Table 1. COPD association results in stage 1 and 2 for lung function sentinel variants analysed in stage 2.

rs number	GWAS gene	Ref allele	Alt allele	Calling algorithm	Stage 1				Stage 2
					Alt allele freq in cases	Alt allele freq in controls	OR	P-value	OR	P-value
rs1344555	MECOM	C	T	SNVer	0.238	0.154	1.72	4.93x10−4	1.03	4.20x10−1
				Syzygy	0.247	0.162	1.69	5.93x10−4
				vipR	0.260	0.180	1.6	9.29x10−3
rs11100860	HHIP	A	G	SNVer	0.337	0.410	0.73	1.44x10−2	0.86	3.31x10−9
				Syzygy	0.340	0.404	0.76	3.28x10−2
				vipR	0.398	0.406	0.97	8.37x10−1
rs153916	SPATA9	C	T	SNVer	0.600	0.530	1.33	2.03x10−2	0.99	5.55x10−1
				Syzygy	0.605	0.536	1.33	2.35x10−2
				vipR	0.576	0.526	1.09	1.33x10−1
rs1985524	HTR4	G	C	SNVer	0.378	0.448	0.75	2.27x10−2	0.88	1.08x10−6
				Syzygy	0.383	0.446	0.77	3.67x10−2
				vipR	0.428	0.446	0.93	5.89x10−1

COPD single variant results for lung function sentinel variants [9] with P < 0.05 when using allele counts for at least two calling algorithms in stage 1 and 2. Full stage 1 results for the 26 lung function loci are presented in S6 Table. OR correspond to the alternative allele.

Abbreviations: Ref = reference, Alt = alternative, freq = frequency, N = number, ac = allele count, OR = odds ratio.