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chr11_69638964_C_A

chr11:69638964 · GRCh38C → Ars3842249receptor_confirmed

nearest gene · CCND1 · 2.2 kb

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

Receptor variant-effect scores

PXR

0.084Neutral

FXR

0.116GoF

AhR

0.327GoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR GoF at normalized 0.327. 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: 0.00
dbSNP: rs3842249
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	0.084	0.116	0.327	not observed
C→G	0.134	0.123	0.433	not observed
C→T	0.012	0.098	0.234	not observed

Every possible base substitution at chr11:69638964, 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.