n-palmitoyl-sphinganine (d18:0/16:0) to sphingomyelin (d18:2/23:1)*

Numerator Metabolite

Structure of n-palmitoyl-sphinganine (d18:0/16:0)
Metabolite Accession: GCST90200064
Name: n-palmitoyl-sphinganine (d18:0/16:0)
Hmdb Id: HMDB11760
Super Pathway: NA
Sub Pathway: NA
Inchikey: GCGTXOVNNFGTPQ

Denominator Metabolite

Structure of sphingomyelin (d18:2/23:1)*
Metabolite Accession: GCST90200126
Name: sphingomyelin (d18:2/23:1)*
Hmdb Id: HMDB0240668
Super Pathway: NA
Sub Pathway: NA
Inchikey: PUTLJICFLAOKRD

Associated Genomic Regions

Region: rs17101394

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:
14
Beta (Ratio):
-0.271
Position:
64232386
SE (Ratio):
0.026
Effect Allele:
A
Z-score (Ratio):
-10.624
Reference Allele:
G
-log10(P):
-59.036
MAF:
0.164
Beta (Num):
-0.112
Novel Locus:
No
SE (Num):
0.021
Beta (Den):
0.159
SE (Den):
0.018
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Ceramide biosynthesis, Sphingolipid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingomyelin metabolism, Sphingolipid metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio reflects the balance between ceramide production and its conversion to sphingomyelin, a key step in sphingolipid metabolism.8[1], 10[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

SGPP1 activity influences ceramide levels, a central molecule in sphingolipid metabolism.1[1], 3[2] Altered ceramide and sphingolipid profiles are linked to insulin resistance and dyslipidemia, impacting HbA1c and triglyceride levels, which are markers for metabolic syndrome.11[3], 12[4], 13[5], 14[6], 15[7]

Phenotype Driver:

Gene-centric:SGPP1

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