Table 2.
Haplotypes associated with DYD for SCS
| Hap ID |
Position (bp) |
Length (Mb) | HapA | HF | β | P -value | Genetic variance % # | Genes within HTB | Other nearby genes ‡ | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Start | End | |||||||||
| BTA5_Hap5* |
5 |
97862816 |
97948752 |
0.09 |
TCAG |
0.35 |
-0.09 |
7.05E-07 |
0.37 |
LOH12CR1, MANSC1 |
CDKN1B |
| BTA6_Hap4* |
6 |
85142067 |
85527109 |
0.39 |
CAGG |
0.34 |
0.09 |
1.84E-07 |
0.44 |
GNRHR, TMPRSS11D |
UBA6 |
| BTA6_Hap8 |
6 |
86642355 |
86904512 |
0.26 |
AGGG |
0.38 |
0.107 |
4.08E-08 |
0.54 |
LOC781988, UGT2A1 |
SULT1B1 |
| BTA6_Hap12* |
6 |
87929420 |
88174863 |
0.25 |
AAGGGC |
0.32 |
0.103 |
3.37E-07 |
0.46 |
GRSF1, MOB1B, DCK |
IGJ, DBP |
| BTA13_Hap10* |
13 |
78383148 |
78858126 |
0.47 |
AAAGGAG |
0.14 |
0.12 |
3.60E-08 |
0.33 |
SLC9A8, RNF114 |
UB2V1, PTGIS |
| BTA13_Hap17* |
13 |
79730805 |
79775537 |
0.04 |
GA |
0.34 |
0.08 |
9.79E-08 |
0.30 |
|
KCNG1, NFATC2 |
| BTA13_Hap34 |
13 |
83917405 |
84002346 |
0.08 |
ACAA |
0.12 |
0.12 |
3.94E-08 |
0.31 |
|
CBLN4 |
| BTA18_Hap6a*† |
18 |
43327273 |
43379174 |
0.05 |
CA |
0.41 |
-0.07 |
4.61E-07 |
0.27 |
RGS9BP, TDRD12 |
CEBPG |
| BTA18_Hap6b*† |
18 |
43327273 |
43379174 |
0.05 |
AG |
0.58 |
0.07 |
7.38E-07 |
0.26 |
RGS9BP, TDRD12 |
CEBPG |
| BTA19_Hap7* | 19 | 50547082 | 50647677 | 0.10 | GAA | 0.19 | -0.11 | 2.64E-08 | 0.39 | RAB40B, FN3KRP | FOXK2, CD7, NPB |
Chr = chromosome; Hap ID = haplotype ID; Mb = megabase; HapA = haplotype alleles; HF = haplotype frequency; β = change per significant haplotype (regression coefficient); HTB = haplotype block; BTA = Bos taurus autosome;
#genetic variance for significant haplotype is based on the formula 2β2f (1-f), where β denotes the change per significant haplotype and f denotes the frequency of the variant; ‡other nearby genes = genes within an area of 1 Mb upstream or downstream of the haplotype block boundaries; genes of known immune functions are written in italic; *haplotype blocks contain SNPs which are significant in GWAS for single marker analyses; † two significant haplotypes were identified in this haplotype block, BTA18_Hap6 (a for the first haplotype and b for the second one); positions follow the University of Maryland bovine genome assembly (UMD3.1); candidate genes are extracted from the Ensembl data base (UMD3.1 Ensembl data base build 73).