sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*

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

Metabolite Accession: GCST90199995
Name: sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs174547

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.260
Position:
61570783
SE (Ratio):
0.014
Effect Allele:
C
Z-score (Ratio):
-18.383
Reference Allele:
T
-log10(P):
-172.107
MAF:
0.339
Beta (Num):
-0.074
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.186
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
FADS2 FADS1 FEN1 TMEM258 MYRF

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.174
Position:
8289519
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
10.218
Reference Allele:
A
-log10(P):
-54.759
MAF:
0.192
Beta (Num):
0.075
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
-0.099
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.149
Position:
12962718
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
-10.801
Reference Allele:
G
-log10(P):
-60.941
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.081
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.4[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1]

Ratio Explanation:

The ratio compares sphingomyelins with C24 acyl chains to those with C20/C22 chains, likely reflecting FADS2 activity on fatty acid precursors for sphingolipid synthesis.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants in FADS2 alter polyunsaturated fatty acid synthesis, which changes sphingomyelin composition.2[1], 5[2] This dysregulation of lipid metabolism is a known risk factor for cholelithiasis (gallstones), a phenotype strongly associated with the genetic loci.6[3], 7[4], 8[5]

Phenotype Driver:

Gene-centric:FADS2

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