Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia

Table 1 Genome-wide Significant SNPs from Novel HLA Locus Identified in Imputation GWAS

SNP	Position	Minor allele	Nearest gene	P imputed^a	Rep case MAF ^b	Rep Cont. MAF ^c	P replication^d	P meta^e	OR (95 % CI) combined^f	P adjusted^g
rs614549	31948604	C	SLC44A4	5.74 × 10⁻⁰⁵	0.32	0.38	5.87 ×10⁻⁰⁵	2.09 × 10⁻⁰⁸	0.80 (0.73, 0.87)	0.26
rs7887	31972526	A	EHMT2	1.18 × 10⁻⁰⁵	0.31	0.37	5.84 ×10⁻⁰⁵	3.70 × 10⁻⁰⁹	0.78 (0.71, 0.86)	NA
rs2844452	31990003	C	C2	1.69 × 10⁻⁰⁵	0.42	0.47	0.00071	4.55 × 10⁻⁰⁸	0.81 (0.74, 0.88)	0.26
rs3020644	32002605	G	C2	1.13 × 10⁻⁰⁵	0.36	0.41	0.00062	2.68 × 10⁻⁰⁸	0.80 (0.73, 0.87)	0.28
rs2280774	32036670	T	NELFE	1.11 × 10⁻⁰⁵	0.29	0.34	0.00096	3.89 × 10⁻⁰⁸	0.81 (0.74, 0.89)	0.83
rs3117116	32474995	C	BTNL2	9.15 × 10⁻⁰⁸	0.15	0.13	0.038	2.65 × 10⁻⁰⁸	1.25 (1.10, 1.41)	0.02

^a P-value from imputation analysis under additive model using discovery GWAS samples
^bMinor allele frequency among replication cases (878)
^cMinor allele frequency among replication controls (2017)
^d P-value from additive model among replication cases and controls
^e P-value from meta-analysis of discovery imputation and replication
^fOdds ratio (OR) and 95 % CI for joint analysis comparing subset of GWAS cases (1498) and replication cases (878) to replication controls (2017) based on observed genotypes; GWAS cases were genotyped at same time as replication cases and controls
^g P-value from joint analysis as in (f) with adjustment for rs7887

ISSN: 2730-6844