sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)* to 1-palmitoleoyl-gpc (16:1)*

Numerator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

Denominator Metabolite

Structure of 1-palmitoleoyl-gpc (16:1)*
Metabolite Accession: GCST90199777
Name: 1-palmitoleoyl-gpc (16:1)*
Hmdb Id: HMDB0010383
Super Pathway: NA
Sub Pathway: NA
Inchikey: LFUDDCMNKWEORN

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):
-0.178
Position:
27730940
SE (Ratio):
0.021
Effect Allele:
T
Z-score (Ratio):
-8.668
Reference Allele:
C
-log10(P):
-39.965
MAF:
0.413
Beta (Num):
-0.090
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.088
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.4[1], 5[2], 6[3], 7[4]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism, Acyl chain remodeling.8[1], 9[2], 10[3]

Ratio Explanation:

The ratio may reflect the balance between sphingomyelin synthesis and lysophosphatidylcholine degradation, potentially influenced by hepatic lipid regulatory genes like GCKR.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter hepatic glucose and lipid metabolism, influencing triglyceride levels.1[1], 11[2], 12[3] This dysregulation is linked to an increased risk of cirrhosis, ischemic heart disease, and type 2 diabetes, phenotypes where sphingolipid and glycerophospholipid imbalances are observed.1[4], 6[5], 13[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