Table 2.
LOAD GWAS loci used to demonstrate the bioinformatics pipeline for prioritizing candidate LOAD genes
| Gene | Variant | Chr | Location | #CTCF | # enhancers | # genes | Interacting genes | Location of nearest Enhancer | CTCF/enhancer overlap | # overlapping regions |
|---|---|---|---|---|---|---|---|---|---|---|
| CELF1 | rs10838725 | 11 | 47,557,871 | 99 | 90 | 24 | CELF1, SPI1, ACP2, AGBL2, ARFGAP2, DDB2, FNBP4, MADD, MTCH2, NRIH3, NUP160, PSMC3, PTPRJ, SLC39A13 | 47,557,800–47,558,200 | CTCF contained within enhancer | 6 |
| Enhancer contained within CTCF but spans beyond right flanking region | 2 | |||||||||
| Enhancer overlaps with left flanking region of CTCF | 6 | |||||||||
| PICALM | rs10792832 | 11 | 85,867,875 | 75 | 116 | 10 | PICALM, SYTL2, EED, CCDC83, CCDC89 | 85,867,400–85,867,800 | CTCF contained within enhancer | 6 |
| Enhancer contained within CTCF but spans beyond right flanking region | 1 | |||||||||
| Enhancer overlaps with left flanking region of CTCF | 2 | |||||||||
| BIN1 | rs6733839 | 2 | 127,892,810 | 65 | 112 | 10 | BIN1, ERCC3, GYPC, IWS1, MYO7B, PROC | 127,893,000–127,893,400 | CTCF contained within enhancer | 4 |
| Enhancer contained within CTCF but spans beyond right flanking region | 1 | |||||||||
| Enhancer overlaps with left flanking region of CTCF | 1 |