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Table 1 SNPs with suggestive association identified within all CHD phenotype approaches in single-population and meta-analysis GWAS. GWAS were performed for 180 (UK), 402 (Swedish), 775 dogs (Finnish) and 1357 (meta-analysis) dogs, respectively. The Finnish-population and meta-analysis GWAS are based on data provided by Mikkola et al. [11] and the Finnish-population GWAS is a repetition of the original GWAS with altered phenotypes (see Materials and methods for further details)

From: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci

SNP ID

Chr

Pos (bp)

AF$

β ± SE

p-value

Trait

Gene(s)§

BICF2S23248027

1

45,161,186

0.39

0.13 ± 0.03

1.14E-05

FIN case-control

TIAM2, TFB1M, CLDN20, NOX3

BICF2S23248027

1

45,161,186

0.39

0.38 ± 0.09

1.17E-05

FIN-FCI

TIAM2, TFB1M, CLDN20, NOX3

BICF2P468585

1

45,382,633

0.39

0.13 ± 0.03

7.28E-06

FIN case-control

NOX3

BICF2P468585

1

45,382,633

0.39

0.40 ± 0.09

4.21E-06

FIN-FCI

NOX3

BICF2P1037296

1

46,268,586

0.42

0.38 ± 0.09

1.56E-05

FIN-FCI

ARID1B

BICF2S22930063

7

11,089,390

0.20

−0.11 ± 0.03

5.96E-06

Meta-analysis case-control

NSL1, TATDN3, ENSCAFG00000029517, FLVCR1, VASH2, ANGEL2, RPS6KC1

BICF2G630561445

7

58,512,418

0.15

0.63 ± 0.13

2.85E-06

UK-FCI

DSC1, DSC2, DSC3

BICF2G630561553

7

58,588,983

0.26

0.54 ± 0.11

1.86E-06

UK-FCI

DSC2, DSC3

BICF2P566919

7

58,676,276

0.16

0.59 ± 0.13

1.44E-05

UK-FCI

 

BICF2G630561779

7

58,791,059

0.15

0.63 ± 0.13

4.35E-06

UK-FCI

 

TIGRP2P100978

7

58,825,151

0.15

0.63 ± 0.13

4.35E-06

UK-FCI

 

BICF2G630561837

7

58,845,222

0.15

0.61 ± 0.13

7.57E-06

UK-FCI

 

BICF2G630562441

7

59,795,168

0.15

0.59 ± 0.13

1.35E-05

UK-FCI

 

BICF2P321938

8

65,857,629

0.33

0.37 ± 0.08

2.59E-06

SWE-FCI

 

BICF2S23027935

9

31,300,189

0.49

0.34 ± 0.08

1.42E-05

FIN-FCI

ANKFN1, NOG

BICF2P742007

9

31,387,114

0.44

0.36 ± 0.08

7.51E-06

FIN-FCI

ANKFN1, NOG

BICF2G630834826

9

31,477,907

0.45

0.34 ± 0.08

1.52E-05

FIN-FCI

ANKFN1, NOG, C17orf67, DGKE

BICF2G630835183

9

32,155,751

0.49

0.35 ± 0.08

9.91E-06

FIN-FCI

 

BICF2G630835188

9

32,166,146

0.48

0.35 ± 0.08

6.99E-06

FIN-FCI

 

BICF2G630835202

9

32,181,375

0.49

0.34 ± 0.08

1.35E-05

FIN-FCI

 

BICF2G630835214

9

32,190,814

0.49

0.34 ± 0.08

1.48E-05

FIN-FCI

 

BICF2G630835223

9

32,271,830

0.47

0.36 ± 0.08

7.23E-06

FIN-FCI

CCDC182

BICF2G630836291

9

34,689,620

0.38

0.35 ± 0.08

1.59E-05

FIN-FCI

MED13, INTS2, BRIP1

BICF2G630836291

9

34,689,620

0.32

0.28 ± 0.06

3.13E-06

Meta-analysis-FCI

MED13, INTS2, BRIP1

BICF2G630836293

9

34,700,358

0.37

0.35 ± 0.08

1.37E-05

FIN-FCI

MED13, INTS2, BRIP1

BICF2G630836293

9

34,700,358

0.32

0.28 ± 0.06

2.57E-06

Meta-analysis-FCI

MED13, INTS2, BRIP1

BICF2G630836294

9

34,723,827

0.37

0.36 ± 0.08

1.05E-05

FIN-FCI

MED13, INTS2, BRIP1

BICF2G630836294

9

34,723,827

0.32

0.28 ± 0.06

2.39E-06

Meta-analysis-FCI

MED13, INTS2, BRIP1

BICF2G630837240

9

36,579,921

0.46

−0.35 ± 0.08

9.21E-06

FIN-FCI

ZNHIT3, MYO19, PIGW, GGNBP2, DHRS11, MRM1, LHX1, AATF

BICF2G630837405

9

36,837,067

0.46

0.36 ± 0.08

3.63E-06

FIN-FCI

LHX1, AATF, ACACA

BICF2G630442661

15

12,679,667

0.15

−0.35 ± 0.08

8.81E-06

Meta-analysis-FCI

SPATA6, SLC5A9, TRABD2B

BICF2P110724

21

39,241,001

0.11

0.85 ± 0.16

4.00E-07*

UK-FCI

SOX6, ENSCAFG00000030220, PLEKHA7

BICF2P689487

21

39,270,633

0.11

0.86 ± 0.16

3.81E-07*

UK-FCI

SOX6, ENSCAFG00000030220, PLEKHA7

TIGRP2P285227

21

39,296,148

0.11

0.85 ± 0.16

4.00E-07*

UK-FCI

SOX6, ENSCAFG00000030220, PLEKHA7

TIGRP2P285228

21

39,304,525

0.11

0.85 ± 0.16

4.00E-07*

UK-FCI

SOX6, ENSCAFG00000030220, PLEKHA7

BICF2P865829

21

39,466,638

0.11

0.83 ± 0.16

3.63E-07*

UK-FCI

ENSCAFG00000030220, PLEKHA7

TIGRP2P333312

25

46,422,704

0.08

−0.27 ± 0.06

1.28E-05

SWE case-control

AGAP1

  1. $AF; allele frequency for the population the significant/ suggestive SNP was identified in (allele frequency within all populations is given in Table S2)
  2. *Genome-wide significant p-value after Bonferroni correction
  3. §Genes located within 200 kb of SNPs. Genes are highlighted in bold if a significant or suggestive SNP was intragenic. Empty entries indicate there are no genes within 200 kb of the SNP
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BMC Genomics

ISSN: 1471-2164

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