Table 2.

Haplotype association analysis in NLGN4X (EUR control population).

N	SNPs in Haplotypes	Control Frequency	Case Frequency	Haplotype	p-Value	Emp. p-Value	Emp. q-Value
6	rs6638575-rs3810688-rs3810687-rs3810686-rs5916269-rs1882260	0.0335	0.1799	GTGCGT	2.58 × 10−6	<1 × 10−5	<1 × 10−5
5	rs6638575-rs3810688-rs3810687-rs3810686-rs5916269	0.0805	0.1799	GTGCG	7.60 × 10−6	<1 × 10−5	<1 × 10−5
5	rs3810688-rs3810687-rs3810686-rs5916269-rs1882260	0.0335	0.1799	TGCGT	2.58 × 10−6	<1 × 10−5	<1 × 10−5
4	rs6638575-rs3810688-rs3810687-rs3810686	0.0805	0.1799	GTGC	7.6 × 10−6	<1 × 10−5	2 × 10−5
4	rs3810688-rs3810687-rs3810686-rs5916269	0.0801	0.1793	TGCG	7.6 × 10−6	<1 × 10−5	2 × 10−5
4	rs3810687-rs3810686-rs5916269-rs1882260	0.0943	0.1793	GCGT	1.3 × 10−5	<1 × 10−5	2 × 10−5
3	rs6638575-rs3810688-rs3810687	0.3538	0.4463	GTG	8.16 × 10−6	<1 × 10−5	<1 × 10−5
3	rs3810688-rs3810687-rs3810686	0.0701	0.1793	TGC	7.6 × 10−6	<1 × 10−5	<1 × 10−5
3	rs3810687-rs3810686-rs5916269	0.4062	0.4445	GCG	8.16 × 10−4	6.99 × 10−4	3.2 × 10−3
3	rs3810686-rs5916269-rs1882260	0.0943	0.1793	CGT	1.3 × 10−5	<1 × 10−5	3 × 10−4
2	rs6638575-rs3810688	0.2109	0.2854	GT	1.08 × 10−4	7 × 10−5	8.3 × 10−4
2	rs3810688-rs3810687	0.0943	0.1793	TG	1.3 × 10−5	2 × 10−5	1.5 × 10−4
2	rs3810687-rs3810686	0.4062	0.4445	GC	8.16 × 10−4	7.3 × 10−4	5 × 10−3
2	rs3810686-rs5916269	0.4062	0.4445	CG	8.16 × 10−4	7.3 × 10−4	5 × 10−3
2	rs5916269-rs1882260	0.4314	0.6259	GT	2.4 × 10−8	<1 × 10−5	<1 × 10−5

Haplotype combinations with significant p-values (p < 0.05), using the EUR control population, after permutation test, have been reported for all the SNPs located on NLGN4X. Empirical p-values and empirical q-values after 100,000 permutations are reported. Only haplotypes having case frequency >0.05 have been presented.