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Table 5 Boundaries of the validated regions that are additively significant on calving interval as well as the most significant SNPs and their associated genes within these regions in discovery and validation populations

From: Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows

   Most strongly associated SNP in discovery Most strongly associated SNP in validation  
BTCa Interval (Mbp)b SNP Position (bP) -log10 (P) Effect ± SE MAFc \( \frac{\sigma_a^2}{\sigma_p^2} \) (%)d SNP Position (bp) -log10 (P) Effect ± SE MAF \( \frac{\sigma_a^2}{\sigma_p^2} \) (%) Genes
5 12.551 - 13.463 rs133249083 13027942 4.139 2.462 ± 0.620 0.329 0.095 rs135584613 13270757 3.229 −3.077 ± 0.893 0.325 0.140 NA
5 88.607 - 89.159 rs135833682 88822777 4.076 −2.191 ± 0.556 0.417 0.083 rs133539520 88861488 2.679 −2.784 ± 0.934 0.313 0.112 ABCC9
9 55.233 - 55.657 rs134339497 55233033 4.325 −2.364 ± 0.580 0.402 0.096 rs136630637 55637401 2.399 −2.559 ± 0.887 0.337 0.098 NA
9 57.397 - 57.735 rs137407787 57396816 4.130 −2.346 ± 0.591 0.358 0.091 rs42550144 57723628 2.408 −2.685 ± 0.929 0.290 0.100 EPHA7
9 60.121 - 60.477 rs43600502 60477358 5.195 −2.642 ± 0.584 0.352 0.114 rs133175600 60130790 2.127 2.813 ± 1.05 0.212 0.087 LOC101902479
11 20.620 – 21.274 rs133774241 20994163 4.318 −2.706 ± 0.665 0.241 0.096 rs137059194 20898669 2.410 −2.467 ± 0.8529 0.458 0.101 LOC783737
11 39.466 - 39.772 rs109315341 39466071 4.126 −2.971 ± 0.749 0.177 0.092 rs133126268 39747182 2.408 −3.706 ± 1.284 0.115 0.094 NA
11 40.896 - 41.299 rs133462686 41298588 4.491 −3.036 ± 0.729 0.182 0.098 rs109834745 40895791 2.414 3.554 ± 1.228 0.139 0.101 LOC101903002
18 4.541 - 4.810 rs109920290 4541123 4.326 2.4 ± 0.589 0.391 0.098 rs110689012 4810082 2.044 3.37 ± 1.29 0.119 0.080 NA
18 37.446 - 37.925 rs41875426 37446338 4.061 2.679 ± 0.682 0.213 0.086 rs137407722 37925382 3.142 4.111 ± 1.213 0.147 0.142 NA
18 53.789 - 54.605 rs41891477 54232476 4.180 −2.302 ± 0.576 0.399 0.091 rs109907036 54028686 3.680 4.065 ± 1.094 0.186 0.168 PRKD2 / PPP5C
18 57.109 - 58.052 rs110801791 57516245 4.675 −3.508 ± 0.824 0.136 0.103 rs41895542 57269152 2.496 3.6 ± 1.219 0.133 0.100 NA
18 61.922 - 62.150 rs133761590 62115202 4.661 2.525 ± 0.594 0.369 0.106 rs137170802 62143810 2.736 −3.018 ± 0.966 0.255 0.116 CACNG6 / VSTM1
22 4.979 - 5.598 rs41996522 5028345 6.076 −2.784 ± 0.564 0.442 0.137 rs41995585 5133660 2.168 −3.028 ± 1.117 0.168 0.086 NA
27 41.873 - 42.109 rs134294374 42079983 5.581 −2.76 ± 0.586 0.367 0.127 rs41586304 41872925 2.295 3.105 ± 1.107 0.176 0.094 NR1D2
27 43.595 - 44.261 rs110746407 43914360 6.075 −2.781 ± 0.564 0.441 0.136   rs43064076 43595406 2.873 −3.831 ± 1.192 0.146 0.123 NA
X 139.211 - 139.509 rs136627433 139508886 4.679 −2.606 ± 0.6098 0.394 0.116   rs110719178 139490243 2.320 −3.327 ± 1.175 0.163 0.101 NA
  1. aBTC: Bos Taurus chromosome
  2. bIntervals containing individually validated SNPs are in bold
  3. c MAF minor allele frequency
  4. d σ 2 a = additive variance; σ 2 p = phenotypic variance