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chr1_633931_T_C

chr1:633931 · GRCh38T → Crs536756579gnomAD AF 1.25e-4receptor_confirmed
nearest gene · OR4F29 · within gene

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

Receptor variant-effect scores

PXR
-5,824LoF
FXR
-2,136LoF
AhR
-192Neutral
− LoF0+ GoF

Strongest effect: FXR LoF at raw -2,136. Impact is low, near neutral.

Raw ft_head_delta is the center bin sum of ALT minus REF on the receptor finetuned ChIP head, in unbounded model output units. A negative value means loss of receptor binding and a positive value means gain. AhR is exploratory, from a single replicate.

Cross-annotations

phyloP conservation
5.30 · conserved
gnomAD
AF 1.25e-4↗
dbSNP
rs536756579↗
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-16,160-4,048-1,888not observed
T→C-5,824-2,136-1921.2e-4
T→G-21,152-4,592-2,608not observed

Every possible base substitution at chr1:633931, 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: PXR

Multi receptor overlap: PXR

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.