Table 2.

Results of association tests with MMP and TIMP gene polymorphisms and nonsyndromic oral clefts.

SNP	Minor Allele	Minor allele frequency		All Clefts (n=494)			Cleft Lip/Palate (n=421)			Cleft Palate (n=73)
		Cases (n=494)	Controls (n=413)	P-value	Odds ratio	95% CI	P-value	Odds ratio	95% CI	P-value	Odds ratio	95% CI
MMP2
rs243865	T	0.17	0.18	0.7534	0.96	0.75–1.23	0.9349	1.01	0.78–1.31	0.1115	0.66	0.40–1.10
rs2285053	T	0.13	0.15	0.2534	0.85	0.65–1.12	0.2577	0.85	0.63–1.13	0.4920	0.83	0.50–1.40
rs243847	C	0.36	0.37	0.8483	0.98	0.81–1.20	0.8652	1.02	0.83–1.25	0.3408	0.84	0.58–1.21
rs2287074	A	0.38	0.39	0.6948	0.96	0.79–1.16	0.7184	0.96	0.79–1.18	0.8303	0.96	0.67–1.37
rs9923304	T	0.37	0.37	0.8485	0.98	0.81–1.19	0.8040	0.97	0.79–1.20	0.9465	0.99	0.69–1.42
rs11639960	G	0.32	0.32	0.8882	0.99	0.81–1.20	0.9595	1.01	0.81–1.24	0.6831	0.92	0.63–1.35
MMP3
rs639752	G	0.48	0.46	0.3896	1.09	0.90–1.31	0.9479	0.99	0.81–1.21	0.0102	1.58	1.11–2.25
rs650108	G	0.32	0.33	0.7042	0.96	0.79–1.17	0.7256	1.04	0.84–1.28	0.0448	0.67	0.45–0.99
rs520540	A	0.45	0.46	0.6774	0.96	0.80–1.16	0.2865	0.90	0.74–1.10	0.0924	1.35	0.95–1.91
rs679620	A	0.45	0.44	0.7039	1.04	0.86–1.25	0.7826	0.97	0.79–1.19	0.0519	1.41	1.00–2.00
rs522616	G	0.28	0.39	0.000003	0.62	0.51–0.76	0.0003	0.68	0.55–0.84	0.0022	0.55	0.37–0.81
rs3025058	5A	0.41	0.41	0.9395	0.99	0.82–1.20	0.5099	0.93	0.76–1.14	0.0821	1.36	0.96–1.93
MMP7
rs11568818	G	0.42	0.42	0.7878	1.03	0.85–1.24	0.6497	1.05	0.86–1.28	0.7246	0.94	0.66–1.34
MMP9
rs3918253	C	0.51	0.47	0.1493	1.15	0.95–1.38	0.0266	0.80	0.66–0.97	0.2550	0.82	0.57–1.16
rs17576	G	0.31	0.32	0.7042	0.96	0.78–1.17	0.8695	0.98	0.79–1.22	0.6280	0.91	0.62–1.33
rs17577	G	0.11	0.12	0.8298	0.97	0.72–1.29	0.6063	0.92	0.68–1.26	0.8139	1.07	0.63–1.80
MMP10
rs17293607	T	0.15	0.18	0.0602	0.78	0.60–1.01	0.0711	0.78	0.59–1.02	0.6971	0.91	0.57–1.45
MMP13
rs478927	G	0.37	0.34	0.1400	1.19	0.94–1.48	0.0905	1.23	0.97–1.57	0.3157	0.78	0.49–1.26
rs2252070	G	0.34	0.33	0.7859	1.03	0.84–1.25	0.6330	1.05	0.85–1.29	0.1854	0.77	0.53–1.13
MMP14
rs1042704	A	0.14	0.13	0.7171	1.05	0.80–1.38	0.9188	0.98	0.73–1.32	0.0551	1.55	0.99–2.44
MMP16
rs7828497	G	0.32	0.26	0.0125	1.30	1.05–1.60	0.0182	1.30	1.05–1.61	0.3107	1.22	0.83–1.78
rs2616490	G	0.39	0.37	0.3350	1.10	0.90–1.32	0.1529	1.16	0.95–1.42	0.2491	0.81	0.56–1.16
MMP25
rs2360167	T	0.24	0.22	0.6027	1.06	0.85–1.32	0.7500	1.04	0.82–1.32	0.4212	1.18	0.79–1.77
MMP27
rs2509010	T	0.23	0.23	0.9885	1.00	0.80–1.25	0.9578	1.01	0.80–1.27	0.7531	1.07	0.71–1.61
rs11225389	A	0.17	0.19	0.1915	0.85	0.67–1.08	0.0977	0.80	0.62–1.04	0.1533	1.35	0.89–2.03
TIMP1
rs5906435	T	0.28	0.25	0.2301	1.16	0.91–1.48	0.7173	1.05	0.81–1.36	0.0446	1.54	1.01–2.36
rs6520279	C	0.43	0.42	0.5119	1.16	0.91–1.48	0.8497	1.02	0.81–1.29	0.4273	1.17	0.79–1.74
TIMP2
rs8179096	T	0.08	0.13	0.0004	0.57	0.41–0.77	0.0018	0.59	0.42–0.82	0.0007	0.23	0.09–0.58
rs9894526	T	0.47	0.45	0.3055	1.10	0.91–1.33	0.2676	1.12	0.92–1.36	0.9223	0.98	0.69–1.40

^*P≤ 0.002 indicates statistical significance under Bonferroni correction (in bold).

The following SNPs were non informative or presented minor allele frequency < 10% in the studied population and therefore excluded from the association analyses: rs28730814 (MMP2), rs3025065 and rs11606831 (MMP3), rs11568818 (MMP7), rs17860973 and rs17860971 (MMP10), rs12295719 (MMP13), rs17123036 (MMP14), rs61995943 and rs12099177 (MMP27), rs9747145 (TIMP2), rs34586282 and rs34334473 (TIMP3), and rs3755724 (TIMP4). TIMP2 rs4789940 showed deviation from Hardy-Weinberg equilibrium and was also excluded from further analyses.