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chr1_3066610_T_C

chr1:3066610 · GRCh38T → CgnomAD AF <0.001%ATAC_only
nearest gene · PRDM16-DT · within gene

For a non-coding regulatory variant the nearest gene by distance is frequently not the regulated gene.

Receptor variant-effect scores

PXR
-0.120LoF
FXR
-0.089Neutral
AhR
-0.144LoF
-1 LoF0+1 GoF

Strongest effect: AhR LoF at p99-scaled -0.144. Impact is small on 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

No external database record for this variant. It is a scored in silico saturation SNV.

Mirrored from ClinVar, GTEx, GWAS Catalog, JASPAR/FIMO, gnomAD and phyloP. See Databases.

Region confidence

In receptor peaks: none