GWAS929753_H QTL Report (Homo sapiens) - Rat Genome Database

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QTL Registration

QTL: GWAS929753_H (high density lipoprotein cholesterol measurement QTL GWAS929753 (human)) Homo sapiens

Symbol: GWAS929753_H
Name: high density lipoprotein cholesterol measurement QTL GWAS929753 (human)
RGD ID: 407280777
Trait: high density lipoprotein cholesterol measurement
Measurement Type: blood high density lipoprotein cholesterol level   (CMO:0000052)    
LOD Score: Not Available
P Value: 2.0E-19
Variance: Not Available
Position
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh381944,912,678 - 44,912,679RGD_MAPPER_PIPELINEGRCh38
GRCh371945,415,935 - 45,415,936RGD_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)
GWAS929753_HHumanblood high density lipoprotein cholesterol level  IAGPrs7256200405850206Based on the EFO term IDGWAS_CATALOGPMID:34887591

Experimental Factor Annotations    Click to see Annotation Detail View
Object SymbolSpeciesTermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
GWAS929753_HHumanhigh density lipoprotein cholesterol measurement  IAGPrs7256200405850206 GWAS_CATALOGPMID:34887591
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

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
155765829LOC127891702H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45415901-45416660194491264444913403Human

Position Markers

Peak: (rs7256200)
Human AssemblyChrPosition (strand)Source
GRCh381944,912,678 - 44,912,679RGD_MAPPER_PIPELINE


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559110SCL22_HSerum cholesterol level QTL 22 (human)3.590.000241Lipid levelLDL cholesterol193190759457907594Human
407244802GWAS893778_Hhigh density lipoprotein cholesterol measurement QTL GWAS893778 (human)4e-10high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)194491267844912679Human
407276097GWAS925073_Hfree cholesterol measurement, high density lipoprotein cholesterol measurement QTL GWAS925073 (human)2e-24free cholesterol measurement, high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)194491267844912679Human
407242462GWAS891438_Hlipid measurement, high density lipoprotein cholesterol measurement QTL GWAS891438 (human)1e-25lipid measurement, high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)194491267844912679Human
407280108GWAS929084_Htaste liking measurement QTL GWAS929084 (human)9e-11taste liking measurement194491267844912679Human
407302205GWAS951181_Hcerebral amyloid deposition measurement QTL GWAS951181 (human)1e-19cerebral cortex integrity trait (VT:0010923)194491267844912679Human
1331657COPD9_HChronic obstructive pulmonary disease QTL 9 (human)1.94Chronic airflow obstructionpost-bronchodilator FEV1193102176057021760Human
407280777GWAS929753_Hhigh density lipoprotein cholesterol measurement QTL GWAS929753 (human)2e-19high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)194491267844912679Human
407332696GWAS981672_Hserum gamma-glutamyl transferase measurement QTL GWAS981672 (human)2e-10serum gamma-glutamyl transferase measurementserum gamma-glutamyltransferase activity level (CMO:0002241)194491267844912679Human


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
GWAS891438_H GCST90092825 Total lipid levels in HDL 115,082 European ancestry individuals G 0.872428 1E-25 25 rs7256200 0.0583104 lipid measurement (EFO:0004529)
high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:35213538
GWAS893778_H GCST90092826 Concentration of HDL particles 115,082 European ancestry individuals G 0.872428 4E-10 9.398 rs7256200 0.0365441 high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:35213538
GWAS925073_H GCST90092896 Free cholesterol levels in medium HDL 115,082 European ancestry individuals G 0.872428 2E-24 23.699 rs7256200 0.0577207 free cholesterol measurement (EFO:0008591)
high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:35213538
GWAS929084_H GCST90094772 F-glutamate liking (derived food-liking factor) 159,473 European ancestry individuals T 0.1225 9E-11 10.046 rs7256200 0.14387 taste liking measurement (EFO:0010155)
 PMID:35585065
GWAS929753_H GCST90239654 High density lipoprotein cholesterol levels 40,963 South Asian ancestry individuals T 0.0719764 2E-19 18.699 rs7256200 0.136949 high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:34887591
GWAS951181_H GCST006904 Cerebral amyloid deposition (PET imaging) 983 European ancestry individuals T 0.17 1E-19 19 rs7256200 0.15 cerebral amyloid deposition measurement (EFO:0007707)
 PMID:30361487
GWAS981672_H GCST90018954 Gamma glutamyl transpeptidase 344,104 European ancestry individuals, 133,471 East Asian ancestry individuals T NR 2E-10 9.699 rs7256200 0.0188 serum gamma-glutamyl transferase measurement (EFO:0004532)
 PMID:34594039
None Available GCST90448456 Memory decline in normal cognition 7,839 European ancestry females, 1,384 African ancestry females ? NR 2E-16 15.699 rs7256200 0.014387 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448452 Memory decline in impaired cognition 4,478 European ancestry males ? NR 2E-12 11.699 rs7256200 0.04344 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448451 Memory decline 11,062 European ancestry males ? NR 2E-20 19.699 rs7256200 0.018934 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448462 Memory decline in normal cognition 7,839 European ancestry females ? NR 4E-19 18.398 rs7256200 0.0167 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448427 Baseline memory 13,154 European ancestry females, 2,487 African ancestry females ? NR 2E-16 15.699 rs7256200 0.119485 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448434 Baseline memory in impaired cognition 3,987 European ancestry females ? NR 2E-16 15.699 rs7256200 0.321696 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448460 Memory decline 13,154 European ancestry females ? NR 7E-30 29.155 rs7256200 0.020525 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448454 Memory decline 13,154 European ancestry females, 2,487 African ancestry females ? NR 2E-25 24.699 rs7256200 0.017494 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448418 Baseline memory 11,062 European ancestry males, 880 African ancestry males ? NR 5E-8 7.302 rs7256200 0.099981 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448424 Baseline memory 11,062 European ancestry males ? NR 2E-9 8.699 rs7256200 0.115171 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448447 Memory decline in normal cognition 4,950 European ancestry males, 391 African ancestry males ? NR 1E-9 9 rs7256200 0.012527 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448433 Baseline memory 13,154 European ancestry females ? NR 2E-20 19.699 rs7256200 0.148778 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90448453 Memory decline in normal cognition 4,950 European ancestry males ? NR 4E-10 9.398 rs7256200 0.013286 memory performance (EFO:0004874)
 PMID:37984853
None Available GCST90454454 Metabolic syndrome 24,171 Taiwanese ancestry cases, 83,059 Taiwanese ancestry controls G 0.09742 5E-9 8.302 rs7256200 0.105261 metabolic syndrome (EFO:0000195)
 PMID:38201907
None Available GCST90448445 Memory decline 11,062 European ancestry males, 880 African ancestry males ? NR 2E-20 19.699 rs7256200 0.018152 memory performance (EFO:0004874)
 PMID:37984853
Database Acc Id Source(s)
GWAS Catalog GCST90239654 GWAS Catalog

RGD Curation Notes
Note Type Note Reference