Additional file 1: of Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes

Table S1. Minnesota Grading System (MGS) – based on the AREDS grading system. Table S2. Demographic characteristics of all RPE samples used in the study including EWAS discovery cohort, independent sample cohort, and expression studies cohort. Table S3. Model parameters used for data analysis. Table S4. Bisulfite Pyrosequencing primer sequences. Table S5. Comparison of demographic characteristics between AMD cases and normal human donor RPE cells in our EWAS discovery cohort, independent sample cohort and combined cohorts. Table S6. RT-qPCR primer sequences. Table S7. Candidate Genes: Literature search results. Table S8. SNPs associated with candidate gene CpG site. Table S9. Histone modifications enriched at differentially methylated CpG loci in various cell types and cell lines represented in the ENCODE data. Table S10. Histone modifications enrichment in Differentially Methylated Regions in AMD. Table S11. Analysis of differentially methylated CpG loci in relation to proposed Cis-Regulatory Elements (CRE) in the RPE/Choroid from the data of T. Cherry et al. (doi: https://doi.org/10.1101/412361, http://biorxiv.org/cgi/content/short/412361v1 , Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic Variation). Table S12. Target differentially methylated CpG probes in relation to ATAC-Seq peaks in identified in RPE tissue in Wang et al, 20187. (DOCX 115 kb)