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. 2016 Aug 10;6:31109. doi: 10.1038/srep31109

Table 3. Commonly significantly associated variants (minor allele frequency [MAF] ≥10%) with milk component traits.

Trait Marker Chr Position RS# or SS# Classification Gene Minor/Major Allele P-Value1 P-Value1 BH FDR Proportion Variance Explained MAF2
Associations with additive and dominant (grey highlight) models
 TD Fat% S14_3590983 14 3590983 rs381816253 Intergenic — G/C 1.86E-05 (2.61E-05) 0.063 (0.077) 0.0228 0.381
  S14_3590986 14 3590986 rs207862021 Intergenic — T/G 1.86E-05 (2.61E-05) 0.063 (0.077) 0.0228 0.381
  S14_1092614 14 1092614 ss1850031881 Intergenic — A/G 5.09E-08 (1.68E-07) 0.0005 (0.001) 0.0367 0.374
  S14_714785 14 714785 ss1850173791 Intergenic — A/G 9.64E-09 (6.43E-09) 0.0001 (7.94E-05) 0.0406 0.315
  S14_714848 14 714848 rs207501095 Intergenic — G/A 6.83E-11(3.50E-10) 1.26E-06(5.19E-06) 0.0522 0.308
  S14_705269 14 705269 rs210465271 Intergenic — C/T 2.10E-07(6.76E-07) 0.002(0.005) 0.0334 0.305
  S14_707436 14 707436 rs436930795 Intergenic — G/A 2.17E-06(1.43E-06) 0.012(0.009) 0.0279 0.289
  S14_707458 14 707458 rs470862327 Intergenic — C/T 2.17E-06(1.43E-06) 0.012(0.009) 0.0279 0.289
  S14_1074199 14 1074199 rs210334336 Intergenic — T/G 2.09E-13(1.53E-11) 1.38E-08(3.77E-07) 0.0657 0.288
  S14_3449027 14 3449027 rs133123595 Intergenic — G/A 1.14E-06(2.79E-06) 0.008(0.015) 0.0294 0.280
  S14_392338 14 392338 rs209328075 Intergenic — T/C 3.72E-13(6.99E-12) 1.38E-08(2.59E-07) 0.0644 0.276
  S14_271158 14 271158 rs132685115 Intronic TONSL T/C 1.19E-09(3.54E-08) 1.47E-05(0.0004) 0.0455 0.2706
  S14_3016578 14 3016578 rs110049376 Intergenic — G/A 2.00E-05(6.39E-06) 0.064(0.032) 0.0227 0.271
  S14_215462 14 215462 ss1850067837 Intronic PPP1R16A A/G 4.14E-06(2.58E-06) 0.019(0.015) 0.0264 0.262
  S14_412791 14 412791 rs135576599 Intronic ADCK5 G/A 1.23E-12(1.54E-14) 3.03E-08(1.14E-09) 0.0616 0.259
  S14_277266 14 277266 rs135581384 Intronic TONSL G/A 2.40E-10(2.70E-11) 3.55E-06(5E-07) 0.0493 0.257
 SCC S17_74300124 17 74300124 rs445429081 Intergenic — C/A 8.53E-06(1.94E-05) 0.019(0.027) 0.0247 0.153
  S16_51178060 16 51178060 ss1850171506 Intergenic — T/C 0.0001(2.32E-05) 0.096(0.029) 0.0185 0.127
  S18_839623 18 839623 ss1850186311 Intergenic — T/G 3.689E-06(7.64E-05) 0.012(0.067) 0.0267 0.123
Associations with additive model
 TD Fat% S14_1028006 14 1028006 rs109714772 Intergenic — G/A 5.078E-06 0.021 0.0259 0.383
  S14_1092930 14 1092930 NA Intergenic — C/T 3.038E-06 0.016 0.0271 0.370
  S20_38406577 20 38406577 rs466001634 Intergenic — G/A 2.938E-05 0.083 0.0218 0.216
TD Protein% S4_114780512 4 114780512 rs384880089 Intergenic — C/T 5.13E-05 0.090 0.0205 0.109
SCC S26_45210692 26 45210692 rs136238567 Intergenic — A/G 9.674E-05 0.083 0.019 0.340
305Fat Yield S14_749654 14 749654 rs110892754 Intergenic — T/C 9.441E-07 0.070 0.0319 0.287
 Associations with dominant model
 TD Fat S14_2513747 14 2513747 rs207542860 Intronic TRAPPC9 T/C 7.079E-06 0.033 0.025 0.335
  S14_1666599 14 1666599 rs207822284 Intergenic — T/C 3.977E-05 0.095 0.021 0.294
  S29_9009252 29 9009252 ss1850314769 Intergenic — C/T 1.782E-05 0.063 0.023 0.370
  S17_48121597 17 48121597 rs109745026 Intergenic — A/G 1.247E-05 0.054 0.024 0.195
 TD Milk Yield S29_9009252 29 9009252 ss1850314769 Intergenic — C/T 1.239E-06 0.092 0.0292 0.370
 SCC S1_47873063 1 47873063 rs210530502 Intergenic — A/G 9.732E-05 0.076 0.019 0.498
  S4_117466216 4 117466216 rs211180730 Intronic CHPF2 T/C 5.837E-05 0.056 0.020 0.497
  S17_75540391 17 75540391 rs470194324 Intronic MZT2B G/C 0.0001309 0.090 0.018 0.198
  S4_116339811 4 116339811 rs459258791 Intronic SSPO C/A 4.545E-05 0.046 0.021 0.165
  S13_53375651 13 53375651 rs444484523 Intergenic — T/G 0.000129 0.090 0.018 0.164

1Values in brackets were obtained with the dominant model.

2MAF: Minor allele frequency.