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Table 1 SNPs significantly associated with milk production traits in the combined population

From: Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits

SNP-ID Gene Amino acid sub Chr Positiona Traitsb P valuec
N7 PDE9A   1 144562226 PP 4.68E-05
C8 DIP2A K → Q 1 147894635 PP 1.01E-05
U71 SLC30A7   3 42465645 PP 1.13E-04
C30 SLC30A7 H → Y 3 42530986 PP 4.88E-06
U36 STXBP1   11 98393605 PP 1.43E-05
C204 EGFL7 I → M 11 104152101 PP 2.71E-07
U41 LY6D   14 1155474 MY,FY,FP,PP 9.62E-05
U42 LY6H   14 1449253 MY,PY,FP 5.84E-05
C109 ZNF34 H → R 14 1494039 MY,FP,PY,PP 1.74E-04
P18 RPL8*   14 1508300 MY,PY,FP 6.63E-05
S12 LOC785799   14 1524572 MY,PY,FP 5.63E-05
P23 GPT*   14 1628421 All 8.08E-08
C110 PPP1R16A A → T 14 1629600 All 2.39E-07
S4 CYHR1*   14 1677522 All 3.14E-08
U46 VPS28*   14 1694862 All 1.99E-09
C111 CPSF1* T → I 14 1736599 All 1.40E-10
C199 DGAT1* K → A 14 1802265 All 2.96E-10
U47 HSF1*   14 1806340 FP 2.95E-08
C112 HEATR7A* Q → R 14 1851040 FP 2.30E-11
C113 HEATR7A* N → S 14 1878165 All 2.66E-10
U48 LOC509113*   14 1907315 All 2.39E-10
N10 MAF1   14 1924112 MY,FP,PP 2.31E-06
P24 GPAA1   14 1946673 MY,FP,PP 1.15E-06
P25 OPLAH   14 1957462 MY,FP,PP 1.48E-06
C114 SPATC1 P → A 14 1977494 MY,FP,PP 1.27E-06
U50 GRINA   14 2019072 FP 6.36E-06
C115 PARP10 G → D 14 2026781 MY,FP,PP 4.39E-07
C116 PARP10 G → S 14 2027812 MY,FP,PP 3.13E-07
C119 LOC786966* D → A 14 2086893 MY,FP,PP 2.97E-06
C120 LOC786966* L → G 14 2087763 All 1.66E-07
C125 EPPK1 R → Q 14 2138115 PP 9.31E-05
P29 PUF60   14 2163044 FP 5.29E-06
P33 LOC506831*   14 2221616 FY,FP,PP 2.29E-04
C127 FAM83H* V → G 14 2231494 MY,FY,FP,PP 1.08E-04
C128 MAPK15 T → M 14 2239085 MY,FY,FP,PP 2.12E-04
C130 PYCRL R → C 14 2308255 PY 2.04E-06
P35 EEF1D*   14 2311270 MY,FP,PP 9.23E-06
P90 EEF1D*   14 2314560 MY,FP,FP 1.21E-04
C132 ZC3H3* P → L 14 2358243 MY,PY,FP,PP 6.77E-06
C133 ZC3H3* A → D 14 2358255 MY,PY,FP,PP 8.05E-06
U52 RHPN1   14 2462476 MY,FP,FP 1.49E-05
C207 RHPN1 T → A 14 2465250 FP,PP 2.29E-04
P89 GPIHBP1*   14 2553652 MY,PY,FP 2.17E-08
C206 CYP11B1 A → V 14 2705205 FP 1.57E-10
N8 CYP11B1   14 2706012 FY,FP 7.98E-05
C198 CYP11B1 E → K 14 2708768 FP 1.87E-05
C136 GML Q → P 14 2715807 FP 1.57E-09
C137 LYNX1 L → F 14 2816429 MY,FP,PP 7.22E-05
S8 GPR20   14 3640627 MY,FP,PP 8.90E-05
C138 PTK2* I → M 14 4061098 MY,FY,FP 3.16E-05
P48 EIF2C2*   14 4129075 MY,FY,FP 1.62E-04
C139 TRAPPC9* C → G 14 4352117 MY,PY,FP 3.45E-07
C140 TRAPPC9* G → R 14 4472220 MY,FY,FP 1.29E-04
U70 KCNK9   14 4743187 MY,FP 6.83E-05
C147 FAM135B M → V 14 5603441 MY,FY,PP 1.24E-04
C194 GHR* F → Y 20 31909476 MY,FY,PP 6.44E-09
P63 PLCXD3   20 33027949 FP,PP 1.96E-04
U60 PLCXD3   20 33229971 PP 7.47E-07
C163 C6 P → L 20 33376024 MY,FP,PP 3.34E-05
C168 C7 T → I 20 33578727 MY,FP,PP 8.33E-05
C169 C7 T → M 20 33582457 PP 2.81E-09
C171 DAB2 A → V 20 35073744 FP,PP 1.88E-05
C175 OSMR R → M 20 35544340 PP 1.56E-05
C176 OSMR M → L 20 35561705 PP 5.21E-05
P72 GDNF   20 36634182 FP,PP 4.81E-07
C184 NIPBL* I → V 20 37238542 FP,PP 1.97E-06
  1. a: based on the UMD_3.1 genome assembly.
  2. b: MY = milk yield, FY = fat yield, PY = protein yield, FP = fat percentage, PP = protein percentage
  3. c: These values were from the combined population. For SNPs whichwere significant for more than one trait, the maximum P values are presented.
  4. *: These genes were selected for mRNA expression analysis.