Skip to main content

Advertisement

Table 3 Lead SNP from genome-wide associated regions for milk yield in Nordic Holstein cattle. Base positions are given as position in UMD 3.1.1 [49]

From: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

BTA base position Imputation accuracy Effect –log10(p) Region Gene Annotation
2 80,753,895 0.9454 1.13 9.95 79,777,813~81,003,948 NABP1 (near) intergenic
3 56,402,959 0.9308 −1.36 11.68 56,152,966~56,653,364 ENSBTAG00000001873 (near) intergenic
4 101,547,644 0.7008 −1.66 12.65 100,921,921~101,798,041 CHRM2 (near) upstream
5 93,953,487 0.9726 −2.10 29.52 93,703,737~94,203,599 MGST1 (near) upstream
5 31005518b 0.9943 1.42 12.25 30,202,453~31,258,920 WNT1 (near) upstream
5 85080296c 0.7619 −1.28 11.24 84,425,435~85,330,671 KRAS (near) intergenic
5 20569435d 0.9944 1.23 9.37 19,600,731~20,820,066 CCER1 (near) intergenic
6 88,847,595 0.9009 −1.78 21.61 88,598,011~89,097,608 GC (near) intergenic
6 46901490b 0.7413 −1.28 11.45 46,181,675~47,152,919 SEL1L3 (near) intergenic
6 38027010c 0.9950 −4.75 9.47 37,669,181~38,279,802 ABCG2 missense
7 65,370,850 0.9848 −1.36 13.58 65,120,872~65,620,985 GLRA1 (near) intergenic
8 73,877,814 0.8453 −1.37 11.14 73,629,406~74,127,901 ENSBTAG00000010829 (near) upstream
8 42062591b 0.9595 −1.27 10.07 41,064,643~42,313,291 KCNV2 (near) intergenic
9 33,478,527 0.8801 −1.25 9.23 32,627,954~33,728,755 ENSBTAG00000015497 (near) intergenic
10 1,989,907 0.9469 −1.15 9.92 1,016,031~2,240,288 ENSBTAG00000047622 (near) intergenic
13 36,822,330 0.9933 −1.66 10.74 36,572,364~37,072,486 MPP7 intron
14a 1,802,667 0.7975 5.98 178.35 1,545,264~2,044,412 DGAT1 intron
15 54,392,611 0.9577 1.57 16.58 53,485,007~54,642,856 PPME1 intron
16 28,384,260 0.9984 1.64 10.50 28,012,864~28,634,313 CNIH3 (near) intergenic
17 66,510,224 0.9438 1.83 11.63 66,119,023~66,760,263 CORO1C intron
18 46,583,346 0.9829 1.86 11.97 46,333,384~46,833,392 UPK1A (near) upstream
19 27,442,452 0.7904 −1.26 9.71 26,592,355~27,692,965 bta-mir-497 (near) downstream
20 29,996,719 0.9580 −2.95 31.02 29,748,423~30,246,822 MRPS30 (near) intergenic
23 25,076,472 0.9797 −1.34 9.23 24,219,868~25,326,583 GCM1 intron
26 37,716,420 0.9790 −1.43 12.28 36,730,021~ 37,966,463 SHTN1 (near) intergenic
28 34,972,377 0.9991 1.18 9.81 34,722,402~35,222,855 ZMIZ1 (near) intergenic
Total number of significant SNPs 55,600
  1. aEight additional SNPs on chromosome 14 had same highest P value. Note, bindicated this SNP was found on second round, cindicated this SNP was found on third round, dindicated this SNP was found on fourth round