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Table 3 Top 20 most significant SNPs, at least 10 Mb apart, in exonic, intronic and UTR regions displaying differential frequencies between groups of cattle divergent for calving interval.

From: Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

Entrez gene/Ensembl ID Chr. Location Allele Frequency in Low CIV pool1 Frequency in High CIV pool1 P value 2 Type/Location3 Predicted effect4 Reference5
GH1 19 49749042 G>T 0.00 0.38 9.2 × 10-15 Exon NSS N/A rs41917096
SST 21 49258728 C>T 0.00 0.34 4.8 × 10-9 Exon NSS N/A novel
NR2F2 21 9510000 A>G 0.00 0.52 9.1 × 10-8 Exon NSS N/A novel
HK3 7 37630361 T>G 0.00 0.30 8.2 × 10-6 Exon NSS N/A novel
STAT5B 19 43679543 G>T 0.00 0.28 1.2 × 10-5 Exon NSS N/A novel
IGFBP5 2 108855684 C>T 0.00 0.54 2.3 × 10-12 5' 2 × pTFBS novel
MAPK9 7 871347 C>T 0.47 0.09 5.3 × 10-12 5' 1 × pTFBS rs43495395
GCK 11 74275999 G>A 0.00 0.39 2.2 × 10-9 5' 8 × pTFBS novel
GHR 20 34207771 C>A 0.00 0.39 8.3 × 10-9 5' None novel
HK1 28 24994609 C>T 0.00 0.18 2.4 × 10-7 3' 1 × miRNA novel
GHRH 13 66803046 A>G 0.65 0.25 3.1 × 10-6 5' None novel
IRS4 X 35195377 C>G 0.00 0.83 4.9 × 10-9 3' None novel
SLC2A1 3 110250920 T>G 0.00 0.38 5.0 × 10-9 3' 4 × miRNA novel
SLC5A1 17 73990477 C>T 0.68 0.18 9.7 × 10-7 3' None rs41255339
ESR2 10 78593544 C>T 0.00 0.21 9.3 × 10-7 3' 1 × miRNA novel
IGF2R 9 100136966 C>T 0.79 0.00 5.5 × 10-20 Intron N/A novel
PIK3R2 7 4996360 C>A 0.00 0.55 2.8 × 10-15 Intron N/A novel
Q95M43 7 14524938 G>A 0.00 0.44 4.4 × 10-9 Intron N/A novel
IGFBP3 4 78896406 A>T 0.00 0.42 8.8 × 10-9 Intron N/A novel
SIRT2 18 48205429 T>A 0.00 0.53 1.6 × 10-8 Intron N/A novel
  1. 1: Frequency of second allele displayed; 2: Benjamini and Hochberg corrected P value; 3: NSS = SNPs resulting in non synonymous substitutions; 4: Predicted effects on transcription factor binding sites in the 5' regulatory regions using MatInspector software package [33] and on microRNA binding sites in the 3' regulatory regions using MicroInspector software [34], detailed information on predicted effects displayed in Tables 6 and 7; 5: SNPs classified according to dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/ accessed 9th September 2011).