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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: 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 63,177,947 0.9885 −1.94 12.35 62,590,679~63,428,175 ENSBTAG00000046854 (near) intergenic
2 124,837,669 0.9886 1.59 12.63 124,587,873~125,089,732 PTPRU intron
2 86095020a 0.9910 1.27 9.53 85,393,563~86,345,056 ANKRD44 intron
3 17,160,521 0.9717 −1.15 8.76 16,197,245~17,415,613 S100A12 (near) upstream
4 103,211,543 0.9321 −1.06 8.74 102,341,267~103,461,820 ATP6V0A4 intron
5 93,511,826 0.8626 −1.37 14.25 93,087,740~93,762,020 LMO3 (near) intergenic
5 21792183a 0.9813 −1.37 10.39 21,542,557~22,042,238 SNORD107 (near) intergenic
5 87923795b 0.9926 1.50 8.97 86,950,758~88,173,798 ETNK1 (near) intergenic
6 88,477,501 0.9962 −2.60 25.98 88,227,821~88,727,537 SLC4A4 intron
6 48,694,003a 0.9785 1.89 12.16 47,720,473~48,944,178 ENSBTAG00000045570 (near) intergenic
6 88847595b 0.9009 −1.82 23.84 88,477,501~89,097,608 GC (near) intergenic
7 41,372,989 0.9999 −1.54 18.14 41,085,164~41,623,965 MGAT1 (near) intergenic
7 72100619a 0.9077 1.59 13.29 71,120,920~72,350,707 EBF1 (near) intergenic
8 93,065,787 0.8573 1.65 10.07 92,816,321~93,315,869 GRIN3A Intron
8 31538155a 1.0000 1.91 9.62 30,550,864~31,788,181 LURAP1L (near) intergenic
9 33,267,855 0.8655 −1.46 11.96 32,627,954~33,518,971 SLC35F1 (near) intergenic
10 93,933,304 0.8370 −1.36 9.90 92,933,459~94,183,400 SEL1L intron
11 35,512,708 0.9999 −1.45 11.82 35,189,581~35,762,749 ENSBTAG00000027786 (near) intergenic
13 37,208,792 0.9279 −1.69 10.90 36,702,834~37,459,042 MKX (near) intergenic
14 1,835,440 0.7471 2.84 48.66 1,448,510~2,085,468 BOP1 intron
14 67981742a 0.7652 1.78 11.60 67,731,848~68,231,920 STK3 intron
16 32,262,983 0.9290 −1.52 12.79 31,268,349~32,513,084 SMYD3 intron
18 57,015,407 0.9754 2.56 17.71 56,767,474~57,265,703 POLD1 intron
18 15057077a 0.9934 1.27 9.99 14,811,219~15,308,407 VPS35 intron
19 27,522,927 0.8500 −1.42 12.55 27,156,952~27,773,922 ASGR1 (near) intergenic
19 61014793a 0.8505 −1.08 8.65 60,313,953~61,265,218 KCNJ2 (near) intergenic
20 69,006,609 0.9920 −1.29 11.27 68,120,719~69,256,618 IRX1 (near) intergenic
20 8830351a 0.9433 −1.71 10.61 8,345,063~9,080,402 ENSBTAG00000012775 (near) intergenic
23 10,974,968 0.9304 −1.18 10.68 10,234,192~11,224,969 FGD2 (near) intergenic
25 36,403,719 1.0000 1.33 10.25 36,112,575~36,654,175 EPO (near) intergenic
26 37,695,494 0.9122 −1.41 14.76 36,699,144~37,945,656 SHTN1 (near) intergenic
27 36,304,978 0.9834 1.06 8.52 36,037,123~36,555,106 ANK1 intron
29 17,620,617 0.9576 1.47 10.37 16,671,270~17,870,637 NARS2 intron
29 35459126a 0.9999 1.61 10.11 34,854,011~35,709,168 NTM intron
Total number of significant SNPs 36,644
  1. Note, aindicated this SNP was found on second round, bindicated this SNP was found on third round
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BMC Genomic Data

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