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chr17_19648780_T_G

chr17:19648780 · GRCh38T → Grs1479279407gnomAD AF 6.57e-6receptor_confirmed

nearest gene · ALDH3A2 · within gene

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

Receptor variant-effect scores

PXR

-0.315LoF

FXR

-0.018Neutral

AhR

0.000Neutral

-1 (LoF)0+1 (GoF)

Strongest effect: PXR LoF at normalized -0.315. 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: -1.10
gnomAD: AF 6.57e-6 · browser
dbSNP: rs1479279407
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	0.154	0.058	0.000	not observed
T→C	0.151	-0.013	-0.034	not observed
T→G	-0.315	-0.018	0.000	6.6e-6

Every possible base substitution at chr17:19648780, 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.