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chr4_88107631_A_C
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 p99-scaled -1.000. Impact is at or beyond the receptor-specific p99 reference magnitude.
The p99-scaled score divides the raw delta by the receptor-specific 99th percentile of |delta| in the reference peak population, then clips to −1 to 1. It is a comparable effect scale, not a percentile rank. AhR is exploratory, from a single replicate.
Cross-annotations
All substitutions at this position
| Substitution | PXR | FXR | AhR | gnomAD AF |
|---|---|---|---|---|
| A→C | -1.000 | -1.000 | -0.336 | not observed |
| A→G | -1.000 | -1.000 | -0.379 | not observed |
| A→T | -1.000 | -1.000 | -0.690 | not observed |
Every possible base substitution at chr4:88107631, each scored independently and shown as p99-scaled scores. 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: PXRFXR
Multi receptor overlap: PXR,FXR
Motif overlap
This base overlaps a significant FIMO hit for HNF4A using JASPAR MA0114.5.
Motif overlap is an independent sequence annotation; the AetherXeno score comes from the receptor-finetuned sequence model and is not inferred from the motif alone. View the locus in UCSC Genome Browser or the JASPAR profile.