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 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 |