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

Numerator Metabolite

Structure of palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

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):
-0.169
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-8.401
Reference Allele:
C
-log10(P):
-37.658
MAF:
0.413
Beta (Num):
-0.082
Novel Locus:
Yes ✔️
SE (Num):
0.015
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

Denominator Metabolite Explanation:

Glycerophospholipid metabolism

Ratio Explanation:

The ratio may reflect the balance between sphingolipid and glycerophospholipid synthesis, potentially influenced by GCKR's role in directing glucose toward lipid synthesis pathways.1[1], 3[2], 7[3], 8[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants are associated with altered hepatic glucose and lipid metabolism, including sphingolipid levels, linking to phenotypes like liver cirrhosis, and dyslipidemia.1[1], 5[2], 9[3], 10[4], 7[5]

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