Table III. Genes having genic and genic plus promoter mean P ≤ 0.05 as well as an association with at least one top 1,000 SNP.

The 13 genes shown are from the intersection of all three parameters shown in Figure 5C. Genes from the intersection of genic P ≤ 0.05 or genic plus promoter P ≤ 0.05 with the top 1,000 SNPs (but not both) are shown in Supplemental Table S8.

Gene	Genic SNPs	Genic Average P Value	Genic Plus Promoter SNPs	Genic Plus Promoter Average P Value	Score	Region	Protein
AT1G01900	4	0.041	7	0.034	1	–	Subtilisin-like Ser protease1.1
AT1G54280	2	0.032	3	0.023	3	17	ATPase E1-E2-type family protein
AT2G03770	2	0.030	6	0.033	1	–	P-loop-containing nucleoside triphosphate hydrolase family
AT2G28170	4	0.014	7	0.039	2	–	Putative Na+/H+ antiporter7
AT3G12970	2	0.017	2	0.017	1	37	Unknown
AT3G46260	7	0.046	7	0.046	2	–	Protein kinase
AT4G37880	8	0.029	9	0.039	1	–	LisH/CRA/RING-U-box domain-containing protein
AT5G10010	3	0.031	4	0.024	2	–	Unknown
AT5G10890	4	0.005	6	0.006	5	73	Myosin heavy chain related
AT5G28150	4	0.042	7	0.047	2	–	Unknown
AT5G44220	2	0.041	2	0.041	13	87	F-box family protein
AT5G45350	8	0.018	15	0.037	4	89	Pro-rich family protein
AT5G46320	2	0.001	6	0.002	16	91	MADS box family protein