stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:1/18:1, d18:2/18:0)

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator 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

Associated Genomic Regions

Region: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.136
Position:
64235556
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
10.847
Reference Allele:
G
-log10(P):
-61.450
MAF:
0.167
Beta (Num):
0.176
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.040
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

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):
0.125
Position:
12959094
SE (Ratio):
0.010
Effect Allele:
A
Z-score (Ratio):
12.847
Reference Allele:
T
-log10(P):
-85.303
MAF:
0.386
Beta (Num):
0.092
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.033
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 metabolism3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism3[1], 4[2]

Ratio Explanation:

The ratio compares saturated (C18:0) to unsaturated sphingomyelins.5[1] ISM1's regulation of upstream lipid synthesis can alter the relative abundance of different sphingomyelin species.2[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

ISM1-mediated changes in sphingolipid metabolism can alter lipoprotein profiles and biliary lipid composition.1[1], 2[2], 6[3] This dysregulation affects LDL-cholesterol levels and is a risk factor for cholelithiasis (gallstones).7[4], 8[5], 6[6]

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