Table 2.

Significant and novel genes (with their P-values) identified by the ‘E + G + Methyl’ approach based on the SCZ1 data

Gene	CHR	No. mQTL	No. CpG	SPU(1)	SPU(2)	References
Source: Hippo
PLCH2a	1	258	49	$3.4\times {10}^{-3}$	$8.5\times {10}^{-6}$	[1, 2]
PLEKHG5	1	103	23	$2.1\times {10}^{-2}$	$1.4\times {10}^{-5}$
NGEFa	2	23	3	$4.6\times {10}^{-1}$	$1.4\times {10}^{-5}$	[2, 3]
PSMG4	6	248	24	$6.7\times {10}^{-5}$	$5.0\times {10}^{-10}$
FAM20C	7	1579	339	$2.6\times {10}^{-1}$	$1.1\times {10}^{-16}$
TOLLIP	11	559	68	$9.5\times {10}^{-1}$	$7.8\times {10}^{-6}$
LRP6	12	163	32	$1.1\times {10}^{-2}$	$9.9\times {10}^{-7}$
MPHOSPH9a	12	7	1	$1.6\times {10}^{-5}$	$1.0\times {10}^{-5}$	[2, 3]
C12orf65a	12	4	1	$1.8\times {10}^{-5}$	$1.6\times {10}^{-5}$	[2]
CDK2AP1a	12	4	2	$2.8\times {10}^{-5}$	$2.4\times {10}^{-6}$	[2]
HMOX2	16	5	4	$1.3\times {10}^{-5}$	$1.2\times {10}^{-5}$
YJEFN3a	19	3	4	$2.2\times {10}^{-6}$	$2.6\times {10}^{-6}$
Source:MCF7
SH3RF1a	4	10	2	$1.1\times {10}^{-2}$	$9.3\times {10}^{-6}$
CREB1	2	3	1	$1.5\times {10}^{-7}$	$7.8\times {10}^{-8}$	[1]
CNOT7	8	5	1	$6.4\times {10}^{-6}$	$5.0\times {10}^{-6}$
VPS37A	8	8	1	$1.3\times {10}^{-6}$	$1.1\times {10}^{-6}$	[3]
PIK3C2A	11	3	1	$2.5\times {10}^{-6}$	$1.8\times {10}^{-5}$	[1, 4, 5]
OGFOD2a	12	4	3	$1.1\times {10}^{-5}$	$1.0\times {10}^{-5}$	[2, 3]
PITPNM2a	12	13	3	$7.1\times {10}^{-5}$	$2.7\times {10}^{-6}$	[2, 3]
CDK2AP1a	12	6	2	$1.1\times {10}^{-6}$	$1.8\times {10}^{-7}$	[2]
XRCC3a	14	5	2	$4.1\times {10}^{-7}$	$2.6\times {10}^{-4}$	[2]
SUGP1a	19	3	1	$2.0\times {10}^{-6}$	$1.8\times {10}^{-6}$	[2]
NDUFA13a	19	2	3	$8.6\times {10}^{-6}$	$5.8\times {10}^{-6}$	[2]
YJEFN3a	19	3	4	$1.7\times {10}^{-6}$	$2.0\times {10}^{-6}$

Note: ‘sig SNP’ give 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); [2] Ripke et al. (2014); [3] Li et al. (2017); [4] Ripke et al. (2011); [5] Ruderfer et al. (2014).

^aNovel genes, not overlapping with a genome-wide significant SNP within a ± 500 kb extension for each gene in the SCZ2 data.