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Table 4 Peak variants for composite milk production traits with co-localized eQTL

From: Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Trait Chr Position Tag variant ID Iteration P-value Gene Top eQTL variant ID Top eQTL variant p-value LD Pearson Pearson window (Mbp)
FP 3 34387618 rs109030498 2 6.0e−13 ELAPOR1 rs109030498 3.2e−30 1 0.832 0.5
FP 5 75698283 rs385866519 1 4.0e−19 CSF2RB rs210641868 9.2e−27 0.910 0.701 1
FP 5 93945738 rs211210569 0 6.7e−106 MGST1 rs209372883 3.2e−43 0.919 0.928 1
FP 10 46483019 rs133089336 0 4.5e−13 USP3 rs208181306 2.0e−31 0.909 0.905 0.5
FP 11 104229609 rs110534892 1 2.6e−14 ABO rs109750996 3.9e−28 0.944 0.727 1
FP 16 67730371 rs380453838 1 2.6e−19 IVNS1ABP rs380453838 4.5e−27 1 0.886 0.5
FP 27 36211708 rs209855549 0 9.7e−132 GPAT4 rs209855549 3.7e−21 1 0.819 0.5
LP 1 154122887 rs42167460 0 1.2e−50 SH3BP5 rs380642859 2.6e−32 0.999 0.859 0.5
LP 3 15433518 rs109749506 1 1.3e−20 KRTCAP2 rs133285846 9.7e−09 0.995 0.940 1
LP 3 15545091 rs379353107 0 2.2e−42 SLC50A1 rs379353107 8.7e−16 1 0.806 0.5
LP 3 53994057 rs211488591 2 6.7e−18 LRRC8C rs466686834 3.5e−39 0.986 0.753 1
LP 19 43036265 rs210324533 3 9.4e−40 GHDC rs381442991 1.8e−22 0.945 0.963 0.5
LP 19 61134515 rs41923843 1 1.1e−46 KCNJ2 rs41923843 1.7e−26 1 0.857 0.5
LP 20 58448763 rs134813825 0 3.2e−18 ANKH rs134813825 2.4e−16 1 0.809 0.5
LP 27 36204066 rs208306200 0 1.9e−21 GPAT4 rs208306200 3.7e−21 1 0.767 0.5
LP 29 9577372 rs380473328 0 2.1e−140 PICALM rs384691767 2.4e−54 0.996 0.845 0.5
PP 3 15520971 rs109098377 2 7.5e−16 KRTCAP2 rs133285846 9.7e−09 0.989 0.928 0.5
PP 3 15550598 rs380597285 0 1.7e−37 SLC50A1 rs380597285 8.7e−16 1 0.832 0.5
PP 5 75680825 rs208925020 4 8.5e−23 CSF2RB rs210641868 9.2e−27 0.947 0.871 1
PP 5 93945738 rs211210569 1 3.7e−42 MGST1 rs209372883 3.2e−43 0.919 0.817 0.5
PP 6 87387870 rs382652853 2 2.9e−45 CSN3 rs208009847 9.9e−33 0.963 0.891 0.5
PP 10 46581015 rs109326466 0 4.0e−38 USP3 rs109326466 2.0e−31 1 0.961 0.5
PP 18 2203,325 rs135350753 0 2.1e−13 FA2H rs137235970 1.9e−27 0.997 0.831 0.5
PP 19 43035006 rs209494359 0 1.6e−40 GHDC rs381442991 1.8e−22 0.945 0.976 0.5
PP 24 58817202 rs208779762 0 5.7e−26 LMAN1 rs207893260 1.3e−27 0.958 0.737 0.5
  1. Peak variants for composite milk production traits with a co-localized eQTL. Co-localized eQTL are defined such that: the Pearson correlation between the –log10(p-values) of the trait QTL and the –log10(p-values) of the eQTL is higher than 0.7; and the LD between the tag variant for the trait QTL and the top eQTL variant is higher than 0.9. The Pearson correlation shown is the highest from two different size windows (0.5 Mbp and 1 Mbp), centred on the top tag variant. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. FP Fat %, LP  Lactose %, PP Protein %
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Genetics Selection Evolution

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