Summary-data based Mendelian randomization identifies gene expression regulatory polymorphisms associated with bovine paratuberculosis by modulation of the nuclear factor Kappa β (NF-κß)-mediated inflammatory response

Table 2 Top 10 most significant cis-eQTL found in the SMR analyses (P-value ≤ 0.05) using GWAS data from a case–control study where cows with multifocal lesions (N = 33) and without lesions (N = 373) were compared

Sample	Chr	Position	Gene ID	Gene symbol	SNP ID	SNP effect	P-value	FDR
ICV	23	27,146,264	ENSBTAG00000049699	U6	rs382341668	0.27394	0.00052194	0.134
	24	60,894,426	ENSBTAG00000035171	SERPINB12	rs477516898	0.13948	0.00171221	0.22
	18	63,798,265	ENSBTAG00000053810		rs432670715	0.220168	0.00404204	0.346
	5	106,389,826	ENSBTAG00000042924	SNORA70	rs464151990	-0.0624398	0.01562814	0.963
	29	1,195,578	ENSBTAG00000054019		rs379620385	0.0697581	0.02785573	0.963
	3	17,894,282	ENSBTAG00000053103		rs109701681	0.00163663	0.03640438	0.963
	3	20,098,666	ENSBTAG00000022741	MGC134040	rs478694916	0.055018	0.03735433	0.963
	14	63,608,763	ENSBTAG00000042171	SNORA70	rs441304008	-0.0235147	0.03771466	0.963
	6	94,896,092	ENSBTAG00000035776	CFAP299	rs459014612	0.0827706	0.04253706	0.963
	22	55,021,464	ENSBTAG00000043073	U6	rs443419569	0.0815626	0.04585341	0.963
PB	11	10,810,645	ENSBTAG00000024058	EGR4	rs383097118	0.222932	4.75E-06	0.002
	3	47,966,652	ENSBTAG00000007101	F3	rs380850681	0.00536243	0.00193635	0.207
	23	16,744,416	ENSBTAG00000015131	SLC29A1	rs137606813	0.00021436	0.00189969	0.207
	1	38,894,238	ENSBTAG00000023652	PROS1	rs385387727	0.00120501	0.00103787	0.207
	19	18,988,823	ENSBTAG00000008788	SLC13A2	rs478589506	0.24342	0.00511518	0.365
	22	6,288,529	ENSBTAG00000022744	TRIM71	rs136689901	0.0169698	0.00434811	0.365
	2	128,473,027	ENSBTAG00000038865	TCEA3	rs482027819	0.0143887	0.00868258	0.532
	3	94,262,264	ENSBTAG00000009674	C3H1orf185	rs466365210	0.216626	0.01357773	0.677
	1	72,577,888	ENSBTAG00000048826		rs109233921	-0.0774901	0.0142077	0.677
	5	106,654,304	ENSBTAG00000008553	B4GALNT3		-0.0420428	0.02157095	0.74

SNP effect- the effect size of a SNP on the phenotype that is mediated by gene expression.
ICV Ileocecal valve, PB Peripheral blood, Chr Chromosome, SNP single nucleotide polymorphism, FDR false discovery rate, ID identification code

ISSN: 1471-2164