Table 2. SNP minor allele frequencies among parents of 297 CL/P cases from four populations.

Gene	No.	SNP name	Physical locationa	Minor allele	High-risk alleleb	Minor allele frequency
						Taiwan	Singapore	Korea	Maryland
PAX7	1	rs766325	18701764	1	1	0.172	0.172	0.138	0.574
	2	rs880810	18739860	1	2	0.139	0.095	0.107	0.077
	3	rs618941	18751458	2	2	0.306	0.319	0.307	0.056
	4	rs553934	18758087	2	2	0.257	0.276	0.250	0.056
	5	rs545793	18761828	2	2	0.372	0.362	0.336	0.204
	6	rs624761	18790183	2	2	0.195	0.207	0.118	0.169
	7	rs609959	18791125	2	2	0.089	0.069	0.053	0.095
PAX3	1	rs3731858	222891375	1	1	0.254	0.271	0.289	0.194
	2	rs7565552	222900773	1	2	0.089	0.143	0.132	0.391
	3	rs1370924	222904097	1	1	0.256	0.284	0.263	0.218
	4	rs1013262	222916284	2	1	0.089	0.144	0.132	0.401
	5	rs1965791	222922214	1	2	0.346	0.415	0.380	0.709
	6	rs6717432	222927785	1	1	0.167	0.237	0.178	0.126
	7	rs1367411	222931347	2	1	0.162	0.161	0.243	0.489
	8	rs1367414	222934296	1	2	0.382	0.398	0.368	0.517
	9	rs7609007	222940422	2	2	0.348	0.297	0.395	0.094
	10	rs1430662	222946520	1	1	0.349	0.297	0.392	0.094
	11	rs4674639	222949598	2	1	0.356	0.398	0.270	0.213
	12	rs930140	222973797	1	2	0.404	0.458	0.327	0.510
	13	rs7600206	222982092	2	1	0.323	0.368	0.257	0.194
PAX6	1	rs3026393	31768791	2	1	0.491	0.422	0.428	0.528
	2	rs644242	31769377	1	2	0.194	0.181	0.132	0.052
	3	rs667773	31771938	1	2	0.194	0.181	0.132	0.052
	4	rs2239789	31772472	2	1	0.491	0.422	0.427	0.524
	5	rs592859	31775911	1	1	0.259	0.333	0.382	0.164
	6	rs3026354	31787233	2	2	0.252	0.333	0.380	0.164
	7	rs2071164	31790118	2	2	0.253	0.333	0.367	0.165
PAX9	1	rs2073241	36198687	1	1	0.491	0.466	0.428	0.353
	2	rs2073247	36200496	1	1	0.489	0.466	0.412	0.348
	3	rs2295218	36204242	2	2	0.491	0.466	0.428	0.351
	4	rs12892031	36207131	1	1	0.218	0.276	0.322	0.391
	5	rs1955734	36208379	1	1	0.217	0.293	0.322	0.436
	6	rs8004187	36210255	2	2	0.217	0.276	0.322	0.389
	7	rs7144276	36214358	2	2	0.221	0.138	0.280	0.067

^aBased on NCBI Human Genome build 35.1.

^bHigh-risk allele was defined as that allele showing over-transmission to cases in TDT (ie OR(transmission)>1.0 ignoring parent-of-origin) regardless of statistical significance.