Table 2.

List of the genome-wide significant cis-eQTLs detected in the liver tissue (those that have been consistently detected in the muscle are shown in bold)¹

liver cis-eQTL										Gene
SSC	N	SNP	Region (Mb)	P-value	q-value	B	δ ± SE	A1	MAF	Acronym	Region (Mb)
1	15	H3GA0004318	251.1–254.7	8.56E-10	2.43E-05	2.43E-05	0.49 ± 0.07	A	0.281	HSDL2	253.1–253.1
1	1	ASGA0006805	253.4–253.4	9.61E-07	2.73E-02	2.73E-02	0.22 ± 0.04	C	0.411	CDC26	253.8–253.9
2	7	MARC0045154	4.6–8.8	2.63E-06	3.22E-02	7.47E-02	0.27 ± 0.06	A	0.146	CTSF	5.8–5.8
2	17	DIAS0003663	82.9–89.7	8.30E-09	1.18E-04	2.36E-04	0.30 ± 0.05	A	0.411	SERINC5	88.8–88.9
4	8	DIAS0000176	96.7–99.8	2.13E-07	2.27E-03	6.04E-03	0.30 ± 0.05	A	0.255	APH1A	98.8–98.8
5	1	H3GA0016032	19.8–19.8	8.25E-07	1.17E-02	2.35E-02	−0.38 ± 0.07	G	0.24	PPP1R1A	19.7–19.7
6	23	ALGA0116876	17.0–21.7	9.05E-16	0.00E+ 00	0.00E+ 00	0.86 ± 0.08	A	0.255	ARL2BP	19.2–19.2
6	13	MARC0031169	70.1–71.6	9.29E-07	3.30E-03	2.64E-02	−0.34 ± 0.04	G	0.276	LZIC	70.2–70.2
6	1	ASGA0104284	80.6–80.6	1.70E-06	4.82E-02	4.82E-02	−0.20 ± 0.04	C	0.141	ZNF436	81.2–81.2
6	14	ALGA0114962	82.1–89.0	6.79E-06	1.76E-02	1.93E-01	−0.32 ± 0.06	A	0.24	BSDC1	88.8–88.8
6	2	ASGA0030033	158.1–158.6	9.06E-07	2.57E-02	2.57E-02	−0.24 ± 0.04	G	0.328	YIPF1	158.4–158.4
7	2	DRGA0007123	9.9–10.4	5.49E-10	1.56E-05	1.56E-05	−0.40 ± 0.05	G	0.24	NOL7	9.9–9.9
8	13	ALGA0112294	10.6–11.3	3.37E-08	1.37E-04	9.58E-04	−0.36 ± 0.06	C	0.406	TAPT1	11.3–11.4
9	2	ASGA0094801	46.6–46.7	3.33E-06	4.73E-02	9.46E-02	−0.54 ± 0.10	G	0.266	THY1	46.6–46.6
10	1	ASGA0046443	10.2–10.2	4.07E-06	1.27E-02	1.16E-01	−0.25 ± 0.05	G	0.229	MARC2	10.1–10.1
10	10	ALGA0106385	48.1–54.6	1.22E-07	2.04E-03	3.46E-03	0.24 ± 0.04	G	0.396	KIAA1217	50.7–51.2
12	2	MARC0042683	24.1–24.7	5.74E-07	1.63E-02	1.63E-02	−0.30 ± 0.06	G	0.297	PNPO	24.1–24.2
12	3	M1GA0016795	42.8–43.1	1.61E-06	2.29E-02	4.58E-02	−0.32 ± 0.06	A	0.464	CRLF3	42.9–42.9
12	9	ALGA0066653	44.0–46.4	6.21E-12	9.00E-08	1.80E-07	0.31 ± 0.04	G	0.5	TMEM97	44.6–44.6
12	3	ALGA0066917	51.0–59.3	3.85E-06	3.65E-02	1.09E-01	0.19 ± 0.04	G	0.333	RABEP1	51.6–51.8
13	1	ALGA0070572	61.1–61.1	1.97E-06	2.80E-02	5.60E-02	−0.40 ± 0.07	A	0.474	ITPR1	61.0–61.3
13	6	ALGA0103755	141.3–148.9	1.73E-07	1.52E-03	4.92E-03	0.44 ± 0.06	A	0.286	GTPBP8	146.9–146.9
14	11	H3GA0038597	6.5–7.2	1.86E-09	4.94E-05	5.28E-05	−0.39 ± 0.06	A	0.401	POLR3D	6.5–6.5
14	22	H3GA0039048	10.1–14.0	8.60E-11	4.10E-07	2.44E-06	0.35 ± 0.05	G	0.469	HMBOX1	12.6–12.8
14	2	DRGA0013801	42.7–43.4	2.70E-07	7.66E-03	7.66E-03	−0.33 ± 0.06	A	0.406	GRK3	43.3–43.4
14	2	ASGA0065623	100.9–100.9	1.21E-06	1.24E-02	3.43E-02	0.37 ± 0.07	A	0.234	LIPA	101.1–101.2
16	5	ALGA0088786	5.7–5.8	1.04E-07	9.88E-04	2.96E-03	0.61 ± 0.10	G	0.406	RETREG1	5.7–5.8
18	8	ASGA0100292	0.2–2.3	4.33E-06	3.08E-02	1.23E-01	−0.15 ± 0.03	A	0.234	ESYT2	0.5–0.6

¹SSC: porcine chromosome, N: Number of SNPs significantly associated with the trait under study, SNP: SNP displaying the most significant association with the trait under study, Region (Mb): region containing SNPs significantly associated with the trait under study, P-value: nominal P-value, q-value: q-value calculated with a false discovery rate approach, B: Bonferroni corrected P-values, δ: allelic effect and its standard error (SE), A₁: minority allele, MAF: frequency of the minority allele