lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

Numerator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Denominator Metabolite

Structure of sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

Associated Genomic Regions

Region: rs12897637

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.271
Position:
64239351
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
-15.638
Reference Allele:
T
-log10(P):
-125.253
MAF:
0.165
Beta (Num):
-0.066
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.205
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814176

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):
-0.178
Position:
12959398
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
-13.301
Reference Allele:
C
-log10(P):
-91.283
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.083
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2], 7[3]

Ratio Explanation:

This ratio reflects altered sphingolipid metabolism, specifically the balance between very-long-chain (C24:0) and other long-chain sphingomyelins, which can impact membrane function and signaling.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 variation likely alters its regulation of lipid metabolism, affecting the sphingomyelin acyl-chain profile.1[1], 2[2], 3[3] This dysregulation is associated with lipoprotein disorders and cholelithiasis, potentially through effects on hepatic lipid processing and bile composition.8[4], 9[5], 10[6], 11[7]

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