Table 2.

Influential Variants identified in two rare variant loci previously found associated with IPF

Chr:Posa	MAb	MAFc	Delta Chi- Square	rs#	SNP-DOC annotation	Nearest Gene	Publications/Clinical Notes
chr5:1294704	A	0.00056	−3.65		coding-synon,ncRNA	TERT
chr5:1295161	G	0.00353	−17.50	rs878855297	ncRNA,untranslated-5	TERT	Familial and sporadic melanoma (Horn et al., 2013) High penetrance, early onset melanoma (Harland et al., 2016) Cancer cell lines, found to abrogate telomerase silencing and promote tumorigenesis (Chiba et al., 2015)
chr5:1295228	A	0.00705	−28.68		unknown	TERT	Familial and sporadic melanoma (Horn et al., 2013; Huang et al., 2013) Cancer cell lines, found to abrogate telomerase silencing and promote tumorigenesis (Chiba et al., 2015) Thyroid cancer (Liu and Xing, 2016)
chr20:62324391	A	0.05008	−6.77	rs41308092d	intron	RTEL
chr20:62324564	T	0.00197	−3.25	rs398123017	ncRNA,nonsense	RTEL	Dyskeratosis congenital (Ballew et al., 2013; Walne et al., 2013) Hoyeraal-Hreidarsson syndrome (Deng et al., 2013) Familial interstitial pneumonia (Cogan et al., 2015) Idiopathic pulmonary fibrosis (Todd et al., 2017)
chr20:62324600	T	0.00098	−2.60	rs373740199	coding-synon,ncRNA,nonsense	RTEL	Dyskeratosis congenital (Ballew et al., 2013) Hoyeraal-Hreidarsson syndrome (Moriya et al., 2016) Idiopathic pulmonary fibrosis (Todd et al., 2017) Early-onset Inflammatory Bowel Disease (Petersen et al., 2017)

^aNCBI Build 37 coordinates

^bMinor allele observed in our data

^cMinor allele frequency observed in our data

^dHaploReg results: promoter histone marks found in skin, GI and enhancer histone marks found in 8 tissues including lung and lung carcinoma cell line