GWAS670660_H QTL Report (Homo sapiens) - Rat Genome Database

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QTL Registration

QTL: GWAS670660_H (cutaneous melanoma, hair color QTL GWAS670660 (human)) Homo sapiens

Symbol: GWAS670660_H
Name: cutaneous melanoma, hair color QTL GWAS670660 (human)
RGD ID: 407021684
Trait: cutaneous melanoma, hair color
LOD Score: Not Available
P Value: 2E-9237
Variance: Not Available
Position
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh381528,120,472 - 28,120,473RGD_MAPPER_PIPELINEGRCh38
GRCh371528,365,618 - 28,365,619RGD_MAPPER_PIPELINEGRCh37
Population Stats: Not Available
JBrowse: View Region in Genome Browser (JBrowse)
Model



Disease Annotations     Click to see Annotation Detail View
skin melanoma  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
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
1317498HERC2HECT and RLD domain containing E3 ubiquitin protein ligase 2152811104028322179Human
156451622LOC128772394melanoma risk locus-associated MPRA allelic enhancer 15:28365618152812040028120544Human

Position Markers

Peak: (rs12913832)
Human AssemblyChrPosition (strand)Source
GRCh381528,120,472 - 28,120,473RGD_MAPPER_PIPELINE


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
406964675GWAS613651_Hsuntan QTL GWAS613651 (human)6e-184suntan152812047228120473Human
406966340GWAS615316_Hhair colour measurement QTL GWAS615316 (human)5e-104hair colour measurementcoat/hair color measurement (CMO:0001808)152812047228120473Human
407039684GWAS688660_Heye colour measurement QTL GWAS688660 (human)1e-200eye colour measurementcoat/hair color measurement (CMO:0001808)152812047228120473Human
407098821GWAS747797_Hhair colour measurement, hair morphology measurement QTL GWAS747797 (human)7e-79hair colour measurement, hair morphology measurementcoat/hair morphological measurement (CMO:0001807)152812047228120473Human
406949577GWAS598553_Hskin pigmentation measurement QTL GWAS598553 (human)5e-147skin pigmentation measurement152812047228120473Human
407097674GWAS746650_Hhair colour measurement, hair morphology measurement QTL GWAS746650 (human)2e-101hair colour measurement, hair morphology measurementcoat/hair morphological measurement (CMO:0001807)152812047228120473Human
407118664GWAS767640_Hglaucoma QTL GWAS767640 (human)4e-08glaucoma152812047228120473Human
1643273BW330_HBody Weight QTL 330 (human)1.050.014Body weightbody mass index152686671952866719Human
406952406GWAS601382_Hhair color QTL GWAS601382 (human)8e-23hair color152812047228120473Human
1643523BW284_HBody Weight QTL 284 (human)1.950.0013Body weight152179288947792889Human
407088860GWAS737836_Hcolorectal health QTL GWAS737836 (human)0.000004colorectal health152812047228120473Human
2289410BW327_HBody weight QTL 327 (human)3.320.0001Body fat amount151998012945980129Human
406967392GWAS616368_Hskin pigmentation QTL GWAS616368 (human)4e-77skin pigmentation trait (VT:0002095)152812047228120473Human
406952291GWAS601267_Hskin sensitivity to sun QTL GWAS601267 (human)4e-14skin sensitivity to sun152812047228120473Human
407005927GWAS654903_Hhair color QTL GWAS654903 (human)1e-77hair color152812047228120473Human
406952166GWAS601142_Hskin sensitivity to sun QTL GWAS601142 (human)9e-10skin sensitivity to sun152812047228120473Human
2289420BW314_HBody weight QTL 314 (human)2.720.0003Body weightlean mass151998012945980129Human
407008748GWAS657724_Heye color QTL GWAS657724 (human)1e-300eye color152812047228120473Human
407097459GWAS746435_Hsuntan, skin pigmentation QTL GWAS746435 (human)9e-13skin pigmentation trait (VT:0002095)152812047228120473Human
406951920GWAS600896_Hskin pigmentation measurement QTL GWAS600896 (human)2e-27skin pigmentation measurement152812047228120473Human
2289430BMD7_HBone mineral density QTL 7 (human)3.320.0001Bone mineral density151998012945980129Human
407021687GWAS670663_Hnevus count, cutaneous melanoma QTL GWAS670663 (human)2e-14nevus count, cutaneous melanoma152812047228120473Human
407021684GWAS670660_Hcutaneous melanoma, hair color QTL GWAS670660 (human)2e-9237cutaneous melanoma, hair color152812047228120473Human
407024120GWAS673096_Hcutaneous melanoma QTL GWAS673096 (human)2e-23cutaneous melanoma152812047228120473Human
407133304GWAS782280_Hnon-melanoma skin carcinoma QTL GWAS782280 (human)0.000001non-melanoma skin carcinoma152812047228120473Human
406949631GWAS598607_Hhair color QTL GWAS598607 (human)3e-51hair color152812047228120473Human
407040509GWAS689485_Hskin pigmentation measurement QTL GWAS689485 (human)1e-17skin pigmentation measurement152812047228120473Human
407001986GWAS650962_Hopen-angle glaucoma QTL GWAS650962 (human)3e-08Corneal astigmatism152812047228120473Human
407127429GWAS776405_Hhair color QTL GWAS776405 (human)5e-141hair color152812047228120473Human
407079810GWAS728786_Hasthma, response to diisocyanate QTL GWAS728786 (human)7e-14asthma, response to diisocyanate152812047228120473Human
407097472GWAS746448_Hsuntan, skin pigmentation QTL GWAS746448 (human)5e-14skin pigmentation trait (VT:0002095)152812047228120473Human
407080192GWAS729168_Hretinal vasculature measurement QTL GWAS729168 (human)4e-10retina blood vessel morphology trait (VT:0002792)152812047228120473Human
407098116GWAS747092_Hskin pigmentation QTL GWAS747092 (human)8e-132skin pigmentation trait (VT:0002095)152812047228120473Human
407134094GWAS783070_Hretinal vasculature measurement QTL GWAS783070 (human)6e-80retina blood vessel morphology trait (VT:0002792)152812047228120473Human
407096072GWAS745048_Hskin pigmentation QTL GWAS745048 (human)1e-148skin pigmentation trait (VT:0002095)152812047228120473Human
407009036GWAS658012_Heye color QTL GWAS658012 (human)3e-52eye color152812047228120473Human
406949648GWAS598624_Hskin pigmentation measurement QTL GWAS598624 (human)6e-126skin pigmentation measurement152812047228120473Human
406983702GWAS632678_Hhair color QTL GWAS632678 (human)2e-308hair color152812047228120473Human
407040930GWAS689906_Hhair colour measurement QTL GWAS689906 (human)8e-105hair colour measurementcoat/hair color measurement (CMO:0001808)152812047228120473Human
407007010GWAS655986_Hsuntan QTL GWAS655986 (human)1e-22suntan152812047228120473Human
407132454GWAS781430_Hage-related macular degeneration QTL GWAS781430 (human)4e-16age-related macular degeneration152812047228120473Human
407007009GWAS655985_Hhair color QTL GWAS655985 (human)1e-167hair color152812047228120473Human
1559411SCL107_HSerum cholesterol level QTL 107 (human)3.88Lipid leveltriglyceride152654355252543552Human
407007014GWAS655990_Heye color QTL GWAS655990 (human)1e-158eye color152812047228120473Human
407088805GWAS737781_Hcolorectal cancer QTL GWAS737781 (human)0.000007colorectal cancer152812047228120473Human
407040933GWAS689909_Heye colour measurement QTL GWAS689909 (human)0.0000006eye colour measurementeye morphological measurement (CMO:0003080)152812047228120473Human
407040938GWAS689914_Heye colour measurement QTL GWAS689914 (human)1e-92eye colour measurementeye morphological measurement (CMO:0003080)152812047228120473Human
407097257GWAS746233_Hhair colour measurement, hair morphology measurement QTL GWAS746233 (human)1e-52hair colour measurement, hair morphology measurementcoat/hair morphological measurement (CMO:0001807)152812047228120473Human
407006381GWAS655357_Hhair color QTL GWAS655357 (human)4e-103hair color152812047228120473Human
407097264GWAS746240_Hhair colour measurement, hair morphology measurement QTL GWAS746240 (human)3e-30hair colour measurement, hair morphology measurementcoat/hair morphological measurement (CMO:0001807)152812047228120473Human
407097270GWAS746246_Hsuntan, skin pigmentation QTL GWAS746246 (human)1e-11skin pigmentation trait (VT:0002095)152812047228120473Human
407097012GWAS745988_Hskin pigmentation QTL GWAS745988 (human)2e-26skin pigmentation trait (VT:0002095)152812047228120473Human
407097018GWAS745994_Hskin pigmentation QTL GWAS745994 (human)3e-27skin pigmentation trait (VT:0002095)152812047228120473Human
407124414GWAS773390_Hhair colour measurement QTL GWAS773390 (human)1e-100hair colour measurementcoat/hair color measurement (CMO:0001808)152812047228120473Human
407006911GWAS655887_Heye color QTL GWAS655887 (human)1e-177eye color152812047228120473Human
407270331GWAS919307_Hbody height QTL GWAS919307 (human)2e-10body height (VT:0001253)body height (CMO:0000106)152812047228120473Human
407008829GWAS657805_Hhair color QTL GWAS657805 (human)9e-88hair color152812047228120473Human
406999101GWAS648077_Hintraocular pressure measurement QTL GWAS648077 (human)0.0000009intraocular pressure measurement152812047228120473Human


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
GWAS598553_H GCST90255688 Skin phototype score 4,933 Iberian ancestry individuals G 0.358605 5E-147 146.302 rs12913832 6.87674 skin pigmentation measurement (EFO:0007009)
 PMID:36672889
GWAS598607_H GCST90255682 Blond vs. brown/black hair color 243 Iberian ancestry cases, 4,702 Iberian ancestry controls G 0.357937 3E-51 50.523 rs12913832 1.61172 hair color (EFO:0003924)
 PMID:36672889
GWAS598624_H GCST90255689 Skin color (Fitzpatrick scale) 4,933 Iberian ancestry individuals G 0.358605 6E-126 125.222 rs12913832 0.330585 skin pigmentation measurement (EFO:0007009)
 PMID:36672889
GWAS600896_H GCST90255690 Skin color 4,985 Iberian ancestry individuals G 0.358375 2E-27 26.699 rs12913832 0.177703 skin pigmentation measurement (EFO:0007009)
 PMID:36672889
GWAS601142_H GCST90255687 Ease of skin tanning 4,973 Iberian ancestry individuals G 0.358335 9E-10 9.046 rs12913832 0.109001 skin sensitivity to sun (EFO:0004795)
 PMID:36672889
GWAS601267_H GCST90255686 Ease of sunburn 4,985 Iberian ancestry individuals G 0.358074 4E-14 13.398 rs12913832 0.201789 skin sensitivity to sun (EFO:0004795)
 PMID:36672889
GWAS601382_H GCST90255683 Brown vs. black hair color 3,750 Iberian ancestry cases, 952 Iberian ancestry controls G 0.33943 8E-23 22.097 rs12913832 0.605471 hair color (EFO:0003924)
 PMID:36672889
GWAS613651_H GCST005897 Low tan response 46,768 European ancestry low tanning cases, 74,528 European ancestry moderate and high tanning controls A NR 6E-184 183.222 rs12913832 0.306 suntan (EFO:0004279)
 PMID:29739929
GWAS615316_H GCST003479 Hair color 6,357 Latin American individuals ? NR 5E-104 103.302 rs12913832 N/A hair colour measurement (EFO:0007822)
 PMID:26926045
GWAS616368_H GCST002907 Perceived skin darkness 9,316 European ancestry individuals A 0.200017073587161 4E-77 76.398 rs12913832 0.21006678 skin pigmentation (EFO:0003784)
 PMID:25963972
GWAS632678_H GCST006989 Brown vs. black hair color 269,394 British ancestry brown hair individuals, 14,526 British ancestry black hair individuals ? NR 2E-308 307.699 rs12913832 2.2291574 hair color (EFO:0003924)
 PMID:30531825
None Available GCST006988 Blond vs. brown/black hair color 39,397 British ancestry blond hair individuals, 283,920 British ancestry brown or black hair individuals ? NR 2E-308 307.699 rs12913832 4.6904316 hair color (EFO:0003924)
 PMID:30531825
GWAS648077_H GCST009725 Intraocular pressure 133,492 European ancestry individuals A 0.21 9E-7 6.046 rs12913832 N/A intraocular pressure measurement (EFO:0004695)
 PMID:31959993
GWAS650962_H GCST90310210 Primary open angle glaucoma (MTAG) at least 29,241 European ancestry cases, at least 350,181 European ancestry controls (MTAG boosted by vertical cup-to-disc ratio and intraocular pressure samples) A NR 3E-8 7.523 rs12913832 0.059673093 open-angle glaucoma (EFO:0004190)
 PMID:37386247
GWAS654903_H GCST000191 Black vs. red hair color 2,287 European ancestry female individuals A NR 1E-77 77 rs12913832 0.44 hair color (EFO:0003924)
 PMID:18483556
GWAS655357_H GCST000190 Black vs. blond hair color 2,287 European ancestry female individuals A NR 4E-103 102.398 rs12913832 0.44 hair color (EFO:0003924)
 PMID:18483556
GWAS655887_H GCST001929 Eye color 3871 European ancestry individuals A NR 1E-177 177 rs12913832 2.82 eye color (EFO:0003949)
 PMID:23548203
GWAS655985_H GCST001932 Hair color 7,070 European ancestry individuals G NR 1E-167 167 rs12913832 0.39 hair color (EFO:0003924)
 PMID:23548203
GWAS655986_H GCST001939 Tanning 9,678 European ancestry individuals G NR 1E-22 22 rs12913832 0.14 suntan (EFO:0004279)
 PMID:23548203
GWAS655990_H GCST001929 Eye color 3871 European ancestry individuals G NR 1E-158 158 rs12913832 2.84 eye color (EFO:0003949)
 PMID:23548203
GWAS657724_H GCST000685 Eye color traits 5,951 European ancestry individuals ? NR 1E-300 300 rs12913832 N/A eye color (EFO:0003949)
 PMID:20463881
GWAS657805_H GCST000707 Hair color 9,126 European ancestry individuals A 0.23 9E-88 87.046 rs12913832 0.97 hair color (EFO:0003924)
 PMID:20585627
None Available GCST000710 Eye color 9,126 European ancestry individuals A 0.23 1E-300 300 rs12913832 2.49 eye color (EFO:0003949)
 PMID:20585627
GWAS658012_H GCST000710 Eye color 9,126 European ancestry individuals A 0.23 3E-52 51.523 rs12913832 8.43 eye color (EFO:0003949)
 PMID:20585627
None Available GCST008519 Skin pigmentation 1,047 Hispanic/Latin American individuals, 684 Cape Verdian individuals, 373 African American individuals G NR 3E-8 7.523 rs12913832 0.21 skin pigmentation measurement (EFO:0007009)
 PMID:31315583
GWAS670660_H GCST010302 Cutaneous melanoma or hair colour 36,760 European ancestry cutaneous melanoma cases, 375,188 European ancestry controls, 352,662 European ancestry individuals A 0.334986 2E-9237 9236.699 rs12913832 N/A cutaneous melanoma (EFO:0000389)
hair color (EFO:0003924)
 PMID:32341527
GWAS670663_H GCST010303 Nevus count or cutaneous melanoma 36,760 European ancestry cutaneous melanoma cases, 375,188 European ancestry controls, 12,930 European ancestry individuals, 52,847 individuals A 0.334986 2E-14 13.699 rs12913832 N/A nevus count (EFO:0004632)
cutaneous melanoma (EFO:0000389)
 PMID:32341527
GWAS673096_H GCST010304 Cutaneous malignant melanoma 36,760 European ancestry cases, 375,188 European ancestry controls G 0.665 2E-23 22.699 rs12913832 1.128923 cutaneous melanoma (EFO:0000389)
 PMID:32341527
None Available GCST007157 Corneal astigmatism 69,140 European ancestry cases, 17,195 European ancestry controls A NR 3E-8 7.523 rs12913832 1.0869565 Corneal astigmatism (EFO:1002040)
 PMID:30306274
GWAS688660_H GCST007453 Eye color 6,236 Latin American individuals ? NR 1E-200 200 rs12913832 N/A eye colour measurement (EFO:0009764)
 PMID:30664655
None Available GCST007451 Skin, hair and eye pigmentation (multivariate analysis) 6,236 Latin American individuals ? NR 1E-200 200 rs12913832 N/A hair colour measurement (EFO:0007822)
eye colour measurement (EFO:0009764)
skin pigmentation measurement (EFO:0007009)
 PMID:30664655
GWAS689485_H GCST007452 Skin pigmentation 6,236 Latin American individuals ? NR 1E-17 17 rs12913832 N/A skin pigmentation measurement (EFO:0007009)
 PMID:30664655
None Available GCST007455 Eye color (brightness) 6,236 Latin American individuals ? NR 1E-200 200 rs12913832 N/A eye colour measurement (EFO:0009764)
 PMID:30664655
GWAS689906_H GCST007454 Hair color 6,236 Latin American individuals ? NR 8E-105 104.097 rs12913832 N/A hair colour measurement (EFO:0007822)
 PMID:30664655
GWAS689909_H GCST007457 Eye color (saturation) 6,236 Latin American individuals ? NR 6E-7 6.222 rs12913832 N/A eye colour measurement (EFO:0009764)
 PMID:30664655
GWAS689914_H GCST007456 Eye color (hue) 6,236 Latin American individuals ? NR 1E-92 92 rs12913832 N/A eye colour measurement (EFO:0009764)
 PMID:30664655
GWAS728786_H GCST002875 Diisocyanate-induced asthma 74 European ancestry cases, 824 European ancestry controls A 0.233 7E-14 13.155 rs12913832 3.48 response to diisocyanate (EFO:0006995)
 PMID:25918132
GWAS729168_H GCST90270397 Retinal arteriolar tortuosity 52,798 European ancestry individuals A 0.218995 4E-10 9.398 rs12913832 0.021 retinal vasculature measurement (EFO:0010554)
 PMID:36757925
GWAS737781_H GCST005150 Colorectal cancer 978 Austrian ancestry colorectal cancer cases, 636 Austrian ancestry advanced colorectal adenoma cases, 4,294 European ancestry controls ? NR 0.000007 5.155 rs12913832 1.252 PMID:29228715
GWAS737836_H GCST005147 Colonoscopy-negative controls vs population controls 855 Austrian ancestry colonoscopy-negative controls, 3,439 European ancestry controls ? NR 0.000004 5.398 rs12913832 1.397 colorectal health (EFO:0008460)
 PMID:29228715
GWAS745048_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 1E-148 148 rs12913832 6.354 skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS745988_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 2E-26 25.699 rs12913832 0.8599 skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS745994_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 3E-27 26.523 rs12913832 0.1766 skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS746233_H GCST007486 Hair morphology traits 4,988 Spanish ancestry individuals ? NR 1E-52 52 rs12913832 1.6129291 hair colour measurement (EFO:0007822)
hair morphology measurement (EFO:0007821)
 PMID:30166351
GWAS746240_H GCST007486 Hair morphology traits 4,988 Spanish ancestry individuals ? NR 3E-30 29.523 rs12913832 0.682465 hair colour measurement (EFO:0007822)
hair morphology measurement (EFO:0007821)
 PMID:30166351
GWAS746246_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 1E-11 11 rs12913832 0.32792723 suntan (EFO:0004279)
skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS746435_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 9E-13 12.046 rs12913832 0.6038 suntan (EFO:0004279)
skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS746448_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 5E-14 13.302 rs12913832 0.2014 suntan (EFO:0004279)
skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS746650_H GCST007486 Hair morphology traits 4,988 Spanish ancestry individuals ? NR 2E-101 100.699 rs12913832 0.3482 hair colour measurement (EFO:0007822)
hair morphology measurement (EFO:0007821)
 PMID:30166351
GWAS747092_H GCST007488 Skin pigmentation traits 4,988 Spanish ancestry individuals ? NR 8E-132 131.097 rs12913832 0.3257 skin pigmentation (EFO:0003784)
 PMID:30166351
GWAS747797_H GCST007486 Hair morphology traits 4,988 Spanish ancestry individuals ? NR 7E-79 78.155 rs12913832 1.602 hair colour measurement (EFO:0007822)
hair morphology measurement (EFO:0007821)
 PMID:30166351
GWAS773390_H GCST006075 Hair color 290,891 European ancestry individuals A 0.246 1E-100 100 rs12913832 0.499 hair colour measurement (EFO:0007822)
 PMID:29662168
GWAS776405_H GCST90095476 Blond vs. brown/black hair color 12,398 European ancestry individuals A NR 5E-141 140.302 rs12913832 1.19021 hair color (EFO:0003924)
 PMID:34737440
GWAS781430_H GCST011317 Age-related macular degeneration 3,544 European ancestry cases, 44,521 European ancestry controls A 0.227 4E-16 15.398 rs12913832 0.22954147 age-related macular degeneration (EFO:0001365)
 PMID:32741009
GWAS782280_H GCST90027058 Non-melanoma skin cancer 18,944 White British ancestry cases, 255,886 White British ancestry controls ? NR 0.000001 6 rs12913832 0.936885 non-melanoma skin carcinoma (EFO:0009260)
 PMID:34290314
GWAS783070_H GCST90095200 Retinal vascular fractal dimension 38,932 British ancestry individuals G 0.7869 6E-80 79.222 rs12913832 0.15454 retinal vasculature measurement (EFO:0010554)
 PMID:34743558
GWAS919307_H GCST90245848 Height 5,314,291 European ancestry, Hispanic or Latin American, East Asian ancestry, African ancestry, South Asian ancestry individuals G 0.6033 2E-10 9.699 rs12913832 0.0097 body height (EFO:0004339)
 PMID:36224396
None Available GCST008373 Glaucoma (PheCode 365) 4,462 British ancestry cases, 397,761 British ancestry controls G 0.21416 4E-8 7.398 rs12913832 N/A PMID:30104761
None Available GCST90448682 25-hydroxyvitamin D levels (skin colour stratified) 409,654 European ancestry individuals A 0.23 3E-13 12.523 rs12913832 0.018 vitamin D measurement (EFO:0004631)
 PMID:37963177
Database Acc Id Source(s)
GWAS Catalog GCST010302 GWAS Catalog

RGD Curation Notes
Note Type Note Reference