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chr1_150410805_C_T

chr1:150410805 · GRCh38C → Trs9651184receptor_confirmed
regulatory target · MRPS21nearest gene · RPRD2 · within gene

Regulatory target MRPS21 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
-0.421LoF
FXR
-0.441LoF
AhR
-0.339LoF
-1 (LoF)0+1 (GoF)

Strongest effect: FXR LoF at normalized -0.441. 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

GTEx liver eQTL
MRPS21, slope 0.22, p 5.0e-6
phyloP conservation
-0.06
dbSNP
rs9651184
Region tier
receptor_confirmed

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

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
C→A-1.000-1.000-1.000not observed
C→G-1.000-1.000-1.000not observed
C→T-0.421-0.441-0.339not observed

Every possible base substitution at chr1:150410805, 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

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