Sequencing depth inconsistencies on open chromatin regions and signals derived from up/downstream orientation-sensitive sequencing read densities, this method infers the tissue of origin of the cfDNA fragments obtained from bisulfite sequencing. The method uses a mathematical formulation to generate signals for orientation-aware cfDNA fragmentation based on the empirical peak periods and positions of up/downstream ends of the reads. The method shown to be useful for inferring the tissue-of-origin, pregnancy identification, cancer detection, and transplant monitoring. This method also provides information on which tissue-of-origin contributes how much to cfDNA reads.