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chr17_6700318_G_T

chr17:6700318 · GRCh38G → Trs1973675960receptor_confirmed
nearest gene · SLC13A5 · within gene

For a non-coding regulatory variant the nearest gene by distance is frequently not the regulated gene.

Receptor variant-effect scores

PXR
38,272GoF
FXR
15,744GoF
AhR
9,472GoF
− LoF0+ GoF

Strongest effect: FXR GoF at raw 15,744. Impact is at or above the receptor peak population 99th percentile, the top 1% or so.

Raw ft_head_delta is the center bin sum of ALT minus REF on the receptor finetuned ChIP head, in unbounded model output units. A negative value means loss of receptor binding and a positive value means gain. AhR is exploratory, from a single replicate.

Cross-annotations

phyloP conservation
2.14 · conserved
dbSNP
rs1973675960↗
Region tier
receptor_confirmed

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

All substitutions at this position

SubstitutionPXRFXRAhRgnomAD AF
G→A-5,568-1,088-1,2806.6e-6
G→C14,2087,0405,376not observed
G→T38,27215,7449,472not observed

Every possible base substitution at chr17:6700318, each scored independently and shown as raw model deltas. 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: PXRFXR

Multi receptor overlap: PXR,FXR

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.