This study investigates age-related macular degeneration (AMD) genetic risk factors through identification of a functional singlenucleotide polymorphism (SNP) and its disease association. We chose ERCC6 because of its roles in the aging process, DNA repair, and ocular degeneration from the gene disruption. Bioinformatics indicated a putative binding-element alteration on the sequence containing C؊6530>G SNP in the 5 flanking region of ERCC6 from Sp1 on the C allele to SP1, GATA-1, and OCT-1 on the G allele. Electrophoretic mobility shift assays displayed distinctive C and G allele-binding patterns to nuclear proteins. Luciferase expression was higher in the vector construct containing the G allele than that containing the C allele. A cohort of 460 advanced AMD cases and 269 age-matched controls was examined along with pathologically diagnosed 57 AMD and 18 age-matched non-AMD archived cases. ERCC6 C؊6530>G was associated with AMD susceptibility, both independently and through interaction with an SNP (rs380390) in the complement factor H (CFH) intron reported to be highly associated with AMD. A disease odds ratio of 23 was conferred by homozygozity for risk alleles at both ERCC6 and CFH compared with homozygozity for nonrisk alleles. Enhanced ERCC6 expression was observed in lymphocytes from healthy donors bearing ERCC6 C؊6530>G alleles. Intense immunostaining of ERCC6 was also found in AMD eyes from ERCC6 C؊6530>G carriers. The strong AMD predisposition conferred by the ERCC6 and CFH SNPs may result from biological epistasis, because ERCC6 functions in universal transcription as a component of RNA pol I transcription complex.Cockayne syndrome ͉ single nucleotide polymorphism ͉ gene regulation ͉ interaction ͉ DNA repair A ge-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in Western countries among the elderly (1). AMD is a significant health problem in the United States, with a current estimate of Ϸ1.75 million persons with advanced AMD in the general population and Ϸ7.3 million people with early stages of AMD defined by large retinal drusen. By the year 2020, it is estimated that Ϸ2.95 million people will suffer advanced AMD, and an additional 6.4 million white individuals will have the early stages of AMD in at least one eye (2).The etiology of AMD remains elusive. To date, age and cigarette smoking have been identified as AMD risk factors (3-8). Various studies have indicated a significant genetic contribution to AMD risk (9). For example, it has been reported that advanced AMD is more prevalent in Caucasian populations as compared with other races that possess higher levels of uveal pigmentation and skin melanin (10). Furthermore, the population-attributed AMD risk related to genetic factors was 23% (11, 12). First-degree relatives of patients with late AMD developed the disease at an increased rate at a relatively young age (12, 13). The higher occurrence of AMD among monozygotic twins and first-degree relatives of AMD patients as compared with spouses and unrelated ...