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chr1_966455_C_A

chr1:966455 · GRCh38C → Ars1642975296receptor_confirmed

nearest gene · PLEKHN1 · 26 bp

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

Receptor variant-effect scores

PXR

-0.187LoF

FXR

-0.072Neutral

AhR

-0.363LoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR LoF at normalized -0.363. 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: -0.09
dbSNP: rs1642975296
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
C→A	-0.187	-0.072	-0.363	not observed
C→G	-0.081	-0.068	-0.222	not observed
C→T	-0.036	0.004	-0.070	6.6e-6

Every possible base substitution at chr1:966455, 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: PXRAhR

Multi receptor overlap: PXR,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.