Table 1.

SNV association test results using logistic regression with 10 covariates, limited to P < 1 × 10⁻³ and MAF < 1%

SNV	CHR	Position (b37)	MAF (%)	MAF Con (%)	MAF Case (%)	MAF UK Pop (%)	OR	P	GWS	ANNOT	Gene
rs140232654	1	111 739 856	0.47	0.35	0.72	0.45	2.12	1.91 × 10−5	N	Missense	DENND2D
rs74440117	7	97 863 152	0.16	0.068	0.29	0.19	4.1	6.01 × 10−5	N	Missense	TECPR1
rs74892550	16	3 707 191	0.75	0.61	0.99	0.69	1.66	0.00024	N	Missense	TRAP1, DNASE1
rs147802928	19	35 941 518	0.12	0.049	0.22	0.1	4.38	0.0003	N	Missense	FFAR2
rs146838872	9	12 694 094	0.07	0.019	0.16	0.074	9.56	0.0003	N	Missense	TYRP1
rs144338731	2	239 038 917	0.39	0.52	0.25	0.36	0.46	0.00044	N	Missense	ESPNL
rs36059660	20	36 640 870	0.92	0.75	1.2	0.88	1.56	0.00048	N	Missense	TTI1
rs118056333	8	70 515 476	0.78	0.64	1	0.68	1.61	0.0005	N	Missense	SULF1
rs61757580	7	13 737 4693	0.68	0.52	0.89	0.69	1.67	0.00059	Y	Missense	DGKI
rs116932219*	13	49 281 261	0.82	0.98	0.6	0.78	0.61	0.00066	N	Missense	CYSLTR2
rs34703321	12	122 361 711	0.94	1.1	0.73	0.99	0.63	0.00066	N	Missense	WDR66
rs79859029	16	31 927 353	0.24	0.17	0.38	0.2	2.3	0.00077	N	Missense	ZNF267
rs139049409	7	87 005 024	0.16	0.25	0.063	0.13	0.25	0.00078	N	Stop	CROT
rs149406506	10	104 231 098	0.12	0.2	0.036	0.13	0.17	0.0008	N	Missense	TMEM180
rs143085034*	13	49 281 101	0.81	0.97	0.6	0.77	0.61	0.00085	N	Missense	CYSLTR2
rs113141749	17	48 594 980	0.36	0.26	0.5	0.34	1.98	0.00089	N	Missense	MYCBPAP
rs55859133	16	30 128 265	0.16	0.099	0.26	0.17	2.82	0.00095	Y	Missense	MAPK3
rs35890409	12	57 569 339	0.76	0.61	0.95	0.68	1.59	0.00096	Y	Missense	LRP1

GWS indicates whether SNV is within one of the genome-wide significant schizophrenia-associated regions reported by the PGC. Cluster plots for SNVs in this table were visually inspected to ensure correct genotype calling. Positions given are for human genome build 37. Variants marked * are close together on the genome. The minor alleles generally occur in the same samples, indicating that these markers are in strong LD. UK population MAF in column ‘MAF UK Pop’ taken from the UK Exome Chip consortium website (http://diagram-consortium.org/uk-exome-chip/).