The subject invention pertains to a method of determining methylation state and chromatin structure of target loci. The method comprises treating the genetic material obtained from the cells with DNA methyltransferase, capturing target genetic loci using a set of oligonucleotides, ligating the target loci with oligonucleotide patches that flank the target loci, treating the target loci flanked by oligonucleotide patches with bisulfite, optionally amplifying the target loci by polymerase chain reaction, sequencing the PCR products, and analyzing the sequences to determine methylation state and chromatin structure of the target loci. The current invention also provides a method to identify genes associated with a disease. The invention also provides a method to detect cells suffering from a disease in a group of cells. The current invention also provides kits suitable for carrying out the method of determining methylation state and chromatin structure of the target loci.