Table 1.

Significantly differentially methylated CpG probes identified in AMD RPE cells

Probe ID	Log2 FC	Adjusted p value	False discovery rate (< 0.2)	Δβ (* > 10%)	Chromosome	Position	Relation to CpG island	UCSC gene name	Relation to gene
cg18486102	1.81	1.08E−12	4.6E−07	*0.20	chr12	50297777	Island	FAIM2	TSS200
cg18934822	− 3.00	1.18E−09	2.5E−04	*− 0.11	chr1	2191402	Open Sea	SKI	Body
cg23169512	− 3.51	2.08E−08	2.9E−03	*− 0.33	chr15	60290666	N_Shore
cg22508626	1.02	7.03E−07	6.0E−02	*0.12	chr6	30879905	N_Shore	GTF2H4	Body
cg01560972	− 3.87	2.03E−06	1.4E−01	*− 0.33	chr11	8190837	S_Shore	RIC3	TSS1500
cg26962595	1.18	2.75E−06	1.6E−01	0.02	chr11	72504889	Island	STARD10	TSS200
cg11897517	1.67	3.87E−06	1.6E−01	0.02	chr6	109761938	Island	SMPD2	5′UTR
cg04838987	− 1.76	3.98E−06	1.6E−01	*− 0.18	chr20	33734406	N_Shore	EDEM2	Body
cg11241206	− 2.82	4.44E−06	1.6E−01	*− 0.35	chr11	27723128	S_Shore	BDNF	TSS1500; 5′UTR
cg03611060	2.51	5.00E−06	1.6E−01	*− 0.14	chr1	59281067	Island
cg26347887	− 2.87	5.16E−06	1.6E−01	*− 0.28	chr2	88927196	Island	EIF2AK3	TSS200

Δβ mean β value AMD—mean β value control, TSS transcription start site, 5′UTR 5′-untranslated region, 3′-UTR 3′-untranslated region, Body gene body, Intragenic intragenic region

Analysis of Illumina 450k BeadChip array data using linear interaction modeling considering independent variables (sex M/F and batch effect) and their interaction with DNA methylation. Significantly differentially methylated CpG probes in contrasts AMD/normal with a FDR of < 20% are shown. cg23169512 is approximately 10 kb from FOXB1, and cg03611061 is within the long intergenic non-protein coding RNA 1135 and 30 kb upstream of JUN proto-oncogene