Table 1 SNPs significantly associated with schizophrenia after Bonferroni correction

From: Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia

SNP-ID	EA beta	Signs concordant	SZ adj. R² (%)	SZ OR (Adj.)	EAF	Power α = 0.05/506 (%)	Chance of direct pleiotropic effect on EA and SZ		Posterior probability of true association with SZ prior belief (π) (%)
SNP-ID	EA beta	Signs concordant	SZ adj. R² (%)	SZ OR (Adj.)	EAF	Power α = 0.05/506 (%)	90% sets	50% sets	0.1%	1.0%	5.0%	10.0%
rs79210963	−0.016	Yes	0.021	0.931	0.89	22.9	H	M	75.0	96.8	99.3	99.7
rs7610856	0.013	No	0.022	0.955	0.41	22.8	M	M	74.9	96.8	99.3	99.7
rs10896636	0.012	No	0.020	0.956	0.67	17.8	H	L	68.7	95.6	99.1	99.5
rs756912	−0.015	Yes	0.022	0.956	0.51	22.7	L	L	74.8	96.7	99.3	99.7
rs6449503	0.018	No	0.020	0.961	0.51	12.9	L	L	60.0	93.7	98.7	99.3
rs7336518	−0.016	Yes	0.014	0.964	0.13	1.5	M	M	13.4	60.6	88.5	93.9
rs143283559	0.014	No	0.017	0.965	0.72	4.6	M	L	32.8	83.0	96.1	98.0
rs11210935	0.015	No	0.014	0.973	0.77	1.2	L	L	10.9	55.1	86.0	92.5
rs77000541	−0.014	Yes	0.018	0.974	0.33	1.6	L	L	14.1	62.2	89.2	94.3
rs2819344	0.014	No	0.017	0.983	0.62	0.3	H	L	3.0	23.3	60.4	75.3
rs4500960	−0.013	No	0.017	1.017	0.47	0.3	L	L	3.0	23.3	60.4	75.3
rs28360516	−0.012	No	0.013	1.027	0.70	1.4	M	L	12.6	59.0	87.8	93.5
rs7522116	0.011	Yes	0.015	1.029	0.56	3.0	M	L	23.8	75.8	94.0	96.9
rs7593947	0.014	Yes	0.018	1.040	0.51	12.5	M	L	59.1	93.5	98.6	99.3
rs11694989	0.011	Yes	0.021	1.044	0.43	17.9	L	L	68.8	95.7	99.1	99.5
rs320700	0.013	Yes	0.024	1.054	0.65	36.4	H	M	85.3	98.3	99.7	99.8
rs3957165	0.015	Yes	0.020	1.056	0.83	14.7	L	L	63.6	94.6	98.9	99.4
rs10791106	0.011	Yes	0.026	1.056	0.54	46.9	L	L	89.9	98.9	99.8	99.9
rs2992632	0.016	Yes	0.025	1.060	0.74	36.8	M	L	85.5	98.3	99.7	99.8
rs10773002	0.022	Yes	0.043	1.087	0.28	91.0	L	L	99.0	99.9	100.0	100.0
rs4378243	0.019	Yes	0.044	1.112	0.85	91.5	L	L	99.1	99.9	100.0	100.0

Notes: The SNPs in the table are ordered by their odds ratio (OR) on schizophrenia (SZ). Effect sizes for SZ (in R² and OR) are downward adjusted for the winner’s curse²⁵. EA (beta) is the standardized beta of a SNP for educational attainment (EA) GWAS. R² was approximated from the winner’s curse adjusted OR ratios, using the formulas described in Methods section. The winner’s curse adjustment took into account that only SNPs with P = 0.05/506 were selected. SNPs with concordant effects on both SZ and EA are marked as ‘yes’ in the sign concordance column. EAF is the effect allele frequency in the SZ GWAS data. Power calculations assumed that the available GWAS sample size for SZ for each SNP consisted of 34,409 cases and 45,670 controls. The chance that a SNP has direct pleiotropic effects on EA and SZ has been evaluated with PAINTOR using sets of SNPs that have a cumulative probability of 90% or 50% to include the causal variant (see Methods and Supplementary Note 3). The posterior probability that these SNPs are truly associated with SZ was calculated using the Bayesian procedure developed by Rietveld et al.²⁵. SNPs highlighted in bold are associations for SZ that have not been emphasized in the previous literature. H high, M medium, L low.

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Table 1 SNPs significantly associated with schizophrenia after Bonferroni correction

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