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Table 3 Summary of the SNPs identified from the RNA-seq datasets in genes mapping within the GWAS regions

From: A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

SSC Interval Top SNP of the GWAS interval # SNPs called Highest LD SNP with highest LD Genotypic frequency (0/0; 0/1; 1/1) # called samples SNP effect Gene Trait
1 I3 rs327733412 3 0.07 rs710447566 0.34; 0.54; 0.11 35 Low KATNAL2 HABN
7 I2 rs336588919 2 0.4 rs330912302 0.63; 0.12; 0.25 32 Low CHD2 NABN
13 I1 rs690794887 21 0.4 rs331304027 0.06; 0.09; 0.85 33 Moderate ULK4 HABN
13 I2 rs327865244 11 0.2 rs323872641 0.49; 0.37; 0.14 35 Low ABHD14A HABN
  1. SSC, Sus scrofa chromosome; # SNPs called, number of SNPs identified in the SNP calling analysis; LD, linkage disequilibrium; Genotypic frequency: allelic frequency for each of the genotypes; # called samples, number of samples with reads in the given SNP position; HABN, head abnormalities; NABN, neck abnormalities
  2. The columns SNP effect and gene refer to the SNP with the highest LD in the region