Table 3.

Lung Function Variants

Chromosome	Previously Reported Variant				Lead Variant in Meta-analysis Window		Linkage Disequilibrium between Previously Reported and Lead Variants
	rs ID	Base Position	Nearest Gene	Meta-analysis P Value	rs ID	Meta-analysis P Value	r2	D′
1	rs2284746	17306675	MFAP2	0.12	rs3170740	0.10	0.91	0.98
1	rs993925	218860068	TGFB2-LYPLAL1	0.56	rs72738847	4.56 × 10−6	0.00	0.34
2	rs2571445 (rs918949)	218683153	TNS1	0.07	rs3791953	1.75 × 10−2	0.00	0.12
2	rs7594321	230224031	DNER	0.09	rs12995479	0.02	0.00	0.02
2	rs12477314	239877148	HDAC4-FLJ43879	2.37 × 10−3	rs35877146	1.26 × 10−3	0.72	0.90
3	rs1529672	25520582	RARB	3.08 × 10−4	rs1529672	3.08 × 10−4	N/A	N/A
3	rs1344555	169300219	MECOM/EVI1	0.68	rs933607	2.29 × 10−4	0.03	0.24
4	rs7671167	89883979	FAM13A	2.45 × 10−15	rs4416442	1.84 × 10−17	0.65	0.99
4	rs10516526	106688904	GSTCD/INTS12/NPNT	7.39 × 10−4	rs11735213	5.12 × 10−5	0.67	0.91
4	rs1032296	145434688	HHIP	4.13 × 10−10	rs13141641	1.26 × 10−18	0.41	0.89
5	rs153916	95036700	SPATA9-RHOBTB3	2.90 × 10−3	rs153916	2.90 × 10−3	N/A	N/A
5	rs11168048	147842353	HTR4	0.01	rs17720155	4.41 × 10−4	0.33	0.78
5	rs11134779 (rs1422795)	156936766	ADAM19	7.98 × 10−3	rs62390771	4.16 × 10−7	0.02	0.38
6	rs6903823*	28322296	ZKSCAN3	0.75	rs3800326	0.10	0.09	1.00
6	rs2857595*	31568469	NCR3-AIF1	0.71	rs2844479	0.03	0.03	0.51
6	rs2070600	32151443	AGER/PPT2	7.05 × 10−6	rs2070600	7.05 × 10−6	N/A	N/A
6	rs7765379	32680928	HLA-DQB1	0.12	rs9275141	5.67 × 10−3	0.14	1.00
6	rs2798641	109268050	ARMC2	1.15 × 10−4	rs2848598	2.06 × 10−5	0.31	0.89
6	rs3817928	142750516	GPR126	5.71 × 10−3	rs9399401	1.91 × 10−4	0.63	0.96
9	rs16909898	98231008	PTCH1	0.12	rs357523	7.77 × 10−3	0.47	0.73
10	rs7068966	12277992	CDC123	0.05	rs10906083	0.03	0.01	0.13
10	rs11001819	78315224	C10orf11	0.39	rs7904646	2.08 × 10−3	0.00	0.33
12	rs11172113	57527283	LRP1	2.28 × 10−4	rs2122692	9.12 × 10−5	0.44	0.80
12	rs1036429 (rs7307510)	96271427	CCDC38	6.35 × 10−3	rs7306887	7.35 × 10−4	0.13	0.87
15	rs12899618	71645120	THSD4	0.01	rs10459646	4.37 × 10−7	0.09	1.00
16	rs12447804	58075282	MMP15	0.16	rs2550370	9.55 × 10−3	0.03	0.63
16	rs2865531 (rs4888380)	75390315	CFDP1	3.09 × 10−3	rs37586	4.88 × 10−4	0.13	1.00
17	rs11654749	69125606	KCNJ2	0.39	rs35883109	0.01	0.00	0.08
21	rs9978142	35652239	KCNE2-LINC00310/C21orf82	0.98	rs73205216	8.96 × 10−5	0.02	1.00

Definition of abbreviations: D′, normalized coefficient of linkage disequilibrium; N/A, not applicable.

For each previously reported variant and lead variant, the P value refers to the association with moderate-to-severe chronic obstructive pulmonary disease in our analysis. Nominally significant associations (P < 0.05) among previously reported variants are shown in bold. Linkage disequilibrium values (r² [between-locus correlation coefficient]) between the previously reported variant and the lead variant in meta-analysis window were obtained using data from 1,000 Genomes Project Phase 1 v3. Proxies for variants not available in our dataset are in parentheses, and P values displayed are for the proxy variant.

^*Risk alleles showing a discordant association direction of effect for chronic obstructive pulmonary disease risk and decreased lung function risk.