Table 2. ITGB3 haplotypes are associated with autism: (a) haplotype structure at the ITGB3 locus. (b) Haplotype family-based association tests performed using HBAT, under an additive model (−e)³².

(a)a
	ITGB3 SNPs
	1	2	3	4	5	6	7	8	9	10	Estimated
Haplotype	rs2317385	rs2056131	rs4525555	rs2015729	rs5918	rs951351	rs15908	rs12603582	rs3809865	rs11650072	Frequency
H1	G	G	C	G	T	G	C	T	A	C	0.158
H2	G	G	T	A	C	G	A	G	T	T	0.125
H3	G	G	C	G	T	G	C	G	A	C	0.103
H4	G	G	T	A	T	G	A	G	A	C	0.102
H5	A	G	T	A	T	G	A	G	A	C	0.097
H6	G	A	C	G	T	G	C	G	A	C	0.083
H7	G	A	C	G	T	G	C	G	T	T	0.074
H8	G	A	C	G	T	G	C	T	A	C	0.058
H9	G	G	C	A	T	A	A	G	A	T	0.041
H10	A	G	C	A	T	G	C	G	T	T	0.027
H11	A	G	C	G	T	G	C	T	A	C	0.011
H12	G	A	C	G	T	G	C	G	A	T	0.011
H13	G	G	T	A	C	G	A	G	A	C	0.010
H14	A	G	T	A	T	G	A	T	A	C	0.009
H15	A	A	T	A	T	G	A	G	A	C	0.007
H16	A	G	C	A	T	A	A	G	A	T	0.006
H17	G	G	T	A	T	G	A	G	T	T	0.005
H18	G	G	C	G	T	G	C	G	T	T	0.005
H19	A	G	T	A	T	G	A	G	A	T	0.005

(b)b
ITGB3 Haplotypes	Estimated frequency	No. of families	S	E(S)	Var(S)	Z	P-value
H1	0.158	79.2	53.241	66.215	30.170	−2.362	0.018
H2	0.125	60.2	55.239	53.866	19.295	0.313	0.754
H3	0.103	55.9	54.993	41.941	21.999	2.783	0.005
H4	0.102	48.0	37.016	38.468	13.996	−0.388	0.698
H5	0.097	55.2	37.996	36.582	15.763	0.356	0.721
H6	0.083	42.0	36.000	34.000	13.500	0.544	0.586
H7	0.074	45.2	37.000	34.458	12.627	0.715	0.474
H8	0.058	36.4	30.375	27.188	10.520	0.983	0.326
H9	0.041	22.5	14.250	14.750	8.281	−0.174	0.862
H10	0.027	17.1	7.000	9.562	4.254	−1.242	0.214

^aOnly haplotypes with estimated frequencies ≥0.005 are listed.

^bHaplotype global P-value for HBAT is P=0.038; whole marker permutation tests yield χ² sum P=0.017 and minimal P=0.011, after 100 000 iterations.

Haplotypes H1 and H3 highlighted in bold are significantly under- and over-transmitted, respectively, from heterozygous parents to the affected offspring.