Skip to main content

Table 4 Single nucleotide polymorphisms (SNPs) with log R ratio (LRR) values associated with carcass weight, carcass fat, and carcass conformation in Charolais (CH), Holstein-Friesians (HF), and Limousins (LM)

From: Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

Chromosome Position Breed Associated trait Marginal R2 a Flanking genes
2 6.92 Mb CH Fat 0.0175 MSTN
2 8.01 Mb CH Fat 0.0136 MSTN
6 55.11 Mb CH Fat 0.0131 ARAP2
8 4.31 Mb CH Fat 0.0142 GALNLT6
13 27.45 Mb CH Fat 0.0240 OPTN, MCM10
2 90.47 Mb HF Weight 0.0287 FZD7, CDK15
21 18.53 Mb HF Weight 0.0194 NTRK3
26 27.13 Mb HF Weight 0.0287 SORCS1
1 24.98 Mb HF Conformation 0.0169 ROBO2, 5S rRNA, U2
7 5.59 Mb HF Conformation 0.0179 PGLS, NIBAN3
11 24.55 Mb HF Conformation 0.0233 ELM4
11 74.95 Mb HF Conformation 0.0176 FAM228A, FAM228B
13 68.22 Mb HF Conformation 0.0176 FAM83D
13 77.51 Mb HF Conformation 0.0157 KCNB1
18 4.24 Mb HF Conformation 0.0169 MON1B
19 17.08 Mb HF Conformation 0.0185 ASIC2
25 21.09 Mb HF Conformation 0.0155 COG7
26 42.62 Mb HF Conformation 0.0158 SPADH1, U6
13 55.30 Mb HF Fat 0.0175 CDH4
19 52.38 Mb HF Fat 0.0168 SLC26A11
22 58.14 Mb HF Fat 0.0146 WNT7A, 5S rRNA
6 44.26 Mb LM Weight 0.0177 5S rRNA, U6, DHX15
6 47.74 Mb LM Weight 0.0174 5S rRNA
11 30.81 Mb LM Weight 0.0167 PPP1R21
2 33.44 Mb LM Fat 0.0242 7SK RNA
5 20.16 Mb LM Fat 0.0124 5S rRNA
5 84.42 Mb LM Fat 0.0142 LMNTD1
7 64.07 Mb LM Fat 0.0131 7SK RNA
10 90.67 Mb LM Fat 0.0172 NRXN3, 5S rRNA
20 30.72 Mb LM Fat 0.0127 U6
20 33.02 Mb LM Fat 0.0143 PLCXD3
20 40.93 Mb LM Fat 0.0221 NPR3
21 37.67 Mb LM Fat 0.0123 U6
27 3.61 Mb LM Fat 0.0226 CSMD1, U6
  1. aThe marginal R2 is the proportion of the variance that was attributable to the fixed effect in a linear mixed model, which for this model is the SNP LRR