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File 1: **Affinity_variant_crms_with_LCL_affinity_types:** Table containing all CRM-TF combinations with at least one haplotype with a non-zero logFC in affinity relative to the highest affinity allele of NA12878.The haplotypes listed include the high affinity NA12878 haplotype and all alternative haplotypes. ***chr_chr_start_end** - Provides the chromosome name, start position and end position of the CRM.* ***TF**- the gene symbol for the transcription factor for which the logFC in affinity for the CRM is given.* ***log fold affinity change** - Gives the logFC change in normalised affinity relative to the highest affinity allele of NA12878 for the given CRM and TF.** *Columns 4-362 contain the number of alleles of each TF CRM haplotype (row) that each of the 359 LCLs has (where each column is a different LCL). For example a 1 means that for given the haplotype (indicated by CRM_chr_start_end, TF and logFC affinity change) the LCL has one allele, a 2 means it has 2 alleles and a zero means that it does not have any alleles of this haplotype.* *allele frequency - the frequency of the allele across the 359 LCLs included in this table.* File 2: **Thresholded_binding_variants_all_tested_associations_supp_table_osf:** Table containing p-values for all tested associations between TF-binding affinity CRM variants and target gene expression using the thresholded approach. Descriptions of column names are given in the file. File 3: **Unthresholded_binding_variants_all_tested_associations_with_eprom_annotations_supp_table_osf** Table containing p-values for all tested associations between TF-binding affinity CRM variants and target gene expression using the unthresholded approach. In addition it includes all genes whose TSSs are within 200bp of the variant CRMs (eprom genes). Descriptions of column names are given in the file.