Table 4.

Ten most highly associated SNPs from the genome-wide association analyses comparing (A) participants with geographic atrophy (GA) to participants with no age-related macular degeneration and (B) participants with choroidal neovascularization (CNV) to participants with no age-related macular degeneration

CHR	GENE	SNP	BP	EA	Freq Cases	Freq Control	INFO	OR	L95	U95	P
(B) CNV vs. no AMD					Freq CNV
SNPs previously associated with overall advanced AMD
10	ARMS2/HTRA1	rs10490924	124214448	T	0.438	0.206	0.98	3.67	3.33	4.05	1.5 × 10−138
1	CFH	rs1061170	196659237	T	0.394	0.629	1	0.36	0.33	0.40	1.2 × 10−108
6	CFB	rs641153	31914180	A	0.052	0.101	0.91	0.45	0.38	0.54	1.0 × 10−17
19	C3	rs2230199	6718387	C	0.239	0.193	0.57*	1.61	1.40	1.85	1.0 × 10−12
4	CFI	rs10033900	110659067	T	0.520	0.463	0.8	1.31	1.19	1.44	6.4 × 10−9
6	C2	rs9332739	31903804	C	0.025	0.045	0.9	0.48	0.37	0.62	1.8 × 10−8
Newly identified SNPs
8	Near TRIB1	rs35691538	126714038	A	0.045	0.032	0.72	1.95	1.51	2.52	1.3 × 10−7
18	Near BRUNOL4	rs8091635	35857547	T	0.399	0.349	0.9	1.27	1.15	1.40	1.7 × 10−7
7	Near TRA2A	rs10262213	23591963	T	0.119	0.151	0.97	0.73	0.65	0.82	1.6 × 10−6
5	ADAM19	rs59795197	156843157	T	0.089	0.117	0.94	0.71	0.61	0.83	3.6 × 10−6
(A) GA vs. no AMD					Freq GA
SNPs previously associated with overall advanced AMD
1	CFH	rs1061170	196659237	T	0.384	0.629	1.00	0.36	0.32	0.40	4.8 × 10−67
10	ARMS2/HTRA1	rs10490924	124214448	T	0.364	0.206	0.94	2.52	2.24	2.83	7.1 × 10−47
19	C3	rs2230199	6718387	C	0.25	0.19	0.56*	1.83	1.56	2.14	4.9 × 10−13
6	CFB	rs641153	31914180	A	0.055	0.101	0.92	0.47	0.37	0.59	1.5 × 10−9
6	C2	rs9332739	31903804	C	0.020	0.045	0.89	0.38	0.26	0.56	1.2 × 10−6
4	CFI	rs10033900	110659067	T	0.521	0.463	0.79	1.32	1.17	1.48	3.9 × 10−6
Newly identified SNPs
6	PECI	rs582301	4124849	A	0.021	0.006	0.91	4.77	2.98	7.64	3.2 × 10−11
6	Near SOD2	rs2842992	160071159	A	0.743	0.797	0.88	0.70	0.61	0.80	3.4 × 10−7
18	Near MBP	rs1789110	74859044	A	0.563	0.625	0.90	0.75	0.67	0.84	4.2 × 10−7
8	Near C8orf42	rs722782	516479	A	0.067	0.106	1.00	0.60	0.48	0.74	1.9 × 10−6

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

^*The INFO score for rs2230199 is less than the QC threshold we used for INFO Score for this analysis. We present the result for this SNP specifically because it is the one that has been previously reported to be associated with overall advanced AMD. Variant rs163494 upstream from C3 had an INFO score >0.6, is in linkage disequilibrium with rs2230199, and was associated with P = 1.2 × 10⁻¹¹