Table 4.

Family based association test (FBAT) results for case and control probands.

Marker	Alleles	freq cases (n=88)	freq controls (n=88)	OR (95% CI)	X2df = 1 p value	Case HWE	Control HWE
IRF6_ rs642961	1	0.93	0.90	1.04 (0.78–1.39)	0.04 (0.832)	0.583	0.212
	2	0.07	0.10
MSX1_ rs4075	1	0.81	0.70	1.25 (0.94–1.67)	2.2.1(0.138)	0.131	0.319
	2	0.19	0.30
MSX1_ rs12532	1	0.62	0.52	1.22 (0.92–1.63)	1.81 (0.179)	0.647	0.865
	2	0.38	0.48
FGFR1_rs13317	1	0.22	0.20	1.04 (0.78–1.39)	1.04 (0.832)	0.409	1
	2	0.78	0.80
FGFR1_C_2080144_10	1	0.41	0.35	1.13 (0.85–1.51)	1.13 (0.437)	0.619	0.360
	2	0.59	0.65
ABC4_rs560426	1	0.51	0.51	1(0.75–1.33)	0.01(0.944)	0.422	0
	2	0.49	0.49
ABC4_rs481931	1	0.88	0.89	0.98(0.74–1.31)	0.01(0.944)	0.832	0
	2	0.12	0.11
ABC4_rs4147811	1	0.88	0.90	0.96(0.72–1.28)	0.05(0.832)	0.159	0
	2	0.12	0.10
8qrs_987525	1	0.66	0.63	1.06(0.80–1.42)	0.13(0.724)	0.848	0.770
	2	0.34	0.37
MAFB_rs13041247	1	0.22	0.27	0.91(0.68–1.21)	0.41(0.525)	0.897	0.105
	2	0.78	0.73
FGFR1_C_2080139_10	1	0.84	0.74	1.16 (0.86–1.55)	1.16 (0.351)	0.771	0.980
	2	0.16	0.26
FGFR1_rs881301	1	0.17	0.26	0.83 (0.62–1.10)	1.63 (0.202)	0.980	0.698
	2	0.83	0.74
FOXE1_rs647843	1	0.31	0.35	0.92 (0.69–1.23)	0.25 (0.621)	0.970	1.0
	2	0.69	0.65
FOXE1_rs894673 (9q22.33)	1	0.31	0.33	0.96 (0.72–1.28)	0.05 (0.832)	0.878	1.0
	2	0.69	0.67
FOXE1_rs3758249_G>A	1	0.31	0.34	0.94 (0.71–1.26)	0.13 (0.72)	1	0.980
	2	0.69	0.66
FGFR2_rs10466215	1	0.21	0.18	1.06 (0.78–1.42)	0.13 (0.720)	0.775	1.0
	2	0.79	0.82
BMP4_rs276188	1	0.78	0.85	0.87 (0.65–1.16)	0.85 (0.358)	0.512	0.970
	2	0.22	0.15
BMP4_rs17563	1	0.94	0.93	1.02(0.77–1.36)	0.01 (0.944)	1	1.0
	2	0.06	0.07

OR=odd ratio HWE = Hardy Weinberg equilibrium

Table 4 shows the allele frequencies for 88 cases and 88 controls (these are matched case and control probands with complete genotype and maternal environment factor data). The odds ratio was calculated between cases and controls for each marker investigated using the chi-square test. There was no significant result observed for any of the markers investigated.