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chr17_47948790_A_G

chr17:47948790 · GRCh38A → Grs1986693gnomAD AF 7.57e-1receptor_confirmed

regulatory target · LRRC46 nearest gene · MIR4315-1 · within gene

Regulatory target LRRC46 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

0.410GoF

FXR

0.393GoF

AhR

0.157GoF

-1 (LoF)0+1 (GoF)

Strongest effect: PXR GoF at normalized 0.410. 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

ClinVar: Benign · Pyridoxal phosphate-responsive seizures · record
GTEx liver eQTL: LRRC46, slope 0.35, p 1.1e-6
phyloP conservation: 0.01
gnomAD: AF 7.57e-1 · browser
dbSNP: rs1986693
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
A→C	0.046	0.030	0.034	not observed
A→G	0.410	0.393	0.157	7.6e-1
A→T	-0.069	0.035	-0.045	not observed

Every possible base substitution at chr17:47948790, 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: PXR

Multi receptor overlap: PXR

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.