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Table 2 QTL regions for each of the trait. Top SNP for each QTL are shown including position, -log10(p)-values, minor allele frequency (MAF), gene information, annotation of the top SNP, allele substitution effect (b.value) and standard error for b.value (SE)

From: Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

CHR Start (bp) End (bp) Length of the QTL region (bp) Significant SNPs in region No of genes with significant SNPs within the QTL region Top SNP Position of the top SNP (bp) - log10(p) MAF Gene Annotation of the top SNP b.value SE
Fat yield              
 5 92,372,732 94,425,668 2,052,936 330 3 rs209818856 93,945,694 27.49 0.38 MGST1 intron variant −2.807 0.253
 14 1,448,510 2271832 823,322 509 49 rs136783505 1,807,140 42.01 0.07 DGAT1/HSF1 downstream variant/intron variant −6.709 0.484
 23 28,567,796 28,591,530 23,734 5 1 rs381390819 28,567,796 9.36 0.45 TRIM26 intron variant 1.148 0.184
 25 8,222,347 11,507,986 3,285,639 883 16 rs379546164 9,870,005 14.40 0.24 CLEC16A intron variant −1.769 0.224
 25 36,226,978 36,227,132 154 2   rs109480808 36,226,978 8.72 0.16   intergenic variant 1.635 0.272
 26 22,144,777 24,793,744 2,648,967 595 32 rs438420348 24,379,571 14.28 0.16 NEURL1 intron variant −2.273 0.290
 26 44,802,991 44,802,991 0 1   rs135624939 44,802,991 9.72 0.28   intergenic variant −1.474 0.231
Milk yield              
 5 112,343,204 11,2450,860 107,656 2 1 rs383553819 112,343,204 8.70 0.36 MKL1 intron variant 1.437 0.239
 14 1,448,510 2,271,832 823,322 455 48 rs133033480 1,743,939 33.01 0.09 CPSF1/ADCK5 downstream variant/splice region variant, intron variant 6.266 0.513
 16 1,322,611 1,322,611 0 1 1 rs108979795 1,322,611 8.58 0.28 LAX1 upstream variant −1.451 0.243
 19 61,447,138 61,449,096 1958 5   rs210324693 61,449,096 8.93 0.32   intergenic variant 1.490 0.244
 20 30,531,217 32,952,019 2,420,802 74 5 rs385640152 31,909,478 15.56 0.11 GHR missense variant −3.877 0.472
 20 37,766,226 39,183,141 1,416,915 34 3 NA 38,828,254 9.54 0.16   intergenic variant −2.250 0.356
 25 2,669,704 2,669,704 0 1   rs209691835 2,669,704 9.21 0.13   intergenic variant −2.855 0.460
 25 3,494,706 3,516,671 21,965 13 4 rs110749311 3,498,960 9.32 0.41 PAM16/GLIS2 downstream variant 1.225 0.196
Protein yield              
 5 112,450,860 112,450,860 0 1   rs109041054 112,450,860 8.88 0.48   intergenic variant −1.473 0.242
 14 1,802,667 1,802,667 0 1 2 NA 1,802,667 8.52 0.06 DGAT1/HSF1 intron variant/downstream variant 3.354 0.564
 25 1,094,996 1,257,612 162,616 12 3 rs136085792 1,103,856 10.83 0.22 UNKL intron variant 1.694 0.250
 25 3,306,363 3,516,671 210,308 40 8 rs110749311 3,498,960 11.70 0.41 PAM16/GLIS2 downstream variant 1.427 0.202