GWAS684093_H QTL Report (Homo sapiens) - Rat Genome Database

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QTL Registration

QTL: GWAS684093_H (free cholesterol in medium LDL measurement QTL GWAS684093 (human)) Homo sapiens

Symbol: GWAS684093_H
Name: free cholesterol in medium LDL measurement QTL GWAS684093 (human)
RGD ID: 407035117
Trait: free cholesterol in medium LDL measurement
LOD Score: Not Available
P Value: 1.0E-14
Variance: Not Available
Position
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh38626,123,274 - 26,123,275RGD_MAPPER_PIPELINEGRCh38
GRCh37626,123,502 - 26,123,503RGD_MAPPER_PIPELINEGRCh37
Population Stats: Not Available
JBrowse: View Region in Genome Browser (JBrowse)
Model



Experimental Factor Annotations    Click to see Annotation Detail View
Object SymbolSpeciesTermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
GWAS684093_HHumanfree cholesterol in medium LDL measurement  IAGPrs115740542405850206 GWAS_CATALOGPMID:36764567
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
1344863H2BC4H2B clustered histone 462611317026123926Human
155230241LOC126859625BRD4-independent group 4 enhancer GRCh37_chr6:26123079-2612427862612271826124075Human

Position Markers

Peak: (rs115740542)
Human AssemblyChrPosition (strand)Source
GRCh38626,123,274 - 26,123,275RGD_MAPPER_PIPELINE


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407130572GWAS779548_Hosteoarthritis QTL GWAS779548 (human)5e-09osteoarthritis62612327426123275Human
1298458BW9_HBody weight QTL 9 (human)2.70.0002Body fat amount6691196032911960Human
407411459GWAS1060435_Hinsomnia QTL GWAS1060435 (human)5e-10apolipoprotein B measurementblood apoliprotein B level (CMO:0000522)62612327426123275Human
407382790GWAS1031766_Hhemoglobin measurement QTL GWAS1031766 (human)2e-580hemoglobin measurementhemoglobin measurement (CMO:0000508)62612327426123275Human
407419609GWAS1068585_Hfree cholesterol measurement QTL GWAS1068585 (human)4e-10free cholesterol measurementblood cholesterol level (CMO:0002280)62612327426123275Human
1358854MULTSCL4_HMultiple sclerosis susceptibility QTL 4 (human)Multiple sclerosis susceptibility6691196032911960Human
407039120GWAS688096_Htotal lipids in LDL measurement QTL GWAS688096 (human)2e-12phospholipids:total lipids ratio, high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)62612327426123275Human
407037648GWAS686624_Hcholesterol in small LDL measurement QTL GWAS686624 (human)4e-12cholesterol in small LDL measurement blood low density lipoprotein phospholipid level (CMO:0001568)62612327426123275Human
407411037GWAS1060013_Hfree cholesterol measurement, low density lipoprotein cholesterol measurement QTL GWAS1060013 (human)4e-19free cholesterol measurement, low density lipoprotein cholesterol measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
407220816GWAS869792_Hosteoarthritis, hip QTL GWAS869792 (human)2e-08osteoarthritis, hip62612327426123275Human
407131538GWAS780514_Hosteoarthritis QTL GWAS780514 (human)0.0000004skin and soft tissue Staphylococcus aureus infection62612327426123275Human
407410644GWAS1059620_Hfree cholesterol measurement, low density lipoprotein cholesterol measurement QTL GWAS1059620 (human)2e-16free cholesterol measurement, low density lipoprotein cholesterol measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
1358857MULTSCL19_HMultiple sclerosis susceptibility QTL 19 (human)Multiple sclerosis susceptibility61958431145584311Human
1643399BMD5_HBone mineral density QTL 5 (human)2.320.0005Bone mineral density6691196032911960Human
407035810GWAS684786_Hesterified cholesterol measurement QTL GWAS684786 (human)2e-11total lipids in medium LDL62612327426123275Human
407410152GWAS1059128_Hfatty acid measurement, linoleic acid measurement QTL GWAS1059128 (human)6e-09fatty acid measurement, linoleic acid measurementblood free fatty acids level (CMO:0000117)62612327426123275Human
407034787GWAS683763_Hcholesteryl ester measurement QTL GWAS683763 (human)7e-10blood lipid amount (VT:0003949)62612327426123275Human
407404713GWAS1053689_HBMI-adjusted waist circumference QTL GWAS1053689 (human)4e-08BMI-adjusted waist circumference62612327426123275Human
1358839MULTSCL5_HMultiple sclerosis susceptibility QTL 5 (human)Multiple sclerosis susceptibility61958431145584311Human
407111207GWAS760183_Hsphingomyelin measurement QTL GWAS760183 (human)5e-12esterified cholesterol measurement62612327426123275Human
407035556GWAS684532_Hcholesteryl ester measurement QTL GWAS684532 (human)3e-10blood lipid amount (VT:0003949)glomerular filtration rate (CMO:0000490)62612327426123275Human
407415854GWAS1064830_Hblood protein measurement QTL GWAS1064830 (human)3e-26blood protein measurementblood protein measurement (CMO:0000028)62612327426123275Human
407410862GWAS1059838_Hlow density lipoprotein cholesterol measurement, phospholipid measurement QTL GWAS1059838 (human)1e-13low density lipoprotein cholesterol measurement, phospholipid measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
1643377BW325_HBody weight QTL 325 (human)2.320.0005Body fat amount6691196032911960Human
1643569GLUCO21_HGlucose level QTL 21 (human)0.021Glucose levelnon-insulin-dependent6691196032911960Human
406942697GWAS591673_Hprotein measurement QTL GWAS591673 (human)4e-18protein measurement62612327426123275Human
407139309GWAS788285_Hosteoarthritis QTL GWAS788285 (human)7e-08osteoarthritis62612327426123275Human
407416482GWAS1065458_Hblood protein measurement QTL GWAS1065458 (human)4e-24blood protein measurementblood protein measurement (CMO:0000028)62612327426123275Human
406942187GWAS591163_Hferritin measurement QTL GWAS591163 (human)8e-20ferritin measurement62612327426123275Human
407220270GWAS869246_Hosteoarthritis QTL GWAS869246 (human)9e-09osteoarthritis62612327426123275Human
1298431RA11_HRheumatoid arthritis QTL 11 (human)0.0000024Joint/bone inflammationrheumatoid arthritis61991188340191709Human
407410149GWAS1059125_Hfree cholesterol measurement, low density lipoprotein cholesterol measurement QTL GWAS1059125 (human)3e-17free cholesterol measurement, low density lipoprotein cholesterol measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
407030828GWAS679804_Hcholesteryl ester measurement QTL GWAS679804 (human)8e-12blood lipid amount (VT:0003949)62612327426123275Human
407035117GWAS684093_Hfree cholesterol in medium LDL measurement QTL GWAS684093 (human)1e-14free cholesterol in medium LDL measurement 62612327426123275Human
407410343GWAS1059319_Hlow density lipoprotein cholesterol measurement, phospholipid measurement QTL GWAS1059319 (human)3e-16low density lipoprotein cholesterol measurement, phospholipid measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
407411367GWAS1060343_Hsphingomyelin measurement QTL GWAS1060343 (human)1e-12sphingomyelin measurement62612327426123275Human
407410489GWAS1059465_Hlow density lipoprotein cholesterol measurement, phospholipid measurement QTL GWAS1059465 (human)2e-14low density lipoprotein cholesterol measurementblood total cholesterol level (CMO:0000051)62612327426123275Human
407132030GWAS781006_Hosteoarthritis QTL GWAS781006 (human)0.000001osteoarthritis62612327426123275Human
407033854GWAS682830_Htotal lipids in small LDL QTL GWAS682830 (human)1e-11total cholesterol measurementblood total cholesterol level (CMO:0000051)62612327426123275Human
407037116GWAS686092_Htotal cholesterol measurement QTL GWAS686092 (human)6e-11low density lipoprotein cholesterol measurementblood low density lipoprotein cholesterol level (CMO:0000053)62612327426123275Human
407410231GWAS1059207_Hlow density lipoprotein cholesterol measurement, lipid measurement QTL GWAS1059207 (human)3e-14low density lipoprotein cholesterol measurement, lipid measurementblood lipid measurement (CMO:0000050)62612327426123275Human


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
GWAS591163_H GCST90247573 Ferritin levels 10,708 European ancestry individuals T 0.94 8E-20 19.097 rs115740542 0.222 ferritin measurement (EFO:0004459)
 PMID:34648354
GWAS591673_H GCST90247620 Ferritin light chain levels 10,708 European ancestry individuals T 0.94 4E-18 17.398 rs115740542 0.211 protein measurement (EFO:0004747)
 PMID:34648354
GWAS679804_H GCST90269514 Cholesteryl esters in LDL (UKB data field 23417) 88,329 European ancestry individuals C 0.0733021 8E-12 11.097 rs115740542 0.0634116 cholesteryl ester measurement (EFO:0010351)
 PMID:36764567
GWAS682830_H GCST90269642 Total lipids in small LDL (UKB data field 23545) 88,329 European ancestry individuals C 0.0733021 1E-11 11 rs115740542 0.0628698 total lipids in small LDL (EFO:0022168)
 PMID:36764567
GWAS683763_H GCST90269638 Cholesteryl esters in medium LDL (UKB data field 23541) 88,329 European ancestry individuals C 0.0733021 7E-10 9.155 rs115740542 0.0573583 cholesteryl ester measurement (EFO:0010351)
 PMID:36764567
GWAS684093_H GCST90269639 Free cholesterol in medium LDL (UKB data field 23542) 88,329 European ancestry individuals C 0.0733021 1E-14 14 rs115740542 0.0718914 free cholesterol in medium LDL measurement (EFO:0022268)
 PMID:36764567
GWAS684532_H GCST90269645 Cholesteryl esters in small LDL (UKB data field 23548) 88,329 European ancestry individuals C 0.0733021 3E-10 9.523 rs115740542 0.0587166 cholesteryl ester measurement (EFO:0010351)
 PMID:36764567
GWAS684786_H GCST90269512 Total esterified cholesterol levels (UKB data field 23415) 88,329 European ancestry individuals C 0.0733021 2E-11 10.699 rs115740542 0.0606256 esterified cholesterol measurement (EFO:0008589)
 PMID:36764567
GWAS686092_H GCST90269497 Total cholesterol levels (UKB data field 23400) 88,329 European ancestry individuals C 0.0733021 6E-11 10.222 rs115740542 0.0591352 total cholesterol measurement (EFO:0004574)
 PMID:36764567
GWAS686624_H GCST90269644 Cholesterol in small LDL (UKB data field 23547) 88,329 European ancestry individuals C 0.0733021 4E-12 11.398 rs115740542 0.06459 cholesterol in small LDL measurement (EFO:0022227)
 PMID:36764567
GWAS688096_H GCST90269522 Total lipids in LDL (UKB data field 23425) 88,329 European ancestry individuals C 0.0733021 2E-12 11.699 rs115740542 0.0649846 total lipids in LDL measurement (EFO:0022308)
 PMID:36764567
None Available GCST90269637 Cholesterol in medium LDL (UKB data field 23540) 88,329 European ancestry individuals C 0.0733021 2E-11 10.699 rs115740542 0.0626577 cholesterol in medium LDL measurement (EFO:0022224)
 PMID:36764567
None Available GCST90269636 Phospholipids in medium LDL (UKB data field 23539) 88,329 European ancestry individuals C 0.0733021 4E-12 11.398 rs115740542 0.0647129 phospholipids in medium LDL measurement (EFO:0022183)
 PMID:36764567
None Available GCST90269635 Total lipids in medium LDL (UKB data field 23538) 88,329 European ancestry individuals C 0.0733021 2E-11 10.699 rs115740542 0.0621918 total lipids in medium LDL (EFO:0022180)
 PMID:36764567
GWAS760183_H GCST90269535 Sphingomyelins levels (UKB data field 23438) 88,268 European ancestry individuals C 0.0732801 5E-12 11.302 rs115740542 0.0602266 sphingomyelin measurement (EFO:0010118)
 PMID:36764567
GWAS779548_H GCST90134284 Osteoarthritis 140,025 European ancestry cases, 344,349 European ancestry controls, 140,025 South Asian ancestry cases, 344,349 South Asian ancestry controls, 140,025 East Asian ancestry cases, 344,349 East Asian ancestry controls, 140,025 African ancestry cases, 344,349 African ancestry controls, 140,025 Hispanic or Latin American cases, 344,349 Hispanic or Latin American controls T 0.93 5E-9 8.302 rs115740542 0.99 PMID:36411363
GWAS780514_H GCST90134285 Osteoarthritis 58,574 European ancestry cases, 262,785 European ancestry controls, 58,574 South Asian ancestry cases, 262,785 South Asian ancestry controls, 58,574 East Asian ancestry cases, 262,785 East Asian ancestry controls, 58,574 African ancestry cases, 262,785 African ancestry controls ? NR 4E-7 6.398 rs115740542 0.9905952 PMID:36411363
GWAS781006_H GCST90134279 Osteoarthritis 54,039 European ancestry cases, 239,780 European ancestry controls ? NR 0.000001 6 rs115740542 0.9365927 PMID:36411363
GWAS788285_H GCST90134288 Osteoarthritis 109,358 European ancestry cases, 303,812 European ancestry controls ? NR 7E-8 7.155 rs115740542 0.9443107 PMID:36411363
GWAS869246_H GCST007093 Osteoarthritis 77,052 European ancestry cases, 378,169 European ancestry controls C 0.07 9E-9 8.046 rs115740542 1.06 PMID:30664745
GWAS869792_H GCST007091 Osteoarthritis (hip) 15,704 European ancestry cases, 378,169 European ancestry controls C 0.07 2E-8 7.699 rs115740542 1.13 osteoarthritis, hip (EFO:1000786)
 PMID:30664745
None Available GCST90013411 Skin and soft tissue infections 6,107 European ancestry cases and 399,239 European ancestry controls C 0.075 4E-7 6.398 rs115740542 1.17 skin and soft tissue Staphylococcus aureus infection (EFO:1001489)
 PMID:33662382
GWAS1031766_H GCST90002314 Hemoglobin concentration 746,431 African American or Afro-Caribbean, African ancestry, European ancestry, East Asian ancestry, Hispanic or Latin American and South Asian ancestry individuals C 0.0544404 2E-580 579.699 rs115740542 N/A hemoglobin measurement (EFO:0004509)
 PMID:32888493
GWAS1053689_H GCST012226 Waist circumference adjusted for body mass index 186,825 British ancestry men C NR 4E-8 7.398 rs115740542 0.0323922 BMI-adjusted waist circumference (EFO:0007789)
 PMID:34021172
None Available GCST90103634 Estimated glomerular filtration rate (creatinine) 1,004,040 European ancestry individuals T 0.9278 3E-10 9.523 rs115740542 0.00316225 glomerular filtration rate (EFO:0005208)
 PMID:34272381
GWAS1059125_H GCST90092885 Free cholesterol levels in LDL 115,082 European ancestry individuals T 0.926399 3E-17 16.523 rs115740542 0.0663069 free cholesterol measurement (EFO:0008591)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1059128_H GCST90092881 Ratio of linoleic acid to total fatty acids 115,006 European ancestry individuals T 0.926411 6E-9 8.222 rs115740542 0.0445895 fatty acid measurement (EFO:0005110)
linoleic acid measurement (EFO:0006807)
 PMID:35213538
GWAS1059207_H GCST90092962 Total lipid levels in small LDL 115,082 European ancestry individuals T 0.926399 3E-14 13.523 rs115740542 0.0604767 low density lipoprotein cholesterol measurement (EFO:0004611)
lipid measurement (EFO:0004529)
 PMID:35213538
GWAS1059319_H GCST90092964 Phospholipid levels in small LDL 115,082 European ancestry individuals T 0.926399 3E-16 15.523 rs115740542 0.0648726 low density lipoprotein cholesterol measurement (EFO:0004611)
phospholipid measurement (EFO:0004639)
 PMID:35213538
None Available GCST90092901 Phospholipids to total lipids ratio in medium HDL 115,082 European ancestry individuals T 0.926399 2E-12 11.699 rs115740542 0.0530652 phospholipids:total lipids ratio (EFO:0020946)
high density lipoprotein cholesterol measurement (EFO:0004612)
 PMID:35213538
GWAS1059465_H GCST90092888 Phospholipid levels in LDL 115,082 European ancestry individuals T 0.926399 2E-14 13.699 rs115740542 0.0605815 low density lipoprotein cholesterol measurement (EFO:0004611)
phospholipid measurement (EFO:0004639)
 PMID:35213538
None Available GCST90092956 Cholesterol levels in small LDL 115,082 European ancestry individuals T 0.926399 2E-14 13.699 rs115740542 0.0609825 total cholesterol measurement (EFO:0004574)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1059620_H GCST90092860 Free cholesterol levels in large LDL 115,082 European ancestry individuals T 0.926399 2E-16 15.699 rs115740542 0.0641466 free cholesterol measurement (EFO:0008591)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1059838_H GCST90092864 Phospholipid levels in large LDL 115,082 European ancestry individuals T 0.926399 1E-13 13 rs115740542 0.0584527 low density lipoprotein cholesterol measurement (EFO:0004611)
phospholipid measurement (EFO:0004639)
 PMID:35213538
None Available GCST90092863 Concentration of large LDL particles 115,082 European ancestry individuals T 0.926399 6E-11 10.222 rs115740542 0.0518371 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1060013_H GCST90092960 Free cholesterol levels in small LDL 115,082 European ancestry individuals T 0.926399 4E-19 18.398 rs115740542 0.0707991 free cholesterol measurement (EFO:0008591)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
None Available GCST90092908 Free cholesterol levels in medium LDL 115,082 European ancestry individuals T 0.926399 3E-17 16.523 rs115740542 0.0670521 free cholesterol measurement (EFO:0008591)
low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1060343_H GCST90092982 Sphingomyelin levels 115,006 European ancestry individuals T 0.926411 1E-12 12 rs115740542 0.0527433 sphingomyelin measurement (EFO:0010118)
 PMID:35213538
GWAS1060435_H GCST90131903 Insomnia 390,751 European ancestry female cases, 1,018,386 European ancestry female controls T NR 5E-10 9.302 rs115740542 0.016 insomnia (EFO:0004698)
 PMID:35835914
GWAS1064830_H GCST90088617 Serum levels of protein TF 5,345 Icelandic ancestry individuals C 0.06851 3E-26 25.523 rs115740542 0.361965 blood protein measurement (EFO:0007937)
 PMID:35078996
GWAS1065458_H GCST90089966 Serum levels of protein NAALAD2 5,360 Icelandic ancestry individuals C 0.06851 4E-24 23.398 rs115740542 0.37297 blood protein measurement (EFO:0007937)
 PMID:35078996
None Available GCST90092809 Apolipoprotein B levels 115,082 European ancestry individuals T 0.926399 5E-10 9.302 rs115740542 0.0494022 apolipoprotein B measurement (EFO:0004615)
 PMID:35213538
None Available GCST90092986 Total esterified cholesterol levels 115,082 European ancestry individuals T 0.926399 5E-12 11.302 rs115740542 0.0530411 esterified cholesterol measurement (EFO:0008589)
 PMID:35213538
None Available GCST90092814 Clinical LDL cholesterol levels 115,082 European ancestry individuals T 0.926399 2E-14 13.699 rs115740542 0.0607717 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:35213538
GWAS1068585_H GCST90092988 Total free cholesterol levels 115,082 European ancestry individuals T 0.926399 4E-10 9.398 rs115740542 0.0486806 free cholesterol measurement (EFO:0008591)
 PMID:35213538
None Available GCST90092985 Total cholesterol levels 115,082 European ancestry individuals T 0.926399 1E-11 11 rs115740542 0.0520967 total cholesterol measurement (EFO:0004574)
 PMID:35213538
Database Acc Id Source(s)
GWAS Catalog GCST90269639 GWAS Catalog

RGD Curation Notes
Note Type Note Reference