TABLE 2.

Colocalization analysis between CD GWAS and whole blood eQTL using eCAVIAR in TNFSF15 and GPR35 locus.

Locus	Gene	SNP	Position (hg19)	Allele		Credible set posterior probabilitya	CLPPb	CD GWASc				Whole blood -cis eQTL
				Risk	Non-risk			RAF Cases	RAF Controls	P value	OR	P valued	Slopee	Distance (BP)f
9q32	TNFSF15	rs6478109	117,568,766	G	A	0.50	0.23	0.706	0.521	3.19 × 10–45	2.10	3.59 × 10–10	−0.75	360
		rs7848647	117,569,046	C	T	0.50	0.23	0.644	0.513	3.29 × 10–45	2.10	3.59 × 10–10	−0.75	640
2q37	GPR35	rs2953153	241,566,012	G	A	0.51	0.20	0.362	0.297	1.38 × 10–7	1.34	4.40 × 10–6	−0.61	21,164
		rs3749172	241,570,249	A	C	0.45	0.17	0.361	0.295	6.65 × 10–8	1.34	4.40 × 10–6	−0.61	25,401

BP, base pair; CD; Crohn’s disease; CLPP, colocalization posterior probability; eQTL, expression quantitative trait loci; GWAS, genome-wide association study; OR, odds ratio; RAF, risk allele frequency; SNP, single nucleotide polymorphism. ^aPosterior probability of each causal variant within the credible set (threshold >0.95). ^bColocalization posterior probability indicates the level of colocalization (threshold >0.01). ^cFrequentist association test of 899 CD and 3,805 controls using SNPTEST. ^deQTL P value calculated using FastQTL. ^eEffect size of gene expression levels of risk versus non-risk alleles. ^fDistance from the SNP position to the transcription start site of the gene.