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chr20_54107656_G_A
For a non-coding regulatory variant the nearest gene by distance is frequently not the regulated gene.
Receptor variant-effect scores
Strongest effect: PXR LoF at normalized -1.000. Impact is at or above the receptor peak population 99th percentile, the top 1% or so.
ft_head_delta_norm = center bin sum of ALT minus REF on the receptor CHIP_TF head, normalized to the peak population 99th percentile and clipped to [−1, 1]. AhR is reported as exploratory, single replicate.
Cross-annotations
- Disrupted motif
- NR1I2 · JASPAR
- phyloP conservation
- 4.33 · conserved
- dbSNP
- rs1413924142
- Region tier
- receptor_confirmed
Mirrored from ClinVar, GTEx, GWAS Catalog, JASPAR/FIMO, gnomAD and phyloP. See Databases.
All substitutions at this position
| Substitution | PXR | FXR | AhR | gnomAD AF |
|---|---|---|---|---|
| G→A | -1.000 | -1.000 | -0.812 | not observed |
| G→C | -1.000 | -1.000 | -0.965 | not observed |
| G→T | -0.660 | -0.914 | -0.391 | 6.6e-6 |
Every possible base substitution at chr20:54107656, each scored independently. The gnomAD column shows which substitution is actually seen in the population versus in silico only. Region confidence is the same for every substitution at this position, so it is shown once in the section below.
Region confidence
In receptor peaks: PXR
Multi receptor overlap: PXR
Binding motif
Logo for the strongest scoring receptor, PXR. The highlighted column marks the approximate affected base within the response element. External browser: UCSC Genome Browser.