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Table 4 Summary of the results from the within-trait expression genome wide association analysis

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

SSC Interval # SNP: transcripts Top eGWAS Top eGWAS location bp Top eGWAS P-value Top eGWAS FDR Top eGWAS MAF Beta Trait RNA abundance correlation Associated gene
4 I1 2 rs318575212 2,412,006 7.36 × 10–3 0.03 0.09 − 0.39 ACRO_5 − 0.33 NCLN
rs332927981 2,415,239
2 rs318575212 2,412,006 1.83 × 10–4 0.03 0.09 − 1.8 ACRO_5 − 0.46 ASCC1
rs332927981 2,415,239
2 rs318575212 2,412,006 2.87 × 10–4 4.83 × 10–2 0.09 − 1.1 ACRO_5 − 0.4 AATF
rs332927981 2,415,239
6 I1 2 rs335394654 65,597,553 5.63 × 10–5 0.02 0.11 − 1.65 ACRO_5 − 0.35 IQCJ
13 I1 31 rs328397029 25,684,259 1.84 × 10–5 2.95 × 10–3 0.09 − 1.03 HABN − 0.38 HARS, ACTR2, EPB41L3, RAB1B
  1. SSC, Sus scrofa chromosome; # SNP: transcripts, number of single nucleotide polymorphisms significantly associated to a transcript; Beta, additive effect; MAF, minor allele frequency; ACRO_5, abnormal acrosomes 5 min; HABN, head abnormalities