Table 2. Associations results for parent-of-origin effects in oral clefts, showing the most significant SNP per locus in both discovery and replication cohorts.

			GWAS data				Replication data				Combined data
SNP ID	Chromosome	Position, hg18	PPAT	PMAT	PPofO	PHET	PPAT	PMAT	PPofO	PHET	PPAT	PMAT	PPofO	PHET
SNPs significant in NSOFC in the combined European and Asian GWAS sample analysis
rs1394156	Chr3	6199872	5.57E-06	0.198	0.024	0.028	0.668	0.630	0.520	0.144	0.001	0.193	0.169	0.008
rs704570	Chr3	100959832	0.225	2.21E-06	0.013	0.213	0.170	0.186	0.997	0.345	0.070	5.60E-06	0.049	0.119
rs4627838	Chr4	175839337	0.885	5.53E-06	1.72E-03	0.007	0.479	0.116	0.519	0.568	0.545	1.41E-05	0.007	0.133
rs11999884	Chr9	91260211	6.68E-06	0.049	0.072	0.439	Failed QC in replication				Failed QC in replication
rs1920435	Chr12	66081140	0.051	1.85E-06	0.047	0.003	Failed QC in replication				Failed QC in replication
rs3814878	Chr16	29949467	0.052	1.69E-07	0.018	0.006	0.272	0.725	0.616	0.411	0.393	7.42E-05	0.025	0.007
SNPs significant in NSOFC in the European GWAS sample analysis
rs4925671	Chr1	245689497	0.816	5.65E-06	0.002	0.005	0.034	0.458	0.043	0.626	0.158	3.87E-04	4.36E-04	0.026
rs10208086	Chr2	3154999	0.287	2.81E-06	0.015	0.070	0.255	0.170	0.873	0.738	0.121	4.57E-05	0.085	0.166
rs820042	Chr2	173853723	5.67E-06	0.751	0.003	0.008	0.414	0.110	0.560	0.405	0.001	0.147	0.166	0.410
rs12543318	Chr8	88937456	0.237	2.24E-06	0.009	0.109	0.433	0.004	0.122	0.462	0.174	1.54E-07	0.004	0.106
rs1519466	Chr9	110900618	0.198	0.075	0.034	6.61E-06	0.209	0.030	0.016	0.317	0.905	0.792	0.792	0.019
rs12264639	Chr10	15368599	0.034	3.44E-05	9.46E-06	0.004	0.386	0.257	0.156	0.024	0.523	0.085	0.091	0.968
rs1533763	Chr11	75578175	0.630	7.66E-06	3.41E-04	0.002	0.411	0.695	0.768	0.620	0.732	0.002	0.050	0.129
rs4944925	Chr11	74037177	0.082	0.022	0.004	5.97E-06	0.817	0.275	0.351	0.765	0.189	0.022	0.011	0.001
rs927053	Chr14	58524433	0.783	6.11E-06	0.001	0.535	0.932	0.697	0.841	0.125	0.901	0.014	0.100	0.473
rs7173522	Chr15	99135612	2.21E-06	0.141	0.025	0.008	0.530	0.107	0.461	0.788	0.001	0.029	0.417	0.057
rs11644607	Chr16	74806998	0.004	0.905	0.028	1.97E-07	0.061	1.000	0.172	0.095	0.001	0.937	0.013	1.72E-06
rs3852922	Chr20	53443077	0.382	7.24E-06	0.010	0.056	0.387	0.274	0.865	0.438	0.899	0.046	0.133	0.525
SNPs significant in NSCL/P in the combined European and Asian GWAS sample analysis
rs719325	Chr2	220376177	8.07E-06	0.692	0.005	0.353	0.002	0.048	0.412	0.403	5.43E-08	0.118	0.007	0.835
rs7618286	Chr3	6194615	2.24E-06	0.654	0.003	0.003	0.060	0.489	0.392	0.356	0.012	0.918	0.067	0.004
rs704570	Chr3	100959832	0.018	3.30E-06	0.119	0.960	0.218	0.304	0.906	0.282	0.009	1.67E-05	0.233	0.462
rs13317017	Chr3	101148211	0.109	4.14E-07	0.016	0.196	0.110	0.262	0.757	0.955	0.024	3.85E-06	0.094	0.319
rs17447439	Chr3	191032117	0.191	6.94E-06	0.049	0.001	1.000	0.062	0.202	0.131	0.320	2.63E-06	0.016	4.61E-04
rs12543318	Chr8	88937456	0.005	4.30E-06	0.176	0.207	0.548	0.010	0.143	0.336	0.010	1.80E-07	0.047	0.113
rs543704	Chr11	91869646	5.40E-06	0.147	0.033	0.031	0.481	0.098	0.092	0.206	7.90E-05	0.942	0.007	0.014
rs2196457	Chr12	94798821	0.269	9.20E-06	9.84E-05	0.001	Failed QC in replication				Failed QC in replication
rs2948150	Chr12	119645972	0.002	0.149	0.001	3.36E-06	0.583	0.729	0.899	0.222	0.161	0.200	0.058	0.035
rs4884077	Chr13	77441896	0.059	0.313	0.040	9.94E-06	0.812	0.172	0.420	0.388	0.081	0.842	0.166	0.001
rs1777697	Chr14	82206283	7.58E-06	0.320	1.20E-04	0.004	0.520	0.894	0.588	0.080	5.11E-05	0.370	0.001	0.001
rs6011617	Chr20	61209037	9.05E-06	0.424	0.009	0.139	Failed QC in replication				Failed QC in replication
SNPs significant in NSCL/P in the European GWAS sample analysis
rs12132001	Chr1	161092955	7.86E-06	0.746	0.003	0.041	0.467	0.648	0.402	0.604	0.026	0.576	0.233	0.409
rs10208086	Chr2	3154999	0.224	4.66E-06	0.024	0.035	0.243	0.166	0.879	0.914	0.095	6.31E-05	0.111	0.231
rs1513121	Chr3	103247757	0.633	3.31E-06	0.001	0.869	0.795	1.000	0.860	0.199	0.615	0.006	0.085	0.264
rs26883	Chr5	4959824	0.349	1.62E-06	0.007	0.035	0.382	0.559	0.853	0.899	0.962	0.004	0.040	0.132
rs9687030	Chr5	76663192	0.221	7.82E-06	0.020	0.134	0.391	0.684	0.732	0.113	0.855	0.009	0.092	0.029
rs12543318	Chr8	88937456	0.311	2.89E-06	0.006	0.103	0.548	0.010	0.143	0.336	0.269	7.85E-07	0.004	0.071
rs2948372	Chr8	12802775	0.146	0.016	0.006	6.13E-06	0.736	1.000	0.812	0.655	0.216	0.209	0.079	0.002
rs890519	Chr8	18949329	5.63E-06	0.776	0.003	0.085	0.494	0.119	0.554	0.267	4.18E-04	0.169	0.120	0.821
rs7922467	Chr10	129643702	0.013	0.025	0.001	7.10E-06	0.083	0.001	0.291	0.918	0.003	0.467	0.089	0.001
rs12426170	Chr12	119597971	0.001	0.365	0.003	8.60E-06	0.473	0.532	0.954	0.356	0.210	0.283	0.099	0.050
rs7988514	Chr13	19763521	0.221	2.89E-06	0.013	0.013	0.860	0.516	0.737	0.610	0.362	0.001	0.069	0.054
rs4429270	Chr15	89828778	0.944	5.82E-06	0.002	0.122	0.462	0.700	0.431	0.663	0.527	0.011	0.171	0.525
rs1610093	Chr19	4505774	0.051	0.028	0.004	8.81E-06	0.790	0.728	0.957	0.715	0.187	0.255	0.082	0.013
rs3852922	Chr20	53443077	0.139	6.67E-07	0.013	0.033	0.852	0.660	0.657	0.289	0.285	0.005	0.215	0.568
SNPs significant in NSCPO in the combined European and Asian GWAS sample analysis
rs11678000	Chr2	229965612	9.43E-08	0.414	0.001	2.56E-04	0.858	0.869	0.808	0.739	7.74E-05	0.463	0.012	0.008
rs512778	Chr6	79401865	0.249	5.93E-06	0.014	0.250	0.056	0.317	0.543	1.000	0.045	1.24E-05	0.078	0.329
rs1483757	Chr12	116245923	3.82E-06	0.115	0.022	0.076	0.448	0.917	0.636	0.414	2.78E-05	0.179	0.034	0.058
rs6539608	Chr12	80976335	1.000	4.50E-06	0.001	0.039	0.768	0.069	0.294	0.639	0.864	1.56E-06	0.001	0.050

Abbreviations: GWAS, genome-wide association studies; HET, heterozygous; LD, linkage disequilibrium; MAT, maternal; NSCL/P, non-syndromic cleft lip with or without cleft palate; NSCPO, non-syndromic cleft palate only; NSOFC, non-syndromic orofacial clefting; PAT, paternal; PofO, parent-of-origin; SNP, single-nucleotide polymorphism.

In bold: SNPs that pass our discovery criteria of P<1 × 10⁻⁵ and show and P≤0.01 in the replication cohort.