sphingomyelin (d18:2/16:0, d18:1/16:1)* to sphingomyelin (d18:2/23:1)*

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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: rs686548

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:
20
Beta (Ratio):
-0.136
Position:
12973521
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
-9.748
Reference Allele:
T
-log10(P):
-50.023
MAF:
0.387
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.061
SE (Den):
0.014
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Ratio Explanation:

The ratio reflects the balance between different sphingomyelin species, which can be influenced by diet and is associated with metabolic health.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

The identified pQTL colocalization for ISM1, a gene linked to lipid metabolism1[1], 2[2], suggests it may influence the sphingomyelin ratio. This altered ratio is associated with cholelithiasis and changes in ALT and LDL cholesterol, possibly by modulating hepatic lipid handling and bile composition.6[3], 7[4], 1[5]

Phenotype Driver:

Gene-centric:ISM1

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