sphingomyelin (d18:2/14:0, d18:1/14:1)* to sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*

Numerator Metabolite

Metabolite Accession: GCST90199975
Name: sphingomyelin (d18:2/14:0, d18:1/14:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator 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

Associated Genomic Regions

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):
-0.168
Position:
12959398
SE (Ratio):
0.012
Effect Allele:
T
Z-score (Ratio):
-13.533
Reference Allele:
C
-log10(P):
-94.411
MAF:
0.387
Beta (Num):
-0.012
Novel Locus:
No
SE (Num):
0.013
Beta (Den):
0.156
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.4[1], 5[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

This ratio compares shorter-chain (C14) to very-long-chain (C21-C23) sphingomyelins, a balance potentially altered by ISM1's regulatory effects on overall lipid homeostasis.1[1], 6[2], 7[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation at the ISM1 locus is linked to this sphingomyelin ratio and risk for cholelithiasis.8[1], 9[2], 10[3] ISM1, a secreted protein, regulates systemic lipid metabolism, which is supported by associations with cholelithiasis, ALT, and LDL-C, suggesting a link between ISM1 function and gallstone disease risk.1[4], 11[5], 12[6], 13[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