Table 1: Top significant local-eQTLs targeting candidate genes for cows fed the control (C) diet.
rsID | Gene.name | Gene type | FDR | Position | Freq | Genotype | Gene position |
rs133674837 | BDH2 | DE | 7.35E-04 | 6:23051485 | 6/8/5 | CC/CA/AA | 6:23047057-23077431 |
rs109975461 | CHRNE | DE | 4.23E-02 | 19:26981374 | 8/6/5 | AA/AG/GG | 19:27118517-27123114 |
rs109947248 | CHRNE | DE | 4.23E-02 | 19:26994134 | 8/6/5 | AA/AG/GG | 19:27118517-27123114 |
rs109341116 | CHRNE | DE | 4.23E-02 | 19:27098154 | 8/6/5 | AA/AG/GG | 19:27118517-27123114 |
rs110896981 | CHRNE | DE | 4.23E-02 | 19:27192150 | 10/4/5 | AA/AG/GG | 19:27118517-27123114 |
rs43318602 | ELOVL6 | DE | 4.23E-02 | 6:16656338 | 15/2/2 | GG/GA/AA | 6:16376642-16510240 |
rs43318545 | ELOVL6 | DE | 4.23E-02 | 6:16678359 | 15/2/2 | GG/GA/AA | 6:16376642-16510240 |
rs43317462 | ELOVL6 | DE | 4.23E-02 | 6:16731878 | 9/8/2 | GG/GA/AA | 6:16376642-16510240 |
rs110036492 | ELOVL6 | DE | 4.23E-02 | 6:16738741 | 8/8/2 | GG/GA/AA | 6:16376642-16510240 |
rs43315610 | ELOVL6 | DE | 4.23E-02 | 6:16755625 | 6/11/2 | GG/GA/AA | 6:16376642-16510240 |
rs43316358 | ELOVL6 | DE | 4.23E-02 | 6:16761983 | 6/11/2 | GG/GA/AA | 6:16376642-16510240 |
rs43317449 | ELOVL6 | DE | 4.23E-02 | 6:16725243 | 9/8/2 | GG/GA/AA | 6:16376642-16510240 |
rs109963253 | GIMAP4 | DE | 3.02E-02 | 4:113638587 | 8/9/2 | GG/GA/AA | 4:113866800-113874303 |
rs134589272 | FDXR | DE | 4.23E-02 | 19: 56624163 | 10/8/1 | GG/GA/AA | 19: 57164031-57175524 |
rs ID = reference SNP cluster ID; Gene Name = name of the targeted genes; Gene type = type of candidate gene: Hub genes (HG) or differentially expressed genes (DE);
FDR = False Discovery Rate of the association between SNP and gene expression, Position = genome position of the SNP, Freq = frequency of each genotypes (A1A1/A1A2/A2A2)
in the cows analysed, Genotype = genotype at the SNP locus (A1A1/A1A2/A2A2), Gene position = genome position of the targeted gene.