lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)* to 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*

Numerator Metabolite

Structure of lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*
Metabolite Accession: GCST90200098
Name: lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: MKOKWBRPIBQYJJ

Denominator Metabolite

Structure of 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Metabolite Accession: GCST90200102
Name: 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Hmdb Id: HMDB0008008
Super Pathway: NA
Sub Pathway: NA
Inchikey: MMUCLZZSNHBNFL

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):
-0.173
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-8.521
Reference Allele:
C
-log10(P):
-38.688
MAF:
0.413
Beta (Num):
-0.079
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.093
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]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.6[1]

Ratio Explanation:

The ratio may reflect a shift in lipid metabolism, where GCKR variants influence both sphingolipid and glycerophospholipid pathways, impacting cellular processes.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter glucose and lipid metabolism, predisposing individuals to type 2 diabetes and hypercholesterolemia.3[1], 7[2], 8[3] The altered metabolic state likely influences the levels of both lactosyl-n-nervonoyl-sphingosine and 1-palmitoleoyl-2-linolenoyl-gpc, leading to the observed associations with cholelithiasis and cardiovascular diseases.

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