Table 3.

Gene Expression and Spirometric Results for the Three Novel IPF Susceptibility Loci

Chr	rsid of Sentinel Variant	Annotation	eQTL		FEV1		FVC		FEV1/FVC
			Lung Tissue	Nonlung Tissue	β [95% CI]	P Value	β [95% CI]	P Value	β [95% CI]	P Value
3	rs78238620	Intron (KIF15)	—	↓ KIF15 ↓ TMEM42	−0.011 [−0.022 to 0.000]	0.069	−0.022 [−0.033 to 0.011]	2.92 × 10−4	0.017 [0.006 to 0.028]	0.005
7	rs12699415	Intron (MAD1L1)	—	↓ MAD1L1	−0.007 [−0.012 to −0.002]	0.011	−0.011 [−0.016 to −0.007]	1.41 × 10−5	0.008 [0.003 to 0.012]	0.005
8	rs28513081	Intron (DEPTOR)	↓ DEPTOR ↓ RP11-760H22.2	↕ DEPTOR ↕ RP11-760H22.2 ↑ KB-1471A8.1 ↑ TAF2	0.001 [−0.004 to 0.006]	0.822	−0.005 [−0.010 to −0.001]	0.045	0.011 [0.006 to 0.016]	4.22 × 10−5

Definition of abbreviations: Chr = chromosome; CI = confidence interval; eQTL = expression quantitative trait loci; IPF = idiopathic pulmonary fibrosis; rsid = reference SNP cluster ID.

Annotation of the variant was taken from Variant Effect Predictor (VEP). A list of all variants included in the credible sets with their annotations and eQTL results can be found in Table E3. For colocalization, only genes where there was a greater than 80% probability of colocalization between the IPF risk signal and gene expression of that gene are reported in this table. In the colocalization column, ↑ denotes that the allele that increases IPF risk was associated with increased expression of the gene, ↓ denotes that the IPF risk allele was associated with decreased expression of the gene, and ↕ denotes that the IPF risk allele was associated with increased expression in some tissues and decreased expression in others. Full results from the eQTL and colocalization analyses can be found in Table E2. The spirometric results for the three novel IPF risk loci are taken from Shrine and colleagues (36) using the allele associated with increased IPF risk as the effect allele, with β being the change in z-score units. Results for all IPF risk variants can be found in Table E6.