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Table 1 Top significant SNPs identified by univariate SSGWAS for significant associations with white blood cell traits at a genome-wise false discovery rate (FDR) of 0.05

From: Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

Traita Bloodb SNP ID SNP statusc SSCd SNP position (bp) MAFe FDR GVar (%)f 1-Mb window start SNP positiong (bp) Dominance effect
± standard error
Additive effecth ± standard error
EOS Blood 3 SNP1: rs336560074 Top lead 4 93,647,202 0.31 0.006 0.46 93,331,316 0.001 ± 0.01 −0.05 ± 0.01i
EOS Blood 3 SNP2: rs346258273 Top lead 10 8,186,695 0.08 0.03 0.35 7,396,201 −0.09 ± 0.04 0.14 ± 0.04
EOS Blood 3 SNP3: rs339860061 Top lead 12 36,308,994 0.13 0.003 0.53 35,450,868 0.002 ± 0.02 −0.06 ± 0.01
MONO Δ13 SNP4: rs321357560 Top floating 2 120,341,201 0.47 0.049 0.12 120,219,793 −0.03 ± 0.02 0.08 ± 0.02
MONO Δ13 SNP5: rs327963623 Top lead 9 105,461,701 0.43 0.049 1.23 105,461,701 −0.02 ± 0.02 −0.08 ± 0.02
  1. aEOS eosinophil concentration, MONO monocyte concentration
  2. bBlood 3: the CBC measures in Blood 3 collected at 2-weeks after the challenge; Δ13: the change of CBC measures from Blood 1 collected at 2-weeks before the challenge to Blood 3 collected at 2-weeks after a polymicrobial infectious challenge
  3. cTop lead: the most significant SNP with a group of supportive SNPs; Top floating: the most significant SNP without a group of supportive SNPs
  4. dSus scrofa chromosome
  5. eMinor allele frequency
  6. fThe largest percentage of additive genetic variance explained by the top significant SNP and its adjacent SNPs in a 1 Mb window
  7. gPositions of the start SNP for the 1 Mb window segment with the largest amount of additive genetic variance
  8. hEstimates of additive effects per additional copy of the “B” allele. When the dominance effect was not significant (p > 0.05) the estimate of the additive effect was based on a model without the dominance effect
  9. iSignificant estimates of additive and dominance effects are highlighted in bold (p < 0.05)