Table 1.

Top SNPs associated with PCs in the Duroc pig breed

PC	CHR	SNP	Position	Minor/major	MAFa	BETAb	p-value	Nearby gene	Typec
PC1	2	ASGA0010593	85596454	G/A	0.425	0.013	5.56E-06	SNORA70	7365
	2	MARC0001645	87106234	A/G	0.384	0.015	1.35E-06	ENSSSCG00000014087	Genic
	2	UMB10000069	87305603	G/A	0.365	0.015	7.70E-07 *	ENSSSCG00000025645	Genic
	2	M1GA0002981	87507128	A/G	0.392	0.014	4.58E-06	AGGF1	Genic
	2	MARC0023062	87571413	G/A	0.394	0.014	6.26E-06	SNORA47	−2363
	2	ASGA0010696	87821516	G/A	0.403	0.014	4.45E-06	PDE8B	Genic
	17	INRA0052583	12436823	A/G	0.428	0.013	5.48E-06	ANK1	−17485
	17	ASGA0075294	12781032	A/G	0.483	−0.013	6.99E-07*	C8ORF40	31476
	17	ASGA0075297	12798139	G/A	0.431	−0.016	6.92E-08*	C8ORF40	14369
	17	DIAS0003526	12823893	G/A	0.431	−0.016	6.92E-08*	C8ORF40	Genic
	17	ALGA0093121	12877758	A/G	0.392	−0.016	5.24E-08*	C8ORF40	−53786
	17	ASGA0075278	12896953	C/A	0.326	−0.016	2.04E-07*	ENSSSCG00000007025	45324
	17	ASGA0075277	13015930	G/A	0.392	−0.016	5.24E-08*	SLC20A2	Genic
PC2	7	ASGA0030822	5278629	C/A	0.328	−0.015	1.09E-06*	BMP6	Genic
	8	ASGA0093827	76550202	A/G	0.086	−0.021	1.09E-06*	SHROOM3	Genic
	9	ASGA0095397	17376220	A/G	0.108	−0.021	1.20E-06	ENSSSCG00000014896	−88,4312
	10	MARC0020616	57676836	A/G	0.050	−0.029	1.32E-06	ARMC3	Genic
	10	ASGA0048292	57954471	G/A	0.050	−0.029	1.32E-06	PIP4K2A	Genic
	10	ASGA0048295	57985436	A/G	0.047	−0.030	1.12E-06	PIP4K2A	Genic
	18	MARC0096007	2334006	A/G	0.182	−0.015	2.30E-06	SHH	330788
	18	MARC0019932	7383149	A/G	0.146	−0.017	6.93E-06	ENSSSCG00000030537	3947
	18	MARC0078684	7813561	A/G	0.138	−0.020	2.53E-07*	TRBV21	Genic
	18	H3GA0050297	7848619	G/A	0.138	−0.020	2.53E-07*	TRBV27	−7443
	X	MARC0070937	44930506	G/A	0.146	−0.017	2.86E-06	ENSSSCG00000026984	−125815
PC3	3	ASGA0015307	98152224	A/G	0.150	−0.016	5.57E-06	FOXN2	−5059
	16	DRGA0016097	36203829	A/G	0.072	0.025	5.45E-06	ENSSSCG00000016898	Genic

^aMAF = Minor allele frequency.

^bBETA = Linear regression coefficient.

^cType = ‘Genic’ means the SNP is located in genic region, value indicate direction and distance (bp) from the SNP to near genic region.

^*<Simple Bonfferoni significance level (1.096E-06).