1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)* to 1-palmitoyl-gpc (16:0)

Numerator Metabolite

Structure of 1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)*
Metabolite Accession: GCST90200083
Name: 1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)*
Hmdb Id: HMDB0011206
Super Pathway: NA
Sub Pathway: NA
Inchikey: PEWXKAOBUSBJLD

Denominator Metabolite

Structure of 1-palmitoyl-gpc (16:0)
Metabolite Accession: GCST90199733
Name: 1-palmitoyl-gpc (16:0)
Hmdb Id: HMDB0010382
Super Pathway: NA
Sub Pathway: NA
Inchikey: ASWBNKHCZGQVJV

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):
-0.158
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-8.099
Reference Allele:
C
-log10(P):
-35.133
MAF:
0.412
Beta (Num):
-0.088
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.070
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:

Ether lipid metabolism

Denominator Metabolite Explanation:

Glycerophospholipid metabolism

Ratio Explanation:

The ratio reflects the balance between ether lipid and glycerophospholipid synthesis. GCKR influences this by regulating the availability of precursors for lipid synthesis.1[1], 4[2], 3[3], 5[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter glucose and lipid metabolism, predisposing individuals to non-alcoholic fatty liver disease (NAFLD) and associated phenotypes like dyslipidemia and type 2 diabetes.2[1], 6[2], 3[3], 7[4], 8[5] The altered metabolite ratio is a downstream consequence of these broader 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