1-palmitoyl-gpe (16:0) to asparagine

Numerator Metabolite

Structure of 1-palmitoyl-gpe (16:0)
Metabolite Accession: GCST90199792
Name: 1-palmitoyl-gpe (16:0)
Hmdb Id: HMDB0011503
Super Pathway: NA
Sub Pathway: NA
Inchikey: YVYMBNSKXOXSKW

Denominator Metabolite

Structure of asparagine
Metabolite Accession: GCST90200452
Name: asparagine
Hmdb Id: HMDB0000168
Super Pathway: NA
Sub Pathway: NA
Inchikey: DCXYFEDJOCDNAF

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):
0.172
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
8.481
Reference Allele:
C
-log10(P):
-38.342
MAF:
0.412
Beta (Num):
0.087
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.085
SE (Den):
0.016
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism

Denominator Metabolite Explanation:

Amino acid metabolism, urea cycle9[1], 10[2], 11[3], 12[4]

Ratio Explanation:

An elevated ratio may reflect a shift towards increased glycerophospholipid breakdown and decreased asparagine synthesis, potentially driven by GCKR's influence on glucose and lipid metabolism.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants are associated with altered glucose and lipid metabolism, increasing the risk for type 2 diabetes and hypercholesterolemia.1[1], 2[2], 3[3], 7[4] The ratio of 1-palmitoyl-gpe to asparagine may reflect these metabolic shifts, contributing to the observed phenotypes of cholelithiasis and ischemic heart disease.

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