Table 1. SNPs associated with male breed-average weight using the array data and imputed data.

Chr	Putative causal variant	Array Position	Array MAF	Array Effect size	Imputation Position	Imputation MAF	Imputation Effect size	LD (r2)
1	N/A	55983871	0.129	-0.071	55922563	0.127	-0.077	0.874
3	41849479	41758863	0.311	-0.031	41780841	0.111	-0.074	0.246
3	N/A	62042184	0.100	0.062	61887587	0.093	0.065	0.849
3	N/A	91103945	0.227	0.067	91110878	0.283	0.094	0.433
4	39182836	39112085	0.334	-0.052	39182836	0.262	-0.060	0.396
4	67040898 67040939	67026055	0.404	-0.033	67040898	0.363	-0.074	0.382
5	N/A	31895829	0.461	-0.029	31689208	0.248	-0.045	0.265
7	N/A	30243851	0.271	-0.044	30183217	0.176	-0.067	0.518
7	N/A	41392649	0.356	-0.041	41351722	0.349	-0.044	0.903
7	43794129	43719549	0.382	-0.067	43724293	0.356	-0.076	0.894
9	N/A	N/A			12034947	0.054	-0.094	N/A
10	8348804	8183593	0.209	-0.135	8379634	0.249	-0.191	0.557
11	N/A	26929946	0.243	-0.045	26929946	0.243	-0.045	1.000
12	33710200	33733595	0.435	0.026	33712492	0.161	0.067	0.148
15	41221438 41220982	41221438	0.465	-0.115	41216098	0.464	-0.114	0.979
18	20443727	20272961	0.151	-0.083	20379945	0.161	-0.116	0.577
20	N/A	21479863	0.085	0.056	21686712	0.110	0.072	0.493
26	N/A	7631562	0.340	0.031	7679257	0.175	0.059	0.075
26	N/A	13224865	0.307	-0.042	12838979	0.232	-0.078	0.154
32	5231894	N/A			5228269	0.164	-0.077	N/A
34	N/A	18559537	0.237	-0.050	18587956	0.258	-0.051	0.849
39	102364864 102369488	102212242	0.345	0.073	102209680	0.342	0.075	0.983

Positions, minor allele frequencies (MAF), and effect sizes for SNPs associated with male breed-average weight using the array data and imputed data, and LD between these pairs of SNPs. Also shown are putative causal variants for loci that have previously been fine-mapped. 20 array QTLs and 20 imputed QTLs (shown in bold) were used in a prediction model.