sphingomyelin (d18:1/20:0, d16:1/22:0)* to sphingomyelin (d18:0/20:0, d16:0/22:0)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/20:0, d16:1/22:0)*
Metabolite Accession: GCST90200001
Name: sphingomyelin (d18:1/20:0, d16:1/22:0)*
Hmdb Id: HMDB0012102
Super Pathway: NA
Sub Pathway: NA
Inchikey: AADLTHQNYQJHQV

Denominator Metabolite

Metabolite Accession: GCST90200123
Name: sphingomyelin (d18:0/20:0, d16:0/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs10799478

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Clumped rQTL variant

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SNP Summary

Chr:
1
Beta (Ratio):
0.154
Position:
224305966
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
9.867
Reference Allele:
T
-log10(P):
-51.200
MAF:
0.405
Beta (Num):
0.037
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.117
SE (Den):
0.015
No CNV overlap
rQTL cluster:
153
Reaction Distance:
NA
Closest Genes:
FBXO28 DEGS1 AC138393.1 NVL CNIH4

Region: rs2244608

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.157
Position:
121416988
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
-9.516
Reference Allele:
A
-log10(P):
-47.770
MAF:
0.317
Beta (Num):
-0.042
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.115
SE (Den):
0.016
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs8012828

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:
14
Beta (Ratio):
0.369
Position:
64233980
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
18.045
Reference Allele:
C
-log10(P):
-165.926
MAF:
0.165
Beta (Num):
0.298
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.070
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis.7[1], 8[2], 9[3]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis.7[1], 8[2], 9[3]

Ratio Explanation:

The ratio reflects the desaturation of sphingomyelin, catalyzed by DEGS1, where lower ratios indicate reduced enzyme activity and an accumulation of saturated sphingomyelins.4[1], 5[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Reduced DEGS1 activity, indicated by a lower ratio, is linked to altered sphingolipid metabolism which has been associated with cardiovascular diseases like coronary atherosclerosis and hypercholesterolemia.10[1], 11[2], 12[3]

Phenotype Driver:

Metabolite-centric[both]

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