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chr5_141919412_T_C

chr5:141919412 · GRCh38T → Crs3855086receptor_confirmed

regulatory target · DELE1 nearest gene · DELE1 · 4.5 kb

Regulatory target DELE1 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

0.231GoF

FXR

0.384GoF

AhR

0.409GoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR GoF at normalized 0.409. 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: DELE1, slope 0.35, p 2.2e-9
phyloP conservation: -0.25
dbSNP: rs3855086
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
T→A	-0.107	-0.158	-0.122	not observed
T→C	0.231	0.384	0.409	not observed
T→G	0.200	0.317	0.415	not observed

Every possible base substitution at chr5:141919412, 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

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.