Table 2. SNPs showing significance in stratified analysis among the three anatomical types of orofacial clefts: NSCLP, NSCLO and NSCPO in Chinese population.

Phenotype	Loci	SNP	BP (hg19)	Allele	F_A	F_U	P*	OR
NSCLP versus NSCLO	1q32.2	rs861020	209977111	A/G	0.23	0.30	2.05E−09	0.72 (0.65–0.80)
	1q32.2	rs642961	209989270	A/G	0.23	0.30	1.16E−09	0.72 (0.64–0.80)
NSCLP versus NSCPO	1q32.2	rs861020	209977111	A/G	0.23	0.17	8.69E−11	1.51 (1.34–1.72)
	1q32.2	rs642961	209989270	A/G	0.23	0.17	9.08E−11	1.51 (1.33–1.72)
	1q32.2	rs2064163	210048819	A/C	0.38	0.44	6.41E−08	0.76 (0.69–0.84)
	1q32.2	rs9430019	210050794	A/G	0.31	0.19	1.29E−25	1.87 (1.66–2.11)
	2p25.1	rs287980	9971366	G/A	0.23	0.27	7.67E−04	0.83 (0.74–0.92)
	2p25.1	rs287982	9972442	G/A	0.23	0.27	8.29E−04	0.83 (0.74–0.93)
	2p24.2	rs10172734	16733054	G/A	0.26	0.33	6.31E−09	0.73 (0.66–0.81)
	2p24.2	rs7552	16733928	A/G	0.24	0.28	6.33E−04	0.83 (0.74–0.92)
	8q21.3	rs1034832	88918331	C/A	0.31	0.35	4.11E−04	0.83 (0.75–0.92)
	12q21.1	rs2304269	72080272	G/A	0.39	0.45	8.58E−07	0.78 (0.71–0.86)
	12q21.1	rs7967428	72089040	G/A	0.40	0.45	1.98E−06	0.79 (0.72–0.87)
	16p13.3	rs2283487	3969886	G/A	0.42	0.47	3.21E−04	0.84 (0.76–0.92)
	16p13.3	rs17136624	3996282	A/G	0.26	0.22	8.59E−04	1.22 (1.08–1.36)
	17p13.1	rs2872615	8914693	G/A	0.43	0.49	2.59E−07	0.78 (0.70–0.85)
	17p13.1	rs1880646	8929845	G/A	0.48	0.53	2.45E−04	0.83 (0.76–0.92)
	17q21.32	rs1838105	45008935	A/G	0.44	0.38	2.28E−05	1.24 (1.12–1.37)
NSCLO versus NSCPO	1q32.2	rs861020	209977111	A/G	0.30	0.17	3.98E−24	2.10 (1.81–2.42)
	1q32.2	rs642961	209989270	A/G	0.30	0.17	2.09E−24	2.11 (1.82–2.43)
	1q32.2	rs2064163	210048819	A/C	0.39	0.44	1.21E−04	0.79 (0.70–0.89)
	1q32.2	rs9430019	210050794	A/G	0.30	0.19	8.70E−18	1.84 (1.60–2.12)
	2p24.2	rs10172734	16733054	G/A	0.25	0.33	6.20E−09	0.68 (0.59–0.77)
	8q21.3	rs1034832	88918331	C/A	0.28	0.35	1.13E−06	0.73 (0.64–0.83)
	10q25.3	rs6585429	118893231	G/A	0.38	0.43	1.11E−03	0.82 (0.72–0.92)
	17p13.1	rs2872615	8914693	G/A	0.42	0.49	1.34E−05	0.77 (0.68–0.86)

F_A, minor allele frequency in cases; F_U, minor allele frequency in controls; NSCLO, non-syndromic cleft lip only; NSCLP, non-syndromic cleft lip with palate; NSCPO, non-syndromic cleft palate only; OR, odds ratio; SNP, single-nucleotide polymorphism.

OR is calculated based on minor allele; alleles are shown as minor allele/major allele.

^*P-value below 1.25 × 10⁻³ (0.05out of 40, the P-value using logistic regression test and Bonferroni correction) was considered to be statistically significant.