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 3 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 diffuse lesions (N = 36) and without lesions (N = 373) were compared

Sample	Chr	Position	Gene ID	Gene symbol	SNP ID	SNP effect	P-value	FDR
ICV	3	20,098,666	ENSBTAG00000022741	MGC134040	rs478694916	0.103	7.53E-05	0.017
	10	25,670,772	ENSBTAG00000039241	OR6S1		0.14	1.85E-03	0.212
	3	114,640,987	ENSBTAG00000044472	5S_rRNA	rs469342481	0.065	9.70E-03	0.741
	3	17,181,908	ENSBTAG00000053743		rs471339029	0.108	0.016	0.754
	22	15,880,322	ENSBTAG00000007969	CIDEC	rs209078215	-0.0008	0.016	0.754
	13	73,824,843	ENSBTAG00000045630		rs801310416	0.086	0.027	0.798
	19	20,354,910	ENSBTAG00000042268	LOC112442820	rs481186610	0.07	0.029	0.798
	7	58,851,099	ENSBTAG00000033759	LOC777593	rs383285289	-0.087	0.03	0.798
	13	63,197,058	ENSBTAG00000010112	BPIFB6	rs110136678	0.001	0.031	0.798
	5	93,655,946	ENSBTAG00000052966	bta-mir-2285be	rs453650622	0.154	0.038	0.8
PB	1	97,501,420	ENSBTAG00000005871	MECOM	rs382448539	0.022	5.22E-04	0.201
	15	21,656,148	ENSBTAG00000015810	C15H11orf34	rs110448688	0.112	1.39E-03	0.267
	1	148,065,848	ENSBTAG00000030585	CLDN14		0.356	3.44E-03	0.441
	16	48,321,792	ENSBTAG00000045373	bta-mir-2320		0.108	7.63E-03	0.734
	15	64,738,340	ENSBTAG00000017150	EHF	rs876546467	0.053	9.83E-03	0.757
	13	74,882,914	ENSBTAG00000002942	SLC2A10	rs41711514	0.002	0.014	0.874
	3	47,966,652	ENSBTAG00000007101	F3	rs380850681	0.004	0.017	0.916
	9	9,801,563	ENSBTAG00000035054	COL9A1	rs435010900	0.04	0.021	0.986
	5	114,503,489	ENSBTAG00000006973	PHF21B	rs444663763	0.027	0.023	0.986
	15	21,822,607	ENSBTAG00000053780		rs109404405	0.029	0.026	0.986

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