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chr17_47841362_A_T

chr17:47841362 · GRCh38A → Trs4453543receptor_confirmed
nearest gene · MIR4315-1 · within gene

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

Receptor variant-effect scores

PXR
-0.825LoF
FXR
-0.033Neutral
AhR
-0.438LoF
-1 (LoF)0+1 (GoF)

Strongest effect: PXR LoF at normalized -0.825. 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
2.15 · conserved
dbSNP
rs4453543
Region tier
receptor_confirmed

Mirrored from ClinVar, GTEx, GWAS Catalog, JASPAR/FIMO, gnomAD and phyloP. See Databases.

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
A→C-1.0000.020-1.000not observed
A→G-0.1640.0250.146not observed
A→T-0.825-0.033-0.438not observed

Every possible base substitution at chr17:47841362, 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

Logo for the strongest scoring receptor, PXR. The highlighted column marks the approximate affected base within the response element. External browser: UCSC Genome Browser.