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chr12_132609027_G_A

chr12:132609027 · GRCh38G → Ars2323974gnomAD AF 2.09e-1receptor_confirmed

regulatory target · LRCOL1 nearest gene · LRCOL1 · within gene

Regulatory target LRCOL1 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

0.503GoF

FXR

0.693GoF

AhR

0.322GoF

-1 (LoF)0+1 (GoF)

Strongest effect: FXR GoF at normalized 0.693. 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

GTEx liver eQTL: LRCOL1, slope 0.44, p 7.9e-11
phyloP conservation: 0.09
gnomAD: AF 2.09e-1 · browser
dbSNP: rs2323974
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
G→A	0.503	0.693	0.322	2.1e-1
G→C	0.348	0.476	0.298	not observed
G→T	0.334	0.436	0.205	not observed

Every possible base substitution at chr12:132609027, 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.