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Table 1 Lead SNPs from genome-wide associated regions for fat 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
1 71,227,484 0.9745 −1.77 9.66 70,442,929~71,477,578 TNK2 intron
2 126,979,882 0.9972 −1.31 11.46 126,041,707~127,230,335 PIGV (near) downstream
2 85991577b 0.9542 1.30 8.91 85,042,155~86,241,732 ANKRD44 intron
3 7,226,390 0.9998 −1.09 9.01 6,264,604~7,476,497 NOS1AP intron
5 93,948,357 0.9906 3.28 62.41 93,698,481~94,198,670 MGST1 intron
5 20284735b 0.9692 −1.30 9.79 20,035,379~20,534,779 5S_rRNA (near) intergenic
6 95,497,933 0.9996 −1.45 14.76 95,248,213~95,747,954 PAQR3 (near) intergenic
6 32950721b 0.4975 6.33 11.39 32,367,171~33,200,834 ENSBTAG00000047255 intron
7 57,287,990 0.8807 −1.66 20.11 57,038,215~57,538,309 KCTD16 intron
9 38,715,137 0.9809 −1.47 8.89 38,345,408~38,965,425 LAMA4 intron
11 88,771,449 0.9876 1.16 10.43 88,521,462~89,021,477 ENSBTAG00000047976 (near) intergenic
11 15323223b 0.8962 −1.32 9.81 14,855,568~15,573,444 TTC27 intron
12 68,965,758 0.9957 −1.10 8.93 68,502,223~69,216,445 ENSBTAG00000045195 (near) intergenic
14a 1,802,265 0.9398 −6.93 240.56 1,549,133~2,049,435 DGAT1 missense
14a 1,802,266 0.9362 −6.93 240.56 1,549,133~2,049,435 DGAT1 missense
14 67981742b 0.7652 1.65 8.71 67,117,232~68,231,920 STK3 intron
14 1321721c 0.4442 1.46 8.82 1,087,168~1,583,427 ENSBTAG00000046435 missense
15 65,891,100 0.9992 1.50 12.99 65,641,131~66,141,839 ELF5 (near) intergenic
15 25044706b 0.9908 −1.17 9.80 24,795,472~25,295,470 ZBTB16 intron
16 31,496,700 0.9501 −1.37 9.32 30,519,873~31,746,789 CNST intron
17 62,543,160 0.9898 1.14 10.49 62,224,291~62,793,298 TBX5 intron
18 18,970,551 0.9442 −1.19 10.30 18,341,203~19,220,732 NKD1 (near) intergenic
19 27,522,927 0.8500 −1.32 10.86 26,625,240~27,773,922 ASGR1 (near) intergenic
20 22,609,736 0.9813 1.53 14.23 21,664,412~22,859,809 MAP3K1 (near) intergenic
20 44186112b 0.9997 1.53 10.20 43,936,468~44,436,133 ENSBTAG00000040572 (near) intergenic
26 20,547,445 0.9993 −1.76 21.46 20,299,309~20,797,570 COX15 intron
26 42408595b 0.9998 −1.21 10.30 41,409,014~42,658,925 TACC2 intron
29 23,609,412 0.7717 2.06 10.73 22,613,737~23,859,451 ENSBTAG00000047094 (near) intergenic
Total number of significant SNPs 52,334
  1. aFourteen additional SNPs on chromosome 14 located near DGAT1 gene had same highest P value (details on those not presented). Note, bindicated this SNP was found on second round, cindicated this SNP was found on third round