You are viewing the site in preview mode

Skip to main content

Table 3 Peak variants for FT-MIR wavenumbers with co-localized eQTL

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

Chr Position Tag variant ID Iter Top wvn (cm−1) N of hits P-value Gene Top eQTL variant ID Top eQTL variant p-value LD Pearson Pearson window (Mb)
1 5120248 rs42317521 2 2794 55 4.0e−18 CLDN8 rs42317521 4.3e−17 1 0.764 0.5
1 144377960 rs208161466 0 2592 22 2.3e−85 SLC37A1 rs208161466 4.1e−15 1 0.710 1.0
1 146481250 rs383691757 1 1071 1 4.7e−15 CSTB rs210595016 1.4e−52 0.992 0.938 0.5
1 154125158 rs207836083 0 1130 142 3.6e−68 SH3BP5 rs207836083 2.6e−32 1 0.816 0.5
3 15411459 rs134900385 1 1022 6 4.3e−19 KRTCAP2 rs133285846 9.7e−09 0.996 0.938 1.0
3 15550598 rs380597285 0 1462 325 1.3e−54 SLC50A1 rs380597285 8.7e−16 1 0.854 0.5
3 34387618 rs109030498 1 1466 157 3.5e−25 ELAPOR1 rs109030498 3.2e−30 1 0.817 0.5
3 53755929 rs209271975 1 1089 15 8.6e−22 LRRC8C rs466686834 3.5e−39 0.99 0.927 0.5
5 75729880 rs384734208 1 1466 44 5.0e−47 CSF2RB rs210641868 9.2e−27 0.926 0.752 1.0
5 75732526 rs210305241 1 1458 5 4.4e−42 NCF4 rs209273109 9.3e−16 0.91 0.813 1.0
5 93945738 rs211210569 0 1171 544 1.8e−131 MGST1 rs209372883 3.2e−43 0.919 0.925 1.0
6 46568418 rs210515595 3 1772 5 7.7e−22 SLC34A2 rs110805476 2.5e−07 0.979 0.805 0.5
6 87388064 rs379473589 1 1436 17 1.1e−97 CSN3 rs208009847 9.9e−33 0.963 0.878 0.5
9 21637056 rs209222932 0 1003 33 9.4e−20 YRMY5A rs209222932 2.8e−36 1 0.634 0.5
9 26534109 rs208123385 0 1462 36 1.9e−24 RNF217 rs208173647 1.3e−16 0.986 0.856 0.5
9 87585031 rs110986237 1 1470 6 7.4e−15 TAB2 rs110986237 9.5e−12 1 0.851 0.5
9 102874726 rs137238900 0 1768 1 1.0e−14 MPC1 rs134094426 6.9e−15 0.969 0.849 0.5
10 46581015 rs109326466 0 1246 15 2.0e−46 USP3 rs109326466 2.0e−31 1 0.961 0.5
11 14180010 rs110527112 1 2760 23 3.6e−29 XDH rs207554031 8.8e−26 0.978 0.709 0.5
11 78868975   1 1112 10 1.2e−19 LAPTM4A rs110552157 1.3e−40 0.998 0.920 0.5
11 103292402 rs383398415 0 2548 1 3.5e−56 PAEP rs109333988 1.2e−29 0.933 0.956 0.5
11 104229609 rs110534892 0 3648 10 1.2e−21 ABO rs109750996 3.9e−28 0.944 0.803 0.5
14 1754287 rs135443540 0 1085 3 1.6e−39 DGAT1 rs137202508 8.9e−42 0.905 0.944 0.5
15 57266467 rs136337092 0 3935 1 2.7e−13 CAPN5 rs136208815 9.3e−46 0.997 0.940 0.5
16 66314547 rs42579412 2 1425 1 1.0e−15 RGL1 rs42579412 6.3e−14 1 0.727 0.5
16 67730371 rs380453838 1 1757 125 3.8e−21 IVNS1ABP rs380453838 4.5e−27 1 0.876 0.5
18 2203322 rs132899112 1 1466 7 1.4e−15 FA2H rs137235970 1.9e−27 0.998 0.875 0.5
19 33517487 rs434248431 0 1100 23 2.9e−46 PMP22 rs434248431 8.6e−38 1 0.832 0.5
19 43036265 rs210324533 1 1029 11 5.3e−43 GHDC rs381442991 1.8e−22 0.945 0.975 0.5
19 57079881 rs381175117 2 1220 9 2.0e−23 HID1 rs109407913 1.2e−32 0.936 0.803 0.5
19 61134515 rs41923843 0 1130 45 3.2e−46 KCNJ2 rs41923843 1.7e−26 1 0.882 0.5
20 58454531 rs135636613 0 1391 23 4.3e−441 ANKH rs135636613 2.4e−16 1 0.860 0.5
22 53519865 rs109233889 0 1235 7 5.3e−15 LTF rs109233889 1.3e−32 1 0.813 0.5
24 58817202 rs208779762 0 1220 23 6.8e−34 LMAN1 rs207893260 1.3e−27 0.958 0.713 1.0
27 36211708 rs209855549 0 1731 157 6.2e−188 GPAT4 rs209855549 3.7e−21 1 0.848 0.5
27 41267242 rs109068627 1 2977 23 3.5e−26 THRB rs109068627 1.7e−22 1 0.704 0.5
29 9546217 rs380868305 0 1130 8 4.6e−186 PICALM rs380868305 2.4e−54 1 0.831 0.5
29 44579245 rs439384463 2 1548 3 4.3e−16 MUS81   3.0e−21 0.924 0.913 0.5
  1. Peak variants for FT-MIR wavenumbers 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. N of hits: number of wavenumbers for which the variant was selected as the representative (most significant) tag variant for a peak
Back to article page

Genetics Selection Evolution

ISSN: 1297-9686