Table 2.

Enrichment of BP in the 0.01% tail of the top interactive A. thaliana SNPs

BP	Enrichment	Nominal P value	ATG number	Locus name	Molecular function	No. of hits
Retrograde transport endosome to golgi	78.3	0.001	AT4G19490	VPS54	Putative homolog of yeast Vps54	14
Cellular response to hypoxia	39.6	0.002	AT4G19520		Disease resistance protein (TIR-NBS-LRR class)	11
				GLUTAMATE	Member of Putative ligand-gated ion channel subunit family	12
Cellular calcium ion homeostasis	28.7	0.005	AT2G24710,	RECEPTOR 2.3
			AT2G24720	GLUTAMATE	Member of Putative ligand-gated ion channel subunit family
				RECEPTOR 2.3

The nominal significance of the observed enrichment was assessed using a null distribution based on 10,000 permutations from a procedure that takesinto account LD patterns (see Materials and Methods).