Table 2.

Markers and haplotypes showing significant evidence of linkage and LD in 79 Taiwanese CL/P case-parent trios

Marker/haplotype
rs599021	rs2235373	rs2235371	rs595918	rs2013162	Allele freq	Trios(N)a	Obsb	Expb	P	Global Pc
Overtransmitted haplotypes
A	G	—	—	—	0.304	76	88	72	0.002	2.7 × 10−5
—	G	C	—	—	0.513	77	111	85	9 × 10−6	3.1 × 10−5
—	G	—	G	—	0.294	73	87	70	0.001	2.9 × 10−5
—	G	—	—	C	0.429	91	107	86	9 × 10−4	4.1 × 10−5
—	—	C	—	C	0.431	92	116	95	7 × 10−4	0.001
—	G	C	—	C	0.429	91	114	93	9 × 10−4	8.7 × 10−5
A	G	C	—	C	0.217	65	62	53	0.037	2.6 × 10−4
C	G	C	—	C	0.212	65	62	51	0.022	2.6 × 10−4
—	G	C	A	C	0.217	65	63	54	0.037	2.6 × 10−4
—	G	C	G	C	0.212	65	63	52	0.022	2.6 × 10−4
Undertransmitted haplotypes
A	A	—	—	—	0.488	79	71	99	5 × 10−6	2.7 × 10−5
A	—	v	G	—	0.575	93	103	125	5.1 × 10−4	0.003
—	A	—	G	—	0.488	79	78	106	5 × 10−6	2.9 × 10−5
—	A	T	—		0.427	77	56	77	5.1 × 10−4	3.1 × 10−5
—	A	—	—	A	0.488	77	67	94	9 × 10−6	4.1 × 10−5
A	A	T	—	—	0.427	77	65	86	5.1 × 10−4	1.1 × 10−4
A	A	—	G	—	0.488	79	75	103	5 × 10−6	8.7 × 10−5
A	A	—	v	A	0.488	77	74	101	9 × 10−6	1.6 × 10−4
—	A	—	G	A	0.488	77	74	101	9 × 10−6	1.6 × 10−4
—	A	T	G	—	0.427	77	67	88	5.1 × 10−4	1.1 × 10−4
A	A	—	G	A	0.488	77	74	101	9 × 10−6	1.6 × 10−4
Haplotypes consisting of 4 SNPs
A	A	T	G	A	0.427	77	72	93	5.1 × 10−4	2.6 × 10−4
A	G	C	A	C	0.217	65	62	53	0.037
C	G	C	G	C	0.212	65	62	51	0.022
A	G	C	G	A	0.084	40	28	23	0.116
A	A	C	G	A	0.060	31	10	16	0.048

^aNumber of informative case-parent trios.

^bObserved and expected frequencies of alleles defining haplotype transmitted.

^cThe P value for a statistical model with whole haplotypes consisted of two, three, or four SNPs.

LD, linkage disequilibrium; CL/P, cleft lip with or without cleft palate; freq, frequency; Obs, observed; Exp, expected.