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.