Home / Variant
chr2_10408451_C_T
Regulatory target HPCAL1 is taken from a GTEx liver eQTL, not from distance. For a non-coding regulatory variant the nearest gene by distance is frequently not the regulated gene.
Receptor variant-effect scores
Strongest effect: PXR GoF at p99-scaled 0.618. 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 |
|---|---|---|---|---|
| C→A | 0.287 | 0.320 | 0.146 | not observed |
| C→G | 0.867 | 0.831 | 0.596 | not observed |
| C→T | 0.618 | 0.569 | 0.427 | 34.3% |
Every possible base substitution at chr2:10408451, 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