The study explores the long-range interaction landscape of gene promoters using chromosome conformation capture carbon copy (5C) to analyze interactions between transcription start sites (TSSs) and distal elements in 1% of the human genome, representing the ENCODE pilot project regions. 5C maps were generated for three cell lines (GM12878, K562, and HeLa-S3) and integrated with ENCODE data. Over 1,000 long-range interactions were identified, including elements resembling enhancers, promoters, and CTCF-bound sites. These interactions showed asymmetry, with a bias for elements located ~120 kb upstream of the TSS. Long-range interactions were often not blocked by CTCF and cohesin sites, indicating that many sites do not demarcate physically insulated gene domains. Only ~7% of interactions were with the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. Promoters and distal elements formed complex networks, revealing their functional relationships in three-dimensional space. The study used 5C to systematically map interactions between promoters and distal elements across 44 ENCODE regions, revealing that long-range interactions are influenced by chromatin features such as open chromatin, active histone marks, and CTCF-bound elements. TSS–E and TSS–P interactions were more cell-type specific than TSS–CTCF interactions. Long-range interactions were enriched for active enhancer-like elements and were significantly correlated with gene expression. The study also found that long-range interactions are often not blocked by CTCF and cohesin sites, indicating that these sites may not always insulate gene domains. The results suggest that long-range interactions are influenced by the spatial organization of the genome and that these interactions play a critical role in gene regulation. The study provides new insights into the three-dimensional organization of the genome and the functional relationships between genes and regulatory elements. The findings highlight the importance of long-range interactions in gene regulation and suggest that additional mechanisms exist for target selection and gene insulation. The study also demonstrates the utility of 5C in mapping long-range interactions and provides a framework for further research into the three-dimensional organization of the genome.The study explores the long-range interaction landscape of gene promoters using chromosome conformation capture carbon copy (5C) to analyze interactions between transcription start sites (TSSs) and distal elements in 1% of the human genome, representing the ENCODE pilot project regions. 5C maps were generated for three cell lines (GM12878, K562, and HeLa-S3) and integrated with ENCODE data. Over 1,000 long-range interactions were identified, including elements resembling enhancers, promoters, and CTCF-bound sites. These interactions showed asymmetry, with a bias for elements located ~120 kb upstream of the TSS. Long-range interactions were often not blocked by CTCF and cohesin sites, indicating that many sites do not demarcate physically insulated gene domains. Only ~7% of interactions were with the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. Promoters and distal elements formed complex networks, revealing their functional relationships in three-dimensional space. The study used 5C to systematically map interactions between promoters and distal elements across 44 ENCODE regions, revealing that long-range interactions are influenced by chromatin features such as open chromatin, active histone marks, and CTCF-bound elements. TSS–E and TSS–P interactions were more cell-type specific than TSS–CTCF interactions. Long-range interactions were enriched for active enhancer-like elements and were significantly correlated with gene expression. The study also found that long-range interactions are often not blocked by CTCF and cohesin sites, indicating that these sites may not always insulate gene domains. The results suggest that long-range interactions are influenced by the spatial organization of the genome and that these interactions play a critical role in gene regulation. The study provides new insights into the three-dimensional organization of the genome and the functional relationships between genes and regulatory elements. The findings highlight the importance of long-range interactions in gene regulation and suggest that additional mechanisms exist for target selection and gene insulation. The study also demonstrates the utility of 5C in mapping long-range interactions and provides a framework for further research into the three-dimensional organization of the genome.