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chr6_2999495_A_G

chr6:2999495 · GRCh38A → Grs2070999gnomAD AF 6.92e-1receptor_confirmed

regulatory target · NQO2-AS1 nearest gene · NQO2 · 320 bp

Regulatory target NQO2-AS1 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

0.038Neutral

FXR

0.028Neutral

AhR

0.122GoF

-1 (LoF)0+1 (GoF)

Strongest effect: AhR GoF at normalized 0.122. Impact is low, near neutral.

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: NQO2-AS1, slope 0.51, p 3.3e-8
phyloP conservation: 0.57
gnomAD: AF 6.92e-1 · browser
dbSNP: rs2070999
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
A→C	0.109	0.021	0.147	not observed
A→G	0.038	0.028	0.122	6.9e-1
A→T	-0.075	-0.138	-0.122	not observed

Every possible base substitution at chr6:2999495, 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

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.