Table 1.
The results of the GWAS meta-analysis for the independent signals reaching p < 10−6 in the discovery stage.
| SNP | Chr | Position (bp) | Nearest gene | Effective allele | Frequency | Discovery stage
|
Replication stage
|
Combined stage
|
Combined stage – sex-specific
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Beta/OR | P-value | I2 | Phet | Beta/OR | P-value | Beta/OR | P-value | Phet | Beta/OR (Males) | P-value (Males) | Beta/OR (Females) | P-value (Females) | ||||||
| EduYears | ||||||||||||||||||
| rs9320913 | 6 | 98691454 | LOC100129158 | A | 0.483 | 0.106 | 4.19×10−9 | 18.3 | 0.097 | 0.077 | 0.012 | 0.101 | 3.50×10−10 | 0.350 | 0.095 | 1.87×10−4 | 0.100 | 1.43×10−6 |
| rs3783006 | 13 | 97909210 | STK24 | C | 0.454 | 0.096 | 2.29×10−7 | 0 | 0.982 | 0.056 | 0.055 | 0.088 | 8.45×10−8 | 0.959 | 0.064 | 1.44×10−2 | 0.108 | 3.35×10−7 |
| rs8049439 | 16 | 28745016 | ATXN2L | T | 0.581 | 0.090 | 7.12×10−7 | 10.7 | 0.229 | 0.065 | 0.026 | 0.086 | 1.15×10−7 | 0.205 | 0.097 | 1.43×10−4 | 0.078 | 1.90×10−4 |
| rs13188378 | 5 | 101958587 | SLCO6A1 | A | 0.878 | −0.136 | 7.49×10−7 | 0 | 0.791 | 0.091 | 0.914 | −0.097 | 1.37×10−4 | 0.646 | −0.134 | 8.21×10−3 | −0.080 | 5.92×10−3 |
| College | ||||||||||||||||||
| rs11584700 | 1 | 202843606 | LRRN2 | A | 0.780 | 0.921 | 2.07×10−9 | 13.8 | 0.179 | 0.912 | 4.86×10−4 | 0.919 | 8.24×10−12 | 0.221 | 0.934 | 6.11×10−4 | 0.911 | 2.12×10−9 |
| rs4851266 | 2 | 100184911 | LOC150577 | T | 0.396 | 1.050 | 2.20×10−9 | 23.7 | 0.049 | 1.049 | 0.003 | 1.050 | 5.33×10−11 | 0.072 | 1.054 | 1.55×10−5 | 1.052 | 6.74×10−8 |
| rs2054125 | 2 | 199093966 | PLCL1 | T | 0.064 | 1.468 | 5.55×10−8 | 7 | 0.325 | 1.098 | 0.225 | 1.376 | 2.12×10−7 | 0.268 | 1.264 | 1.74×10−2 | 1.503 | 1.95×10−7 |
| rs3227 | 6 | 33770273 | ITPR3 | C | 0.498 | 1.043 | 6.02×10−8 | 5 | 0.363 | 1.010 | 0.280 | 1.037 | 3.24×10−7 | 0.415 | 1.046 | 9.44×10−5 | 1.029 | 1.37×10−3 |
| rs4073894 | 7 | 104254200 | LHFPL3 | A | 0.207 | 1.076 | 4.41×10−7 | 0 | 0.765 | 1.003 | 0.467 | 1.062 | 5.55×10−6 | 0.513 | 1.050 | 2.18×10−2 | 1.073 | 1.74×10−5 |
| rs12640626 | 4 | 176863266 | GPM6A | A | 0.580 | 1.041 | 4.94×10−7 | 10.9 | 0.234 | 1.000 | 0.495 | 1.034 | 7.48×10−6 | 0.420 | 1.038 | 1.59×10−3 | 1.031 | 7.61×10−4 |
The rows in bold are the independent signals reaching p < 5 × 10−8 in the discovery stage. “Frequency” refers to allele-frequency in the combined-stage meta-analysis. “Beta/OR” refers to the effect size in the EduYears analysis and to the Odds Ratio in the College analysis. All p-values are from the sample-size-weighted meta-analysis (fixed effects). The p-value in the replication stage meta-analysis was calculated from a one-sided test. I2 represents the % heterogeneity of effect size between the discovery stage studies. phet is the heterogeneity p-value.