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chr20_62146682_C_G

chr20:62146682 · GRCh38C → Grs6142715gnomAD AF 6.56e-1receptor_confirmed

regulatory target · LSM14B nearest gene · SS18L1 · within gene

Regulatory target LSM14B 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

0.195GoF

FXR

0.527GoF

AhR

0.263GoF

-1 (LoF)0+1 (GoF)

Strongest effect: FXR GoF at normalized 0.527. 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: LSM14B, slope -0.34, p 9.4e-8
phyloP conservation: -0.02
gnomAD: AF 6.56e-1 · browser
dbSNP: rs6142715
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	0.002	-0.006	-0.067	1.4e-5
C→G	0.195	0.527	0.263	6.6e-1
C→T	0.091	0.194	0.110	not observed

Every possible base substitution at chr20:62146682, 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.