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Input.1      Gene.1 (+1234), Gene.2 (+35000)
Input.2      Gene.3 (-45434)
Input.3      NONE

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The first column of the output is the user-given name of the input genomic region (the "name" field of the BED). The second column contains a comma-delimited list of all genes to which the genomic region is associated and the distance (in bp) from the middle of the input genomic region to the transcription start site (TSS) of the gene (or NONE if the genomic region is not associated with any gene). The distance also has strand information: '+' indicates that the input genomic region is downstream of the TSS and '-' indicates that the input genomic region is upstream of the TSS.

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