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chr11_124954054_G_A

chr11:124954054 · GRCh38G → Ars3809056gnomAD AF 1.85e-1receptor_confirmed

regulatory target · CCDC15-DT nearest gene · CCDC15 · 147 bp

Regulatory target CCDC15-DT is taken from a GTEx liver eQTL, not from distance. For a non-coding regulatory variant the nearest gene by distance is frequently not the regulated gene.

Receptor variant-effect scores

PXR

0.050Neutral

FXR

0.010Neutral

AhR

0.000Neutral

-1 (LoF)0+1 (GoF)

Strongest effect: PXR Neutral at normalized 0.050. Impact is low, near neutral.

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

GTEx liver eQTL: CCDC15-DT, slope 0.62, p 1.5e-15
phyloP conservation: -0.17
gnomAD: AF 1.85e-1 · browser
dbSNP: rs3809056
Region tier: receptor_confirmed

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

All substitutions at this position

Substitution	PXR	FXR	AhR	gnomAD AF
G→A	0.050	0.010	0.000	1.8e-1
G→C	0.003	-0.030	-0.117	6.6e-6
G→T	0.013	0.003	-0.070	1.1e-1

Every possible base substitution at chr11:124954054, 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: AhR

Multi receptor overlap: AhR

Binding motif

PXR DR3 (AGGTCAxxxAGGTCA) · JASPAR MA1148

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