1. 90 85 80 75 70 65 40 44 48 52 56 90 80 70 60 50 38 40 42 44 46 48 50 52 90 80 70 60 50 40 30 25 30 35 40 45 50 55 Normal r = 0.043 p = 0.678 Methylation Level of LINE1 (%) Background r = 0.063 p = 0.559 Methylation Level of LINE1 (%) ESCC r = 0.502 p < 0.001 Methylation Level of LINE1 (%) Methylation Level of Alu (%) Supplementary Figure 1

2. a b HOXA9 NEFH p < 0.001 p < 0.001 p < 0.001 p < 0.001 100 60 50 p < 0.001 80 40 60 Methylation Level (%) 30 40 20 p = 0.276 20 10 0 0 ESCC Normal Background ESCC Normal Background (n = 89) (n = 93) (n = 95) (n = 89) (n = 93) (n = 95) c d UCHL1 MT1M p < 0.001 p < 0.001 p < 0.001 p < 0.001 100 80 80 60 60 p = 0.018 Methylation Level (%) 40 40 p = 0.118 20 20 0 0 ESCC ESCC Normal Background Normal Background (n = 89) (n = 93) (n = 89) (n = 93) (n = 95) (n = 95) Supplementary Figure 2

3. a b c Supplementary Figure 3