palmitoyl-sphingosine-phosphoethanolamine (d18:1/16:0) to 1-stearoyl-gpe (18:0)

Numerator Metabolite

Metabolite Accession: GCST90200237
Name: palmitoyl-sphingosine-phosphoethanolamine (d18:1/16:0)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of 1-stearoyl-gpe (18:0)
Metabolite Accession: GCST90199772
Name: 1-stearoyl-gpe (18:0)
Hmdb Id: HMDB0011130
Super Pathway: NA
Sub Pathway: NA
Inchikey: BBYWOYAFBUOUFP

Associated Genomic Regions

Region: rs1260326

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
-0.165
Position:
27730940
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
-8.631
Reference Allele:
C
-log10(P):
-39.643
MAF:
0.413
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.090
SE (Den):
0.015
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.8[1], 9[2]

Ratio Explanation:

This ratio may reflect the balance of sphingolipid versus glycerophospholipid synthesis, which is influenced upstream by GCKR's regulation of hepatic glucose and lipid flux.2[1], 10[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR gene variants are strongly associated with altered hepatic glucose/lipid metabolism, influencing triglyceride levels, liver fat accumulation (cirrhosis/NASH), and T2D risk.2[1], 11[2], 12[3], 13[4], 14[5] This ratio likely serves as a downstream biomarker of these GCKR-driven metabolic shifts.

Phenotype Driver:

Gene-centric:GCKR

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data