Table 2. Correlations between haplotype means for each phenotype measured for a given gene with a significant eQTL.

Gene ID	Within diet			Between diet
	DR	C	HS	DR vs. C	C vs. HS	DR vs. HS
Mipp2	*	0.99	0.99	0.58	0.40	0.44
dsh	0.99	*	0.99	0.52	0.64	0.03
Pi3K21B	*	0.99	0.98	0.43	0.26	0.48
Lip4	0.76	*	0.89	0.09	0.89	0.61
PRAS40	0.24	*	0.52	0.62	0.53	0.64
hppy	0.58	*	0.73	0.42	0.76	0.31
Pi3K59F	0.93	*	0.81	0.50	0.33	0.15
slif	0.86	0.75	*	0.48	0.18	0.21
REPTOR	*	0.98	0.99	0.72	0.34	0.01
Ilp5	0.99	0.93	*	0.82	0.74	0.78
step	0.64	0.82	*	0.61	0.69	0.89

For each gene, the * indicates the treatment with the highest peak location for a given gene. The correlations reported here for each gene are the correlations between the estimated haplotype means stemming from mapping expression within the * treatment and the estimated haplotype means stemming from mapping expression within and between (difference) all other treatments. All correlations include only haplotypes with at least three observations in our set of RIXs.