Table 2. P-values from individual and SNP-set approaches for the VSTM4 gene.

Region (SNP-set)	Total Number of SNPs	Additional SNPs with p-value less than 0.002 (p-value)1	GATES	VEGAS-SUM	VEGAS-MAX	LR-PC	LR
VSTM4	5	rs12245255 (0.00016)	0.0006	0.0034	0.011	0.0021	0.02
VSTM4+/−5kb	6	rs4298825 (0.003) rs4488117 (0.002)	0.0011	0.0023	0.035	0.0046	0.14
VSTM4+/−10kb	10	rs6537494 (0.0016)	0.0014	0.0014	0.060	0.0047	0.20
VSTM4+/−15kb	15	rs4240498 (0.0008) rs7074818 (0.0016)	0.0020	0.0007	0.16	0.013	0.22
VSTM4+/−25kb	25	none	0.0030	0.0010	0.24	0.015	0.12
VSTM4+/−50kb	38	none	0.0034	0.0024	0.33	0.041	0.003

1. To find the total number of significant SNPs in each SNP-set include all significant SNPs located in and above the row of interest.