Table 3.

Replication of MWAS Association Findings (H₀: b ₂ = 0) in Blood With q-Value < 0.1 in Postmortem Brain Samples

Chr	SNP	Position (bp)	MWAS				Replication			Gene
			T	P-value	q-value	Effect	T	P-value	Effect
2	rs605832	31454545	−5.65	2.0E-08	0.010	−0.301	−0.91	1.8E-01	−0.232
3	rs9827299	71353372	−6.59	6.3E-11	0.000	−0.351	0.79	7.8E-01	0.202	FOXP1
3	rs3796293	190332093	−5.49	4.7E-08	0.015	−0.292	−2.88	3.0E-03	−0.732	IL1RAP
15	rs56153788	86170992	−5.33	1.1E-07	0.028	−0.284	0.70	7.5E-01	0.177	AKAP13
16	rs2542671	54209836	−5.26	1.6E-07	0.032	−0.280	−0.06	4.8E-01	−0.015
17	rs9912900	71057060	−5.17	2.7E-07	0.044	−0.276	0.69	7.5E-01	0.175	SLC39A11
17	rs2589133	78793476	−5.05	5.1E-07	0.071	−0.296	−1.52	6.8E-02	−0.386	RPTOR

Note: “Chr.” is chromosome. Position is for reference genome build hg19/GRCh37. Signs of the T statistics (T) give the direction of effect in the MWAS and replication, respectively, where a negative value indicates a decreased methylation level in the SZ cases. Effect is effects size calculated by Cohen’s d (mean difference between the cases and controls divided by a pooled estimate of the standard deviation) is calculated for the replication sample only. Gene is name of the gene allowing for a ±20 Kb flanking region. CpG-SNPs in bold reach significance in the replication after a Bonferroni correction for multiple testing.