Fig. 2

CfDNA fragmentation hotspots are enriched at active gene-regulatory regions in healthy. a The overlap of cfDNA fragmentation hotspots (BH01, healthy) and CGI transcription starting sites (TSSs), non-CGI TSSs, 5′exon boundary (no TSS or CTCF within ± 2 kb), transcription termination sites (TTSs) (no TSS or CTCF within ± 2 kb), CTCF transcription factor binding sites (no TSS within ± 4 kb), and random genomics regions. b The DNA accessibility levels from hematopoietic cells around the cfDNA fragmentation hotspots (BH01, healthy). c The histone modification levels from monocytes around the cfDNA fragmentation hotspots (BH01, healthy). d The H3K4me1 histone modification levels from hematopoietic (solid lines) and non-hematopoietic (dashed lines) cells around the cfDNA fragmentation hotspots (BH01, healthy). e The enrichment of hotspots at tissue-specific chromHMM states (Enhancer and TssFlank). Odds ratio is compared with matched random regions (matched chromosome and length, repeated 10 times). The error bar is based on the 95% confidence interval. p-value is calculated based on the Fisher exact test. f The receiver operating characteristic (ROC)  curve for the prediction of open chromatin regions by using cfDNA fragmentation level at the hotspots from the constitutively open and closed regions. g The overlap of cfDNA fragmentation hotspots (BH01, healthy) and 3′end of transposons (Alu, L1, and LTR). h The cfDNA methylation level from healthy individuals (Sun et al. 2015 PNAS) [21] around the 3′end of Alu that overlapped or not overlapped with the cfDNA fragmentation hotspots (BH01, healthy)