (1.31–2.11) | 2.49 × 10−5 | 0.003 | 0.184 | 0.860 | 1.000 | 0.086 | 0.989 | 0.662 | 0.999 |
| Ma et al., 2009 [32] | Autism | NA | rs10038113 | C(minor)/T(major) | 0.67 (0.56–0.81) | 2.75 × 10−5 | 0.012 | 0.521 | 0.744 | 1.000 | 0.063 | 0.985 | 0.678 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6079540 | A (minor allele) | 0.75 (0.66–0.84) | 2.90 × 10−5 | 0.034 | 0.979 | 0.019 | 0.950 | 0.001 | 0.399 | 0.037 | 0.975 |
| Anney et al., 2010 [30] | Autism | HAT1 | rs6731562 | G (minor allele) | 1.51 (1.27–1.81) | 3.30 × 10−5 | 0.006 | 0.471 | 0.562 | 0.999 | 0.017 | 0.946 | 0.383 | 0.998 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6074787 | A (minor allele) | 1.33 (1.18–1.50) | 3.40 × 10−5 | 0.047 | 0.975 | 0.067 | 0.986 | 0.003 | 0.776 | 0.147 | 0.994 |
| Kuo et al., 2015 [33] | ASD | GLIS1 | rs12080933 | A (minor allele) | 1.48 (1.23–1.78) | 3.57 × 10−5 | 0.013 | 0.557 | 0.707 | 1.000 | 0.053 | 0.983 | 0.648 | 0.999 |
| Kuo et al., 2015 [33] | ASD | FSTL4 | rs11741756 | T (minor allele) | 1.67 (1.31–2.13) | 3.64 × 10−5 | 0.004 | 0.194 | 0.903 | 1.000 | 0.157 | 0.995 | 0.785 | 1.000 |
| Kuo et al., 2015 [33] | ASD | STYK1 | rs7953930 | G (minor allele) | 1.65 (1.30–2.09) | 3.83 × 10−5 | 0.004 | 0.215 | 0.888 | 1.000 | 0.133 | 0.994 | 0.761 | 1.000 |
| Anney et al., 2010 [30] | Autism | NA | rs4078417 | C (minor allele) | 1.50 (1.26–1.79) | 4.10 × 10−5 | 0.007 | 0.500 | 0.509 | 0.999 | 0.014 | 0.933 | 0.339 | 0.998 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs4141463 | A (minor allele) | 0.75 (0.66–0.85) | 4.30 × 10−5 | 0.049 | 0.967 | 0.118 | 0.993 | 0.007 | 0.873 | 0.243 | 0.997 |
| Kuo et al., 2015 [33] | ASD | OR2M3 | rs11204613 | G (minor allele) | 0.58 (0.45–0.75) | 4.60 × 10−5 | 0.003 | 0.144 | 0.920 | 1.000 | 0.185 | 0.996 | 0.799 | 1.000 |
| Anney et al., 2010 [30] | ASD | MACROD2 | rs6079537 | G (minor allele) | 1.32 (1.17–1.49) | 5.40 × 10−5 | 0.062 | 0.981 | 0.103 | 0.991 | 0.007 | 0.878 | 0.249 | 0.997 |
| Anney et al., 2010 [30] | Autism | GSG1L | rs205409 | G (minor allele) | 0.69 (0.58–0.81) | 1.10 × 10−4 | 0.011 | 0.663 | 0.353 | 0.998 | 0.009 | 0.896 | 0.271 | 0.997 |
| Anney et al., 2010 [30] | Autism | POU5F2 | rs10258862 | G (minor allele) | 1.43 (1.21–1.71) | 1.80 × 10−4 | 0.027 | 0.700 | 0.764 | 1.000 | 0.112 | 0.992 | 0.799 | 1.000 |
Abbreviations: ASD, Autism spectrum disorders; A, Adenine; C, Cytosine; G, Guanine; T, Thymine; D, Deletion; I, Insertion; FPRP, false positive rate probability; BFDP, Bayesian false discovery probability; OR, odds ratio; CI, confidence interval; GWAS, Genome-Wide Association Studies; NA, not available.