Table 3 |
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|
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. |
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|
Entrez gene/Ensembl ID |
Chr. |
Location |
Allele |
Frequency in Low CIV pool1 |
Frequency in High CIV pool1 |
P value2 |
Type/Location3 |
Predicted effect4 |
Reference5 |
|
|
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|
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 |
|
|
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|
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). |
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|
Mullen et al. BMC Genomics 2012 13:16 doi:10.1186/1471-2164-13-16 |
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