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. 2019 Jul 1;51:34. doi: 10.1186/s12711-019-0473-7

Table 2.

The 59 QTL regions identified by GWAS, the most likely candidate variant, and number of traits affected by the QTL

QTL region Best candidate varianta Number of traitsd
N BTA From (bp) To (bp) # variants #genes bp Variant ID Rank R2 MAF Effect SE − log10P Gene Functional annotation Trait most strongly affected CMP Proteins Fatty acids Minerals
1 1 144,389,419 144,398,814 6 1 144,395,375 rs136069703 1 0.97 0.38 29.5 0.951 210.4 SLC37A1 Intron P 3 1 1 4
2 2 5,718,384 6,567,522 111 5 5,865,070 rs136830094 1 0.91 0.22 − 0.02 0.003 15.6 INPP1 Downstream Lactose 0 1 0 2
3 2 131,808,301 131,888,417 88 1 131,816,616 rs133677653 1 0.91 0.49 − 0.05 0.003 41.4 ALPL Intron κ-CN 1 3 0 1
4 3 7,442,755 8,149,715 56 5 7,935,102 rs383033753 7 0.50 0.14 − 0.65 0.096 10.7 FCGR2B Intron CYDM 2 0 1 0
5 3 15,514,034 15,928,379 401 7 15,525,599 rs110073735 1 0.99 0.03 − 2.78 0.410 10.9 EFNA1 Intron Lactose 1 0 0 3
6 3 34,235,208 34,355,357 35 4 34,327,146 rs210558120 1 0.34 0.43 0.26 0.035 12.9 KIAA1324 Intron aSC 2 0 0 0
7 4 49,033,707 49,153,995 39 2 49,033,707 rs380575157 1 0.47 0.20 0.02 0.001 30.7 CBLL1 Upstream pH0_PCC 2 3 0 2
8 4 75,743,094 79,803,738 59 5 77,825,429 rs385069094 1 0.57 0.01 − 2.34 0.360 10.1 GCK Intron Mg 0 1 0 3
9 4 92,588,016 92,966,245 227 7 92,624,543 rs379514460 1 0.34 0.03 − 29.0 4.226 11.2 FSCN3 Upstream Ca 0 0 0 1
10 5 29,947,476 31,423,430 315 25 29,947,476 rs442522314 2 0.63 0.09 − 2.26 0.383 8.4 COX14 Downstream Lactose 0 0 0 1
11 5 93,892,583 93,945,738 9 1 93,943,700 rs210744452 1 0.77 0.05 0.11 0.010 27.7 MGST1 Intron FC 2 0 7 0
12 5 117,126,900 119,221,867 51 3 117,972,265 rs525880746 1 0.79 0.04 42.4 2.186 83.0 GRAMD4 Upstream Ca 7 4 1 6
13 6 37,857,989 38,326,250 268 8 38,326,250 rs382477515 1 0.37 0.42 − 0.10 0.017 9.5 IBSP Upstream β-CN 0 1 0 0
14 6 46,555,489 47,082,793 89 3 46,876,802 rs110408618 1 1.00 0.17 27.8 1.189 120.5 SEL1L3 Intron K 4 5 1 4
15 6 87,125,482 87,961,577 143 7 87,392,899 rs382350292 3 0.53 0.23 0.03 0.002 76.4 CSN3 Downstream K10/RSC 8 8 0 1
16 6 108,967,622 109,145,154 91 5 109,026,822 rs208213463 1 0.93 0.47 − 8.42 0.904 19.9 GAK Intron Ca 2 2 0 2
17 7 958,741 1,146,962 359 4 975,515 rs383246531 1 0.93 0.37 − 1.56 0.180 17.4 47695b Intron Lactose 0 0 0 2
18 7 41,576,519 46,646,915 399 23 46,452,656 rs209828204 6 0.87 0.07 1.36 0.127 26.0 FSTL4 Downstream aPCC 2 2 0 1
19 9 102,731,669 103,130,410 207 3 102,885,120 rs134445867 15 0.90 0.03 − 0.14 0.023 9.3 MPC1 Intron C4_C10 0 0 1 0
20 10 1,984,741 2,326,212 86 1 2,096,282 rs385793060 67 0.99 0.35 − 2.04 0.380 7.1 47622b Upstream Na 0 0 0 1
21 10 48,359,318 50,266,445 213 1 49,459,919 rs109896326 1 1.00 0.14 0.30 0.046 9.8 RORA Intron UNSAT 0 0 4 0
22 10 99,714,774 99,843,583 20 0 99,714,774 rs440530756 1 0.22 0.02 − 0.18 0.028 9.8 – Intergenic PUNSAT 0 0 2 0
23 11 9,023,594 9,684,851 11 3 9,684,851 rs384459785 8 0.62 0.07 − 2.82 0.385 12.6 POLE4 Intron CYFAT-PROT 3 0 3 0
24 11 14,152,677 15,493,112 132 6 14,284,886 rs384594145 48 0.90 0.10 − 0.01 0.001 18.7 XDH Upstream pH0_PCC 1 0 0 1
25 11 86,907,041 86,916,295 9 1 86,912,990 rs481567394 1 0.21 0.05 0.02 0.003 16.7 ATP6V1C2 Intron pH0_PCC 1 0 0 0
26 11 103,273,963 103,322,890 214 4 103,301,982 rs109907194 48 0.89 0.46 − 1.09 0.017 559.7 PAEP Intron ΣWP 8 7 2 3
27 12 68,616,690 77,578,414 337 7 70,162,028 rs721489054 22 0.83 0.17 0.22 0.019 29.0 ABCC4 Intron C14:0 0 0 7 2
28 13 20,094,707 22,437,171 291 4 21,053,894 rs378591536 7 0.34 0.07 − 0.24 0.034 12.1 23216b Intron C14:0 0 0 1 0
29 13 45,394,264 48,611,254 75 4 46,734,011 rs379821485 18 0.76 0.15 − 0.01 0.001 10.6 RF0026 Downstream pH0_PCC 1 0 1 0
30 13 52,289,279 55,114,121 80 9 54,938,610 rs110422533 2 1.00 0.39 − 6.60 1.007 10.3 GID8 Synonymous K 0 0 2 1
31 13 64,648,620 64,870,118 19 3 64,812,464 rs43717459 1 0.33 0.10 − 0.24 0.027 18.9 ACSS2 Intron C4–C10 0 0 1 0
32 13 79,225,285 79,326,265 6 1 79,326,265 rs109862148 3 0.38 0.07 − 0.04 0.007 8.9 FAM65C Downstream αs2-CN 0 1 0 0
33 14 1,622,956 1,881,116 27 9 1,629,753 rs109035586 1 0.36 0.33 0.17 0.007 122.7 GPT Upstream FC 6 6 10 4
34 15 39,854,757 40,283,508 140 2 39,885,845 rs134953698 2 0.79 0.18 − 0.04 0.005 10.4 ARNTL Intron PUNSAT 0 0 1 0
35 15 52,993,384 54,612,060 341 10 53,943,342 rs381948106 1 0.47 0.04 17.5 2.747 9.7 RAB6A Intron P 0 0 2 2
36 16 1,607,369 3,050,452 10 0 1,609,129 rs42450079 1 0.54 0.28 − 0.04 0.005 17.0 – Intergenic κ-CN 2 6 0 0
37 16 60,539,357 63,891,341 178 3 60,646,127 rs137615589 72 0.75 0.14 0.02 0.004 9.8 38238b Upstream aSC 2 1 0 0
38 16 67,700,538 67,811,269 167 2 67,758,163 rs42465711 1 1.00 0.4 0.31 0.044 11.9 SWT1 Intron CYDM 2 1 2 1
39 16 70,170,086 71,493,899 59 1 71,432,479 rs109766366 5 0.79 0.43 − 0.23 0.032 12.3 PROX1 Intron UNSAT 0 0 4 2
40 17 29,348,215 30,211,790 203 9 29,938,428 rs207509104 21 0.55 0.36 0.10 0.015 10.3 LARP1B Synonymous C4–C10 0 0 1 0
41 17 52,753,338 53,240,467 283 6 53,072,959 rs448501071 5 1.00 0.06 − 0.32 0.019 62.4 BRI3BP Intron C4–C10 2 3 2 1
42 18 10,566,605 11,091,131 68 5 11,002,789 rs41867427 2 0.61 0.06 14.3 2.071 11.3 CRISPLD2 Intron aSC 2 0 0 1
43 19 51,304,834 51,538,272 67 2 51,383,847 rs136067046 1 0.83 0.32 0.20 0.013 49.4 FASN Upstream C14:0 0 0 9 0
44 19 55,229,384 57,240,571 267 10 57,151,350 rs42848485 1 0.63 0.46 9.07 1.079 16.4 FADS6 Intron Ca 2 1 1 1
45 19 60,407,923 62,177,206 142 0 61,135,270 rs41923848 1 0.91 0.13 − 2.28 0.210 26.6 – Intergenic Lactose 0 3 0 3
46 20 58,245,970 58,457,768 87 1 58,446,058 rs137085630 22 0.99 0.06 − 1.01 0.036 176.5 ANKH Intron Citrate 5 4 2 5
47 21 40,120,343 44,138,058 63 2 41,638,428 rs137153434 25 0.21 0.12 0.07 0.009 12.7 G2E3 Upstream PC 3 1 0 1
48 22 32,877,755 33,466,544 46 2 32,877,755 rs208141216 10 0.30 0.08 0.08 0.007 25.7 FAM19A4 Intron PC 8 1 1 2
49 22 55,186,094 55,273,619 72 1 55,254,221 rs43597796 1 0.93 0.49 0.00 0.001 12.6 ATP2B2 Intron pH0_PCC 1 1 0 0
50 22 61,257,725 61,312,492 18 1 61,284,069 rs109001472 1 1.00 0.47 − 0.09 0.008 28.3 KLF15 Intron C4–C10 0 0 2 0
51 24 50,420,365 50,550,020 114 2 50,465,348 rs383068825 4 0.53 0.34 − 10.7 1.282 16.0 SKA1 Downstream K 1 1 0 2
52 24 58,744,952 58,825,217 23 3 58,817,202 rs208779762 1 0.93 0.43 − 6.57 0.807 15.4 LMAN1 Upstream P 1 1 0 1
53 25 2,994,081 3,261,509 28 3 3,241,838 rs137696417 16 0.61 0.18 − 0.03 0.007 6.5 ADCY9 Downstream κ-CN 0 1 0 0
54 25 25,642,563 29,605,418 82 11 26,498,356 rs137150057 1 1.00 0.34 − 0.11 0.020 11.3 FAM57B 5′UTR C18:0 1 1 6 0
55 26 20,727,700 21,427,109 61 4 21149234 rs136334180 11 1.00 0.31 0.39 0.035 27.6 SCD Upstream UNSAT 0 0 11 0
56 26 32,773,808 33,925,908 95 2 33,233,277 rs385554497 36 0.27 0.02 1.55 0.270 8.1 ACSL5 intron aPCC 1 0 0 0
57 27 36,165,492 36,235,730 11 1 36,212,352 rs208675276 1 0.54 0.41 0.65 0.040 60.4 GPAT4c 5′ UTR C16:0 3 0 7 1
58 28 6,008,464 7,038,810 141 3 6,027,037 rs382911338 1 0.37 0.18 − 0.01 0.001 17.1 PCNX2 Intron pH0_PCC 1 2 0 1
59 29 9,253,006 9,622,389 145 3 9,343,362 rs133715120 6 0.61 0.33 − 2.76 0.264 24.9 EED Intron Lactose 0 3 1 4

aWhen a gene was present in the confidence interval of the QTL, the best candidate variant was the genic variant with the most significant effects (intergenic variants were discarded)

b47695, 47622, 23216, and 38238 for ENSBTAG00000047695, ENSBTAG00000047622, ENSBTAG00000023216, and ENSBTAG00000038238, respectively

cAlso named AGPAT6

dNumber of milk cheese-making (CMP), protein, fatty acid, and mineral composition traits with significant effects