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Table 4 Analysis of genetic variants for known traits and diseases

From: Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare

PMID Chromosome Coordinate Gene Gene Name Phenotype Associated Genotype QH Genotype
20353955 [32] 1 108,249,293 TRPM1 transient receptor potential cation channel Leopard complex spotting and congenital stationary night blindness C/C C/T T/T
17498917 [12] 1 128,056,148 PPIB peptidyl-prolyl cis-trans isomerase B Hereditary equine regional dermal asthenia A/A G/A
20419149 [33] 1 138,235,715 MYO5A myosin-Va isoform 1 Lavender foal syndrome Del 1 bp Neg
8995760 [34] 3 36,259,552 MC1R melanocyte-stimulating hormone receptor Chestnut coat color T/T C/T
11086549 [17] 3 36,259,554 MC1R melanocyte-stimulating hormone receptor Chestnut coat color A/A G/G
16284805 [35] 3 77,735,520 KIT mast/stem cell growth factor receptor Sabino spotting A/A A/T T/T
18253033 [36] 3 77,740,163 KIT mast/stem cell growth factor receptor Tobiano spotting pattern A/A A/G G/G
21070277 [6] 4 38,969,307 PDK4 pyruvate dehydrogenase kinase isozyme 4 Racing performance A/A A/C C/C
21070277 [6] 4 38,973,231 PDK4 pyruvate dehydrogenase kinase isozyme 4 Racing performance A/A A/G G/G
12230513 [37] 5 20,256,789 LAMC2 laminin subunit gamma-2 precursor Junctional epidermolysis bullosa Ins C Neg
17029645 [38] 6 73,665,304 PMEL17 melanocyte protein 17 precursor Silver coat color T/T T/C C/C
19016681 [39] 8 45,603,643-45,610,231 LAMA3 laminin alpha-3 Junctional epidermolysis bullosa Del 6,589 Neg
9103416 [40] 9 35,528,429 DNAPK DNA-dependent protein kinase catalytic subunit Severe combined immunodeficiency Del 5 bp Neg
15318347 [41] 10 9,554,699 RYR1 ryanodine receptor 1 isoform 2 Malignant hyperthermia G/G G/C C/C
21059062 [19] 10 15,884,567 CKM creatine kinase M-type Racing performance A/A A/G G/G
18358695 [7] 10 18,940,324 GYS1 glycogen [starch] synthase muscle Polysaccharide storage myopathy A/A A/G G/G
7623088 [42] 11 15,500,439 SCN4A sodium channel protein type 4 subunit alpha Equine hyperkalemic periodic paralysis G/G G/C C/C
18802473 [43] 14 26,701,092 SLC36A1 proton-coupled amino acid transporter 1 Champagne dilution C/C C/G G/G
9580670 [44] 17 50,624,658 EDNRB endothelin B receptor precursor Lethal white foal syndrome AG/AG TC/TC
20932346 [18] 18 66,493,737 MSTN growth/differentiation factor 8 precursor Optimum racing distance T/T T/T
12605854 [45] 21 30,666,626 SLC45A2 membrane-associated transporter protein isoform Cream coat color A/A A/G G/G
21059062 [19] 22 22,684,390 COX4I2 cytochrome c oxidase subunit 4 isoform 2 Racing performance T/T T/C T/T
11353392 [46] 22 25,168,567 ASIP agouti-signaling protein precursor Black and bay color Del 11 bp ND
18641652 [47] 25 6,574,013-6,581,600 STX17 syntaxin 17 Gray coat color Dup 4,600 Neg
  1. Abbreviations: Del, Deletion; Ins, Insertion; Neg, Negative; ND, Not Determined; Dup, Duplication