Table 2. Top 25 gene sets from the pathway-based VSEA test.

Gene set	Pathway ID	P-value	Number of genes	Average single-SNP rank
Rac 1 cell-motility signaling pathway	h_rac1Pathway	<0.001	18	56 573
Actinin binding	GO:0042805	<0.001	4	1821
Sulfur amino-acid metabolic process	GO:0000096	<0.001	17	72 336
Vasculogenesis	GO:0001570	<0.001	17	69 199
Fatty-acid biosynthetic process	GO:0006633	0.001	51	66 381
Neuron differentiation	GO:0030182	0.001	106	47 424
Gene silencing	GO:0016458	0.002	17	79 722
Estrogen-responsive protein Efp controls cell cycle and breast tumors growth	h_EfpPathway	0.003	6	37 582
Calpain and friends in cell spread	h_ucalpainPathway	0.003	11	41 681
Rho cell-motility signaling pathway	h_rhoPathway	0.004	17	78 688
Phosphoinositide binding	GO:0035091	0.004	163	62 020
Limonene and pinene degradation	hsa00903	0.005	28	54 080
rRNA binding	GO:0019843	0.005	14	58 365
Fatty-acid metabolic process	GO:0006631	0.006	120	67 524
Mitosis	GO:0007067	0.006	152	86 502
Drug transport	GO:0015893	0.006	13	36 267
Hydrolyase activity	GO:0016836	0.007	47	72 672
Two-component signal transduction system (phosphorelay)	GO:0000160	0.007	8	43 192
Response to bacterium	GO:0009617	0.007	12	27 606
Ubiquitin-mediated proteolysis	hsa04120	0.008	39	67 463
Histone deacetylase activity	GO:0004407	0.008	12	81 299
Semaphorin receptor activity	GO:0017154	0.008	5	5989
DNA repair	GO:0006281	0.009	200	79 037
Glycerolipid metabolic process	GO:0046486	0.01	21	39 609
Myelination	GO:0042552	0.01	19	53 658

Bolded gene sets previously implicated in CHD.