Table 4

Analysis of genetic variants for known traits and diseases

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


Abbreviations: Del, Deletion; Ins, Insertion; Neg, Negative; ND, Not Determined; Dup, Duplication

Doan et al. BMC Genomics 2012 13:78   doi:10.1186/1471-2164-13-78

Open Data