Table 3. SNPs significantly associated with variation in principal components of nutritional indices at P < 10−6.
| PC | Diet | SNP | P | Effect | MAF | Gene | FBgn | Type | Function | Reference |
|---|---|---|---|---|---|---|---|---|---|---|
| PC1 | HGD | 2L.15990382 | 9.79E-07 | −0.988 | 0.465 | CR43412 | FBgn0263331 | Down (435) | Nonprotein coding | Tweedie et al. 2009 |
| X.16918901 | 9.24E-07 | 1.046 | 0.300 | CG43997 | FBgn0264739 | Down (923) | Unknown | NA | ||
| PC2 | HGD | 3L.1235270 | 7.76E-08 | −1.015 | 0.309 | CG33966 | FBgn0053966 | 3′ UTR | Vitamin E binding | Tweedie et al. 2009 |
| 3L.1235273 | 8.26E-07 | −0.927 | 0.324 | CG33966 | FBgn0053966 | 3′ UTR | Vitamin E binding | Tweedie et al. 2009 | ||
| 3L.2644168 | 9.74E-07 | 0.974 | 0.264 | CG14949 | FBgn0035358 | Up (744) | Unknown | NA | ||
| 3L.17498584 | 9.88E-07 | 0.970 | 0.270 | Oatp74D | FBgn0036732 | Intron | Organic anion transport | Tweedie et al. 2009 | ||
| PC3 | HGD | X.20411124 | 5.38E-07 | −0.977 | 0.222 | RunxB | FBgn0259162 | Intron | DNA binding | Boutros et al. 2004 |
| PC4 | HGD | 3R.14205878 | 2.25E-07 | −0.976 | 0.178 | CG7675 | FBgn0038610 | Intron | Glucose/ribitol reductase | Tweedie et al. 2009 |
| 3R.14206166 | 2.70E-08 | −1.016 | 0.200 | CG7675 | FBgn0038610 | Intron | Glucose/ribitol reductase | Tweedie et al. 2009 | ||
| 3R.14206170 | 2.34E-07 | −0.924 | 0.211 | CG7675 | FBgn0038610 | Intron | Glucose/ribitol reductase | Tweedie et al. 2009 | ||
| X.8316242 | 5.06E-07 | −1.630 | 0.080 | NA | NA | NA | NA | NA | ||
| PC5 | HGD | 2L.18537420 | 8.35E-07 | −0.817 | 0.181 | Pde11 | FBgn0085370 | Syn. | Phosphodiesterase | Day et al. 2005 |
| 2L.19068086 | 9.35E-07 | −1.693 | 0.036 | CG10702 | FBgn0032752 | Intron | Protein phosphorylation | Tweedie et al. 2009 | ||
| CG17343 | FBgn0032751 | Intron | Regulation of mitotic anaphase | Tweedie et al. 2009 | ||||||
| 3L.12761401 | 1.40E-07 | −1.800 | 0.035 | CG32113 | FBgn0052113 | Syn. | Vesicle-mediated transport | Tweedie et al. 2009 | ||
| 3R.22249607 | 4.98E-07 | −1.144 | 0.085 | CG6503 | FBgn0040606 | Down (813) | Unknown | NA | ||
| PC1 | LGD | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| PC2 | LGD | 2L.14109774 | 3.30E-07 | 1.122 | 0.225 | CG31769 | FBgn0051769 | Syn. | Unknown | NA |
| 2R.6893862 | 6.94E-07 | 1.126 | 0.196 | luna | FBgn0040765 | Intron | DNA binding | Boutros et al. 2004 | ||
| X.12603566 | 9.74E-07 | 0.889 | 0.373 | Smr | FBgn0263865 | Intron | Regulation of mitotic cell cycle | Pile et al. 2002 | ||
| PC3 | LGD | 3R.25503463 | 7.36E-07 | 0.884 | 0.302 | CAP-D2 | FBgn0039680 | Intron | Mitotic sister chromatin segregation | Boutros et al. 2004 |
| 3R.25504118 | 9.66E-07 | 1.009 | 0.269 | CAP-D2 | FBgn0039680 | Syn. | Mitotic sister chromatin segregation | Boutros et al. 2004 | ||
| PC4 | LGD | 2R.4176279 | 6.74E-07 | 1.640 | 0.042 | NA | NA | NA | NA | NA |
| 3L.12262931 | 6.95E-07 | 0.666 | 0.442 | Pbgs | FBgn0036271 | 3′ UTR | Porphobolinogin synthase | Golombieski et al. 2008 | ||
| 3L.12412047 | 4.3E-07 | 2.33 | 0.021 | NA | NA | NA | NA | NA | ||
| 3L.13348431 | 1.72E-07 | 1.682 | 0.042 | CG17687 | FBgn0036348 | Down (391) | Unknown | NA | ||
| PC5 | LGD | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Effect, effect size of minor allele; MAF, minor allele frequency. SNPs labeled NA are not within 1000 bp of an annotated gene. Lines with all NAs indicate no SNPs met significance threshold.