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.

Entrez gene/Ensembl ID

Chr.

Location

Allele

Frequency in Low CIV pool1

Frequency in High CIV pool1

P value2

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: 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/ webcite accessed 9th September 2011).

Mullen et al. BMC Genomics 2012 13:16   doi:10.1186/1471-2164-13-16

Open Data