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Integrative analysis of the interactome with previous  epigenome and transcriptome datasets from the same tissues revealed a strong  correlation between the chromatin contacts and chromatin state at distal  enhancers, as well as gene expression patterns at predicted target genes. We  predicted target genes of 15,098 candidate enhancers and used them to annotate  target genes of homologous candidate enhancers in the human genome that harbor  risk variants of human diseases. 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To fill this gap, here we  mapped chromatin contacts between gene promoters and distal sequences across the  genome in seven mouse fetal tissues and across six developmental stages of the  forebrain. We identified 248,620 long-range chromatin interactions centered at  14,138 protein-coding genes and characterized their tissue-to-tissue variations  and developmental dynamics. Integrative analysis of the interactome with previous  epigenome and transcriptome datasets from the same tissues revealed a strong  correlation between the chromatin contacts and chromatin state at distal  enhancers, as well as gene expression patterns at predicted target genes. We  predicted target genes of 15,098 candidate enhancers and used them to annotate  target genes of homologous candidate enhancers in the human genome that harbor  risk variants of human diseases. 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