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chr3_129433705_C_T

chr3:129433705 · GRCh38C → Trs3138354receptor_confirmed

nearest gene · MBD4 · within gene

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

Receptor variant-effect scores

PXR

-0.344LoF

FXR

-0.423LoF

AhR

-0.299LoF

-1 (LoF)0+1 (GoF)

Strongest effect: FXR LoF at normalized -0.423. 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: 0.57
dbSNP: rs3138354
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
C→A	0.284	0.374	0.195	not observed
C→G	-0.222	-0.281	-0.195	not observed
C→T	-0.344	-0.423	-0.299	not observed

Every possible base substitution at chr3:129433705, 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: FXR

Multi receptor overlap: FXR

Binding motif

FXR IR1 (AGGTCAxTGACCT) · JASPAR MA1602

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