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chr20_13452813_C_G

chr20:13452813 · GRCh38C → Grs6134875gnomAD AF 6.57e-6receptor_confirmed
nearest gene · TASP1 · within gene

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

Receptor variant-effect scores

PXR
-0.439LoF
FXR
-0.469LoF
AhR
-0.264LoF
-1 (LoF)0+1 (GoF)

Strongest effect: FXR LoF at normalized -0.469. Impact is moderate.

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

phyloP conservation
-1.02
gnomAD
AF 6.57e-6 · browser
dbSNP
rs6134875
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-0.420-0.418-0.250not observed
C→G-0.439-0.469-0.2646.6e-6
C→T-0.089-0.088-0.067not observed

Every possible base substitution at chr20:13452813, 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: FXRAhR

Multi receptor overlap: FXR,AhR

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.