LOC126805599 (CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6658990-6660189) - 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)
Gene: LOC126805599 (CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6658990-6660189) Homo sapiens
Analyze
Symbol: LOC126805599
Name: CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6658990-6660189
RGD ID: 153351501
Description: This genomic region was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. [provided by RefSeq, Sep 2022]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3816,598,930 - 6,600,129 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3716,658,990 - 6,660,189 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.016,124,594 - 6,125,793 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35650434  


Genomics

Variants

.
Variants in LOC126805599
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.32-36.23(chr1:2844760-8007940)x1 copy number loss See cases [RCV000051086] Chr1:2844760..8007940 [GRCh38]
Chr1:2761325..8068000 [GRCh37]
Chr1:2751185..7990587 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
NM_014851.4(KLHL21):c.1298A>G (p.Lys433Arg) single nucleotide variant not specified [RCV004288624] Chr1:6599176 [GRCh38]
Chr1:6659236 [GRCh37]
Chr1:1p36.31		 uncertain significance
NM_014851.4(KLHL21):c.1232C>T (p.Pro411Leu) single nucleotide variant not specified [RCV004316730] Chr1:6599242 [GRCh38]
Chr1:6659302 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.33-36.31(chr1:629044-7008678)x1 copy number loss See cases [RCV000051995] Chr1:629044..7008678 [GRCh38]
Chr1:564424..7068738 [GRCh37]
Chr1:554287..6991325 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:629025-8537745)x1 copy number loss See cases [RCV000051993] Chr1:629025..8537745 [GRCh38]
Chr1:564405..8597804 [GRCh37]
Chr1:554268..8520391 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.32-36.23(chr1:3472163-7842947)x1 copy number loss See cases [RCV000053720] Chr1:3472163..7842947 [GRCh38]
Chr1:3388727..7903007 [GRCh37]
Chr1:3378587..7825594 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
GRCh38/hg38 1p36.32-36.13(chr1:3006193-17688934)x1 copy number loss See cases [RCV000053714] Chr1:3006193..17688934 [GRCh38]
Chr1:2922757..18015429 [GRCh37]
Chr1:2912617..17888016 [NCBI36]
Chr1:1p36.32-36.13		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:859215-8747647)x1 copy number loss See cases [RCV000052045] Chr1:859215..8747647 [GRCh38]
Chr1:794595..8807706 [GRCh37]
Chr1:784458..8730293 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
NM_014851.4(KLHL21):c.1054G>A (p.Val352Met) single nucleotide variant not specified [RCV004084649] Chr1:6599420 [GRCh38]
Chr1:6659480 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.32-36.21(chr1:4898439-13111056)x1 copy number loss See cases [RCV000053724] Chr1:4898439..13111056 [GRCh38]
Chr1:4958499..13178528 [GRCh37]
Chr1:4858359..13101115 [NCBI36]
Chr1:1p36.32-36.21		 pathogenic
NM_014851.4(KLHL21):c.1384G>A (p.Ala462Thr) single nucleotide variant not specified [RCV004072362] Chr1:6599090 [GRCh38]
Chr1:6659150 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.33-36.23(chr1:844347-8171914)x1 copy number loss See cases [RCV000136554] Chr1:844347..8171914 [GRCh38]
Chr1:779727..8231974 [GRCh37]
Chr1:769590..8154561 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.32-36.23(chr1:2868477-7332569)x1 copy number loss See cases [RCV000141437] Chr1:2868477..7332569 [GRCh38]
Chr1:2785042..7392629 [GRCh37]
Chr1:2774902..7315216 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
NM_014851.4(KLHL21):c.1190A>G (p.His397Arg) single nucleotide variant not specified [RCV004147225] Chr1:6599284 [GRCh38]
Chr1:6659344 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.33-36.22(chr1:844347-12470133)x1 copy number loss See cases [RCV000136695] Chr1:844347..12470133 [GRCh38]
Chr1:779727..12530188 [GRCh37]
Chr1:769590..12452775 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic|likely pathogenic
GRCh38/hg38 1p36.32-36.21(chr1:4898439-12911913)x1 copy number loss See cases [RCV000137461] Chr1:4898439..12911913 [GRCh38]
Chr1:4958499..12971757 [GRCh37]
Chr1:4858359..12894344 [NCBI36]
Chr1:1p36.32-36.21		 pathogenic
GRCh38/hg38 1p36.31-36.21(chr1:6303641-15799093)x1 copy number loss See cases [RCV000137948] Chr1:6303641..15799093 [GRCh38]
Chr1:6363701..16125588 [GRCh37]
Chr1:6286288..15998175 [NCBI36]
Chr1:1p36.31-36.21		 pathogenic|likely benign
GRCh38/hg38 1p36.33-36.31(chr1:821713-7000838)x1 copy number loss See cases [RCV000138896] Chr1:821713..7000838 [GRCh38]
Chr1:757093..7060898 [GRCh37]
Chr1:746956..6983485 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:902111-9556305)x1 copy number loss See cases [RCV000141577] Chr1:902111..9556305 [GRCh38]
Chr1:837491..9616363 [GRCh37]
Chr1:827354..9538950 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844347-6916587)x1 copy number loss See cases [RCV000133943] Chr1:844347..6916587 [GRCh38]
Chr1:779727..6976647 [GRCh37]
Chr1:769590..6899234 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
NM_014851.4(KLHL21):c.1074C>G (p.Ser358Arg) single nucleotide variant not specified [RCV004164850] Chr1:6599400 [GRCh38]
Chr1:6659460 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.33-36.23(chr1:844347-7870545)x1 copy number loss See cases [RCV000142709] Chr1:844347..7870545 [GRCh38]
Chr1:779727..7930605 [GRCh37]
Chr1:769590..7853192 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.31-36.13(chr1:6554885-16056011)x3 copy number gain See cases [RCV000142906] Chr1:6554885..16056011 [GRCh38]
Chr1:6614945..16382506 [GRCh37]
Chr1:6537532..16255093 [NCBI36]
Chr1:1p36.31-36.13		 pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:911300-9329925)x1 copy number loss See cases [RCV000142615] Chr1:911300..9329925 [GRCh38]
Chr1:846680..9389984 [GRCh37]
Chr1:836543..9312571 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:914086-9567122)x1 copy number loss See cases [RCV000141970] Chr1:914086..9567122 [GRCh38]
Chr1:849466..9627180 [GRCh37]
Chr1:839329..9549767 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:898721-7811306)x1 copy number loss See cases [RCV000142651] Chr1:898721..7811306 [GRCh38]
Chr1:834101..7871366 [GRCh37]
Chr1:823964..7793953 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
NM_014851.4(KLHL21):c.1036T>A (p.Ser346Thr) single nucleotide variant not specified [RCV004302764] Chr1:6599438 [GRCh38]
Chr1:6659498 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic
NM_014851.4(KLHL21):c.1097C>T (p.Ala366Val) single nucleotide variant KLHL21-related disorder [RCV003979152] Chr1:6599377 [GRCh38]
Chr1:6659437 [GRCh37]
Chr1:1p36.31		 likely benign
NM_014851.4(KLHL21):c.1242C>T (p.Asn414=) single nucleotide variant KLHL21-related disorder [RCV003934083] Chr1:6599232 [GRCh38]
Chr1:6659292 [GRCh37]
Chr1:1p36.31		 likely benign
NM_014851.4(KLHL21):c.1183T>A (p.Tyr395Asn) single nucleotide variant not specified [RCV004406856] Chr1:6599291 [GRCh38]
Chr1:6659351 [GRCh37]
Chr1:1p36.31		 uncertain significance
NM_014851.4(KLHL21):c.1168G>A (p.Asp390Asn) single nucleotide variant not specified [RCV004406855] Chr1:6599306 [GRCh38]
Chr1:6659366 [GRCh37]
Chr1:1p36.31		 uncertain significance
NM_014851.4(KLHL21):c.1156G>A (p.Val386Met) single nucleotide variant not specified [RCV004406854] Chr1:6599318 [GRCh38]
Chr1:6659378 [GRCh37]
Chr1:1p36.31		 uncertain significance
NM_014851.4(KLHL21):c.1046A>T (p.Tyr349Phe) single nucleotide variant not specified [RCV004406853] Chr1:6599428 [GRCh38]
Chr1:6659488 [GRCh37]
Chr1:1p36.31		 uncertain significance
NM_014851.4(KLHL21):c.1364A>G (p.Gln455Arg) single nucleotide variant not specified [RCV004631554] Chr1:6599110 [GRCh38]
Chr1:6659170 [GRCh37]
Chr1:1p36.31		 uncertain significance
GRCh38/hg38 1p36.31-36.13(chr1:5363826-18360302)x1 copy number loss See cases [RCV000142771] Chr1:5363826..18360302 [GRCh38]
Chr1:5423886..18686796 [GRCh37]
Chr1:5323746..18559383 [NCBI36]
Chr1:1p36.31-36.13		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298451OSTEAR17_HOsteoarthritis QTL 17 (human)2.40.0004Joint/bone inflammationosteoarthritis11125188105Human
407236229GWAS885205_Hwhite matter hyperintensity measurement QTL GWAS885205 (human)0.0000001white matter hyperintensity measurement165989586598959Human
407167133GWAS816109_Happendicular lean mass QTL GWAS816109 (human)3e-13appendicular lean mass165994456599446Human
1298463BP9_HBlood pressure QTL 9 (human)3.9Blood pressurehypertension susceptibility1125188105Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC126805599 COSMIC
GTEx LOC126805599 GTEx
Human Proteome Map LOC126805599 Human Proteome Map
NCBI Gene LOC126805599 ENTREZGENE