sphingomyelin (d18:1/14:0, d16:1/16:0)* to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/14:0, d16:1/16:0)*
Metabolite Accession: GCST90199945
Name: sphingomyelin (d18:1/14:0, d16:1/16:0)*
Hmdb Id: HMDB0012097
Super Pathway: NA
Sub Pathway: NA
Inchikey: KYICBZWZQPCUMO

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

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
14
Beta (Ratio):
0.479
Position:
64239629
SE (Ratio):
0.019
Effect Allele:
G
Z-score (Ratio):
25.153
Reference Allele:
T
-log10(P):
-319.782
MAF:
0.166
Beta (Num):
0.421
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 metabolism3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism3[1], 4[2]

Ratio Explanation:

The ratio reflects the balance between shorter-chain (numerator) and very-long-chain (denominator) sphingomyelins, potentially modulated by SGPP1's role in supplying precursors for ceramide synthesis.1[1], 5[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SGPP1 function likely dysregulates the balance of sphingomyelin species. This can impact lipoprotein metabolism, platelet function, and insulin signaling, leading to lipidaemias, and changes in platelet count, HbA1c, and triglycerides.6[1], 7[2], 8[3], 9[4]

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