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chr22_41235029_C_T

chr22:41235029 · GRCh38C → Trs1321339970receptor_confirmed
nearest gene · CHADL · within gene

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

Receptor variant-effect scores

PXR
-25728LoF
FXR
-9280LoF
AhR
-15232LoF
− (LoF)0+ (GoF)

Strongest effect: FXR LoF at raw -9280. Impact is high, in the upper range toward the 99th percentile.

Raw ft_head_delta is the center bin sum of ALT minus REF on the receptor finetuned ChIP head, in model output units (unbounded). Sign gives direction: negative is loss of binding (LoF), positive is gain (GoF). AhR is reported as exploratory, single replicate.

Cross-annotations

phyloP conservation
-0.20
dbSNP
rs1321339970↗
Region tier
receptor_confirmed

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

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
C→A-16256-3776-9344not observed
C→G-21344-8320-12288not observed
C→T-25728-9280-15232not observed

Every possible base substitution at chr22:41235029, each scored independently and shown as raw model deltas. 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

Multi receptor overlap: FXR

Binding motif

Logo for the strongest scoring receptor, FXR. The highlighted column marks the approximate affected base within the response element. External browser: UCSC Genome Browser.