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Table 2 Information for the SNPs genotyped in this study and summary statistics for the 848 genotyped Irish Holstein-Friesian AI sires

From: DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle

Gene/Expressed allele BTA SNP ID1 Nucleotide position of SNP SNP gene position Alleles (1/2)2 Frequency allele 1 (p)3 Heterozygosity Deviation from HWE
CALCR/maternal 4 rs42940189 11,049,538 Exonic (non-syn) G/A 0.90 0.15 < 0.001
  4 rs42940187 11,039,296 Exonic (syn) C/T 0.86 0.23 0.03
GRB10/ isoform-dependent 4 GRB10_p.A5394141C 5,394,141 Intronic C/A 0.95 0.09 0.11
  4 rs43375833 5,334,910 Intronic C/T 0.67 0.42 0.14
ZNF215/ maternal 15 rs42575466 44,945,003 Exonic (syn) G/A 0.95 0.09 < 0.00001
  15 rs42575474 44,934,196 Intronic G/A 0.67 0.43 0.46
PEG3/ paternal 18 PEG3_p.A64370595G 64,370,595 Upstream G/A 0.69 0.44 0.36
  18 PEG3_p.C64367437T 64,367,437 Upstream C/T 0.66 0.45 0.81
  18 rs17871322 64,362,259 Exonic (syn) G/A 0.66 0.46 0.43
ZIM2/ paternal expression in humans; polymorphic expression in mice 18 rs41899915 64,234,488 Exonic (syn) C/G 0.80 0.32 0.43
  18 rs41899913 64,233,519 3'UTR G/C 0.83 0.28 0.85
  18 rs41899911 64,232,216 3'UTR C/T 0.80 0.32 0.41
  18 rs41899910 64,231,503 3'UTR T/C 0.70 0.40 0.28
RASGRF1/ paternal 21 RASGRF1_p.C25039690T 25,039,690 Intronic A/G 0.59 0.42 < 0.001
PHLDA2/ maternal 29 rs42194502 50,555,723 3'UTR A/T 0.90 0.18 0.17
TSPAN32/ maternal 29 rs42637579 51,123,847 Intronic G/A 0.63 0.42 < 0.01
  29 rs42637578 51,123,729 Exonic (syn) T/C 0.94 0.11 0.32
  1. Genotype and allele frequencies and the significance of deviations from Hardy-Weinberg equilibrium (HWE) based on P-values obtained from χ2-test results are shown for all 17 SNPs. All SNP nucleotide positions were obtained from the Build 4.0 of the B. taurus genome sequence on the ENSEMBL database (http://www.ensembl.org) or the UCSC genome browser (http://genome.ucsc.edu). The ORF gene model positions for each SNP are given. For exonic SNPs, amino acid sequence changing SNPs (i.e. non-synonymous SNPs, denoted 'non-syn') and non-amino acid sequence changing SNPs (i.e. synonymous SNPs, denoted 'syn') are shown. The imprinting status of each gene is based on data from human and mice and, where possible, cattle, sheep and pigs [14, 16].
  2. 1 Where possible, SNP identities (IDs) are given as per their entry in the dbSNP database [43]; [http://www.ncbi.nlm.nih.gov/projects/SNP]. Where no dbSNP ID was available, SNPs were labelled as per nomenclature used by Magee et al. [8] as detailed in the main body text of the manuscript.
  3. 2 Alleles 1 and 2 represent the major and minor alleles, respectively, at a given SNP
  4. 3 The frequency of allele 1 (p), the major allele at a SNP locus