Home / Variant

chr6_52666801_T_G

chr6:52666801 · GRCh38T → Grs1769066955receptor_confirmed

nearest gene · LOC730101 · within gene

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

Receptor variant-effect scores

PXR

2,880Neutral

FXR

784Neutral

AhR

3,136GoF

− LoF0+ GoF

Strongest effect: AhR GoF at raw 3,136. Impact is low, near neutral.

Raw ft_head_delta is the center bin sum of ALT minus REF on the receptor finetuned ChIP head, in unbounded model output units. A negative value means loss of receptor binding and a positive value means gain. AhR is exploratory, from a single replicate.

Cross-annotations

phyloP conservation: 3.60 · conserved
dbSNP: rs1769066955↗
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	4,160	1,168	3,392	not observed
T→C	6,720	1,744	5,184	not observed
T→G	2,880	784	3,136	not observed

Every possible base substitution at chr6:52666801, each scored independently and shown as raw model deltas. 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

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.