Table 1. Conditional FDR<0.05, non MHC SNPs associated with schizophrenia given multiple sclerosis.

Locus #	SNP	Location	Gene	SCZ P	FDR SCZ	FDR SCZ|MS
1	rs1625579	1p21.3	AK094607a,b (MIR137HG)	5.52E-06	4.92E-02	3.69E-02
2	rs17180327	2q31.3	CWC22b,c	6.37E-06	5.19E-02	3.95E-03
3	rs7646226	3p21-p14	PTPRGb,c	5.51E-06	4.92E-02	2.43E-02
4	rs9462875	6p21.1	CUL9b,c	1.20E-05	6.59E-02	4.14E-02
5	rs10257990	7p22	MAD1L1a,b	5.53E-06	4.92E-02	1.63E-02
6	rs10503253	8p23.2	CSMD1a,b	3.96E-06	4.70E-02	4.04E-02
	rs10503256	8p23.2	CSMD1a,b	2.27E-06	4.32E-02	1.29E-02
7	rs6990941	8q21.3	MMP16a,b	2.48E-06	4.32E-02	1.48E-02
8	rs396861	9p24	AK3	6.89E-06	5.19E-02	4.53E-02
9	rs4532960	10q24.32	AS3MT b	2.65E-06	4.32E-02	1.29E-02
10	rs12411886	10q24.32	CNNM2a,b	1.79E-06	4.10E-02	1.86E-02
11	rs11191732	10q25.1	NEURLb	2.55E-06	4.32E-02	2.69E-02
12	rs1025641	10q26.2	C10orf90	7.51E-06	5.54E-02	4.87E-02
13	rs2852034	11q22.1	CNTN5	1.12E-05	6.00E-02	2.90E-02
14	rs540723	11q23.3	STT3Ab	1.82E-06	4.10E-02	2.56E-02
15	rs7972947	12p13.3	CACNA1Ca,b	7.12E-06	5.54E-02	4.87E-02
16	rs2007044	12p13.3	CACNA1Ca,b	2.74E-05	9.43E-02	1.75E-02
17	rs12436216	14q13.2	KIAA0391b	7.40E-06	5.54E-02	4.87E-02
18	rs1869901	15q15	PLCB2b	3.66E-06	4.70E-02	4.04E-02
19	rs4887348	15q25	NTRK3	4.69E-05	1.39E-01	3.05E-02
20	rs4309482	18	AK093940	9.66E-06	6.00E-02	1.34E-02

Independent complex or single-gene loci (r²<0.2) with SNP(s) with a conditional FDR (SCZ|MS)<0.05 in schizophrenia (SCZ) given association in multiple sclerosis (MS). All significant SNPs are listed and sorted in each LD block and independent loci are listed consecutively (Locus #). Chromosome location (Location), closest gene (Gene), P-value of SCZ (SCZ P-value) and false discovery rate of SCZ, FDR (SCZ) are also listed. All data were first corrected for genomic inflation.

^aLoci identified by GWASs without leveraging genetic pleiotropy structure between phenotypes.

^bLoci identified using conditional FDR method on SCZ with CVD.

^cLoci identified using conditional FDR method on SCZ with BD.