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Table 3 Top SNPs from the GWAS on different case-control analyses of the FCI hip score

From: Genetic dissection of canine hip dysplasia phenotypes and osteoarthritis reveals three novel loci

Trait

Chr

Locus

Alleles

N per SNP

SNP(s)

P-value from FASTA, corrected with the inflation factor lambda (λ = 1.010–1.024)

1st case-control analysis (normal hips or mild-to-severe CHD; FCI scores)

1

45,382,633

45,161,186

46,279,297

46,268,586

C/A

G/C

A/G

C/A

693

693

689

692

BICF2P468585

BICF2S23248027

BICF2P357728

BICF2P1037296

7.03 × 10–7

1.30 × 10–6

2.52 × 10–6

9.51 × 10–6

2nd case-control analysis (normal hips or moderate-to-severe CHD; FCI scores)

9

36,837,067

36,886,621

G/A

A/G

520

517

BICF2G630837405

TIGRP2P126345

4.96 × 10–6

7.75 × 10–6

3rd case-control analysis (mild CHD or moderate-to-severe CHD; FCI scores)

9

36,837,067

36,886,621

G/A

A/G

340

338

BICF2G630837405

TIGRP2P126345

4.12 × 10–6

7.48 × 10–6

  1. SNPs with P-values < 1.0 × 10–5 are listed. The SNPs and their corresponding P-values are in bold font if the P-value passed the threshold for genome-wide significance (1.82 × 10–6) determined with the estimated number of independent tests from SimpleM (see methods). N refers to the number dogs in analysis after exclusion of dogs by FASTA because they lack either the phenotype or a covariate. Covariates for the 1st analysis: age at radiographing and genotyping batch. Covariates for the 2nd analysis: age at radiographing, genetic cluster, genotyping batch and birth month. Covariates for the 3rd analysis: genetic cluster, genotyping batch and birth month. See also Additional file 1