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Table 1 Peak variants for FT-MIR wavenumbers with highly significant protein sequence association effects

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

Chr Position Tag variant ID N of hits Top wvn (cm−1) Iter P-value Protein coding variant ID LD Gene Impact Description
3 7908611 rs137763930 11 940 1 6.7e−20 rs110560331 0.976 FCRLA L c.233-3 T > C
3 7931694 rs211402696 20 1462 2 1.2e−23 rs381714237 0.989 FCGR2B H c.899dupC
3 15411459 rs134900385 6 1022 1 4.3e−19 rs382689947 0.994 FAM189B M c.1237 T > C
3 15411459 rs134900385 6 1022 1 4.3e−19 rs134844772 0.990 GBA M c.1080C > A
3 15411459 rs134900385 6 1022 1 4.3 e−19 rs132659643 0.999 HCN3 M c.1699A > G
3 15411459 rs134900385 6 1022 1 4.3e−19 rs109330809 0.990 MTX1 L c.508-6 T > C
3 15517871 rs109328483 6 1007 1 4.4e−19 rs136761456 0.992 SCAMP3 M c.151G > C
3 15517871 rs109328483 6 1007 1 4.4e−19 rs43706482 0.994 THBS3 L c.2075-3 T > C
3 15550598 rs380597285 327 1462 0 1.3e−54 rs109816684 0.994 SLC50A1 L c.282 + 7G > A
5 75729880 rs384734208 50 1466 1 5.0e−47 rs207628090 0.930 CSF2RB M c.41 T > C
5 75758989 rs210094995 2 1447 0 5.8e−40 rs210937722 0.926 NCF4 M c.841G > C
5 118246868 rs136859160 308 1261 0 3.0e−44 rs456403270 0.937 TBC1D22A M c.1063C > T
6 38027010 rs43702337 455 1119 0 7.3e−948 rs43702337 1 ABCG2 M c.1742A > C
6 87181619 rs43703011 17 3633 2 2.5e−22 rs43703011 1 CSN2 M c.245C > A
6 87274397 rs378808772 3 1283 2 9.9e−51 rs43703010 0.974 CSN1S1 M c.620A > G
6 87390576 rs43703015 18 1473 1 4.0e−108 rs43703015 1 CSN3 M c.470 T > C
11 103304757 rs109625649 329 1593 0 1.2e−134 rs109625649 1 PAEP M c.401 T > C
11 104242578 rs207688357 11 1462 0 5.5e−33 rs207688357 1 ABO H c.233 + 1G > C
12 69612955 rs383509255 132 1716 0 6.4e−45 rs208744187 0.950 TGDS M c.204A > C
14 1726650 rs133611586 6 3514 1 1.6e−75   0.992 WDR97 L c.2656-5_2656-4insG
14 1732043 rs437406031 384 2846 1 6.3e−42 rs450710918 0.990 ENS..39978 M c.352G > A
14 1732043 rs437406031 384 2846 1 6.3e−42 rs476736066 0.997 MROH1 M c.3549G > C
14 1755742 rs384226556 5 2656 0 4.0e−20 rs209542297 0.9998 CPSF1 L c.4287 T > C
14 1802265 rs109234250 310 1716 0 1.5e−2607 rs109234250 1 DGAT1 M c.694G > A
14 1802265 rs109234250 310 1716 0 1.5e−2607 rs134364612 0.999 SLC52A2 M c.724A > G
14 66328304 rs446084949 19 1029 1 2.7e−20 rs446084949 1 SPAG1 M c.2044G > A
15 28347165 rs210034037 5 1537 0 7.7e−35 rs208325660 0.999 RNF214 M c.314G > A
15 53940444 rs382926661 23 1205 1 4.2e−19 rs380220394 0.993 DNAJB13 L c.69-4 T > C
16 24977696 rs111027377 62 2742 2 4.8e−25 rs109896036 0.988 MTARC1 L c.628-5C > T
16 24977696 rs111027377 62 2742 2 4.8e−25 rs110899826 0.988 MTARC1 M c.581C > G
19 42428366 rs209808022 4 1250 1 3.1e−25 rs209302038 0.991 KRT9 M c.196C > T
19 42488389 rs379667889 8 1447 0 7.8e−34 rs209756857 0.969 KRT42 L c.57 + 7C > T
19 42488389 rs379667889 8 1447 0 7.8e−34 rs383013355 0.963 KRT16 M c.896A > G
19 42488389 rs379667889 8 1447 0 7.8e−34 rs208923483 0.966 KRT17 M c.146G > C
19 42488389 rs379667889 8 1447 0 7.8e−34 rs385937063 0.966 KRT17 L c.1233C > T
19 43036265 rs210324533 11 1029 1 5.3e−43 rs207799702 0.944 KAT2A L c.700-7C > G
19 43036265 rs210324533 11 1029 1 5.3e−43 rs209410283 0.945 KCNH4 M c.408C > G
19 43036265 rs210324533 11 1029 1 5.3e−43 rs377779402 0.945 KCNH4 H c.2663 + 2 T > C
19 43053995 rs481837688 24 1212 1 6.6e−26 rs481837688 1 STAT5A M c.2305C > A
19 51303887 rs41921224 65 1499 0 1.9e−35 rs41921160 0.993 CCDC57 M c.1907 T > C
19 57087981 rs41920620 6 1216 0 1.8e−21 rs469721022 0.999 HID1 L c.1147-7G > C
28 6559147 rs133101552 3 1261 0 8.6e−23 rs133101552 1 KCNK1 M c.934C > A
29 41821270 rs207854419 14 1257 1 4.6e−30 rs384900272 0.998 NXF1 M c.1555G > A
  1. Peak variants and association effects for FT-MIR wavenumbers classified as highly significant. Highly significant effects are classified such that: the –log10(p-value) for the effect was greater than 1.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.975, 1]; or the –log10(p-value) for the effect was greater than 2 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.95, 0.975]; or the –log10(p-value) for the effect was greater than 2.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.925, 0.95]. Bonferroni threshold: –log10(6.2e–13). N of hits: number of wavenumbers for which the variant was selected as the representative (most significant) tag variant for a peak. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. L Low impact splice region variant, M  Moderate impact missense variant, H High impact splice donor
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Genetics Selection Evolution

ISSN: 1297-9686