Table 1.

Most significant linkage disequilibrium results in the cleft lip and palate families with and without dental anomalies as an additional affection status.

Cleft Lip and Palate + Dental Anomalies
chromosome	snp	cM	p-value	Gene
1	rs2013162	206.3571	0.002	IRF6
1	rs2279455	91.89721	0.008	TGFBR3
1	rs674433	206.3533	0.01	IRF6
1	rs3738480	147.8039	0.02	PRUNE
1	rs786908	88.96538	0.04	PKN2
2	rs377122	70.67868	0.03	TGFA
2	rs7583130	202.7306	0.04	SUMO1	close to
3	rs9849690	185.8107	0.02	EPHB3	close to
3	rs1515490	191.0796	0.04	p63/TP73L
4	rs6841268	139.5262	0.04	SLC7A11
4	rs7677751	54.96539	0.04	PDGFRA
5	rs4559013	170.7842	0.04	FGF18
5	rs3934591	170.8002	0.05	FGF18
6	rs9320231	108.1769	0.005	SCML4
6	rs6921044	140.3791	0.006	BC039503
6	rs969282	134.2468	0.008	TCF21
6	rs971402	112.5946	0.008	LAMA4
6	rs2503791	153.7521	0.009	MTRF1L
6	rs7772821	132.9342	0.01	TAAR6
6	rs9206	151.7713	0.01	MTHFD1L
6	rs3757316	151.8665	0.01	Corf211
6	rs1555091	127.4783	0.02	AK127472
6	rs9491385	125.6747	0.02	IBRDC1	close to
6	rs1546943	116.6082	0.02	NT5DC1
6	rs485640	125.4073	0.03	IBRDC1
6	rs2503322	127.499	0.03	RSPO3
6	rs2811674	134.3728	0.03	SLC2A12
6	rs3800223	108.6792	0.03	SNX3
6	rs238590	115.4712	0.03	HS3ST5
6	rs6570847	148.7266	0.04	SASH1
6	rs1741820	122.7632	0.04	HSF2
6	rs1267948	122.8153	0.04	SERINC1
6	rs576247	122.7886	0.05	HSF2
6	rs2802288	109.0029	0.05	FOXO3A
6	rs6913898	151.474	0.05	MTHFD1L
6	rs911477	109.3696	0.05	ARMC2
9	rs4742741	98.61916	0.0004	ANKS6
9	rs843258	102.6709	0.007	CYLC2
9	rs1930135	98.49069	0.009	GABBR2
9	rs1020884	97.23761	0.01	FOXE1
9	rs4743088	97.23837	0.01	FOXE1
9	rs2636879	114.1241	0.01	COL27A1
9	rs4443717	107.0198	0.01	ZNF462
9	rs418919	99.11206	0.02	TGFBR1	close to
9	rs4129220	94.46965	0.03	FBP1
9	rs337572	98.5662	0.03	ANKS6
9	rs1555573	99.20898	0.03	DQ673940
9	rs773515	91.06249	0.03	AUH
9	rs3747496	97.1669	0.03	KIAA1529
9	rs4743077	97.17104	0.03	KIAA1529
9	rs2416682	118.5309	0.03	TLR4
9	rs3794486	105.5419	0.04	TMEM38B
9	rs1979993	105.6141	0.04	TMEM38B
9	rs3793524	109.299	0.04	PTPN3
9	rs1059273	97.92906	0.04	TRIM14
9	rs4743348	99.25561	0.05	TGFBR1	close to
9	rs2281732	97.92456	0.05	TRIM14
14	rs2536143	72.25479	0.03	DPF3
14	rs221430	79.13787	0.04	NRXN3
14	rs1018466	36.193	0.04	PAX9	close to
15	rs2879515	32.65859	0.01	SLC12A5	close to
15	rs878960	24.48003	0.02	GABRB3
15	rs690	56.62203	0.03	LIPC
15	rs1426223	24.50339	0.05	GABRB3
17	rs1810132	35.11953	0.0005	ERBB2
17	rs2015729	42.70949	0.002	ITGB3
17	rs2292699	42.71729	0.005	ITGB3
17	rs890397	45.45893	0.01	DLX3/DLX4
17	rs1905339	37.83582	0.01	STAT3	close to
17	rs8071740	22.54986	0.02	WSB1	close to
17	rs744166	37.76773	0.02	STAT3
17	rs2313430	35.18334	0.04	IKZF3
17	rs9906933	37.66357	0.04	STAT5B
18	rs2215502	24.03802	0.02	CDH2	close to
20	rs819133	32.33398	0.02	AHCY
20	rs6123674	55.19635	0.04	BMP7
21	rs4817579	33.83209	0.02	GART
Cleft Lip and Palate
chromosome	snp	cM	p-value	Gene
1	rs674433	206.3533	0.001	IRF6
1	rs2013162	206.3571	0.001	IRF6
1	rs513287	167.3959	0.003	PRRX1
1	rs2279455	91.89721	0.01	TGFBR3
1	rs4245660	78.25275	0.02	GIPC2
1	rs1051740	222.3264	0.03	EPHX1
1	rs786908	88.96538	0.03	PKN2
1	rs1007512	75.2837	0.05	LHX8	close to
2	rs7583130	202.7306	0.01	SUMO1	close to
2	rs4328603	9.611782	0.01	ADAM17
2	rs2280509	202.7229	0.03	FZD7
2	rs6705408	9.580829	0.03	ADAM17
2	rs2276338	9.596387	0.03	ADAM17
2	rs377122	70.67868	0.04	TGFA
2	rs512535	21.17943	0.04	OSR1	close to
3	rs9849690	185.8107	0.02	EPHB3	close to
5	rs7715062	7.959907	0.04	MTRR	close to
6	rs2503791	153.7521	0.003	MTRF1L	close to
6	rs971402	112.5946	0.003	LAMA4
6	rs7772821	132.9342	0.005	TAAR6
6	rs9320231	108.1769	0.01	SCML4
6	rs6921044	140.3791	0.01	BC039503
6	rs969282	134.2468	0.02	TCF21	close to
6	rs1546943	116.6082	0.02	NT5DC1
6	rs1983721	117.0122	0.02	RWDD1
6	rs485640	125.4073	0.02	IBRDC1
6	rs911477	109.3696	0.03	ARMC2
6	rs718174	108.4799	0.03	OSTM1
6	rs3734679	107.6221	0.03	PDSS2
6	rs2503322	127.499	0.03	RSPO3
6	rs3800229	109.1037	0.03	FOXO3A
6	rs2811674	134.3728	0.03	SLC2A12
6	rs3127657	107.2111	0.04	QRSL1
6	rs549332	116.5613	0.04	NT5DC1
6	rs1555091	127.4783	0.04	AK127472
6	rs9400504	112.213	0.04	FYN
8	rs6987534	38.41887	0.02	FGFR1
8	rs3925	38.40082	0.03	FGFR1
9	rs4742741	98.61916	0.001	ANKS6
9	rs418919	99.11206	0.005	TGFBR1	close to
9	rs1020884	97.23761	0.01	FOXE1	close to
9	rs4743088	97.23837	0.01	FOXE1	close to
9	rs2636879	114.1241	0.01	COL27A1
9	rs1930135	98.49069	0.01	GABBR2
9	rs4129220	94.46965	0.01	FBP1
9	rs2281732	97.92456	0.02	TRIM14
9	rs1059273	97.92906	0.02	TRIM14
9	rs843258	102.6709	0.02	CYLC2
9	rs1555573	99.20898	0.02	DQ673940
9	rs995294	109.8189	0.03	PALM2-AKAP2
9	rs3794486	105.5419	0.03	TMEM38B
9	rs3750396	88.85173	0.03	AK127258
9	rs4743348	99.25561	0.03	TGFBR1	close to
9	rs1320547	93.79928	0.04	BARX1	close to
9	rs1462090	97.24908	0.05	FOXE1	close to
9	rs773515	91.06249	0.05	AUH
11	rs10790332	119.0589	0.02	PVRL1
12	rs11065374	119.8629	0.01	TCF1	close to
12	rs1039302	119.699	0.02	UNQ1887
14	rs1018466	36.193	0.01	PAX9	close to
15	rs690	56.62203	0.02	LIPC
17	rs1810132	35.11953	0.0006	ERBB2
17	rs2015729	42.70949	0.001	ITGB3
17	rs2292699	42.71729	0.01	ITGB3
17	rs890397	45.45893	0.01	DLX3/DLX4	close to
17	rs2056131	42.68874	0.01	ITGB3
17	rs8071740	22.54986	0.01	WSB1	close to
17	rs4461115	43.15458	0.03	ITGB3	close to
18	rs2215502	24.03802	0.003	CDH2	close to