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chr20_35327174_G_A

chr20:35327174 · GRCh38G → Ars1057251137gnomAD AF 6.57e-6receptor_confirmed

nearest gene · UQCC1 · within gene

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

Receptor variant-effect scores

PXR

-0.332LoF

FXR

-0.047Neutral

AhR

-0.195LoF

-1 (LoF)0+1 (GoF)

Strongest effect: PXR LoF at normalized -0.332. 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: 0.25
gnomAD: AF 6.57e-6 · browser
dbSNP: rs1057251137
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	-0.332	-0.047	-0.195	6.6e-6
G→C	-0.207	0.021	-0.098	not observed
G→T	-0.279	-0.042	-0.189	not observed

Every possible base substitution at chr20:35327174, 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: PXRFXR

Multi receptor overlap: PXR,FXR

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.