Table 3.
List of SNPs in the Bos taurus autosomes showing significant (−log10 (p) ≥ 4.00) associations with SCS in the Romanian Brown breed.
| Parity 1 | Informative SNP 2 |
SNP rsID | Chr:Position 3 | A1 | A2 | SNP Effect 4 | –log10 (p) | Nearest Gene 5 |
Distance (bp) |
|---|---|---|---|---|---|---|---|---|---|
| L1 | |||||||||
| AX-106741653 | NA | 7:8272794 | C | A | 6.14 × 10−9 | 5.37 | AKAP8 | 514640 | |
| AX-115114947 | NA | 7:8276425 | G | A | 6.14 × 10−9 | 5.37 | AKAP8 | 511009 | |
| AX-106739297 | rs108991944 | 11:37261133 | A | C | 1.54 × 10−9 | 4.41 | CLHC1 | 526855 | |
| AX-124375018 | rs42894728 | 6:20276795 | G | A | 7.39 × 10−9 | 4.33 | NA | NA | |
| AX-171466608 | rs42228650 | 7:27601185 | G | A | 5.65 × 10−10 | 4.29 | MEGF10 | 219169 | |
| AX-106727011 | NA | 13:76008898 | G | A | −3.96 × 10−9 | 4.24 | NA | NA | |
| AX-117090125 | rs110642171 | 6:39688028 | A | G | −2.65 × 10−9 | 4.19 | NA | NA | |
| AX-117084655 | rs109189476 | 2:88162563 | C | T | 6.31 × 10−10 | 4.14 | SATB2 | 86169 | |
| AX-106731475 | NA | 8:75798051 | T | C | 2.67 × 10−9 | 4.14 | NA | NA | |
| AX-124381310 | NA | 24:34453446 | A | G | −1.98 × 10−9 | 4.08 | GATA6 | 96211 | |
| L2 | |||||||||
| AX-124381305 | rs43358795 | 3:97560648 | A | G | −3 × 10−10 | 5.38 | SPATA6 | 809734 | |
| AX-169513997 | rs133252983 | 13:77447650 | G | T | 5.07 × 10−9 | 4.61 | NA | NA | |
| AX-117080179 | rs110709131 | 2:46155190 | G | A | 3.47 × 10−9 | 4.56 | NA | NA | |
| AX-117083483 | rs133489631 | 2:46126141 | T | C | 3.47 × 10−9 | 4.56 | NA | NA | |
| AX-124350324 | rs42797639 | 9:20734430 | C | T | −9.3 × 10−10 | 4.19 | NA | NA | |
| AX-124377880 | rs41981703 | 21:40381539 | A | C | 1.02 × 10−8 | 4.15 | NA | NA | |
| AX-106735825 | rs43585636 | 9:14745626 | C | A | 3.02 × 10−9 | 4.09 | COL12A1 | 123884 | |
| AX-117085949 | rs43585209 | 9:14767890 | A | G | 3.02 × 10−9 | 4.09 | COL12A1 | 101620 | |
| AX-106726354 | NA | 5:94517415 | A | G | 5.58 × 10−9 | 4.08 | EPS8 | 156339 | |
| L3 | |||||||||
| AX-115109333 | NA | 22:26294371 | A | G | 6.59 × 10−9 | 5.17 | NA | NA | |
| AX-124375014 | rs110955314 | 29:19740081 | C | A | −1.57 × 10−8 | 4.38 | LUZP2 | 519687 | |
| AX-106753982 | NA | 21:23675656 | A | G | −6.09 × 10−9 | 4.35 | RAMAC | 30303 | |
| AX-106735391 | rs110359025 | 19:16700029 | C | T | −7.19 × 10−9 | 4.21 | NA | NA | |
| AX-106735614 | rs43256975 | 1:108154057 | A | G | −3.37 × 10−9 | 4.1 | IL12A | 131225 | |
| AX-115115579 | rs110825674 | 19:50547082 | T | C | −9.06 × 10−9 | 4.06 | NA | NA | |
| AX-106730586 | rs109619272 | 20:22823334 | A | G | 4.48 × 10−9 | 4.03 | ANKRD55 | 184056 |
1 Parity 1 (L1), 2 (L2) and 3 (L3). 2 SNPs are sorted in descending order with respect to the significance of the association analysis between each SNP and SCS. 3 SNP position based on the UMD3.1 genome assembly of Bos taurus. 4 SNP effect is calculated relative to the A2 allele (if the effect is positive, then A2 increases the phenotype relative to A1). 5 Nearest gene: genes downstream/upstream relative to the SNP, within a ±1 MBp range (2 MBp total). NA: not available; SNP: single nucleotide polymorphism; Chr: chromosome; A1 and A2: allele 1 and 2.