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chr6_2999372_T_G

chr6:2999372 · GRCh38T → Grs1332215199receptor_confirmed
nearest gene · NQO2 · 443 bp

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

Receptor variant-effect scores

PXR
-1.000predicted occupancy decrease
FXR
-0.915predicted occupancy decrease
AhR
-0.482predicted occupancy decrease
-1 decrease0+1 increase

Strongest effect: PXR predicted occupancy decrease 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

phyloP conservation
-0.63
dbSNP
rs1332215199↗
Region tier
receptor_confirmed

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

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
T→A-1.000-1.000-0.776not observed
T→C-1.000-1.000-0.541<0.001%
T→G-1.000-0.915-0.482not observed

Every possible base substitution at chr6:2999372, 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