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chr15_40755400_G_A

chr15:40755400 · GRCh38G → Ars7174551gnomAD AF 4.92e-1receptor_confirmed

regulatory target · CCDC32 nearest gene · RMDN3 · 64 bp

Regulatory target CCDC32 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

-0.161LoF

FXR

-0.010Neutral

AhR

-0.427LoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR LoF at normalized -0.427. 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

GTEx liver eQTL: CCDC32, slope 0.44, p 4.9e-14
phyloP conservation: -0.01
gnomAD: AF 4.92e-1 · browser
dbSNP: rs7174551
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	-0.161	-0.010	-0.427	4.9e-1
G→C	0.249	0.484	0.854	not observed
G→T	-0.052	0.242	0.022	not observed

Every possible base substitution at chr15:40755400, 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

AhR::ARNT XRE (TNGCGTG) · JASPAR MA0006

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