Table 2

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

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


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 webcite) or the UCSC genome browser (http://genome.ucsc.edu webcite). 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].

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 webcite]. 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.

2 Alleles 1 and 2 represent the major and minor alleles, respectively, at a given SNP

3 The frequency of allele 1 (p), the major allele at a SNP locus

Magee et al. BMC Genetics 2010 11:93   doi:10.1186/1471-2156-11-93

Open Data