The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]
Transcription factors with Perturb-seq knockdown data for LDLR. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = LDLR upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of LDLR, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr19:10,835,171–10,836,835 | 253.5 kb | Distal (>10kb) Multiome | 1096 | |
| chr19:10,870,403–10,872,620 | 218.3 kb | Distal (>10kb) Multiome | 714 | |
| chr19:10,928,331–10,929,395 | 160.8 kb | Distal (>10kb) Multiome | 860 | |
| chr19:10,960,232–10,961,863 | 128.6 kb | Distal (>10kb) Multiome | 1016 | |
| chr19:11,089,041–11,091,015 | 174 bp | At TSS Multiome | 964 | |
| chr19:11,137,551–11,138,233 | 48.4 kb | Distal (>10kb) Multiome | 584 | |
| chr19:11,155,520–11,156,298 | 66.4 kb | Distal (>10kb) Multiome | 754 | |
| chr19:11,196,759–11,198,184 | 108.2 kb | Distal (>10kb) Multiome | 728 | |
| chr19:11,243,345–11,243,968 | 154.0 kb | Distal (>10kb) Multiome | 448 | |
| chr19:11,262,060–11,262,653 | 173.0 kb | Distal (>10kb) Multiome | 406 | |
| chr19:11,339,100–11,339,837 | 250.2 kb | Distal (>10kb) Multiome | 506 | |
| chr19:11,346,053–11,346,958 | 257.0 kb | Distal (>10kb) Multiome | 676 | |
| chr19:11,355,078–11,355,735 | 265.9 kb | Distal (>10kb) Multiome | 382 | |
| chr19:11,361,368–11,362,625 | 272.2 kb | Distal (>10kb) Multiome | 256 | |
| chr19:11,374,474–11,375,717 | 285.5 kb | Distal (>10kb) Multiome | 866 | |
| chr19:11,380,761–11,382,262 | 291.9 kb | Distal (>10kb) Multiome | 798 | |
| chr19:11,382,830–11,384,509 | 294.9 kb | Distal (>10kb) Multiome | 761 |
Genomic view of the LDLR locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.