The eQTL folder has the code for generating enhancer-gene links from eQTL data taken from the source - https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL.tar.gz.
python eqtl.py
Running the above command generates linksDBeqtl and linksDBnumeqtl files that are the concatention of all the files of respective nature generated from different tissue variant gene pair files.
$ head linksDBeqtl
7 HUMAN|HGNC=23517|UniProtKB=Q8N2H3 10_100169983_A_G_b37 4.57077e-11 23 2
7 HUMAN|HGNC=23517|UniProtKB=Q8N2H3 10_100170037_A_G_b37 7.59471e-11 23 2
7 HUMAN|HGNC=23517|UniProtKB=Q8N2H3 10_100170209_T_C_b37 4.57077e-11 23 2
12 HUMAN|HGNC=28228|UniProtKB=Q96DD0 1_100502868_T_TATAC_b37 4.09143e-08 23 2
16 HUMAN|HGNC=28228|UniProtKB=Q96DD0 1_100555192_A_G_b37 1.5892e-07 23 2
62 HUMAN|HGNC=25613|UniProtKB=Q69YN2 10_101854930_CA_C_b37 5.74856e-06 23 2
63 HUMAN|HGNC=25613|UniProtKB=Q69YN2 10_101863410_C_A_b37 3.37568e-06 23 2
88 HUMAN|HGNC=17452|UniProtKB=Q9HBK9 10_104585405_A_T_b37 2.15079e-08 23 2
92 HUMAN|HGNC=7642|UniProtKB=Q99747 18_10497034_G_A_b37 2.43176e-06 23 2
317 HUMAN|HGNC=28769|UniProtKB=Q6UX65 1_111733724_G_C_b37 1.98817e-07 23 2
$ head linksDBnumeqtl
enhancer gene tissue number_of_eQTL assay
1026 HUMAN|HGNC=378|UniProtKB=O43823 23 1 2
12 HUMAN|HGNC=28228|UniProtKB=Q96DD0 23 1 2
1212 HUMAN|HGNC=264|UniProtKB=P29275 23 1 2
1213 HUMAN|HGNC=264|UniProtKB=P29275 23 1 2
1295 HUMAN|HGNC=19359|UniProtKB=Q5VWW1 23 1 2
1410 HUMAN|HGNC=28793|UniProtKB=O95568 23 1 2
1411 HUMAN|HGNC=28793|UniProtKB=O95568 23 1 2
16 HUMAN|HGNC=28228|UniProtKB=Q96DD0 23 1 2
1630 HUMAN|HGNC=11984|UniProtKB=Q6ZVM7 23 1 2