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Table 2 Lead SNPs from genome-wide associated regions for protein yield in Nordic Holstein cattle. Base positions are given as position in UMD 3.1.1 [49]

From: RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle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
1 63177947 0.9885 −1.94 12.35 61838881~ 63178271 ENSBTAG00000046854 (near) intergenic
2 124837669 0.9886 1.59 12.63 124834921~ 124837676 PTPRU Intron
3 17160521 0.9717 −1.15 8.76 15377852~ 17160986 S100A12 (near) Upstream
5 93511826 0.8626 −1.37 14.25 93087740~ 93511841 LMO3 (near) intergenic
5 21792183a 0.9813 −1.37 10.39 20072875~ 21792190 SNORD107 (near) intergenic
5 87923795b 0.9926 1.50 8.97 85996611~ 87924188 ETNK1 (near) intergenic
6 88477501 0.9962 −2.60 25.98 87154594~ 88477524 SLC4A4 Intron
6 48477272a 0.7329 1.49 13.59 46907022~ 48477298 ENSBTAG00000045570 (near) intergenic
6 88749792b 0.3222 −1.66 12.13 86831016~ 88749854 GC (near) intergenic
7 41372989 0.9999 −1.54 18.14 41085164~ 41373119 MGAT1 (near) intergenic
7 72100619a 0.9077 1.59 13.29 70118741~ 72100721 EBF1 (near) intergenic
8 93065787 0.8573 1.65 10.07 91065857~ 93066321 GRIN3A Intron
8 31538155a 1.0000 1.91 9.62 30388755~ 31538625 LURAP1L (near) intergenic
9 33267855 0.8655 −1.46 11.96 32627954~ 33267856 SLC35F1 (near) intergenic
10 93933304 0.8370 −1.36 9.90 92043775~ 93933391 SEL1L Intron
11 35512708 0.9999 −1.45 11.82 33534073~ 35512724 ENSBTAG00000027786 (near) intergenic
13 37208792 0.9279 −1.69 10.90 35572625~ 37208843 MKX (near) intergenic
13 77657858a 0.9906 1.17 9.52 76677111~ 77908632 PREX1 intron
14 1835440 0.7471 2.84 48.66 1448510~ 1836166 BOP1 Intron
14 67981742a 0.7652 1.78 11.60 65984180~ 67981772 STK3 (near) intergenic
16 32262983 0.9290 −1.52 12.79 30519873~ 32263130 SMYD3 Intron
18 57015407 0.9754 2.56 17.71 55015676~ 57015473 POLD1 Intron
18 15272231a 0.6697 −1.16 9.53 15032157~ 15272234 SNORA11(near) downstream
19 27522927 0.8500 −1.42 12.55 26422519~ 27522980 RNASEK (near) downstream
19 61014793a 0.8505 −1.08 8.65 60995058~ 61014874 KCNJ2 (near) intergenic
20 69006609 0.9920 −1.29 11.27 68120719~ 69006661 IRX1 (near) intergenic
20 9282667a 0.6747 1.71 10.93 7765154~ 9282923 MRPS27 intron
23 10974968 0.9304 −1.18 10.68 9127211~ 10975139 FGD2 (near) intergenic
25 36403719 1.0000 1.33 10.25 36112575~ 36403849 EPO (near) intergenic
26 37695494 0.9122 −1.41 14.76 36684176~ 37695588 KIAA1598 (near) intergenic
27 36304978 0.9834 1.06 8.52 35875452~ 36305040 ANK1 intron
29 17620617 0.9576 1.47 10.37 15650574~ 17620644 NARS2 intron
29 35459126a 0.9999 1.61 10.11 33464929~ 35459620 NTM intron
  Total number of significant SNPs 38,439
  1. aindicated this SNP was found on second round, b indicated this SNP was found on third round