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Table 2 Most significant SNP marker for FTI and the underlying female fertility traits

From: Genome-wide association study for female fertility in Nordic Red cattle

Trait namea Marker name rsname −log10(P) Annotationb Ensemble Gene name Gene description Proportion of additive genetic variance explained by the SNP
BTA1  
FTI Chr1:128614529 rs137748444 11.49 intergenic_variant     1.17
AISC Chr1:127295226 rs43271631 9.89 intron_variant ENSBTAG00000002232 TRPC1 Bos taurus transient receptor potential cation channel, subfamily C, member 1 0.89
AISH Chr1:128189301 rs136231770 11.75 upstream_gene_variant ENSBTAG00000021886 GRK7 Bos taurus G protein-coupled receptor kinase 7 1.21
ICF Chr1:128663781 Chr1:128663781c 7.32 intergenic_variant     0.67
IFLC Chr1:127295226 rs43271631 12.24 intron_variant ENSBTAG00000002232 TRPC1 Bos taurus transient receptor potential cation channel, subfamily C, member 1 1.26
IFLH Chr1:128189301 rs136231770 12.49 upstream_gene_variant ENSBTAG00000021886 GRK7 Bos taurus G protein-coupled receptor kinase 7 1.32
NRRC Chr1:127295226 rs43271631 7.37 intron_variant ENSBTAG00000002232 TRPC1 Bos taurus transient receptor potential cation channel, subfamily C, member 1 0.72
NRRH Chr1:128106801 rs43262199 8.36 intergenic_variant     0.93
BTA2  
FTI Chr2:133075293 rs42761190 8.51 intergenic_variant     0.90
AISC Chr2:133079214 rs42761183 6.17 intergenic_variant     0.57
AISH Chr2:132321329 rs209242168 13.30 intron_variant ENSBTAG00000040215 EIF4G3 Uncharacterized protein 1.44
ICF Chr2:133126588 rs109245794 9.98 upstream_gene_variant ENSBTAG00000012217 PLA2G2F Bos taurus phospholipase A2, group IIF 0.95
IFLC Chr2:133077462 rs42761186 6.00 intergenic_variant     0.57
IFLH Chr2:132321329 rs209242168 10.50 intron_variant ENSBTAG00000040215 EIF4G3 Uncharacterized protein 1.13
NRRC Chr2:131498393 rs110082997 6.92 intergenic_variant     0.74
NRRH Chr2:132321329 rs209242168 13.01 intron_variant ENSBTAG00000040215 EIF4G3 Uncharacterized protein 1.51
BTA3  
FTI Chr3:33388881 rs43336559 14.22 intergenic_variant     1.56
AISC Chr3:33388881 rs43336559 15.78 intergenic_variant     1.47
AISH Chr3:30770425 rs134664378 23.07 intron_variant ENSBTAG00000014299 RHOC Bos taurus ras homolog gene family, member C 2.48
ICF Chr3:31574900 rs43334971 8.05 intron_variant     0.80
IFLC Chr3:33388881 rs43336559 11.99 intergenic_variant     1.24
IFLH Chr3:35629755 rs109158850 15.86 intron_variant ENSBTAG00000031575 VAV3 vav 3 guanine nucleotide exchange factor 1.69
NRRC Chr3:33388483 rs381207703 18.34 intergenic_variant     1.87
NRRH Chr3:32024752 rs43332934 21.55 upstream_gene_variant ENSBTAG00000014102 WDR77 Bos taurus WD repeat domain 77 2.41
BTA5  
FTI Chr5:62781359 rs135099682 10.79 intergenic_variant     1.15
AISC Chr5:62781359 rs135099682 9.99 intergenic_variant     0.89
AISH Chr5:62781359 rs135099682 13.87 intergenic_variant     1.37
ICF Chr5:61879166 rs207754946 8.01 intergenic_variant     0.76
IFLC Chr5:61625072 rs434505378 10.16 intergenic_variant     0.97
IFLH Chr5:62781359 rs135099682 13.45 intergenic_variant     1.34
NRRC Chr5:64863598 rs383102267 6.74 intergenic_variant     0.59
NRRH Chr5:61836879 rs211681535 6.95 intergenic_variant     0.69
BTA6  
FTI Chr6:43511992 rs41983284 13.59 intron_variant ENSBTAG00000004653 GPR125 G protein-coupled receptor 125 1.54
AISC Chr6:43223916 rs133258175 12.17 intergenic_variant     1.15
AISH Chr6:44642153 rs209918674 20.98 intergenic_variant     1.99
ICF Chr6:42542483 rs110363606 7.77 intron_variant ENSBTAG00000047743 KCNIP4 Bos taurus Kv channel interacting protein 4 0.71
IFLC Chr6:45794025 rs109808198 12.17 intergenic_variant     1.26
IFLH Chr6:41455222 rs43610453 16.21 intron_variant ENSBTAG00000005108 SLIT2 Slit homolog 2 (Drosophila) 1.59
NRRC Chr6:42245672 rs109518200 12.48 intron_variant ENSBTAG00000047743 KCNIP4 Bos taurus Kv channel interacting protein 4 1.27
NRRH Chr6:44642153 rs209918674 17.63 intergenic_variant     1.80
BTA6  
FTI Chr6:98115824 rs208894094 11.29 intergenic_variant     1.26
AISC Chr6:98115824 rs208894094 6.38 intergenic_variant     0.58
AISH Chr6:99400480 rs379908987 14.72 intron_variant ENSBTAG00000022449 SCD5 Bos taurus stearoyl-CoA desaturase 5 1.51
ICF Chr6:98048673 rs133357086 10.91 intergenic_variant     1.06
IFLC Chr6:98115824 rs208894094 8.88 intergenic_variant     0.92
IFLH Chr6:99400480 rs379908987 13.58 intron_variant ENSBTAG00000022449 SCD5 Bos taurus stearoyl-CoA desaturase 5 1.42
NRRC Chr6:98385129 rs210763629 4.43 intergenic_variant     0.45
NRRH Chr6:96953202 rs110379023 12.73 intron_variant ENSBTAG00000035776 C4orf22 Chromosome 4 open reading frame 22 1.19
BTA13  
FTI Chr13:58664049 rs378998625 14.85 intron_variant ENSBTAG00000013574 ANKRD60 Ankyrin repeat domain 60 1.75
AISC Chr13:56125951 rs109185706 12.69 intergenic_variant     1.18
AISH Chr13:59923876 rs41700956 16.72 intergenic_variant     2.28
ICF Chr13:59112800 rs42555672 12.19 downstream_gene_variant ENSBTAG00000013574 ANKRD60 Ankyrin repeat domain 60 1.26
IFLC Chr13:57020976 rs109484180 13.17 intergenic_variant     1.37
IFLH Chr13:59923876 rs41700956 16.77 intergenic_variant     2.29
NRRC Chr13:60559073 rs41699546 6.44 intergenic_variant     0.60
NRRH Chr13:57048934 rs110280398 12.14 intergenic_variant     1.23
BTA15  
FTI Chr15:34677367 rs41763261 15.90 intron_variant ENSBTAG00000001410 GRAMD1B GRAM domain containing 1B 1.68
AISC Chr15:34737376 rs110670590 10.87 intron_variant ENSBTAG00000001410 GRAMD1B GRAM domain containing 1B 0.99
AISH Chr15:33428419 rs382278362 9.99 intergenic_variant     0.97
ICF Chr15:34702074 rs41763326 9.86 intron_variant ENSBTAG00000001410 GRAMD1B GRAM domain containing 1B 0.89
IFLC Chr15:34677367 rs41763261 15.55 intron_variant ENSBTAG00000001410 GRAMD1B GRAM domain containing 1B 1.55
IFLH Chr15:33428419 rs382278362 10.81 intergenic_variant     1.08
NRRC Chr15:34829707 rs378927222 11.19 intergenic_variant     1.67
NRRH Chr15:34802991 rs208575577 11.65 intergenic_variant     1.50
BTA20  
FTI Chr20:67116858 rs133488500 11.44 intergenic_variant     1.39
AISC Chr20:67623217 rs110045690 13.52 intergenic_variant     1.22
AISH Chr20:68086468 rs208936479 15.87 intergenic_variant     1.68
ICF Chr20:66806800 rs384363430 10.20 intergenic_variant     0.93
IFLC Chr20:67124570 rs42467155 13.09 intergenic_variant     1.50
IFLH Chr20:68084517 rs383590013 15.71 intergenic_variant     1.71
NRRC Chr20:67623217 rs110045690 10.79 intergenic_variant     1.05
NRRH Chr20:68086468 rs208936479 12.82 intergenic_variant     1.46
BTA24  
FTI Chr24:31820659 rs137134841 18.50 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 2.17
AISC Chr24:31820659 rs137134841 15.00 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 1.48
AISH Chr24:31817915 rs381174897 25.32 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 2.80
ICF Chr24:31442858 rs43737972 7.94 intergenic_variant     0.70
IFLC Chr24:31820659 rs137134841 14.49 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 1.58
IFLH Chr24:31817915 rs381174897 22.20 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 2.50
NRRC Chr24:30565598 rs42446963 11.49 intergenic_variant     1.16
NRRH Chr24:31817915 rs381174897 18.03 intron_variant ENSBTAG00000007383 ZNF521 Zinc finger protein 521 2.13
  1. A marker is significant if the –log10(P) > 8.25
  2. aFTI: fertility index, AIS: number of inseminations per conception, ICF: length in days of the interval from calving to first insemination, IFL: days from first to last insemination, and NRR: 56-day non-return rate (Suffix h: heifers and suffix c: cows)
  3. bIn case the SNP marker is annotated as a downstream_gene_variant or an upstream_gene_variant the gene closest located to this SNP is mentioned
  4. cSNP marker did not have an rs id
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