Table 1. Numbers of significant genes identified by analyzing the SCZ1 data.

	Enhancer		Enhancer + gene body		Gene body (STD)	TWAS
	MCF7	Hippo	MCF7	Hippo		YFS	NTR	METSIM	CMC
# genes	8589	3363	9127	4600	22842	4697	2452	4665	5412
SPU(1)	14/12/11a	8/6/6	20/19/18	15/13/14	36/32/34	14/11/14	10/6/10	8/5/7	16/10/13
SPU(2)	35/25/29	9/9/9	39/29/33	46/34/40	89/77/84	31/25/26	27/19/26	23/14/23	39/25/34

The numbers a/b/c in each cell indicate the numbers of (a) significant genes; (b) significant genes that covered one or more genome-wide significant SNPs within an extended gene region $\pm 500$ kb in the SCZ1 data; (c) significant genes that covered one or more genome-wide significant SNPs within an extended gene region $\pm 500$ kb in the SCZ2 data.

^aSome genome-wide significant loci in the SCZ1 data were no longer significant in the SCZ2 data. For example, gene CUL9 contained some significant SNPs in the SCZ1 data (with the most significant SNP $p=1.2\times {10}^{-8}$) but did not contain any significant SNPs in the SCZ2 data (with the smallest $p=9.6\times {10}^{-7}$).