Table 2.

Top hits from meta-analysis of CL/P, CP, or all OFCs in all populations

Analysis	Locus	CHR	BP	SNP	Minor Allele	Major Allele	P1	POFC TDT OR [95%CI]	GENEVA TDT OR [95%CI]	POFC CC OR [95%CI]
CL/P	8q24	8	129976136	rs55658222	A	G	8.30E-44	2.08 [1.77–2.44]	2.13 [1.78–2.54]	1.91 [1.59–2.29]
	1q32	1	209984470	rs75477785	G	T	4.16E-29	0.58 [0.49–0.69]	0.57 [0.49–0.65]	0.56 [0.45–0.69]
	17p13	17	8947708	rs12944377	C	T	8.32E-21	0.73 [0.65–0.82]	0.66 [0.58–0.74]	0.73 [0.63–0.85]
	1p22	1	94558110	rs66515264	T	G	4.14E-17	1.49 [1.3–1.71]	1.506 [1.31–1.73]	1.32 [1.12–1.56]
	1p36	1	18972776	rs9439713	A	G	6.02E-13	1.33 [1.17–1.51]	1.481 [1.27–1.73]	1.34 [1.16–1.56]
	20q12	20	39261054	rs6072081	G	A	1.87E-12	0.88 [0.79–0.98]	0.70 [0.63–0.78]	0.77 [0.67–0.88]
	8q21	8	88868340	rs12543318	C	A	8.75E-12	1.3 [1.18–1.46]	1.30 [1.17–1.45]	1.16 [1.02–1.33]
	10q25	10	118846294	rs10886040	G	C	8.82E-11	1.35 [1.18–1.53]	1.31 [1.17–1.46]	1.21 [1.03–1.42]
	13q31	13	80679302	rs11841646	A	T	3.62E-10	1.29 [1.15–1.45]	1.33 [1.17–1.50]	1.21 [1.05–1.39]
	17q22	17	54773238	rs227731	G	T	1.77E-09	1.22 [1.09–1.36]	1.24 [1.12–1.38]	1.28 [1.12–1.47]
	2p24	2	16729357	rs7566780	G	A	4.28E-09	1.35 [1.20–1.51]	1.20 [1.08–1.34]	1.17 [1.02–1.34]
	3q28	3	189553372	rs76479869	T	C	1.16E-08	1.38 [1.08–1.75]	1.79 [1.41–2.29]	1.58 [1.18–2.13]
	15q24	15	74889163	rs11072494	T	C	2.40E-08	0.80 [0.71–0.91]	0.84 [0.75–0.95]	0.73 [0.63–0.85]
	3q12	3	99691522	rs68092024	C	T	5.24E-08	0.82 [0.73–0.92]	0.74 [0.66–0.84]	0.89 [0.77–1.03]
	4q21	4	77549559	rs6838801	T	G	5.63E-08	1.18 [1.05–1.32]	1.24 [1.11–1.38]	1.28 [1.11–1.48]
	12q13	12	53357335	rs2363632	G	T	1.51E-07	0.829 [0.71–0.96]	0.73 [0.64–0.84]	0.79 [0.66–0.96]
	5q13	5	67483732	rs6449957	C	T	1.54E-07	0.79 [0.71–0.89]	0.85 [0.76–0.95]	0.82 [0.72–0.94]
	8q12	8	32333570	rs1878918	C	G	2.72E-07	1.15 [1.03–1.28]	1.29 [1.15–1.45]	1.20 [1.05–1.37]
	17q21	17	45005703	rs3785888	C	T	4.01E-07	1.16 [1.04–1.29]	1.14 [1.03–1.27]	1.36 [1.19–1.55]
CP	1p36	1	24669457	rs41268753	T	C	7.73E-08	2.0 [0.75–5.39]	2.40 [1.15–5.02]	6.34 [3.31–12.17]
	5p13	5	36048396	rs1287275	T	C	7.79E-06	1.31 [0.68–2.51]	2.0 [1.28–3.12]	3.09 [1.82–5.22]
All Clefts	8q24	8	129964873	rs17242358	A	G	6.21E-37	1.93 [1.67–2.24]	1.82 [1.55–2.12]	1.71 [1.43–2.03]
	1q32	1	209992501	rs1109430	A	G	9.56E-22	0.62 [0.56–0.72]	0.67 [0.59–0.76]	0.60 [0.49–0.75]
	17p13	17	8947708	rs12944377	C	T	1.11E-16	0.76 [0.68–0.84]	0.74 [0.67–0.82]	0.75 [0.65–0.87]
	1p22	1	94558110	rs66515264	T	G	6.14E-15	1.44 [1.26–1.64]	1.40 [1.24–1.59]	1.26 [1.07–1.48]
	20q12	20	39261054	rs6072081	G	A	9.17E-13	0.88 [0.79–0.97]	0.74 [0.68–0.81]	0.78 [0.68–0.89]
	8q21	8	88868340	rs12543318	C	A	7.61E-11	1.28 [1.15–1.41]	1.26 [1.15–1.38]	1.13 [0.99–1.29]
	10q25	10	118846294	rs10886040	G	C	8.05E-11	1.34 [1.18–.51]	1.26 [1.14–1.39]	1.19 [1.03–1.39]
	1p36	1	18972776	rs9439713	A	G	3.73E-10	1.27 [1.13–1.44]	1.30 [1.14–1.49]	1.30 [1.13–1.50]
	9q22	9	100619719	rs12347191	C	T	1.33E-09	0.80 [0.72–0.90]	0.78 [0.69–0.88]	0.80 [0.70–0.92]
	2p24	2	16729357	rs7566780	G	A	1.25E-08	1.30 [1.17–1.45]	1.18 [1.07–1.29]	1.16 [1.02–1.32]
	13q31	13	80679302	rs11841646	A	T	3.39E-08	1.29 [1.15–1.44]	1.19 [1.07–1.33]	1.17 [1.02–1.34]
	17q21	17	45019731	rs6504622	C	T	1.13E-07	0.88 [0.79–0.97]	0.86[0.78–0.94]	0.76 [0.67–0.86]
	8q12	8	32380835	rs10088648	A	T	1.34E-07	0.85 [0.76–0.94]	0.82 [0.74–0.91]	0.83 [0.73–0.95]
	3q28	3	189553372	rs76479869	T	C	3.20E-07	1.33 [1.05–1.67]	1.56 [1.27–1.93]	1.52 [1.14–2.02]

¹Genome-wide significant SNPs are in bold (based on the Bonferroni-corrected genome-wide significant p-value (p < 5 × 10⁻⁸))