Molecular Vision: Ryu, Mol Vis 2010; 16:2811-2821. Table 2

Table 2. Replication of single nucleotide polymorphisms (SNPs) associated with age related macular degeneration (AMD) in the age-related eye disease study (AREDS) genome-wide association study (GWAS) and Replication subjects.

					Minor allele frequency		Log-additive p-values
Chromosome	SNP	Nearby gene	Base pair position (build 36.3)	Minor allele	Cases	Controls	HWE p-value	Adjusted for population stratification	Adjusted for population stratification and known loci†	Replication p-value
1	rs11208590	RIMS3	40880736	C	0.3	0.41	0.23	5.49E-05	0.00096	0.49
1	rs2297634	ABCA4	94349556	C	0.52	0.38	0.66	2.27E-05	0.00422	0.71
1	rs1853883	CFHR4	1.95E+08	C	0.31	0.6	0.2	3.41E-18	-	*
1	rs2054780	YOD1	2.05E+08	T	0.15	0.07	0.91	9.69E-05	0.00387	0.94
1	rs287614	OBSCN	2.27E+08	A	0.51	0.38	0.29	8.59E-05	0.00393	0.24¹
1	rs1150910	OBSCN	2.27E+08	A	0.51	0.38	0.29	7.33E-05	0.00341	0.24¹
3	rs2055451 ⁵	ROBO1	79924819	T	0.25	0.37	0.2	9.34E-06	9.06E-05	0.11
4	rs1447338	-	1.81E+08	G	0.22	0.35	0.51	5.02E-06	0.00587	0.17
4	rs13129209	-	1.81E+08	T	0.29	0.41	0.38	5.94E-05	0.03675	0.65
6	rs429608	SKIV2L	32038441	A	0.08	0.17	0.07	2.49E-06	0.03228	*
7	rs2267742	ADCYAP1R1	31107071	A	0.05	0.11	0.35	6.96E-05	0.00677	0.39
7	rs10275700	-	85428174	T	0.43	0.55	0.7	0.00007	0.00109	0.01²
7	rs10274362	-	85449561	G	0.52	0.4	0.48	9.73E-05	0.00191	0.01²
7	rs988426	-	85454805	T	0.42	0.55	0.96	7.43E-05	0.00121	0.01²
10	rs2014307	ARMS2	1.24E+08	T	0.27	0.43	0.45	7.48E-08	-	*
15	rs2713935	-	54333504	C	0.44	0.57	0.25	3.62E-05	0.00179	0.62³
15	rs6493856	TEX9	54474651	A	0.51	0.38	0.53	0.000098	0.0081	0.93⁴
16	rs8056814	CTRB1#	73809828	A	0.05	0.13	0.17	4.16E-05	0.0012	0.02
17	rs4268798	METT10D#	2313335	C	0.39	0.52	0.04	5.11E-05	0.0025	0.47
18	rs9950970 ⁵	DCC#	49117806	C	0.3	0.43	0.58	2.87E-05	4.81E-05	0.65
18	rs1367634 ⁵	DCC#	49118666	T	0.3	0.43	0.45	4.87E-05	7.41E-05	0.6
18	rs12954274 ⁵	DCC#	49119872	C	0.3	0.43	0.65	3.46E-05	5.44E-05	0.61
18	rs8086078	FBXO15	69950556	C	0.03	0.08	0.37	0.000072	0.00021	0.83
19	rs2230199	C3	6669387	C	0.29	0.18	0.3	4.89E-05	-	*
20	rs6137194 ⁵	-	20896861	C	0.38	0.25	0.7	4.35E-05	0.000046	0.8
22	rs9608466 ⁵	SEZ6L	24891478	A	0.04	0.11	0.84	1.68E-05	3.89E-06	0.34
4	rs6532378 ⁵	GRID2	93761791	A	0.33	0.34	0.64	0.0093	4.58E-05	0.28⁶
9	rs972925 ⁵	OR1Q1	1.24E+08	A	0.17	0.17	0.43	0.0043	7.44E-05	0.19
21	rs2838378 ⁵	-	44030783	C	0.42	0.44	0.41	0.0127	4.79E-05	0.06⁷

SNPs associated with AMD with a p-value of less than 0.0001 using the log-additive model with correction for population stratification are shown, except that only the most significant SNP in already established AMD risk loci are included. The last three rows show SNPs associated with AMD only after correction for known SNPs. The significance of attempted replication in the Replication subjects is shown in the last column. The association with AMD was not replicated for any of the SNPs. †The SNPs used for conditioning are listed in the methods section. *These SNPs are located within loci already known to be associated with AMD. No replication was attempted. Note that CFHR4 is near CFH and SKIV2L is near C2/CFB. # Loci genotyped on Illumina platform (based on allele distribution p-values provided on the dbGaP website) and previously reported [26] ¹ The p-value for rs435776 was used to represent rs287614 (r²=1) and rs1150910 (r²=0.96) ²The p-value for rs10245061 was used to represent rs10275700 (r²=0.89), rs10274362 (r²=1), and rs988426 (r²=0.89) ³ The p-value for rs2725854 was used to represent rs2713935 (r²=0.83) ⁴ The p-value for rs7170307 was used to represent rs6493856 (r²=0.86) ⁵ These SNPs were significantly associated with AMD after adjustment for known AMD SNPs and loci (please see Figure 3D) ⁶ The p-value for rs1349350 was used to represent rs6532378 (r²=1) ⁷ The p-value for rs1041456 was used to represent rs2838378 (r²=0.96).