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Table 4 Significant SNPs and candidate genes from multiple-trait analysis for four sire fertility traits

From: Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

Chr

Position (bp)

P values

Genomic location

Candidate genes

(within ± 100 kb)a

N of QTLb

BTA3

147,935

2.2433e-05

Intergenic

ENSBTAG00000000584, TBX19

0

71,522,570

2.1323e-05

Intergenic

—

0

BTA4

18,040,294

2.4781e-05

Intergenic

—

0

47,200,188

2.5485e-05

Intergenic

SYPL1

0

59,888,193

9.0367e-06

Intron

ELMO1

0

82,878,864

9.7487e-07

Intergenic

LSM8

3

BTA5

6,106,039

2.7083e-06

Intergenic

ZDHHC17

0

13,310,594

9.9233e-07

Intergenic

—

0

32,058,789

1.0382e-05

Intergenic

H1-7, ENSBTAG00000032429, ENSBTAG00000032428, CCDC184, ASB8, PFKM

0

53,516,007

2.3608e-05

Intergenic

—

6

BTA6

7,494,351

1.3907e-05

Intergenic

ENSBTAG00000051854*

2

16,046,562

2.6665e-05

Intergenic

—

0

BTA7

56,985,760

2.23e-05

Intron

PRELID2, GRXCR2

0

64,117,199

1.5768e-05

Intergenic

—

2

65,880,766

2.3775e-05

Intergenic

ENSBTAG00000053039*, LARP1

0

65,887,207

2.5969e-06

Intergenic

68,359,300

1.6201e-05

Intergenic

ENSBTAG00000030297, TIMD4, ENSBTAG00000050582*, ENSBTAG00000049542*

0

68,430,783

1.5884e-05

Intergenic

69,170,746

2.7112e-05

Intron

CYFIP2, NIPAL4, ADAM19, SOX30

0

83,320,343

2.8225e-06

Intron

XRCC4, VCAN

1

100,056,219

8.7549e-06

Intron

ST8SIA4

2

BTA9

15,828,286

7.3866e-06

Intergenic

—

2

15,843,031

2.5491e-05

Intergenic

74,655,065

1.7472e-05

Intron

MAP3K5

4

BTA10

13,081,096

2.3448e-05

Intron

MEGF11

0

55,196,388

9.9519e-06

Intergenic

RSL24D1

0

77,838,554

2.8177e-05

Downstream

FUT8

0

77,968,781

1.3016e-05

Intergenic

BTA11

58,988,314

1.1679e-05

Intergenic

—

0

63,929,970

1.3355e-05

Intergenic

—

0

BTA12

60,487,742

4.3234e-06

Intergenic

—

0

63,535,854

1.6981e-05

Intergenic

—

0

63,538,393

2.1305e-05

Intergenic

BTA13

13,568,203

2.023e-05

Intergenic

—

0

14,812,273

1.4407e-05

Intergenic

—

0

41,317,365

1.2933e-05

Intergenic

—

0

53,595,922

1.5122e-05

Intron

ENSBTAG00000054594, ENSBTAG00000011638, ENSBTAG00000054447, ENSBTAG00000027221, GINS1, PCMTD2, MYT1

2

BTA14

78,863,167

3.3468e-05

Intergenic

—

0

BTA15

30,636,699

1.2166e-05

Intergenic

TRIM29

3

60,970,873

2.5168e-05

Intergenic

FSHB, ARL14EP

2

BTA16

23,387,972

1.0853e-05

Intergenic

SLC30A10, EPRS1

0

BTA17

18,332,441

2.8154e-05

Intron

RAB33B, NAA15, NDUFC1, MGARP, ENSBTAG00000015811, ELF2

3

18,371,778

2.706e-05

Intron

18,408,888

2.8364e-05

Intron

18,458,616

2.3968e-05

Intergenic

33,971,794

2.9933e-05

Intergenic

ENSBTAG00000052376*

5

48,501,570

3.3186e-05

Intron

TMEM132C

2

73,040,719

1.7853e-05

Intergenic

TANGO2, ENSBTAG00000049742*, DGCR8, TRMT2A, ENSBTAG00000049062, RANBP1, ZDHHC8, CCDC188, ENSBTAG00000052630*, RTN4R, PRODH, DGCR6L

8

BTA19

3,507,732

6.9599e-06

Intergenic

—

0

6,425,261

2.0337e-05

Intron

PCTP, ENSBTAG00000053407, ENSBTAG00000039563

0

23,803,632

4.6828e-05

Intron

RAP1GAP2, ENSBTAG00000049401, OR1D3B, OR1D3

2

23,811,867

3.2146e-05

Intron

BTA20

6,792,445

2.1451e-05

Intron

FAM169A, NSA2, GFM2, HEXB, LOC786974

0

44,069,982

8.8349e-06

Intergenic

—

0

53,664,202

1.0238e-05

Intron

CDH18

0

BTA21

3,550,200

1.2359e-05

Intergenic

—

0

BTA22

529,021

3.8026e-05

Intron

VOPP1, LANCL2

0

756,892

2.5524e-05

Intron

37,660,216

4.9522e-05

Intergenic

THOC7, C22H3orf49, ENSBTAG00000051113*, SNTN

3

42,471,770

2.3695e-05

Intron

CFAP20DC

3

44,200,445

1.8137e-06

Intron

ARHGEF3

0

59,781,347

1.759e-05

Intron

MGLL, ABTB1, PODXL2

0

BTA24

1,516,807

1.8306e-05

Intergenic

—

0

20,595,336

4.1116e-05

Intron

FHOD3

1

57,446,121

5.5515e-06

Intron

NEDD4L, ENSBTAG00000051924*

0

57,476,264

2.8706e-05

Exon

61,476,879

2.1094e-05

Intron

BCL2

1

BTA25

26,121,115

1.2696e-05

Intron

EIF3CL, CLN3, ENSBTAG00000050361, IL27, NUPR1, SGF29, SULT1A1, SLX1A, ENSBTAG00000008632, CORO1A, MAPK3, GDPD3, YPEL3, TBX6, PPP4C, ALDOA, ENSBTAG00000050743

1

27,554,453

2.3765e-05

Intergenic

ITGAD, COX6A2, ARMC5, TGFB1I1, SLC5A2, RUSF1, AHSP, OR7A53, OR7A153, SEPTIN14, ZNF713, MRPS17

1

39,147,647

6.6288e-05

Intron

MMD2, ENSBTAG00000051446, RADIL, PAPOLB, AP5Z1, ENSBTAG00000050145*, FOXK1

1

40,290,599

1.0271e-05

Intergenic

CARD11

0

40,356,262

5.4215e-05

Intergenic

BTA26

10,927,671

1.4324e-06

Intergenic

ENSBTAG00000054811*, LIPA

1

27,142,712

2.691e-05

Intergenic

ENSBTAG00000055185*

0

30,565,345

4.8874e-05

Intergenic

XPNPEP1, ENSBTAG00000054944, ADD3

0

48,212,324

5.1946e-05

Intergenic

ENSBTAG00000053738*

5

BTA27

13,351,474

3.8108e-05

Intron

ENSBTAG00000047749

1

25,506,261

6.2859e-05

Intron

TNKS

1

BTA28

5,066,852

2.9294e-05

Intergenic

—

1

19,499,175

7.0726e-06

Intron

JMJD1C

0

29,298,316

2.2431e-06

Intron

NUDT13, ECD, FAM149B1, DNAJC9, MRPS16, CFAP70, ANXA7

0

37,896,374

1.0502e-05

Intron

NRG3

1

BTA29

4,807,970

5.4737e-05

Intergenic

—

1

14,612,904

3.5086e-05

Intergenic

—

1

  1. aCandidate genes are represented by gene symbol when available, otherwise by the Ensembl gene ID. The long noncoding RNA genes are marked by asterisk (*). The genes directly linked to SNPs are further denoted in bold
  2. bThe number of known and reproduction-associated QTL found in Cattle QTL Database v43 (www.animalgenome.org)