sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/14:0, d16:1/16:0)*

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

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

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):
-0.185
Position:
12959094
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-10.784
Reference Allele:
T
-log10(P):
-60.764
MAF:
0.386
Beta (Num):
-0.068
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
0.118
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.10[1], 11[2], 12[3], 13[4], 14[5], 15[6], 16[7]

Denominator Metabolite Explanation:

Sphingolipid metabolism.10[1], 11[2], 12[3], 13[4], 14[5], 15[6], 16[7]

Ratio Explanation:

The ratio likely reflects altered sphingolipid metabolism influenced by ISM1, potentially impacting the balance between longer-chain (numerator) and shorter-chain (denominator) sphingomyelins.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

ISM1's role in lipid metabolism may influence the sphingomyelin profile.1[1], 3[2], 5[3], 6[4], 7[5], 8[6] Altered sphingomyelin levels and ISM1 are linked to changes in LDL cholesterol and have a reported association with cholelithiasis, suggesting a gene-to-phenotype link mediated by lipid alterations.17[7], 18[8], 19[9], 20[10], 4[11], 21[12], 22[13]

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