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

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

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):
-0.162
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-7.958
Reference Allele:
C
-log10(P):
-33.979
MAF:
0.413
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.087
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:

Sphingolipid biosynthesis.6[1], 7[2], 8[3], 9[4]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.10[1], 11[2], 12[3], 13[4], 14[5], 15[6]

Ratio Explanation:

The ratio may reflect the balance between sphingolipid and glycerophospholipid metabolism, potentially influenced by shared precursors or regulatory processes involving PLB1 and ATRAID.16[1], 17[2], 10[3], 18[4], 7[5], 19[6]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

The GCKR gene influences both glucose and lipid metabolism, and its variants are linked to an increased risk of cirrhosis, ischemic heart disease, and gout.1[1], 2[2], 4[3], 5[4] These associations may be mediated through downstream effects on lipid profiles and metabolic stress.1[5], 20[6]

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