Home / Variant

chr19_49451759_G_C

chr19:49451759 · GRCh38G → Crs2293011receptor_confirmed

nearest gene · SNAR-A3 · within gene

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

Receptor variant-effect scores

PXR

0.770GoF

FXR

0.174GoF

AhR

0.955GoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR GoF at normalized 0.955. Impact is high, in the upper range toward the 99th percentile.

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: -0.19
dbSNP: rs2293011
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	0.489	0.191	0.820	not observed
G→C	0.770	0.174	0.955	not observed
G→T	0.344	0.035	0.438	not observed

Every possible base substitution at chr19:49451759, 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

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.