Table 2.

Significant haplotypes on ULK4 gene by haplo.glm or haplo.score (in addition to those indicated in Table 1)

SNP# in haplotype block	Location	Hap name	Hap freq	LBL (OR)	LBL (BF)	Haplo GLM (p value)	Haplo score (p value)	Haplo score overall test (p value)
8–12	41497115–41657184	00001	0.0014	2.471	1.430	0.040*	0.010*	0.005*
9–13	41504594–41722969	00010	0.0016	2.022	1.123	0.035*	0.016*	0.005*
10–14	41504679–41722976	00100	0.0016	2.155	1.050	0.036*	0.016*	0.064
		00001	0.0019	0.218	1.743	0.000*	0.130	0.064
11–15	41607541–41723054	01000	0.0016	2.118	1.394	0.037*	0.016*	0.085
		00001	0.0011	0.305	1.151	0.000*	0.252	0.085
12–16	41657184–41723090	10000	0.0016	2.137	1.281	0.036*	0.016*	0.041*
		00010	0.0011	0.307	1.278	0.000*	0.252	0.041*
		00100	0.0019	0.226	1.773	0.000*	0.130	0.041*
26–30	41796016–41841618	00001	0.0033	2.036	1.340	0.047*	0.040*	0.331
		10000	0.0016	0.286	1.355	0.000*	0.161	0.331
27–31	41796025–41841716	00010	0.0032	1.945	1.051	0.045*	0.040*	0.565
28–32	41831203–41841811	00100	0.0032	1.900	0.989	0.047*	0.040*	0.357
		00001	0.0018	0.248	1.595	0.000*	0.132	0.357
30–34	41841618–41861013	10000	0.0030	1.877	1.036	0.039*	0.046*	0.649
		01001	0.0016	0.565	0.737	0.000*	0.487	0.649
39–43	41925423–41939990	01010	0.0012	0.555	0.809	0.000*	0.543	0.219
40–44	41937000–41939992	10010	0.0016	0.821	0.798	0.000*	0.495	0.253
		10100	0.0012	0.606	0.791	0.000*	0.549	0.253
44–48	41939992–41949348	01001	0.0004	2.228	1.270	NA	0.000*	1.000
		10001	0.0010	1.813	0.915	0.000*	0.104	1.000
47–51	41949301–41952774	00001	0.0048	1.881	1.407	0.046*	0.043*	0.000*
48–52	41949348–41952781	00010	0.0048	1.842	1.252	0.049*	0.040*	0.011*
49–53	41949359–41952838	00100	0.0048	1.900	1.293	0.049*	0.040*	0.161
50–54	41949479–41952852	01000	0.0047	2.000	1.449	0.032*	0.037*	0.299
51–55	41952774–41952898	10000	0.0045	2.163	1.838	0.023*	0.023*	0.218

Major allele is coded as 0. SNP# corresponds to the order of SNP in the gene among SNPs with MAF ≥0.001 and no more than 25 % missing genotypes. The blocks shown in bold in the first column are reported in Table 1 also but for a different haplotype

Hap haplotype, Hap freq haplotype frequency (obtained from hapassoc); NA, this haplotype was not returned by haplo.glm as its frequency is below pooling tolerance of 0.001

*Significant p value