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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From: RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle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
2 80753895 0.9454 1.13 9.95 79587952~ 80754103 NABP1 (near) intergenic
3 56402959 0.9308 −1.36 11.68 56392727~ 56402961 ENSBTAG00000001873 (near) intergenic
4 101547644 0.7008 −1.66 12.65 100921921~ 101547648 CHRM2 (near) upstream
5 93953487 0.9726 −2.10 29.52 91953587~ 93953619 MGST1 (near) upstream
5 23022794a 0.7617 1.38 12.93 21101742~ 23022797 EEA1 (near) intergenic
5 85080296b 0.7619 −1.28 11.24 84425435~ 85080331 ENSBTAG00000009778 (near) intergenic
6 88847595 0.9009 −1.78 21.61 88612186~ 88847596 GC (near) intergenic
6 46901490a 0.7413 −1.28 11.45 46181675~ 46901554 SEL1L3 (near) intergenic
6 38027010b 0.9950 −4.75 9.47 36909885~ 38027583 ABCG2 missense
7 65370850 0.9848 −1.36 13.58 65256765~ 65370922 GLRA1 (near) intergenic
8 73877814 0.8453 −1.37 11.14 71877875~ 73877845 ENSBTAG00000010829 (near) upstream
8 42062591a 0.9595 −1.27 10.07 40245362~ 42062776 KCNV2 intergenic
9 33478527 0.8801 −1.25 9.23 31790030~ 33478670 NUS1 (near) intergenic
10 1989907 0.9469 −1.15 9.92 448434~ 1990092 ENSBTAG00000047622 (near) intergenic
13 36822330 0.9933 −1.66 10.74 36663680~ 36822395 MPP7 Intron
14# 1802667 0.7975 5.98 178.35 1702853~ 1797137 DGAT1 Intron
14 67577503a 0.8898 −2.16 11.04 66624772~  67828111 OSR2 intergenic
15 54392611 0.9577 1.57 16.58 52771707~ 54393036 PPME1 Intron
16 28384260 0.9984 1.64 10.50 28012864~ 28384605 CNIH3 (near) Intergenic
17 66510224 0.9438 1.83 11.63 66119023~ 66510712 CORO1C Intron
18 46583346 0.9829 1.86 11.97 44583383~ 46583963 UPK1A (near) upstream
19 27442452 0.7904 −1.26 9.71 26592355~ 27442492 bta-mir-497 (near) upstream
20 29996719 0.9580 −2.95 31.02 27997007~ 29996870 MRPS30 (near) intergenic
23 25076472 0.9797 −1.34 9.23 23690289~ 25076491 GCM1 Intron
26 37716420 0.9790 −1.43 12.28 36730021~  37966463 TRPA1 intergenic
28 34972377 0.9991 −1.29 9.81 33464705~ 34972672 ZMIZ1 intergenic
Total number of significant SNPs 57,808
  1. #Eight additional SNPs on chromosome 14 had same highest P value. a indicated this SNP was found on second round, b indicated this SNP was found on third round