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chr3_14141910_T_C

chr3:14141910 · GRCh38T → Crs1043943gnomAD AF 6.52e-1receptor_confirmed

regulatory target · XPC nearest gene · TMEM43 · within gene

Regulatory target XPC 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

-0.503LoF

FXR

-0.743LoF

AhR

-0.879LoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR LoF at normalized -0.879. 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

ClinVar: Benign/Likely benign · record
GTEx liver eQTL: XPC, slope 0.28, p 6.5e-13
phyloP conservation: -1.33
gnomAD: AF 6.52e-1 · browser
dbSNP: rs1043943
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	-0.501	-0.732	-0.898	not observed
T→C	-0.503	-0.743	-0.879	6.5e-1
T→G	-0.497	-0.732	-0.843	not observed

Every possible base substitution at chr3:14141910, 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

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.