Table 1 Top variants at 25 QTL for fat and protein percentages in milk
QTL | Top variant | Fat percentage | Protein percentage | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Chr | Position | NCBI rs-ID | Alternate allele | Candidate gene(s) | Allele substitution effect (±standard error) | Effect direction (and evidence of heterogeneity) across three populationsa | P meta | Allele substitution effect (±standard error) | Effect direction (and evidence of heterogeneity) across three populationsa | P meta | |
1c | 1 | 144,441,562 | rs136426342 | G | SLC37A1 | −0.05 (±0.015) | --- (0.44) | 1.2e-03 | −0.09 (±0.016) | --- (0.37) | 8.5e-09 |
2 | 3 | 15,540,709 | rs207616487 | C |  | −0.19 (±0.038) | ?-- (0.11) | 5.6e-07 | −0.49 (±0.05) | --- (0.26) | 3.0e-22 |
3 | 3 | 34,387,618 | rs109030498 | T |  | 0.06 (±0.014) | +++ (0.18) | 9.1e-05 | 0.14 (±0.016) | +++ (0.88) | 1.1e-17 |
4c | 4 | 56,528,040 | rs381550282 | A |  | 0.08 (±0.022) | +++ (0.61) | 2.0e-04 | 0.15 (±0.024) | +++ (0.74) | 2.5e-10 |
5c | 5 | 75,656,328 | rs210334611 | T | TST | −0.11 (±0.019) | --- (0.27) | 6.1e-09 | −0.15 (±0.021) | --- (0.48) | 6.2e-13 |
6 | 5 | 93,948,357 | rs209372883 | C | MGST1 | −0.34 (±0.016) | --- (1.1e-3) | 9.8e-100 | −0.17 (±0.018) | --- (0.23) | 6.3e-21 |
7 | 5 | 118,100,512 | rs384440535 | T | TBC1D22A | −0.07 (±0.015) | + − - (0.09) | 1.1e-05 | −0.12 (±0.017) | --- (0.28) | 3.0e-12 |
8 | 6 | 38,027,010 | rs43702337 | C | ABCG2 | −0.66 (±0.075) | ??- (1) | 1.1e-18 | −1.13 (±0.093) | ??- (1) | 4.3e-34 |
9 | 6 | 87,154,594 | rs109193501 | G | CSN1S1 | 0.10 (±0.016) | +++ (1.5e-4) | 4.1e-10 | 0.30 (±0.018) | +++ (9.1e-3) | 4.9e-68 |
10 | 10 | 46,550,543 | rs208077205 | A |  | 0.15 (±0.023) | +++ (0.68) | 3.7e-10 | 0.22 (±0.025) | +++ (0.51) | 8.2e-18 |
11 | 11 | 103,296,192 | rs381989107 | C | PAEP | −0.14 (±0.013) | --- (1.0e-3) | 6.1e-27 | −0.05 (±0.014) | --- (0.43) | 6.8e-04 |
12b | 14 | 1,802,266 | rs109326954 | A | DGAT1 | 1.58 (±0.02) | −++ (1.9e-12) | 8.4e-1436 | 0.91 (±0.024) | −++ (2.3e-5) | 1.9e-308 |
|  |  | 1,800,399 | rs208317364 | A |  | 1.59 (±0.02) | −++ (2.8e-14) | 1.2e-1437 | 0.91 (±0.024) | −++ (6.2e-6) | 1.1e-308 |
13 | 14 | 66,871,289 | rs439256148 | C |  | −0.29 (±0.037) | + − - (0.25) | 4.4e-15 | −0.51 (±0.048) | --- (0.50) | 1.6e-26 |
14 | 15 | 53,938,718 | rs386031410 | A |  | −0.17 (±0.034) | + − - (0.25) | 8.1e-07 | −0.31 (±0.037) | + − - (0.43) | 6.3e-17 |
15c | 15 | 74,830,325 | rs42364320 | T |  | −0.09 (±0.014) | --- (0.92) | 2.1e-10 | −0.02 (±0.016) | + − - (0.68) | 0.13 |
16 | 16 | 1,607,723 | rs382661583 | T |  | −0.19 (±0.022) | --- (0.33) | 1.3e-17 | −0.31 (±0.024) | --- (0.27) | 1.6e-38 |
17c | 16 | 67,735,669 | rs385934483 | A |  | −0.1 (±0.013) | --- (0.28) | 1.9e-13 | −0.07 (±0.015) | --- (0.09) | 5.8e-06 |
18 | 19 | 51,386,735 | rs137372738 | T | FASN | −0.11 (±0.013) | --- (0.22) | 5.9e-16 | 0.01 (±0.014) | +++ (0.96) | 0.72 |
19 | 20 | 31,909,478 | rs385640152 | T | GHR | −0.39 (±0.028) | --- (4.1e-4) | 2.9e-45 | −0.56 (±0.031) | --- (0.19) | 1.6e-74 |
20 | 24 | 58,811,405 | rs380879212 | A | LMAN1 | 0.07 (±0.016) | +++ (0.59) | 4.5e-05 | 0.14 (±0.017) | +++ (0.91) | 1.9e-15 |
21 | 25 | 27,926,446 | rs801168123 | A |  | 0.27 (±0.09) | ?++ (0.44) | 2.6e-03 | 0.55 (±0.093) | ?++ (0.45) | 4.5e-09 |
22 | 27 | 36,221,754 | rs208624037 | G | AGPAT6 | −0.12 (±0.015) | --- (0.002) | 6.1e-16 | −0.03 (±0.016) | --- (0.39) | 0.11 |
23 | 28 | 35,868,970 | NA | A | MBL1 | 0.17 (±0.054) | ? +? (1) | 1.7e-03 | 0.42 (±0.056) | ? +? (P = 1) | 7.1e-14 |
24c | 29 | 9,576,277 | rs384716744 | T |  | 0.06 (±0.015) | +++ (0.07) | 6.1e-05 | 0.14 (±0.016) | +++ (0.01) | 1.1e-16 |
25 | 29 | 41,836,992 | rs471090482 | G |  | −0.16 (±0.04) | ??- (1) | 5.8e-05 | −0.35 (±0.045) | ??- (1) | 6.6e-15 |