Table 1. Genome wide significant variants following SCZ meta analysis.

Gene	rsID	CHR	BP (hg18)	Freq	Pval	Direction effect	A1	A2	HetPVal	Imputed
SDCCAG8	rs10927013	1	241655779	0.436	8.09 × 10−9	++++++++++++++++	G	T	0.91	Y
	rs2039839	1	241665293	0.564	1.28 × 10−8	−−−−−−−−−−−−−−−−	A	G	0.93	I
	rs6703335	1	241675590	0.562	3.71 × 10−9	−−−−−−−−−−−−−−−+	A	G	0.91	I
ITIH1	rs2710323	3	52790945	0.466	2.97 × 10−8	−++−++−+++++++++	C	T	0.39	A
MHC	rs9379858	6	26475668	0.106	1.42 × 10−8	+++−++−++−++++++	C	T	0.35	A
	rs3799380	6	26575161	0.220	2.80 × 10−8	+++−++−+++++++++	C	T	0.82	I
	rs6456728	6	26585758	0.779	2.36 × 10−8	−−−+−−+−−−−−−−−−	A	G	0.82	I
	rs7749305	6	27554545	0.100	2.57 × 10−8	+++−++++++++++++	C	T	0.29	Y
	rs6904596	6	27599278	0.896	3.06 × 10−8	−−−+−−−−−−−−−−−−	A	G	0.27	A
	rs17750424	6	27809101	0.085	1.99 × 10−8	++++++++++++++++	C	T	0.38	Y
	rs17693963	6	27818144	0.904	1.61 × 10−9	+++−++++++++++++	A	C	0.36	I A5
	rs34706883	6	27913234	0.909	3.14 × 10−8	++++++++++++++++	A	C	0.39	Y
	rs13212651	6	27914964	0.909	3.34 × 10−8	++++++++++++++++	A	G	0.39	Y
	rs13194781	6	27923618	0.909	3.51 × 10−8	++++++++++++++++	A	G	0.42	A
	rs13199772	6	27942064	0.909	3.40 × 10−8	++++++++++++++++	A	G	0.42	Y
MAD1L1	rs10275045	7	1887352	0.403	2.16 × 10−8	−+−+−−−−−−−+−−−+	C	T	0.36	N
	rs12537914	7	1914885	0.365	2.03 × 10−8	−+−+−−−−−−−+−−−−	C	T	0.47	Y
	rs4721184	7	1917310	0.369	2.74 × 10−8	+−+−+++++++−+++−	C	T	0.47	Y
	rs2056480	7	1920827	0.632	1.54 × 10−8	−−−+−−−−−−−+−−−+	A	G	0.56	I
	rs4721190	7	1921258	0.596	3.83 × 10−8	−−−+−−−−−−−+−−−+	A	G	0.69	I A5
	rs12699477	7	1935479	0.352	8.78 × 10−9	+−+++++++++−++++	C	T	0.67	A
	rs2280550	7	1943082	0.639	3.80 × 10−8	−+−+−−−−−−−+−−−+	A	G	0.49	Y
	rs12666575	7	1970947	0.358	8.27 × 10−10	−−−−−−+−−−−+−−−+	C	T	0.19	A
	rs4721295	7	2003195	0.378	6.23 × 10−10	+−++++−++++−+++−	G	T	0.07	I
	rs1107592	7	2007958	0.62	5.64 × 10−9	+−++++−++++−+++−	A	G	0.04	I A5
	rs3778969	7	2106516	0.633	6.43 × 10−9	−−−−−−+−−−−+−−−+	A	G	0.16	N
	rs10224497	7	2116493	0.574	1.09 × 10−8	++++++−++++−+++−	A	G	0.13	I A5
	rs10239050	7	2124916	0.615	1.11 × 10−8	+−++++−++++−+++−	A	G	0.12	A
	rs3800913	7	2129763	0.604	4.03 × 10−8	++++++−++++−+++−	A	G	0.15	A
	rs3800917	7	2134465	0.64	2.29 × 10−9	−+−−−−+−−−−+−−−+	A	G	0.22	I
	rs3778991	7	2138981	0.656	2.21 × 10−9	−−−−−−+−−−−+−−−−	A	G	0.20	A
	rs3778994	7	2142381	0.616	2.53 × 10−9	−−−−−−+−−−−+−−−−	A	C	0.21	A5
	rs4721441	7	2150586	0.356	9.41 × 10−10	++++++−++++−++++	C	T	0.29	Y
	rs3779003	7	2151428	0.347	2.33 × 10−9	−−−−−−+−−−−+−−−−	C	T	0.23	I A5
	rs3757440	7	2239462	0.647	1.98 × 10−8	++++++++++−−+++−	A	G	0.28	I A5
	rs7787274	7	2242519	0.651	1.08 × 10−8	−−−−−−−−−−−+−−−+	A	G	0.21	Y
	rs7799006	7	2244752	0.350	1.24 × 10−8	−−−−−−−−−−−+−−−+	C	T	0.23	A
CSMD1	rs6558872	8	4225547	0.571	4.75 × 10−8	−−−−+−−−−+−−−−−+	A	G	0.46	I A5
TSNARE1	rs10098073	8	143307411	0.535	9.05 × 10−9	++−+++++++++++++	A	C	0.93	I
	rs4129585	8	143310840	0.566	2.38 × 10−8	++++++++++++++++	A	C	0.99	I

The final column lists the imputation status of each SNP. Y: imputed in all cohorts; N: not imputed; I: imputed in cohorts genotypes on the Illumina chips; A: imputed in cohorts genotyped on the Affymetrix chips; A5: imputed in cohorts genotyped on the Affymetrix 5.0 and 500 arrays.