sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)* to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

Numerator Metabolite

Metabolite Accession: GCST90200053
Name: sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Metabolite Accession: GCST90200134
Name: sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: JONXXLXMISNQNG

Associated Genomic Regions

Region: rs12878001

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):
0.366
Position:
64239629
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
21.579
Reference Allele:
T
-log10(P):
-236.136
MAF:
0.165
Beta (Num):
0.308
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
-0.058
SE (Den):
0.021
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Ratio Explanation:

This ratio reflects a shift in the N-acyl chain length distribution of sphingomyelins, potentially influenced by SGPP1-mediated changes in sphingolipid precursor availability.5[1], 6[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Variation in SGPP1 likely alters the ceramide/S1P balance, impacting the sphingomyelin N-acyl chain profile.7[1], 6[2] This dysregulation affects lipoprotein metabolism, platelet function, and glucose homeostasis, leading to the observed lipid disorders, and changes in platelet count and HbA1c.8[3], 9[4], 10[5], 11[6]

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