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Table 2 Most significantly associated SNP for female fertility traits in the regions selected based on QTL segregating for the fertility index

From: Identification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data

  BTA20
Trait name 2 SNP MAF -log 10 (P-value) Annotation 1 Ensemble name Gene name Gene description
FTI Chr20:24457090 0.20 11.42 intergenic_variant    
AISc Chr20:24457090 0.20 10.56 intergenic_variant    
AISh Chr20:24457090 0.20 5.99 intergenic_variant    
ICF Chr20:24814046 0.22 12.21 intergenic_variant    
IFLc Chr20:24457090 0.20 11.88 intergenic_variant    
IFLh Chr20:24811587 0.24 8.89 intergenic_variant    
NRRc Chr20:24457090 0.20 7.69 intergenic_variant    
NRRh Chr20:24457090 0.20 5.68 intergenic_variant    
  BTA23
FTI Chr23:30817360 0.42 9.51 intergenic_variant    
AISc Chr23:30586684 0.38 12.43 missense_variant ENSBTAG00000005885 F1N1L2 Olfactory receptor
AISh Chr23:30634587 0.39 9.63 intergenic_variant    
ICF Chr23:30364272 0.02 5.82 intergenic_variant    
IFLc Chr23:30831993 0.47 10.75 downstream_gene_variant ENSBTAG00000044946   Novel miRNA
IFLh Chr23:30634587 0.39 8.66 intergenic_variant    
NRRc Chr23:30090044 0.37 11.13 missense_variant ENSBTAG00000008943 ZSCAN12 Bos taurus zinc finger and SCAN domain containing 12
NRRh Chr23:30602861 0.43 10.22 upstream_gene_variant ENSBTAG00000040307 F1N7S5 Olfactory receptor
  BTA7
FTI Chr7:79631927 0.07 8.98 intergenic_variant    
AISc Chr7:78685481 0.06 5.73 intergenic_variant    
AISh Chr7:78685062 0.06 13.16 intergenic_variant    
ICF Chr7:78287019 0.07 12.3 intergenic_variant    
IFLc Chr7:78685481 0.06 6.54 intergenic_variant    
IFLh Chr7:78685481 0.06 14.86 intergenic_variant    
NRRc Chr7:78380148 0.08 4.28 intergenic_variant    
NRRh Chr7:78685062 0.06 10.50 intergenic_variant    
  BTA9 QTL1
FTI Chr9:39070817 0.34 6.79 intergenic_variant    
AISc Chr9:40178726 0.48 8.22 intergenic_variant    
AISh Chr9:39056106 0.29 10.86 intergenic_variant    
ICF Chr9:43897568 0.16 9.19 intron_variant ENSBTAG00000017527 AIM1 absent in melanoma 1
IFLc Chr9:43027665 0.30 7.12 intron_variant ENSBTAG00000019175 SOBP sine oculis binding protein homolog (Drosophila)
IFLh Chr9:40147543 0.47 8.30 intergenic_variant    
NRRc Chr9:40176331 0.48 7.59 intergenic_variant    
NRRh Chr9:39056106 0.29 8.37 intergenic_variant    
  BTA9 QTL2
FTI Chr9:103675274 0.14 9.01 intergenic_variant    
AISc Chr9:102992258 0.37 7.52 intron_variant ENSBTAG00000021741 RPS6KA2 ribosomal protein S6 kinase, 90 kDa, polypeptide 2
AISh Chr9:103880081 0.43 9.57 intron_variant ENSBTAG00000005557 MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
ICF Chr9:103664731 0.14 10.66 intergenic_variant    
IFLc Chr9:104308602 0.44 9.45 intron_variant ENSBTAG00000013176 SMOC2 SPARC related modular calcium binding 2
IFLh Chr9:103861364 0.39 12.27 intron_variant&feature_truncation ENSBTAG00000005557 MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
NRRc Chr9:103788916 0.20 4.46 intergenic_variant    
NRRh Chr9:103861364 0.39 9.21 intron_variant&feature_truncation ENSBTAG00000005557 MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
  BTA25
FTI Chr25:26810616 0.27 9.37 upstream_gene_variant ENSBTAG00000031852 TBC1D10B TBC1 domain family, member 10B
AISc Chr25:26864302 0.39 7.40 downstream_gene_variant ENSBTAG00000010851 SEPHS2 selenophosphate synthetase 2
AISh Chr25:27783308 0.17 8.86 downstream_gene_variant ENSBTAG00000047734 C16orf58 chromosome 16 open reading frame 58
ICF Chr25:29847729 0.39 10.27 intergenic_variant    
IFLc Chr25:26810616 0.27 10.77 upstream_gene_variant ENSBTAG00000031852 TBC1D10B TBC1 domain family, member 10B
NRRc Chr25:27784063 0.17 6.45 downstream_gene_variant ENSBTAG00000047734 C16orf58 chromosome 16 open reading frame 58
NRRh Chr25:27784062 0.17 7.56 downstream_gene_variant ENSBTAG00000047734 C16orf58 chromosome 16 open reading frame 58
  1. 1In case the SNP marker is annotated as a downstream_gene_variant or an upstream_gene_variant the gene closest located to this SNP is listed.
  2. 2Fertility index (FTI); number of inseminations per conception in cows (AISc) and heifers (AISh); the length in days of the interval from calving to first insemination in cows (IFC); days from first to last insemination in cows (IFLc) and heifers (IFLh) and 56-day non-return rate in cows (NRRc) and heifers (NRRh).