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chr17_1546464_A_C

chr17:1546464 · GRCh38A → Creceptor_confirmed
nearest gene · PITPNA · within gene

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

Receptor variant-effect scores

PXR
-0.813LoF
FXR
-1.000LoF
AhR
-1.000LoF
-1 (LoF)0+1 (GoF)

Strongest effect: FXR LoF at normalized -1.000. Impact is at or above the receptor peak population 99th percentile, the top 1% or so.

ft_head_delta_norm = center bin sum of ALT minus REF on the receptor CHIP_TF head, normalized to the peak population 99th percentile and clipped to [−1, 1]. AhR is reported as exploratory, single replicate.

Cross-annotations

Disrupted motif
HNF4A · JASPAR
phyloP conservation
0.33
Region tier
receptor_confirmed

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

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
A→C-0.813-1.000-1.000not observed
A→G-0.793-1.000-1.000not observed
A→T-0.736-1.000-1.000not observed

Every possible base substitution at chr17:1546464, each scored independently. 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.