Table 6 The lead SNP and its nearest genes in the multi-trait meta-analysis of milk yield (MY) and mastitis resistance (MR)
Chr | Lead SNP (bp) | rsid | − log10(p) | Nearest gene (distance) | Annotation | Single-trait significanta |
|---|---|---|---|---|---|---|
1 | 62876378 | – | 11.43 | ENSBTAG00000046854 (483,497 bp) | Intergenic | Novel |
2 | 81179721 | rs110121625 | 10.92 | TMEFF2 | Intron | MY |
2 | 96376739 | – | 8.92 | RF00001 (13,015 bp) | Intergenic | Novel |
3 | 47643148 | rs378327566 | 12.42 | PTBP2 (732,492Â bp) | Intergenic | MY |
3 | 91848036 | – | 11.21 | USP24 | Intron | Novel |
4 | 10938389 | rs211526380 | 11.12 | TFPI2 (97,090Â bp) | Intergenic | MR |
4 | 59012300 | rs136891032 | 10.53 | ENSBTAG00000020620 (287,400Â bp) | Intergenic | Novel |
4 | 101547644 | – | 12.03 | CHRM2 (4968 bp) | Upstream | MY |
5 | 31352419 | – | 13.58 | LALBA (2537 bp) | Downstream | MR, MY |
5 | 93953487 | rs210234664 | 28.36 | MGST1 (3325Â bp) | Upstream | MY |
6 | 23474516 | rs109255104 | 16.50 | MANBA | Intron | MR |
6 | 88729872 | rs109803407 | 44.04 | GC | Intron | MR, MY |
7 | 18085661 | rs133896398 | 8.98 | FBN3 (9071Â bp) | Intergenic | Novel |
7 | 41607423 | rs208385619 | 13.33 | ENSBTAG00000039706 (16,819Â bp) | Intergenic | MR, MY |
7 | 65370850 | rs109644389 | 12.99 | GLRA1 (258,214Â bp) | Intergenic | MY |
8 | 25684799 | – | 11.38 | ADAMTSL1 | Intron | MR |
8 | 41148951 | – | 10.90 | ENSBTAG00000014467 (197,503 bp) | Intergenic | MY |
8 | 61253437 | rs43552270 | 10.23 | MELK (22,888Â bp) | Intergenic | Novel |
8 | 73877814 | rs381189656 | 12.11 | ENSBTAG00000010829 (171Â bp) | Upstream | MY |
9 | 86108587 | rs209751747 | 10.90 | SAMD5 (87,968Â bp) | Intergenic | MR |
10 | 2752616 | rs209970861 | 9.26 | YTHDC2 (318,445Â bp) | Intergenic | Novel |
10 | 39050124 | – | 8.56 | ENSBTAG00000004692 (137,772 bp) | Intergenic | Novel |
10 | 49633928 | rs43587750 | 10.44 | RORA | Intron | Novel |
10 | 67479321 | rs109694327 | 12.49 | SAMD4A | Intron | MR |
10 | 74236917 | rs380306966 | 12.27 | SNAPC1 (58,791Â bp) | Intergenic | Novel |
10 | 90272296 | rs381454149 | 9.06 | ADCK1 (137,647Â bp) | Intergenic | Novel |
11 | 13025259 | – | 9.43 | DYSF | Intron | Novel |
11 | 58017848 | rs380589113 | 8.64 | LRRTM4 (415,739Â bp) | Intergenic | Novel |
11 | 88743727 | rs380133715 | 8.53 | ID2 (156,561Â bp) | Intergenic | MR |
12 | 25763482 | rs210185748 | 11.55 | NBEA (29,504Â bp) | Intergenic | Novel |
13 | 21477118 | rs135125951 | 8.87 | RF00026 (80,513Â bp) | Intergenic | Novel |
13 | 36822330 | rs379020207 | 10.39 | MPP7 | Intron | MY |
13 | 46391099 | rs42442665 | 10.13 | ADARB2 | intron | MY |
13 | 62017506 | rs211080099 | 20.20 | PDRG1 (2545Â bp) | Upstream | MR |
13 | 76532010 | rs42057265 | 10.31 | ZMYND8 | Intron | Novel |
14 | 1793616 | rs384957047 | 183.77 | DGAT1 (1735Â bp) | Upstream | MY |
14 | 36478894 | rs43757971 | 9.46 | XKR9 (1379Â bp) | Upstream | Novel |
14 | 61344981 | rs42484846 | 12.22 | ZFPM2 | Intron | MR |
15 | 27475189 | rs208648732 | 18.08 | RF00285 (140,736Â bp) | Intergenic | Novel |
15 | 45384070 | rs43100874 | 19.84 | ENSBTAG00000048176 (4269Â bp) | Upstream | MY |
15 | 84666672 | rs382250433 | 9.54 | MS4A13 (102Â bp) | Upstream | Novel |
16 | 30309951 | rs384258494 | 11.26 | STUM | Intron | MR |
16 | 47836093 | rs207941573 | 11.92 | ACOT7 | Intron | MR |
16 | 59908679 | rs451830006 | 10.94 | BRINP2 (45,408Â bp) | Intergenic | MR |
17 | 66530413 | rs209525123 | 11.00 | CORO1C | Intron | MY |
18 | 13625299 | rs209154036 | 9.53 | ZNF469 (115,323Â bp) | Intergenic | Novel |
18 | 43909571 | rs464881101 | 17.12 | ENSBTAG00000004994 (17,651Â bp) | Intergenic | MR |
18 | 57501622 | – | 10.88 | KLK14 (2325 bp) | upstream | Novel |
19 | 7941510 | rs209798151 | 9.51 | TRIM25 | Intron | Novel |
19 | 27442452 | rs483221509 | 9.52 | bta-mir-497 (689Â bp) | Upstream | MY |
19 | 41169414 | rs134338592 | 16.40 | WIPF2 | Intron | MR |
20 | 10123208 | rs207633790 | 11.45 | GTF2H2 (4035Â bp) | Downstream | MY |
20 | 29996719 | – | 30.18 | MRPS30 (75,496 bp) | Intergenic | MY |
20 | 63369153 | rs133899283 | 10.93 | FAM173B (241,983Â bp) | Intergenic | MY |
22 | 25185357 | rs110721487 | 9.50 | CNTN6 | Intron | Novel |
23 | 11294868 | – | 16.92 | CMTR1 (8638 bp) | Intergenic | MR |
23 | 32139475 | rs477621057 | 12.23 | CARMIL1 | Intron | Novel |
25 | 3655364 | rs379765871 | 11.68 | CDIP1 | Intron | Novel |
25 | 35354412 | rs383829107 | 8.62 | CUX1 | Intron | MR |
26 | 24938054 | rs460832137 | 11.68 | SFR1 (7550Â bp) | Intergenic | MY |
26 | 37716420 | rs381336935 | 11.55 | SHTN1 (26,088Â bp) | Intergenic | MY |
28 | 1921500 | rs383708617 | 8.69 | RF00001 (26,734Â bp) | Intergenic | Novel |
28 | 34972377 | rs137526033 | 16.36 | ZMIZ1 (60,078Â bp) | Intergenic | MY |
29 | 45895253 | rs209161829 | 10.19 | POLD4 (4347Â bp) | Downstream | Novel |