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chr6_3157575_C_T

chr6:3157575 · GRCh38C → Trs909965gnomAD AF 6.19e-1receptor_confirmed

regulatory target · TUBB2B nearest gene · TUBB2A · 31 bp

Regulatory target TUBB2B 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

-0.409LoF

FXR

0.034Neutral

AhR

-0.098Neutral

-1 (LoF)0+1 (GoF)

Strongest effect: PXR LoF at normalized -0.409. 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

ClinVar: Benign · record
GTEx liver eQTL: TUBB2B, slope 0.76, p 1.2e-22
phyloP conservation: -2.87
gnomAD: AF 6.19e-1 · browser
dbSNP: rs909965
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	-0.022	0.010	0.110	not observed
C→G	0.053	-0.010	-0.073	6.6e-6
C→T	-0.409	0.034	-0.098	6.2e-1

Every possible base substitution at chr6:3157575, 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

PXR DR3 (AGGTCAxxxAGGTCA) · JASPAR MA1148

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