An in situ method for detecting spatial proximity relationships between nucleic acid sequences in a cell, comprising: treating a provided sample of one or more cells or cellular nuclei, whereby nucleic acids are held in a fixed position relative to one another; optionally, wherein the cells are cell cycle synchronized; optionally, wherein the genome is treated to accentuate interactions between contiguous regions of the genome; fragmenting the nucleic acids present in the cells or cellular nuclei, wherein the fragmented nucleic acids are fragmented to create 5' overhanging ends; optionally, wherein the fragmented nucleic acids are DNA; optionally, wherein fragmenting the nucleic acid present in the one or more cells comprises enzymatic digestion with an endonuclease that leaves 5' overhanging ends; filling in the overhanging ends with at least one labeled nucleotide, wherein the labeled nucleotide is used to isolate the nucleic acids; joining in intact nuclei the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having one or more junctions, wherein the site of the one or more junctions comprises one or more labeled nucleic acids; wherein joining the fragmented nucleic acids comprises contacting the sample of one or more cells or cellular nuclei with a ligase, wherein the junction comprises a ligation junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; optionally, wherein the labeled nucleotide is isolated with a specific binding agent that specifically binds to the label; optionally, wherein the specific binding agent is attached to a solid surface; optionally, purifying the nucleic acids present in the sample; optionally, selecting end ligated fragments that are between about 300 and 500 base pairs in length; optionally, end repairing the nucleic acid fragments; optionally, attaching sequencing adapters to the ends of the end joined nucleic acid fragments; and determining the sequence at the one or more junctions of the one or more end joined nucleic acid fragments, thereby detecting spatial proximity relationships between nucleic acid sequences in a cell; optionally, wherein determining the sequence at the one or more junctions of the one or more end joined nucleic acid fragments comprises using a probe that specifically hybridizes to the nucleic acid sequences both 5' and 3' of a junction of the one or more end joined nucleic acid fragments. treating a provided sample of one or more cells or cellular nuclei, whereby nucleic acids are held in a fixed position relative to one another; optionally, wherein the cells are cell cycle synchronized; optionally, wherein the genome is treated to accentuate interactions between contiguous regions of the genome; fragmenting the nucleic acids present in the cells or cellular nuclei, wherein the fragmented nucleic acids are fragmented to create 5' overhanging ends; optionally, wherein the fragmented nucleic acids are DNA; optionally, wherein fragmenting the nucleic acid present in the one or more cells comprises enzymatic digestion with an endonuclease that leaves 5' overhanging ends; filling in the overhanging ends with at least one labeled nucleotide, wherein the labeled nucleotide is used to isolate the nucleic acids; joining in intact nuclei the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having one or more junctions, wherein the site of the one or more junctions comprises one or more labeled nucleic acids; wherein joining the fragmented nucleic acids comprises contacting the sample of one or more cells or cellular nuclei with a ligase, wherein the junction comprises a ligation junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; optionally, wherein the labeled nucleotide is isolated with a specific binding agent that specifically binds to the label; optionally, wherein the specific binding agent is attached to a solid surface; optionally, purifying the nucleic acids present in the sample; optionally, selecting end ligated fragments that are between about 300 and 500 base pairs in length; optionally, end repairing the nucleic acid fragments; optionally, attaching sequencing adapters to the ends of the end joined nucleic acid fragments; and determining the sequence at the one or more junctions of the one or more end joined nucleic acid fragments, thereby detecting spatial proximity relationships between nucleic acid sequences in a cell; optionally, wherein determining the sequence at the one or more junctions of the one or more end joined nucleic acid fragments comprises using a probe that specifically hybridizes to the nucleic acid sequences both 5' and 3' of a junction of the one or more end joined nucleic acid fragments.