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chr6_56399929_T_C

chr6:56399929 · GRCh38T → Crs643246gnomAD AF 4.09e-1receptor_confirmed
regulatory target · RCC2P7nearest gene · COL21A1 · 5.8 kb

Regulatory target RCC2P7 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
-1.000LoF
FXR
-0.875LoF
AhR
-0.623LoF
-1 (LoF)0+1 (GoF)

Strongest effect: PXR LoF at normalized -1.000. Impact is at or above the receptor peak population 99th percentile, the top 1% or so.

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
RCC2P7, slope -0.47, p 2.8e-11
GWAS Catalog
Glutamine levels · record
phyloP conservation
-1.01
gnomAD
AF 4.09e-1 · browser
dbSNP
rs643246
Region tier
receptor_confirmed

Mirrored from ClinVar, GTEx, GWAS Catalog, JASPAR/FIMO, gnomAD and phyloP. See Databases.

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
T→A-1.000-0.951-0.672not observed
T→C-1.000-0.875-0.6234.1e-1
T→G-1.000-1.000-1.000not observed

Every possible base substitution at chr6:56399929, 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: FXRAhR

Multi receptor overlap: FXR,AhR

Binding motif

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