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Table 3 Significant SNPs and candidate genes from multiple-trait analysis for nine cow fertility and reproduction 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
BTA1 34,156,863 6.8092e-06 Intergenic CADM2 0
BTA2 44,192,878 1.7484e-05 Intron CACNB4 0
BTA3 13,060,985 1.5004e-05 Intergenic ENSBTAG00000053098, ENSBTAG00000052866*, ENSBTAG00000054932, ENSBTAG00000051454 0
67,686,622 2.6373e-05 Intron ST6GALNAC5 0
67,687,557 2.2745e-05 Intron
67,687,632 1.0234e-05 Intron
67,687,904 1.6141e-05 Intron
67,688,010 8.0894e-06 Intron
67,688,259 1.4877e-05 Intron
67,691,020 1.2185e-05 Intron
67,691,132 9.1178e-06 Intron
67,691,448 2.7514e-05 Intron
67,691,487 1.6939e-05 Intron
67,691,717 2.6505e-05 Intron
67,693,137 1.9264e-05 Intron
67,693,371 2.0276e-05 Intron
BTA4 52,090,769 3.731e-06 Intergenic TES, ENSBTAG00000055251 0
86,337,952 2.7549e-05 Intron PTPRZ1 0
86,338,437 5.4702e-06 Intron
BTA5 59,741,942 2.5619e-05 Downstream OR9K2, OR9K15, OR9K1, OR9K2F, OR9K1B 1
61,923,964 1.5754e-05 Intergenic None 2
98,326,111 2.4699e-05 Intergenic None 0
BTA8 9,613,389 1.6984e-05 Intron KIF13B, HMBOX1 0
48,903,003 2.4027e-06 Intergenic ENSBTAG00000048940*, TMC1, ENSBTAG00000052698 0
49,280,626 6.2112e-06 Intergenic ENSBTAG00000052764*, ANXA1 0
49,282,386 7.11e-06 Intergenic
49,282,702 8.1027e-06 Intergenic
52,344,611 2.7461e-05 Intron PCSK5 0
97,982,105 1.9975e-05 Intergenic None 0
98,998,669 2.7653e-05 Intron PTPN3 0
100,989,652 2.3223e-05 Intron ECPAS, ZNF483, PTGR1, DNAJC25, GNG10 0
BTA9 21,350,462 2.972e-06 Intergenic None 0
73,443,174 2.0733e-05 Intron AHI1, ENSBTAG00000046495 0
91,316,160 2.1955e-05 Intergenic ENSBTAG00000020723, ENSBTAG00000049872, SCAF8 1
BTA10 15,091,095 1.0356e-05 Intergenic PIAS1, CALML4, CLN6, FEM1B, ITGA11 2
15,499,538 2.5633e-05 Intron CORO2B 0
15,737,285 1.2939e-05 Intergenic ANP32A, ENSBTAG00000051138*, SPESP1 0
27,718,962 6.5343e-06 Downstream OR4F67B, OR4G18, OR4K36, OR4G8, OR4G9, OR4G2 0
30,942,681 2.4868e-05 Intron DPH6 0
BTA11 89,383,411 1.5143e-05 Intergenic None 3
BTA12 74,138,771 2.0551e-05 Intergenic HS6ST3, ENSBTAG00000045566, OXGR1 0
74,922,982 3.4154e-05 Intergenic ENSBTAG00000052185* 2
BTA13 20,203,933 6.2166e-07 Intergenic ENSBTAG0000002675, ENSBTAG00000052951 0
BTA14 2,204,649 8.1819e-06 Intergenic ENSBTAG00000048964* 1
40,827,215 1.0856e-05 Intergenic ENSBTAG00000039499 0
79,535,150 3.2796e-06 Intergenic None 0
BTA15 54,978,763 2.5073e-05 Intergenic MOGAT2, ENSBTAG00000053794, LOC785379, ENSBTAG00000017443, ENSBTAG00000015091, ENSBTAG00000052936 1
73,049,607 1.3516e-05 Intergenic None 0
BTA17 4,778,666 1.7939e-05 Intron FHDC1, ARFIP1 1
7,455,065 4.1422e-05 Intron LRBA 0
32,848,516 5.4123e-07 Intergenic None 0
36,481,658 9.3183e-06 Intron FSTL5 1
BTA18 61,968,892 2.8497e-05 Intergenic EPN1, U2AF2, CCDC106, ZNF581, ZNF580, ZNF524, ZNF784, FIZ1, ZNF579, SBK2, SSC5D, NAT14, ZNF628, C19orf85, ENSBTAG00000050011, ISOC2, SHISA7 0
63,182,112 3.3624e-05 Intergenic ENSBTAG00000049178, RPS9, TSEN34, MBOAT7, TMC4, LENG1, CNOT3, PRPF31, TFPT, NDUFA3 6
BTA19 59,744,349 4.8366e-06 Intergenic None 0
BTA20 56,959,618 2.3978e-05 Intron MARCHF11 4
60,163,003 4.01e-05 Intergenic None 0
BTA21 16,945,728 2.5982e-05 Intergenic AGBL1 0
60,917,828 2.6523e-06 Intron C21H14orf132 0
BTA22 56,807,677 1.3049e-05 Intron PPARG, ENSBTAG00000052393* 0
BTA23 2,330,898 2.7799e-05 Intergenic None 0
28,726,064 3.9504e-06 Upstream JSP.1, ENSBTAG00000037421, BOLA, TRIM26, TRIM15, TRIM10 0
BTA24 45,122,975 4.3551e-05 Intergenic None 0
57,019,331 7.1833e-06 Intergenic ATP8B1 1
BTA25 8,675,209 3.4891e-05 Intron GRIN2A 0
8,702,138 2.0848e-06 Intergenic
27,413,783 6.8667e-06 Exon ITGAM, ITGAX, ITGAD, COX6A2, ARMC5, TGFB1I1 1
BTA27 24,754,025 1.5149e-05 Intron CLDN23, LOC527981 1
43,998,949 1.466e-06 Intergenic ZNF385D 1
BTA28 19,657,628 8.5e-06 Intron JMJD1C, REEP3 0
BTA29 13,752,854 2.5963e-05 Intergenic None 0
37,010,381 1.9927e-05 Intergenic ENSBTAG00000050640*, SNX19, ENSBTAG00000022460, MS4A8, MS4A18 2
  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)