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Table 5 Genome-wide eQTL for 497 candidate genes expressed in the gluteus medius (GM) muscle of Duroc pigs

From: Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

Ensembl ID SSC N SNP Region (Mb) q-value B δ ± SE A1 MAF
ENSSSCG00000004064 1 27 rs81289665 5.69–10.57 4.34E−03 1.30E−02 − 0.45 ± 0.09 G 0.42
ENSSSCG00000004071 1 6 rs81278169 12.26–13.05 8.75E−04 8.75E−04 0.51 ± 0.09 A 0.40
ENSSSCG00000014432 2 1 rs80929229 149.45–149.45 3.71E−03 2.97E−02 − 0.47 ± 0.10 A 0.10
ENSSSCG00000014432 2 9 rs81290831 150.27–151.35 2.72E−03 1.91E−02 − 0.46 ± 0.09 A 0.11
ENSSSCG00000005976 4 6 rs80965603 14.33–15.13 1.55E−02 3.10E−02 0.24 ± 0.05 C 0.28
ENSSSCG00000005976 4 1 rs81261174 29.68–29.68 4.40E−02 3.08E−01 0.23 ± 0.05 C 0.29
ENSSSCG00000032907 4 3 rs80955389 89.79–89.95 4.01E−02 1.00E+00 − 0.24 ± 0.06 C 0.48
ENSSSCG00000032907 4 32 rs80977488 90.00–99.43 4.25E−04 4.25E−04 0.35 ± 0.06 G 0.36
ENSSSCG00000032907 4 4 rs80889119 103.32–103.47 4.01E−02 1.00E+00 0.31 ± 0.08 G 0.45
ENSSSCG00000033497 6 4 rs81388022 68.99–69.13 1.85E−02 7.41E−02 0.34 ± 0.07 C 0.23
ENSSSCG00000027659 6 25 rs81389074 80.81–82.56 8.02E−04 1.36E−02 − 0.30 ± 0.06 A 0.15
ENSSSCG00000038994 6 19 rs81389074 80.81–82.15 6.32E−03 1.14E−01 0.85 ± 0.18 A 0.15
ENSSSCG00000027659 6 2 rs81309503 111.39–111.40 3.98E−02 1.00E+00 − 0.26 ± 0.06 G 0.15
ENSSSCG00000025087 6 2 rs81393449 156.12–156.13 4.27E−02 8.55E−02 − 0.42 ± 0.09 A 0.09
ENSSSCG00000003844 6 3 rs81345502 157.59–158.65 1.13E−06 1.13E−06 0.30 ± 0.05 G 0.43
ENSSSCG00000003844 6 1 rs81333128 162.74–162.74 2.37E−02 7.10E−02 0.21 ± 0.04 A 0.34
ENSSSCG00000001455 7 12 rs339209635 23.40–26.06 9.64E−03 1.98E−02 0.60 ± 0.12 A 0.49
ENSSSCG00000024596 8 1 rs81237638 37.96–37.96 1.60E−02 6.55E−01 − 0.33 ± 0.08 G 0.33
ENSSSCG00000024596 8 22 rs81402024 83.19–89.67 1.58E−02 1.23E−01 − 0.37 ± 0.08 C 0.37
ENSSSCG00000024596 8 39 rs81402439 90.31–99.95 1.58E−02 2.99E−01 0.34 ± 0.08 G 0.33
ENSSSCG00000024596 8 11 rs81310686 100.02–101.17 1.58E−02 4.81E−01 0.34 ± 0.08 A 0.31
ENSSSCG00000024596 9 1 rs81420190 14.32–14.32 4.59E−02 1.00E+00 − 0.30 ± 0.08 C 0.24
ENSSSCG00000015129 9 4 rs81408352 24.50–28.89 6.62E−03 1.28E−01 − 0.27 ± 0.06 G 0.10
ENSSSCG00000015129 9 28 rs81318704 35.15–39.98 6.62E−03 1.39E−01 − 0.25 ± 0.06 A 0.12
ENSSSCG00000015129 9 10 rs81410722 45.90–47.65 2.64E−05 5.28E−05 − 0.25 ± 0.04 G 0.17
ENSSSCG00000015129 9 3 rs81226448 54.24–54.49 2.97E−02 7.72E−01 − 0.15 ± 0.03 C 0.28
ENSSSCG00000015129 9 1 rs81412811 65.10–65.10 4.49E−02 1.00E+00 − 0.19 ± 0.05 C 0.12
ENSSSCG00000017895 12 9 rs81436670 50.91–53.86 4.50E−07 1.36E−06 0.40 ± 0.06 G 0.33
ENSSSCG00000023829 14 1 rs80875259 31.27–31.27 1.24E−06 3.74E−02 − 0.36 ± 0.07 G 0.42
ENSSSCG00000014791 17 1 rs81466737 47.44–47.44 9.17E−07 2.76E−02 0.33 ± 0.07 A 0.22
  1. SSC, Sus scrofa chromosome; N, number of SNPs significantly associated with the gene under study; SNP, corresponds to the most significant associated SNP; Region (Mb), region containing the SNPs significantly associated with the gene under study; P-value, nominal P-value of association between gene expression and SNP; q-value, q-value calculated with a false discovery rate approach; B, Bonferroni corrected P-values; δ, effect size of the marker and its standard error (SE); A1, minor allele; MAF, minor allele frequency