One locus showed significant SNP heterogeneity between phenotyping definitions (rs12124523 intronic variant in NEGR1, common factor association p = 8.4 × 10−14, Q heterogeneity p = 2.9 × 10−10, I2 = 0.71) with a stronger association found in self-reported depression studies (self-report odds ratio [OR] = 1.081, confidence interval [CI] = 1.065–1.098; other cohorts OR = 1.008, CI = 0.999–1.018). Here, NEGR1 is linked to depressive symptom measurement.