Table 2 Lead variants of genome-wide significant loci for white matter hyperintense lesion volume in the JPSC-AD Study and UK Biobank meta-analysis
Chr:Pos | Location | Lead variant | Ref/Alt | Nearest gene | Annotation | JPSC-AD | UKB | meta Beta (SE) | meta P | P for het | I2 (%) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EAF | Beta (SE) | P | EAF | Beta (SE) | P | ||||||||||
A) Newly discovered signal from the results of meta-GWAS | |||||||||||||||
6:134326285 | 6q23.2 | rs1002559 | C/T | SLC2A12 | Intronic | 0.223 | 0.044 (0.017) | 1.70E-02 | 0.192 | 0.053 (0.010) | 1.53E-07 | 0.050 (0.009) | 6.61E-09 | 0.66 | 0 |
B) Known signals from the results of meta-GWAS | |||||||||||||||
2:43104975 | 2p21 | rs62137163 | T/C | HAAO | Intergenic | 0.007 | 0.095 (0.089) | 2.50E-01 | 0.181 | -0.064 (0.010) | 7.56E-10 | -0.061 (0.010) | 2.10E-09 | 0.07 | 68.3 |
2:56150864 | 2p16.1 | rs3762515 | T/C | EFEMP1 | 5 Prime UTR variant | 0.044 | 0.024 (0.035) | 4.50E-01 | 0.097 | 0.146 (0.013) | 5.97E-28 | 0.131 (0.012) | 9.05E-26 | 1.11E-03 | 90.6 |
2:188221793 | 2q32.1 | rs36146505 | C/T | CALCRL | Intronic | 0.067 | -0.039 (0.029) | 1.70E-01 | 0.295 | -0.046 (0.009) | 8.92E-08 | -0.046 (0.008) | 3.67E-08 | 0.8 | 0.0 |
2:203683990 | 2q33.2 | rs79633844 | G/A | ICA1L | Intronic | 0.005 | -0.132 (0.101) | 1.80E-01 | 0.128 | -0.070 (0.012) | 4.39E-09 | -0.071 (0.012) | 2.18E-09 | 0.54 | 0.0 |
3:183373567 | 3q27.1 | rs10470355 | G/A | KLHL24 | Intronic | 0.381 | -0.047 (0.015) | 1.30E-03 | 0.262 | -0.077 (0.009) | 1.20E-17 | -0.069 (0.008) | 3.35E-19 | 0.09 | 66.0 |
5:82862328 | 5q14.2-q14.3 | rs35544841 | GA/G | VCAN | Intronic | 0.270 | 0.002 (0.016) | 9.80E-01 | 0.199 | 0.087 (0.010) | 2.13E-18 | 0.064 (0.008) | 4.64E-14 | 8.60E-06 | 95.1 |
6:151020020 | 6q25.1 | rs12202497 | T/A | PLEKHG1 | Intronic | 0.344 | 0.025 (0.015) | 9.30E-02 | 0.404 | 0.072 (0.008) | 6.24E-19 | 0.061 (0.007) | 6.48E-18 | 0.01 | 86.9 |
8:8729761 | 8p23.1 | rs907183 | C/G | MFHAS1 | Intronic | 0.784 | 0.064 (0.018) | 2.30E-04 | 0.457 | 0.045 (0.008) | 1.32E-08 | 0.048 (0.007) | 2.50E-11 | 0.34 | 0.0 |
8:11860251 | 8p23.1 | rs10103228 | G/T | DEFB134 | Intergenic | 0.929 | 0.062 (0.028) | 2.90E-02 | 0.610 | 0.043 (0.008) | 1.23E-07 | 0.044 (0.008) | 1.26E-08 | 0.51 | 0.0 |
10:105599770 | 10q24.33 | rs11191822 | G/T | SH3PXD2A | Intronic | 0.650 | -0.061 (0.015) | 2.80E-05 | 0.362 | -0.050 (0.008) | 1.04E-09 | -0.053 (0.007) | 3.17E-13 | 0.52 | 0.0 |
10:127675607 | 10q26.2 | rs3812683 | C/A | FANK1 | Intronic | 0.405 | 0.049 (0.015) | 7.60E-04 | 0.417 | 0.039 (0.008) | 9.09E-07 | 0.042 (0.007) | 3.48E-09 | 0.58 | 0.0 |
13:111040681 | 13q34 | rs11838776 | A/G | COL4A2 | Intronic | 0.084 | 0.022 (0.026) | 4.40E-01 | 0.279 | 0.057 (0.009) | 1.13E-10 | 0.054 (0.008) | 1.74E-10 | 0.21 | 38.2 |
16:51442679 | 16q12.1 | rs1948948 | T/C | SALL1 | Intergenic | 0.888 | -0.017 (0.023) | 5.70E-01 | 0.442 | -0.066 (0.008) | 9.31E-17 | -0.061 (0.008) | 5.24E-16 | 0.04 | 75.3 |
16:87237568 | 16q24.2 | rs12928520 | T/C | C16orf95 | Intergenic | 0.155 | 0.093 (0.020) | 2.70E-06 | 0.444 | 0.068 (0.008) | 3.34E-17 | 0.071 (0.007) | 1.02E-21 | 0.25 | 25.8 |
17:19194812 | 17p11.2 | rs1969161 | A/G | EPN2 | Intronic | 0.011 | 0.035 (0.070) | 6.90E-01 | 0.814 | 0.068 (0.010) | 2.80E-11 | 0.067 (0.010) | 2.71E-11 | 0.64 | 0.0 |
17:43141966 | 17q21.31 | rs4525538 | G/A | NMT1 | Intronic | 0.386 | 0.068 (0.015) | 6.00E-06 | 0.629 | 0.072 (0.008) | 2.17E-18 | 0.071 (0.007) | 5.94E-23 | 0.82 | 0.0 |
17:73871773 | 17q25.1 | rs3744020 | A/G | TRIM47 | Intronic | 0.159 | 0.134 (0.020) | 1.70E-11 | 0.188 | 0.145 (0.010) | 4.90E-47 | 0.143 (0.009) | 3.23E-57 | 0.61 | 0.0 |
X:13808841 | Xp22.2 | rs6527976 | G/A | GPM6B | Intronic | 0.759 | -0.036 (0.014) | 1.11E-02 | 0.602 | -0.043 (0.007) | 7.74E-11 | -0.042 (0.006) | 3.14E-12 | 0.65 | 0.0 |
X:152601840 | Xq28 | rs5970447 | T/C | ZNF275 | Intronic | 0.324 | -0.010 (0.013) | 4.32E-01 | 0.303 | -0.057 (0.007) | 1.01E-15 | -0.046 (0.006) | 1.06E-13 | 1.71E-03 | 90.1 |
