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

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

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
		2	rs332927981	2,415,239	7.36 × 10^–3	0.03	0.09	− 0.39	ACRO_5	− 0.33	NCLN
		2	rs318575212	2,412,006	1.83 × 10^–4	0.03	0.09	− 1.8	ACRO_5	− 0.46	ASCC1
		2	rs332927981	2,415,239	1.83 × 10^–4	0.03	0.09	− 1.8	ACRO_5	− 0.46	ASCC1
		2	rs318575212	2,412,006	2.87 × 10^–4	4.83 × 10^–2	0.09	− 1.1	ACRO_5	− 0.4	AATF
		2	rs332927981	2,415,239	2.87 × 10^–4	4.83 × 10^–2	0.09	− 1.1	ACRO_5	− 0.4	AATF
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

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

ISSN: 1297-9686