sphingomyelin (d18:2/24:1, d18:1/24:2)* to glycosyl ceramide (d18:1/23:1, d17:1/24:1)*

Numerator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200119
Name: glycosyl ceramide (d18:1/23:1, d17:1/24:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs4814175

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:
12959094
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
-8.892
Reference Allele:
T
-log10(P):
-41.958
MAF:
0.386
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.110
SE (Den):
0.020
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]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio likely reflects the balance of sphingolipid metabolic pathways, where both metabolites are derived from a common precursor, ceramide.5[1], 7[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

ISM1's regulation of hepatic lipid synthesis and its correlation with LDL-C and ALT suggest a mechanism where altered sphingolipid metabolism impacts liver function and cholesterol homeostasis, increasing the risk for cholelithiasis.8[1], 9[2], 1[3], 10[4]

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