sphingomyelin (d18:1/18:1, d18:2/18:0) to sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

Denominator Metabolite

Metabolite Accession: GCST90200047
Name: sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)
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):
-0.120
Position:
12959398
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
-9.320
Reference Allele:
C
-log10(P):
-45.899
MAF:
0.387
Beta (Num):
-0.033
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.087
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 biosynthesis

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

The ratio reflects differential activity in sphingolipid metabolism. A higher ratio may indicate altered synthesis or breakdown of specific sphingomyelin species, potentially influenced by ISM1.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 may regulate lipid metabolism, affecting the balance of sphingomyelin species. This dysregulation is linked to cholelithiasis and altered LDL-cholesterol and ALT levels, possibly by influencing bile composition and hepatic lipid handling.3[1], 4[2], 5[3], 6[4], 7[5]

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