GWAS1002851_H QTL Report (Homo sapiens) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
QTL Registration

QTL: GWAS1002851_H (low density lipoprotein cholesterol measurement, phospholipids:total lipids ratio QTL GWAS1002851 (human)) Homo sapiens

Symbol: GWAS1002851_H
Name: low density lipoprotein cholesterol measurement, phospholipids:total lipids ratio QTL GWAS1002851 (human)
RGD ID: 407353875
Trait: low density lipoprotein cholesterol measurement, phospholipids:total lipids ratio
Measurement Type: blood low density lipoprotein cholesterol level   (CMO:0000053)    
LOD Score: Not Available
P Value: 1.0E-78
Variance: Not Available
Position
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh386160,668,275 - 160,668,276RGD_MAPPER_PIPELINEGRCh38
GRCh376161,089,307 - 161,089,308RGD_MAPPER_PIPELINEGRCh37
Population Stats: Not Available
JBrowse: View Region in Genome Browser (JBrowse)
Model



Experimental Data Annotations    Click to see Annotation Detail View

Clinical Measurement
Object SymbolSpeciesTermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
GWAS1002851_HHumanblood low density lipoprotein cholesterol level  IAGPrs56393506405850206Based on the EFO term IDGWAS_CATALOGPMID:35213538

Experimental Factor Annotations    Click to see Annotation Detail View
Object SymbolSpeciesTermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
GWAS1002851_HHumanlow density lipoprotein cholesterol measurement  IAGPrs56393506405850206 GWAS_CATALOGPMID:35213538
GWAS1002851_HHumanphospholipids:total lipids ratio  IAGPrs56393506405850206 GWAS_CATALOGPMID:35213538
Experimental Data Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. RGD GWAS Catalog Import Pipeline RGD pipeline to import data from GWAS Catalog and create human variant and QTL records

Region

Position Markers

Peak: (rs56393506)
Human AssemblyChrPosition (strand)Source
GRCh386160,668,275 - 160,668,276RGD_MAPPER_PIPELINE


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407142693GWAS791669_Hcoronary artery disease QTL GWAS791669 (human)3e-103coronary artery disease6160668275160668276Human
406910403GWAS559379_Hlipoprotein A measurement, apolipoprotein A 1 measurement QTL GWAS559379 (human)3e-105lipoprotein A measurement, apolipoprotein A 1 measurementblood apolipoprotein AI level (CMO:0000520)6160668275160668276Human
407367778GWAS1016754_Hstroke, type 2 diabetes mellitus, coronary artery disease QTL GWAS1016754 (human)6e-12stroke, type 2 diabetes mellitus, coronary artery disease6160668275160668276Human
407350754GWAS999730_Hlow density lipoprotein cholesterol measurement, cholesteryl esters:total lipids ratio QTL GWAS999730 (human)9e-100low density lipoprotein cholesterol measurement, cholesteryl esters:total lipids ratioblood low density lipoprotein cholesterol level (CMO:0000053)6160668275160668276Human
407257827GWAS906803_Hcholesteryl esters to total lipids in medium LDL percentage QTL GWAS906803 (human)5e-73cholesteryl esters to total lipids in medium LDL percentage 6160668275160668276Human
407258115GWAS907091_Hphospholipids:total lipids ratio QTL GWAS907091 (human)8e-72phospholipids:total lipids ratio6160668275160668276Human
407091268GWAS740244_Hsleep duration, low density lipoprotein cholesterol measurement QTL GWAS740244 (human)3e-17sleep duration, low density lipoprotein cholesterol measurementblood low density lipoprotein cholesterol level (CMO:0000053)6160668275160668276Human
407384783GWAS1033759_Hlarge artery stroke QTL GWAS1033759 (human)2e-08large artery stroke6160668275160668276Human
407062442GWAS711418_Hlarge artery stroke QTL GWAS711418 (human)0.0000001large artery stroke6160668275160668276Human
407354092GWAS1003068_Hlow density lipoprotein particle size measurement QTL GWAS1003068 (human)2e-65low density lipoprotein particle size measurementblood low density lipoprotein particle diameter (CMO:0002693)6160668275160668276Human
407215497GWAS864473_Hglycoprotein measurement QTL GWAS864473 (human)4e-18glycoprotein measurement6160668275160668276Human
407261321GWAS910297_Hphospholipids:total lipids ratio QTL GWAS910297 (human)4e-57phospholipids:total lipids ratio6160668275160668276Human
407146772GWAS795748_Hcoronary artery disease QTL GWAS795748 (human)5e-34coronary artery disease6160668275160668276Human
407348725GWAS997701_HIschemic stroke QTL GWAS997701 (human)0.000002total cholesterol measurementblood total cholesterol level (CMO:0000051)6160668275160668276Human
407353875GWAS1002851_Hlow density lipoprotein cholesterol measurement, phospholipids:total lipids ratio QTL GWAS1002851 (human)1e-78low density lipoprotein cholesterol measurement, phospholipids:total lipids ratioblood low density lipoprotein cholesterol level (CMO:0000053)6160668275160668276Human
1643404BMD3_HBone mineral density QTL 3 (human)2.420.0005Bone mineral density6157563614170805979Human
406910581GWAS559557_Hlipoprotein A measurement QTL GWAS559557 (human)8e-285lipoprotein A measurement6160668275160668276Human
407353182GWAS1002158_Hchylomicron measurement, very low density lipoprotein cholesterol measurement, phospholipids:total lipids ratio QTL GWAS1002158 (human)7e-92chylomicron measurement, very low density lipoprotein cholesterol measurement, phospholipids:total lipids ratioblood very low density lipoprotein cholesterol level (CMO:0000648)6160668275160668276Human
407390805GWAS1039781_Hangina pectoris QTL GWAS1039781 (human)2e-29angina pectoris6160668275160668276Human
1643367BW323_HBody weight QTL 323 (human)2.420.0005Body fat amount6157563614170805979Human


Additional Information

GWAS QTLs Related by Peak Marker
Data has come from the GWAS Catalog   
The highlighted row represents the current QTL
QTL GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG Peak Marker Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GWAS559379_H GCST004399 Lipoprotein(a) levels adjusted for apolipoprotein(a) isoforms 13,781 European ancestry individuals T NR 3E-105 104.523 rs56393506 7.07 lipoprotein A measurement (EFO:0006925)
apolipoprotein A 1 measurement (EFO:0004614)
 PMID:28512139
GWAS559557_H GCST004398 Lipoprotein (a) levels 13,781 European ancestry individuals T NR 8E-285 284.097 rs56393506 13.6 lipoprotein A measurement (EFO:0006925)
 PMID:28512139
GWAS740244_H GCST009366 LDL cholesterol levels x long total sleep time interaction (2df test) 2,913 African American long sleepers, 358 Chinese ancestry long sleepers, 110 Asian ancestry long sleepers, 7,583 European ancestry long sleepers, 1,036 Hispanic/Latino long sleepers, up to 11,862 African American controls, 1,432 Chinese ancestry controls, 444 Asian ancestry controls, at least 31,744 European ancestry controls, 4,066 Hispanic/Latino controls ? NR 3E-17 16.523 rs56393506 2.382 sleep duration (EFO:0005271)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:31719535
GWAS791669_H GCST010866 Coronary artery disease 25,892 Japanese ancestry cases, 95,342 European ancestry cases, 142,336 Japanese ancestry controls, 385,488 European ancestry controls ? NR 3E-103 102.523 rs56393506 0.14927 coronary artery disease (EFO:0001645)
 PMID:33020668
GWAS795748_H GCST010479 Coronary artery disease 15,302 Japanese ancestry cases, 76,014 European and East Asian ancestry cases, 36,140 Japanese ancestry controls, 264,785 European and East Asian ancestry controls T 0.16 5E-34 33.302 rs56393506 1.15 coronary artery disease (EFO:0001645)
 PMID:32469254
GWAS864473_H GCST90269577 Glycoprotein acetyls levels (UKB data field 23480) 88,329 European ancestry individuals T 0.171679 4E-18 17.398 rs56393506 0.0544764 glycoprotein measurement (EFO:0004555)
 PMID:36764567
GWAS906803_H GCST90269718 Cholesteryl esters to total lipids in medium LDL percentage (UKB data field 23621) 88,329 European ancestry individuals T 0.171679 5E-73 72.302 rs56393506 0.114975 cholesteryl esters to total lipids in medium LDL percentage (EFO:0022252)
 PMID:36764567
GWAS907091_H GCST90269676 Phospholipids to total lipids in chylomicrons and extremely large VLDL percentage (UKB data field 23579) 85,701 European ancestry individuals T 0.170303 8E-72 71.097 rs56393506 0.115094 phospholipids:total lipids ratio (EFO:0020946)
 PMID:36764567
GWAS910297_H GCST90269716 Phospholipids to total lipids in medium LDL percentage (UKB data field 23619) 88,329 European ancestry individuals T 0.171679 4E-57 56.398 rs56393506 0.101241 phospholipids:total lipids ratio (EFO:0020946)
 PMID:36764567
GWAS997701_H GCST90308666 Ischemic stroke at least 26,047 African, African American ancestry individuals, at least 268,697 East Asian ancestry individuals, at least 1,479,471 European ancestry individuals, at least 15,080 Hispanic or Latin American individuals, at least 21,934 South Asian ancestry individuals T NR 0.000002 5.699 rs56393506 1.033 Ischemic stroke (HP:0002140)
 PMID:37601974
GWAS999730_H GCST90092907 Cholesteryl esters to total lipids ratio in medium LDL 115,082 European ancestry individuals C 0.828806 9E-100 99.046 rs56393506 0.117849 low density lipoprotein cholesterol measurement (EFO:0004611)
cholesteryl esters:total lipids ratio (EFO:0020944)
 PMID:35213538
GWAS1002158_H GCST90093049 Phospholipids to total lipids ratio in chylomicrons and extremely large VLDL 111,638 European ancestry individuals C 0.830282 7E-92 91.155 rs56393506 0.114199 chylomicron measurement (EFO:0008596)
very low density lipoprotein cholesterol measurement (EFO:0008317)
phospholipids:total lipids ratio (EFO:0020946)
 PMID:35213538
GWAS1002851_H GCST90092913 Phospholipids to total lipids ratio in medium LDL 115,082 European ancestry individuals C 0.828806 1E-78 78 rs56393506 0.104415 low density lipoprotein cholesterol measurement (EFO:0004611)
phospholipids:total lipids ratio (EFO:0020946)
 PMID:35213538
GWAS1003068_H GCST90092889 Average diameter for LDL particles 115,082 European ancestry individuals C 0.828806 2E-65 64.699 rs56393506 0.093157 low density lipoprotein particle size measurement (EFO:0008593)
 PMID:35213538
GWAS1016754_H GCST90274723 Cardiometabolic multimorbidity 14,835 European ancestry cases, 352,312 European ancestry controls T 0.172197 6E-12 11.222 rs56393506 0.110328 stroke (EFO:0000712)
coronary artery disease (EFO:0001645)
 PMID:38409652
GWAS1033759_H GCST90104538 Large artery stroke 213 African American cases, 20,030 African American controls, 1,735 East Asian ancestry cases, 237,242 East Asian ancestry controls, 6,399 European ancestry cases, 1,234,808 European ancestry controls, 167 Hispanic cases, 4,146 Hispanic controls, 705 South Asian ancestry cases, 7,672 South Asian ancestry controls T 0.1562 2E-8 7.699 rs56393506 1.16 large artery stroke (EFO:0005524)
 PMID:36180795
None Available GCST90134518 Total cholesterol levels 58,701 Korean ancestry individuals T NR 0.000002 5.699 rs56393506 1.53 total cholesterol measurement (EFO:0004574)
 PMID:35884923
GWAS1039781_H GCST90018932 Unstable angina pectoris 9,481 European ancestry cases, 446,987 European ancestry controls, 5,891 East Asian ancestry cases, 146,214 East Asian ancestry controls T NR 2E-29 28.699 rs56393506 0.2 angina pectoris (EFO:0003913)
 PMID:34594039
None Available GCST005840 Ischemic stroke (large artery atherosclerosis) 4,373 European ancestry cases, 297,290 European ancestry controls, 1,626 East Asian ancestry cases, 28,195 East Asian ancestry controls, 355 South Asian ancestry cases, 6,707 South Asian ancestry controls, 259 African American cases, 15,146 African American controls, 34 Asian ancestry cases, 333 Asian ancestry controls, 41 Latin American cases, 692 Latin American controls T 0.16 1E-7 7 rs56393506 1.17 large artery stroke (EFO:0005524)
 PMID:29531354
Database Acc Id Source(s)
GWAS Catalog GCST90092913 GWAS Catalog

RGD Curation Notes
Note Type Note Reference