Table 1. A selection of key genes involved in piebald.

GeneID	Chr	Mb	Normalised Gene Expression1					SNP2	Allele Frequency3		P-value4	OR4
			NOR	PBB	PBW	RSB	RSW		Piebald	Non_Piebald
ATRN	13	55.4	6.15	8.43	8.42	7.59	8.99	OAR13_55578882	0.67	0.44	5.96E-03	2.57
C1QL1	11	46.9	NA	NA	NA	NA	NA	s27884	0.19	0.5	1.47E-04	4.33
CD9	3	225.7	9.63	9.32	9.01	8.33	9.58	s65742	0.29	0.58	6.34E-04	3.3
DOCK7	1	38.6	2.47	4.18	4.36	4.67	4.18	OAR1_38581202	0.67	0.74	3.05E-01	1.45
EFNA5	5	112.9	8.44	9.15	8.91	8.59	9.15	s72651	0.58	0.79	4.40E-03	2.71
FGFR1OP	8	95.4	7.87	6.73	7.28	6.75	7.09	OAR8_95443730	0.9	0.81	1.80E-01	1.98
FRY	10	29.2	6.78	8.5	8.19	7.97	8.81	OAR10_29223007	0.69	0.42	1.54E-03	2.99
GLI3	4	84	5.85	7.48	7.58	6.81	8.39	OAR4_83976143	0.67	0.78	9.95E-02	1.82
IGFBP7	6	78.9	11.37	10.35	9.7	9.87	10.7	s49104	0.54	0.88	8.45E-07	5.92
KRT31	11	43.8	14.06	11.25	12.11	12.77	12.57	OAR11_43737226	0.71	0.67	6.55E-01	1.18
LARP7	6	15.7	6.29	7.99	7.71	6.51	8.76	s14758	0.46	0.67	7.80E-03	2.44
MAML2	15	13.4	7.05	7.57	8.31	7.34	8.6	s71238	0.88	0.65	2.62E-03	3.84
MYH10	11	29.3	5.36	5.77	5.97	6.43	7.54	s29973	0.46	0.74	2.74E-04	3.42
PDGFRA	6	76.2	6.12	5.33	6.22	5.99	6.1	OAR6_76377079	0.31	0.62	2.34E-04	3.56
PTK2	9	16.2	5.06	6.12	5.75	4.78	5.73	s22485	0.58	0.35	5.20E-03	2.55
PTPN18	2	121.1	6.99	7.19	7.87	7.54	8.69	s23889	0.71	0.46	2.68E-03	2.87
SHISA9	24	13.2	7.23	7.57	8.31	8.38	8.88	OAR24_13240468	0.9	0.63	4.28E-04	5.16
SILV	3	174.6	8.16	8.87	8.51	9.15	9.22	s59363	0.79	0.87	2.01E-01	1.73
SLC11A2	3	144.3	7.76	7.44	7.52	7.89	8.05	OAR3_144283427	0.88	0.64	2.03E-03	3.96
SP3	2	143.5	6.2	7.36	8.33	7.49	8.29	OAR2_143746835	0.54	0.78	1.63E-03	2.96
TBX15	1	101.9	4.38	3.67	4.96	5.29	4.53	OAR1_101890858	0.54	0.6	4.46E-01	1.29
TMEM158	19	57.1	6.18	6.95	6.76	6.41	7.77	s04445	0.79	0.41	4.57E-06	5.47

A selection of key genes differentially expressed (DE; P<0.01) in at least one of the seven contrasts and/or near a SNP associated with the piebald conditions (P<0.001).

¹The mean normalised gene expression is given for each of five tissue types (NOR, PBB, PBW, RSB and RSW as define in Figure 2A). Values for piebald tissue (PBB or PBW) that are higher than in the normal tissue (NOR) indicate up regulation (eg ATRN).

²SNP with the highest association within a 1 Mb region centered on the gene.

³Allele frequencies are given in both the piebald and non-piebald animal populations.

⁴Both the P-value and associated odd ratio (OR) are given for SNP². See Table S1 for full list of 312 key genes. Genes in bold type correspond to genes located at the intersection between the regulatory and the epistatic network (Figure 3).