Table 3.

Significant and novel genes identified by both SPU(1) and SPU(2) with the ‘E + G + Methyl’ approach, but not by the STD, ‘E + G,’ and TWAS based on the SCZ2 data

Gene	CHR	No. mQTL	No. CpG	SPU(1)	SPU(2)	References
Source: Hippo
CHRM3	1	2	2	$2.7\times {10}^{-7}$	$2.5\times {10}^{-7}$
KCNS3	2	12	4	$9.8\times {10}^{-1}$	$3.3\times {10}^{-7}$	[1]
EFR3B	2	3	1	$5.6\times {10}^{-7}$	$5.2\times {10}^{-7}$	[1]
CHL1	3	1340	191	$9.5\times {10}^{-1}$	$1.8\times {10}^{-9}$
PSMG4	6	248	24	$4.0\times {10}^{-4}$	$0.0\times {10}^0$
FAM20C	7	1579	339	$5.8\times {10}^{-1}$	$0.0\times {10}^0$
C7orf50	7	805	135	$1.1\times {10}^{-1}$	$8.8\times {10}^{-9}$
DRD4	11	109	39	$6.3\times {10}^{-3}$	$7.7\times {10}^{-7}$
TOLLIP	11	559	68	$4.4\times {10}^{-1}$	$9.1\times {10}^{-10}$
LRP6	12	163	32	$3.5\times {10}^{-4}$	$1.6\times {10}^{-13}$
FAM177A1	14	9	2	$2.3\times {10}^{-6}$	$8.9\times {10}^{-7}$
MADCAM1	19	404	85	$3.0\times {10}^{-4}$	$3.4\times {10}^{-6}$
CSNK1G2	19	68	17	$3.1\times {10}^{-8}$	$4.7\times {10}^{-9}$
Source:MCF7
PRADC1	2	2	1	$4.6\times {10}^{-6}$	$4.7\times {10}^{-6}$
CREB1	2	3	1	$1.0\times {10}^{-6}$	$7.6\times {10}^{-7}$	[1]
ZNF623	8	13	3	$1.2\times {10}^{-5}$	$3.1\times {10}^{-6}$

Note: ‘sig SNP’ gives the P-value of the most significant SNP within a ± 500 kb extension for each gene in the SCZ2 data; the previously reported gene-SCZ associations appear in ‘References’: [1] Goes et al. (2015).