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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).
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BMC Genomic Data

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