Metabolomics (Nightingale)

Summary

Number of traits: 141
Training cohort: INTERVAL
Training sample size: 37,359

External validation cohorts: UK Biobank, ORCADES, VIKING
Number of traits externally validated: 141, 141 and 141
External cohort sample sizes: 116,830, 1,884 and 2,046
Evaluation Metric: Spearman correlation coefficient, r squared (r2)

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All genetic scores are provided under a CC-BY license.

Validation performance of genetic scores

drawing

(a1): Spearman correlation performance comparison between internal and external validation (UKB);
(a2): Spearman correlation performance comparison between internal and external validation (ORCADES);
(a3): Spearman correlation performance comparison between internal and external validation (VIKING);
(b): The number of traits whose genetic scores are in different performance ranges in terms of explained variance (R2) between internal and external validation.

Explore traits and their genetic scores:

Trait ID Biomarker Name Group Subgroup #SNP r2 EXT1.r2 EXT2.r2 EXT3.r2
sldlce Cholesteryl esters in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 400 0.13 0.06 0.08 0.05
sldlc Cholesterol in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 388 0.13 0.06 0.09 0.06
mldlce Cholesteryl esters in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 392 0.13 0.05 0.07 0.04
mldlc Cholesterol in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 388 0.13 0.06 0.08 0.05
ldlc LDL cholesterol Cholesterol 392 0.13 0.07 0.1 0.06
mldll Total lipids in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 381 0.12 0.06 0.08 0.06
lldlc Cholesterol in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 393 0.12 0.07 0.1 0.07
lldlfc Free cholesterol in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 406 0.12 0.08 0.1 0.07
mldlp Concentration of medium LDL particles Lipoprotein subclasses Medium LDL (average diameter 23 nm) 379 0.12 0.05 0.06 0.05
sldll Total lipids in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 374 0.12 0.08 0.09 0.07
lldlce Cholesteryl esters in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 392 0.12 0.07 0.1 0.07
sldlp Concentration of small LDL particles Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 377 0.12 0.06 0.08 0.06
lldll Total lipids in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 395 0.12 0.07 0.1 0.07
idlfc Free cholesterol in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 405 0.12 0.08 0.09 0.06
lldlp Concentration of large LDL particles Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 391 0.12 0.07 0.1 0.07
idlpl Phospholipids in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 395 0.11 0.08 0.11 0.07
mldlfc Free cholesterol in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 350 0.11 0.08 0.09 0.07
lldlpl Phospholipids in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 371 0.11 0.07 0.09 0.07
xsvldlpl Phospholipids in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 426 0.11 0.06 0.08 0.06
idll Total lipids in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 398 0.11 0.08 0.1 0.07
idlp Concentration of IDL particles Lipoprotein subclasses IDL (average diameter 28.6 nm) 396 0.11 0.07 0.09 0.06
idlc Cholesterol in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 384 0.11 0.08 0.09 0.07
mldlpl Phospholipids in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 356 0.1 0.07 0.09 0.07
sldlfc Free cholesterol in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 319 0.1 0.09 0.1 0.08
idlce Cholesteryl esters in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 372 0.1 0.07 0.09 0.06
apob Apolipoprotein B Apolipoproteins 384 0.1 0.07 0.09 0.08
gly Glycine Amino acids 330 0.1 0.18 0.17 0.16
sldlpl Phospholipids in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 332 0.1 0.09 0.1 0.09
hdld Average diameter for HDL particles Lipoprotein particle sizes 375 0.1 0.12 0.12 0.14
xlhdlpl Phospholipids in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 365 0.09 0.1 0.1 0.12
xsvldll Total lipids in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 378 0.09 0.08 0.1 0.07
idltg Triglycerides in IDL Lipoprotein subclasses IDL (average diameter 28.6 nm) 360 0.09 0.09 0.12 0.13
xsvldlp Concentration of very small VLDL particles Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 373 0.09 0.08 0.1 0.08
serumc Total cholesterol Cholesterol 329 0.09 0.07 0.08 0.07
xsvldltg Triglycerides in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 387 0.09 0.09 0.11 0.1
estc Total esterified cholesterol Cholesteryl esters 311 0.09 0.07 0.08 0.07
freec Total free cholesterol Free cholesterol 344 0.09 0.07 0.08 0.07
xsvldlfc Free cholesterol in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 345 0.09 0.07 0.09 0.07
xlhdlp Concentration of very large HDL particles Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 334 0.09 0.11 0.1 0.12
lhdlce Cholesteryl esters in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 316 0.09 0.1 0.11 0.12
lhdlc Cholesterol in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 313 0.08 0.1 0.11 0.13
lldltg Triglycerides in large LDL Lipoprotein subclasses Large LDL (average diameter 25.5 nm) 307 0.08 0.08 0.11 0.13
xlhdll Total lipids in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 327 0.08 0.1 0.09 0.11
vldld Average diameter for VLDL particles Lipoprotein particle sizes 376 0.08 0.04 0.05 0.06
svldlpl Phospholipids in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 375 0.08 0.06 0.07 0.07
ldltg Triglycerides in LDL Triglycerides 310 0.08 0.08 0.09 0.12
svldltg Triglycerides in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 367 0.08 0.08 0.07 0.07
svldlp Concentration of small VLDL particles Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 348 0.08 0.07 0.08 0.08
svldll Total lipids in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 348 0.08 0.07 0.07 0.08
lhdlfc Free cholesterol in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 294 0.08 0.1 0.11 0.12
lhdll Total lipids in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 306 0.08 0.1 0.11 0.13
mldltg Triglycerides in medium LDL Lipoprotein subclasses Medium LDL (average diameter 23 nm) 289 0.08 0.05 0.07 0.1
lvldlce Cholesteryl esters in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 322 0.08 0.06 0.04 0.06
lhdlp Concentration of large HDL particles Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 304 0.08 0.11 0.11 0.12
mvldlce Cholesteryl esters in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 313 0.08 0.02 0.03 0.03
svldlfc Free cholesterol in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 360 0.08 0.04 0.05 0.06
mvldll Total lipids in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 341 0.08 0.06 0.05 0.06
mvldlpl Phospholipids in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 333 0.08 0.04 0.04 0.05
mvldlp Concentration of medium VLDL particles Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 341 0.08 0.04 0.04 0.05
lhdltg Triglycerides in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 231 0.08 0.1 0.12 0.13
vldltg Triglycerides in VLDL Triglycerides 343 0.08 0.07 0.05 0.06
sldltg Triglycerides in small LDL Lipoprotein subclasses Small LDL (average diameter 18.7 nm) 339 0.08 0.05 0.06 0.08
mvldltg Triglycerides in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 339 0.07 0.07 0.05 0.06
xxlvldltg Triglycerides in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 300 0.07 0.05 0.03 0.03
lvldlc Cholesterol in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 323 0.07 0.06 0.04 0.06
hdltg Triglycerides in HDL Triglycerides 281 0.07 0.07 0.09 0.09
xsvldlc Cholesterol in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 322 0.07 0.07 0.09 0.07
serumtg Total triglycerides Triglycerides 339 0.07 0.07 0.06 0.06
xxlvldlpl Phospholipids in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 311 0.07 0.07 0.03 0.04
vldlc VLDL cholesterol Cholesterol 316 0.07 0.05 0.07 0.07
xxlvldlp Concentration of chylomicrons and extremely large VLDL particles Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 305 0.07 0.06 0.03 0.04
mvldlfc Free cholesterol in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 330 0.07 0.02 0.03 0.04
xxlvldll Total lipids in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 306 0.07 0.05 0.03 0.04
mvldlc Cholesterol in medium VLDL Lipoprotein subclasses Medium VLDL (average diameter 44.5 nm) 321 0.07 0.02 0.03 0.03
lvldll Total lipids in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 312 0.07 0.06 0.04 0.05
lvldlp Concentration of large VLDL particles Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 313 0.07 0.07 0.05 0.05
xlhdltg Triglycerides in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 236 0.07 0.07 0.1 0.14
xlvldlce Cholesteryl esters in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 304 0.07 0.05 0.03 0.05
la Linoleic acid Fatty acids 305 0.07 0.03 0.05 0.06
lvldltg Triglycerides in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 306 0.07 0.06 0.04 0.05
lvldlpl Phospholipids in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 313 0.07 0.07 0.05 0.06
xlvldll Total lipids in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 301 0.07 0.06 0.04 0.04
svldlc Cholesterol in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 308 0.07 0.06 0.08 0.07
xlvldlp Concentration of very large VLDL particles Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 299 0.07 0.07 0.04 0.05
lhdlpl Phospholipids in large HDL Lipoprotein subclasses Large HDL (average diameter 12.1 nm) 273 0.07 0.1 0.1 0.12
xlvldltg Triglycerides in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 297 0.07 0.06 0.03 0.04
faw6 Omega-6 fatty acids Fatty acids 283 0.07 0.03 0.06 0.06
xlvldlc Cholesterol in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 303 0.07 0.06 0.03 0.05
lvldlfc Free cholesterol in large VLDL Lipoprotein subclasses Large VLDL (average diameter 53.6 nm) 302 0.07 0.07 0.05 0.06
shdltg Triglycerides in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 284 0.07 0.08 0.07 0.09
xxlvldlfc Free cholesterol in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 283 0.07 0.07 0.04 0.04
xxlvldlc Cholesterol in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 300 0.07 0.07 0.03 0.05
pufa Polyunsaturated fatty acids Fatty acids 282 0.07 0.03 0.07 0.07
xlhdlfc Free cholesterol in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 258 0.07 0.07 0.06 0.08
xlvldlfc Free cholesterol in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 288 0.07 0.06 0.03 0.04
xxlvldlce Cholesteryl esters in chylomicrons and extremely large VLDL Lipoprotein subclasses Chylomicrons and extremely large VLDL (particle diameters from 75 nm upwards) 279 0.07 0.07 0.04 0.05
xsvldlce Cholesteryl esters in very small VLDL Lipoprotein subclasses Very small VLDL (average diameter 31.3 nm) 289 0.07 0.07 0.08 0.06
xlvldlpl Phospholipids in very large VLDL Lipoprotein subclasses Very large VLDL (average diameter 64 nm) 290 0.07 0.06 0.03 0.04
svldlce Cholesteryl esters in small VLDL Lipoprotein subclasses Small VLDL (average diameter 36.8 nm) 286 0.07 0.06 0.08 0.07
mhdltg Triglycerides in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 301 0.07 0.07 0.08 0.07
xlhdlc Cholesterol in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 261 0.06 0.09 0.08 0.11
hdlc HDL cholesterol Cholesterol 223 0.06 0.07 0.09 0.1
xlhdlce Cholesteryl esters in very large HDL Lipoprotein subclasses Very large HDL (average diameter 14.3 nm) 256 0.06 0.09 0.08 0.11
unsat Degree of unsaturation Fatty acids 230 0.06 0.07 0.08 0.1
totfa Total fatty acids Fatty acids 292 0.06 0.0 0.06 0.07
mufa Monounsaturated fatty acids Fatty acids 279 0.06 0.0 0.05 0.06
sfa Saturated fatty acids Fatty acids 225 0.05 0.0 0.05 0.06
pc Phosphatidylcholines Other lipids 209 0.05 0.06 0.07 0.06
sm Sphingomyelins Other lipids 217 0.05 0.05 0.07 0.07
totcho Total cholines Other lipids 201 0.05 0.05 0.07 0.06
ldld Average diameter for LDL particles Lipoprotein particle sizes 199 0.05 0.0 0.01 0.0
totpg Phosphoglycerides Other lipids 189 0.05 0.05 0.07 0.06
shdlce Cholesteryl esters in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 148 0.05 0.01 0.01 0.01
apoa1 Apolipoprotein A1 Apolipoproteins 165 0.04 0.06 0.09 0.07
faw3 Omega-3 fatty acids Fatty acids 165 0.04 0.04 0.1 0.08
shdlpl Phospholipids in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 167 0.04 0.02 0.03 0.01
shdlc Cholesterol in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 122 0.03 0.01 0.01 0.01
dha Docosahexaenoic acid Fatty acids 119 0.03 0.04 0.07 0.06
gp Glycoprotein acetyls Inflammation 107 0.03 0.04 0.03 0.03
mhdlce Cholesteryl esters in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 112 0.03 0.03 0.05 0.04
mhdlc Cholesterol in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 109 0.03 0.03 0.05 0.04
shdlfc Free cholesterol in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 144 0.03 0.01 0.01 0.0
his Histidine Amino acids 51 0.03 0.02 0.02 0.02
mhdlpl Phospholipids in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 127 0.03 0.03 0.05 0.03
mhdll Total lipids in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 119 0.03 0.03 0.05 0.03
mhdlp Concentration of medium HDL particles Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 121 0.03 0.03 0.04 0.03
mhdlfc Free cholesterol in medium HDL Lipoprotein subclasses Medium HDL (average diameter 10.9 nm) 107 0.03 0.03 0.04 0.03
gln Glutamine Amino acids 87 0.02 0.04 0.05 0.06
shdlp Concentration of small HDL particles Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 109 0.02 0.02 0.02 0.01
shdll Total lipids in small HDL Lipoprotein subclasses Small HDL (average diameter 8.7 nm) 103 0.02 0.02 0.02 0.01
tyr Tyrosine Amino acids Aromatic amino acids 99 0.02 0.02 0.03 0.03
phe Phenylalanine Amino acids Aromatic amino acids 54 0.02 0.0 0.0 0.0
ala Alanine Amino acids 41 0.01 0.01 0.01 0.02
crea Creatinine Fluid balance 34 0.01 0.0 0.01 0.01
val Valine Amino acids Branched-chain amino acids 24 0.01 0.01 0.01 0.02
leu Leucine Amino acids Branched-chain amino acids 20 0.01 0.0 0.0 0.01
ile Isoleucine Amino acids Branched-chain amino acids 26 0.01 0.0 0.0 0.01
ace Acetate Ketone bodies 1 0.0 0.0 0.0 0.0
glc Glucose Glycolysis related metabolites 5 0.0 0.0 0.01 0.01
acace Acetoacetate Ketone bodies 14 0.0 0.0 0.0 0.0
pyr Pyruvate Glycolysis related metabolites 1 0.0 0.0 0.0 0.0