Table 2.

Genome-wide association “discovery” analysis comparing participants with choroidal neovascularization to participants with geographic atrophy

CHR	GENE	SNP	BP	EA	Freq CNV	Freq GA	INFO	OR	L95	U95	P
Most highly associated SNPs
10	ARMS2/HTRA1	rs10490924	124214448	T	0.438	0.364	0.92	1.47	1.28	1.69	4.3 ×10−9
11	Near QSER1	rs4755455	32903318	C	0.186	0.13	0.94	1.59	1.33	1.90	2.1 ×10−7
12	KCTD10	rs56209061	109905685	A	0.052	0.083	0.97	0.55	0.43	0.70	1.4 ×10−6
2	Near BC017935	rs1108738	227078645	T	0.012	0.025	0.53	0.23	0.12	0.43	3.2 ×10−6
19	Near LILRA4	rs10405172	54856550	T	0.818	0.787	0.33	1.85	1.43	2.39	3.8 ×10−6
12	Near NUDT4	rs7973431	93641198	T	0.335	0.276	0.91	1.38	1.20	1.58	3.9 ×10−6
5	Near RASA1	rs62367737	86393085	A	0.914	0.889	0.38	2.12	1.55	2.90	4.6 ×10−6
10	Near ADARB2	rs34167775	1942152	A	0.051	0.085	0.94	0.57	0.45	0.72	5.0 ×10−6
20	NFATC2	rs11697536	50108389	T	0.04	0.03	0.16	7.61	3.21	18.03	5.0 ×10−6
17	Near UTP18	rs4794243	49449132	T	0.624	0.669	0.50	0.67	0.56	0.80	5.5 ×10−6
SNPs previously associated with overall advanced AMD (other than ARMS2/HTRA1 above)
16	CETP	rs3764261	56993324	A	0.369	0.34	0.99	1.13	1.00	1.27	0.054
22	TIMP3	rs9621532	31414511	A	0.967	0.956	1.00	1.29	0.96	1.73	0.10
19	C3	rs2230199	6718387	C	0.239	0.254	0.59	0.87	0.73	1.04	0.11
6	C2	rs9332739	31903804	C	0.025	0.02	0.89	1.30	0.84	2.00	0.24
6	FRK/COL10A1	rs1999930	116387134	T	0.262	0.253	0.95	1.05	0.92	1.20	0.49
3	COL8A1	rs13095226	99396272	T	0.880	0.871	1.00	1.07	0.89	1.27	0.49
1	CFH	rs1061170	196659237	T	0.394	0.384	0.99	1.03	0.92	1.16	0.63
6	VEGFA	rs4711751	43828582	T	0.534	0.537	0.73	0.99	0.86	1.14	0.86
4	CFI	rs10033900	110659067	T	0.52	0.521	0.85	0.99	0.86	1.14	0.88
6	CFB	rs641153	31914180	A	0.052	0.055	0.86	0.98	0.74	1.29	0.90
15	LIPC	rs10468017	58678512	T	0.257	0.256	0.80	1.01	0.86	1.18	0.94
9	ABCA1	rs1883025	107664301	T	0.256	0.257	0.92	1.00	0.86	1.14	0.95

CHR= chromosome, SNP= single nucleotide polymorphism, BP= base position, EA= Effective allele (frequency and odds ratios are based on this allele), Freq = frequency, INFO= information content, OR= odds ratios, L95 = lower 95% confidence interval, U95= upper 95% confidence interval, AMD=age-related macular degeneration

P values - comparing effective allele frequencies in patients with choroidal neovascularization vs. patients with geographic atrophy