Home / Variant

chr10_58268989_C_A

chr10:58268989 · GRCh38C → Ars3831305receptor_confirmed

nearest gene · CISD1 · 172 bp

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

Receptor variant-effect scores

PXR

0.225GoF

FXR

0.126GoF

AhR

0.187GoF

-1 (LoF)0+1 (GoF)

Strongest effect: PXR GoF at normalized 0.225. 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: -0.04
dbSNP: rs3831305
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	0.225	0.126	0.187	not observed
C→G	0.119	0.025	0.105	not observed
C→T	0.099	0.060	0.152	not observed

Every possible base substitution at chr10:58268989, 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.