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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)