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chr3_125935397_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: AhR LoF at p99-scaled -0.589. Impact is large relative to the receptor-specific p99 scale.
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 |
|---|---|---|---|---|
| G→A | -0.397 | -0.530 | -0.589 | 0.0013% |
| G→C | -0.196 | -0.187 | -0.238 | not observed |
| G→T | -0.328 | -0.312 | -0.446 | not observed |
Every possible base substitution at chr3:125935397, 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: FXR