Table 1 The results of the GWAS meta-analysis for the independent signals reaching P < 10−6 in the discovery stage.

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 percent heterogeneity of effect size between the discovery-stage studies. Phet is the heterogeneity P value. bp, base pair.

SNPChrPosition
(bp)
Nearest geneReference
allele
FrequencyDiscovery stageReplication stageCombined stageCombined stage–sex-specific analysis
Beta/ORP valueI2PhetBeta/ORP valueBeta/ORP valuePhetBeta/OR
(males)
P value
(males)
Beta/OR
(females)
P value
(females)
EduYears
rs9320913698691454LOC100129158A0.4830.1064.19×10−918.30.0970.0770.0120.1013.50×10−100.3500.0951.87×10−40.1001.43×10−6
rs37830061397909210STK24C0.4540.0962.29×10−700.9820.0560.0550.0888.45×10−80.9590.0641.44×10−20.1083.35×10−7
rs80494391628745016ATXN2LT0.5810.0907.12×10−710.70.2290.0650.0260.0861.15×10−70.2050.0971.43×10−40.0781.90×10−4
rs131883785101958587SLCO6A1A0.878–0.1367.49×10−700.7910.0910.914–0.0971.37×10−40.646–0.1348.21×10−3-0.0805.92×10−3
College
rs115847001202843606LRRN2A0.7800.9212.07×10−913.80.1790.9124.86×10−40.9198.24×10−120.2210.9346.11×10−40.9112.12×10−9
rs48512662100184911LOC150577T0.3961.0502.20×10−923.70.0491.0490.0031.0505.33×10−110.0721.0541.55×10−51.0526.74×10−8
rs20541252199093966PLCL1T0.0641.4685.55×10−870.3251.0980.2251.3762.12×10−70.2681.2641.74×10−21.5031.95×10−7
rs3227633770273ITPR3C0.4981.0436.02×10−850.3631.0100.2801.0373.24×10−70.4151.0469.44×10−51.0291.37×10−3
rs40738947104254200LHFPL3A0.2071.0764.41×10−700.7651.0030.4671.0625.55×10−60.5131.0502.18×10−21.0731.74×10−5
rs126406264176863266GPM6AA0.5801.0414.94×10−710.90.2341.0000.4951.0347.48×10−60.4201.0381.59×10−31.0317.61×10−4