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Table 2 Significant SNPs and candidate genes from multiple-trait analysis for six heifer 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
BTA2 70,633,250 1.7755e-06 Intergenic EN1 0
80,773,959 8.2906e-06 Intron TMEFF2 0
98,894,327 1.703e-05 Intergenic 0
BTA3 83,818,837 9.9389e-06 Exon PATJ 0
89,878,033 1.2513e-06 Intergenic 98
BTA4 2,476,516 1.0209e-05 Intergenic 0
17,304,670 2.5726e-06 Intergenic 0
36,768,135 2.6301e-05 Intergenic ENSBTAG00000053333* 0
77,892,378 2.4934e-05 Intergenic HECW1 0
BTA6 31,807,526 1.248e-05 Intergenic 2
54,108,303 9.9442e-06 Intergenic 1
BTA7 6,177,026 5.1964e-06 Intron CPAMD8, F2RL3, SIN3B, NWD1 1
8,193,333 2.7732e-05 Exon CASP14, CCDC105, SLC1A6, ENSBTAG00000053903, OR7C19, OR7A85, ENSBTAG00000051946 0
62,865,717 8.3985e-06 Intergenic FAT2, SPARC, ENSBTAG00000054940, ATOX1 0
97,438,333 1.6934e-05 Intergenic 0
100,189,059 2.344e-05 Intergenic ST8SIA4 2
BTA9 21,350,462 1.1343e-05 Intergenic 0
71,191,104 1.5112e-05 Intergenic 0
95,975,870 2.4538e-05 Intergenic ENSBTAG00000052316, SOD2, WTAP, ACAT2, TCP1, MRPL18, PNLDC1 5
BTA10 41,323,422 2.7906e-05 Intergenic 0
81,606,975 1.5652e-05 Intron SLC10A1, SMOC1 1
BTA12 45,686,110 1.8064e-05 Intergenic 0
45,712,972 2.0906e-05 Intergenic
69,768,461 1.8444e-05 Intergenic 0
77,682,412 2.495e-05 Intron NALCN 4
BTA13 3,327,860 1.1246e-05 Intergenic ANKEF1 0
42,023,779 3.7745e-05 Downstream NXT1, GZF1, NAPB, ENSBTAG00000027420, MGC133636, CST8, ENSBTAG00000015949 0
42,049,979 3.7745e-05 Intron
BTA14 18,883,604 1.0029e-05 Intergenic 3
54,326,109 7.0163e-06 Intergenic 1
61,221,242 3.2749e-05 Intergenic CTHRC1, FZD6, BAALC 3
67,859,596 1.5109e-05 Intergenic PTDSS1 0
BTA15 45,999,990 2.9729e-05 Intergenic OR6A2, OR6B18, ENSBTAG00000027525, OR6B17, ENSBTAG00000037603, OR2D4, OR2D3G, OR2AG1E, OR2AG1G, OR2AG1, OR2AG2 0
BTA18 39,676,071 1.3142e-05 Intron ZNF19, ZNF23, ENSBTAG00000053994*, CALB2, CMTR2, ENSBTAG00000051512 0
39,750,065 2.1267e-05 Intergenic
39,767,356 8.5276e-06 Exon
39,797,494 1.8113e-07 Downstream
39,854,578 9.5369e-06 Upstream
39,905,828 2.4327e-05 Intron
41,105,349 4.5111e-05 Intron ZNF536 2
41,112,039 2.5866e-05 Intron
BTA19 39,685,286 4.588e-05 Exon PLXDC1, CACNB1, RPL19, ENSBTAG00000050597, STAC2, ENSBTAG00000008368, FBXL20 0
46,856,509 2.2533e-05 Intron EFCAB3, METTL2A, TLK2 2
53,776,030 3.7096e-06 Intron DNAH17, PGS1, SOCS3 0
53,779,550 2.1366e-06 Intron
BTA20 12,849,264 2.7392e-05 Intron ENSBTAG00000049964 0
15,673,813 3.5073e-06 Intergenic HTR1A 0
15,788,934 4.5398e-07 Intergenic
15,839,035 3.8454e-05 Intergenic
29,868,266 8.7288e-06 Intergenic ENSBTAG00000054476 0
29,957,655 1.2013e-06 Intergenic
29,957,766 3.1125e-05 Intergenic
29,959,061 1.8094e-05 Intergenic
51,156,345 1.4415e-05 Intron CDH12 0
62,043,263 3.4353e-05 Intron CTNND2 0
62,043,442 3.5997e-05 Intron
BTA21 17,250,280 2.0376e-05 Intron AGBL1 0
BTA22 2,072,527 1.8504e-05 Intergenic EOMES 0
5,159,344 4.422e-05 Intron TGFBR2, GADL1 1
9,601,560 4.4335e-05 Intergenic ARPP21 0
9,634,144 1.8949e-05 Intergenic
11,393,650 1.341e-05 Intron CTDSPL, VILL, PLCD1, DLEC1 0
11,701,385 2.9746e-05 Intron ACAA1, ENSBTAG00000054286, MYD88, OXSR1, ENSBTAG00000050531*, SLC22A14, XYLB, ACVR2B 0
11,737,948 4.1052e-06 Downstream
35,777,156 2.4904e-05 Intron MAGI1 0
51,337,027 3.512e-05 Intron CELSR3, SLC26A6, TMEM89, UQCRC1, ENSBTAG00000049917*, ENSBTAG00000052088*, ENSBTAG00000049028*, UCN2, PFKFB4, SHISA5, ENSBTAG00000048942, TREX1, ATRIP, TMA7, CCDC51 2
55,900,928 4.9063e-05 Intergenic TAMM41, TRH, TMCC1 1
BTA23 5,726,221 2.9329e-05 Intergenic 0
25,235,958 5.2155e-05 Intron GSTA1, GSTA5, GSTA3, GSTA4, CILK1, FBXO9, GCM1 0
25,819,703 4.2745e-05 Intergenic ENSBTAG00000013919, ENSBTAG00000048364, ENSBTAG00000038397, ENSBTAG00000015565, BOLA-DRA, BTNL2, ENSBTAG00000034945, ENSBTAG00000007618 0
26,689,257 1.4214e-05 Intergenic 0
28,036,775 4.1923e-06 Intron ENSBTAG00000051047, ENSBTAG00000007075, ENSBTAG00000053433, POU5F1, TCF19, CCHCR1, PSORS1C2, CDSN, C23H6orf15 1
28,634,425 3.1365e-05 Intergenic BOLA-NC1, JSP.1, ENSBTAG00000037421, BOLA 0
30,058,286 2.9988e-05 Intron ZNF311, ENSBTAG00000052294*, TRIM27, ENSBTAG00000053198 0
34,904,897 1.9645e-05 Intergenic GHE4, PRP2, PRP14, PRP9 0
34,928,894 5.2141e-05 Intron
BTA24 13,978,039 3.8859e-05 Intron PIK3C3 0
58,070,140 2.9176e-05 Intron ZNF532, ENSBTAG00000022829, SEC11C 0
BTA25 38,933,869 4.7617e-05 Intron FBXL18, ENSBTAG00000050734*, TNRC18, SLC29A4, WIPI2 3
BTA27 13,585,281 3.5455e-05 Intron TENM3 1
23,857,214 4.66e-05 Intron DLC1 0
30,435,395 1.768e-05 Intergenic 0
34,758,502 1.2659e-05 Intron ADAM2, ADAM3A 3
BTA28 10,602,903 3.7999e-05 Intergenic RYR2, ZP4 1
24,802,568 6.4777e-05 Intron PBLD, HNRNPH3, RUFY2, DNA2, SLC25A16 0
39,062,420 5.1602e-05 Intergenic GHITM, C10orf99, CDHR1 0
BTA29 27,630,533 1.1083e-05 Intergenic OR8G5, OR8G47, OR8D2, OR8B1U, OR8B1S, OR8B1AE, ENSBTAG00000051999, OR8B3G, ENSBTAG00000050103, OR8B3 0
  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)