Schematic diagram of CpG islands and retroelement distributions in the 5'-end regions of 20 genes. A total of 32 CpG amplicon sites from 20 genes were examined using the methylation-specific PCR (MSP) primer sets. The CpG islands of the CDH1, RABGEF1, STAG1, and MYBPC2 genes were neighbored by the high-density Alu elements at distances of ≤ 1 kb. The VDR, ESR2, MLH1, FLJ43855, MYBPC2, PTEN, and CDKN2A genes confronted by a low density of Alu, L1, and LTR elements at a distance of 2–6 kb were examined at the boundary of CpG islands. The PAX5, RUNX2, and RUNX3 genes contained long CpG islands bordered by a few retroelements at distances of > 6 kb. The genes containing no CpG islands are confronted by the L1 elements (MAGEA2 and TFF2), a low density of Alu elements (SERPINB5 and DDX53), or a high density of Alu and L1 elements (MSLN). The VDR, CDKN2A, RUNX2, RUNX3, KIAA1752, and MUC8 genes were examined at the intragenic CpG sites of the CpG islands as well. The MSP primer sites were located in close proximity to the transcription start sites without CpG islands.