sphingomyelin (d18:2/16:0, d18:1/16:1)* to glycosyl ceramide (d18:1/23:1, d17:1/24:1)*

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

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: rs686548

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
20
Beta (Ratio):
-0.185
Position:
12973521
SE (Ratio):
0.022
Effect Allele:
A
Z-score (Ratio):
-8.454
Reference Allele:
T
-log10(P):
-38.109
MAF:
0.387
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.015
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:

Sphingomyelin synthesis, ceramide metabolism.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Glycosphingolipid biosynthesis, ceramide metabolism.8[1], 9[2], 10[3], 11[4]

Ratio Explanation:

The ratio reflects the balance between two major ceramide utilization pathways; ISM1 may influence this by altering lipid metabolism and substrate availability for sphingolipid synthesis.8[1], 5[2], 1[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 influences lipid metabolism, which is linked to cholelithiasis.1[1], 2[2], 3[3], 4[4] Studies show a protective effect of sphingomyelin against cholelithiasis, a relationship that is significantly mediated by LDL cholesterol.12[5], 13[6], 14[7] Elevated ALT and LDL-C are also associated with ISM1 and cholelithiasis.15[8], 16[9], 17[10]

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