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chr19_344781_A_T

chr19:344781 · GRCh38A → Trs1278347815gnomAD AF <0.001%ATAC_only
nearest gene · MIER2 · within gene

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

Receptor variant-effect scores

PXR
-0.222predicted occupancy decrease
FXR
-0.056small predicted occupancy change
AhR
-0.336predicted occupancy decrease
-1 decrease0+1 increase

Strongest effect: AhR predicted occupancy decrease at p99-scaled -0.336. Impact is moderate 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.

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
A→G-0.271-0.066-0.503<0.001%
A→T-0.222-0.056-0.336<0.001%

Every possible base substitution at chr19:344781, 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: none