Table 3. Association of CNTNAP2 SNPs rs2107856 and rs2141388 allele T, both with LOXL1 common-risk haplotype G-G, composed of both G alleles of the two LOXL1 coding SNPs rs1048661 and rs3825942.

Groups	LOXL1 haplotypes	Cases	Controls	SNP	Cases, Controls	χ2	P-value	OR	95% CI
Discovery	G-G carriers	144	59	rs2107856	0.292, 0.169	6.557	0.0104	2.02	1.17–3.48
				rs2141388	0.292, 0.169	6.557	0.0104	2.02	1.17–3.48
	Non-G-G carriers	16	21	rs2107856	0.406, 0.119	8.139	0.0043	5.06	1.57–16.32
				rs2141388	0.406, 0.119	8.139	0.0043	5.06	1.57–16.32
Replication	G-G carriers	580	273	rs2107856	0.285, 0.234	4.750	0.0293	1.30	1.03–1.65
				rs2141388	0.285, 0.233	5.000	0.0254	1.31	1.03–1.66
	Non-G-G carriers	30	91	rs2107856	0.350, 0.253	2.132	0.1443	1.59	0.85–2.98
				rs2141388	0.350, 0.250	2.257	0.1330	1.62	0.86–3.03
Combined	G-G carriers	724	332	rs2107856	0.286, 0.223	9.288	0.0023	1.40	1.13–1.73
				rs2141388	0.286, 0.222	9.609	0.0019	1.41	1.13–1.75
	Non-G-G carriers	46	112	rs2107856	0.370, 0.228	6.677	0.0098	1.99	1.18–3.37
				rs2141388	0.370, 0.225	6.916	0.0085	2.02	1.19–3.42

The results are shown for the discovery group (160 patients, 80 control individuals), the replication group (610 patients, 364 control individuals) and the combined groups (770 patients, 444 control individuals).