LOC130056830 (ATAC-STARR-seq lymphoblastoid active region 9236) - 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   new 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
Gene: LOC130056830 (ATAC-STARR-seq lymphoblastoid active region 9236) Homo sapiens
Analyze
Symbol: LOC130056830
Name: ATAC-STARR-seq lymphoblastoid active region 9236
RGD ID: 329818093
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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
GRCh381540,161,203 - 40,161,302 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01537,968,090 - 37,968,189 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Colon cancer  (IAGP)
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130056830
26 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001211.6(BUB1B):c.10G>A (p.Val4Met) single nucleotide variant BUB1B-related condition [RCV003935141]|Inborn genetic diseases [RCV002515823]|Mosaic variegated aneuploidy syndrome 1 [RCV000475422]|not specified [RCV000120414] Chr15:40161230 [GRCh38]
Chr15:40453431 [GRCh37]
Chr15:15q15.1		 likely benign|not provided
NM_001211.6(BUB1B):c.26G>T (p.Gly9Val) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV001911639] Chr15:40161246 [GRCh38]
Chr15:40453447 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.9G>T (p.Ala3=) single nucleotide variant Colorectal cancer [RCV003316390]|Mosaic variegated aneuploidy syndrome 1 [RCV000459103]|not provided [RCV001651155]|not specified [RCV000246516] Chr15:40161229 [GRCh38]
Chr15:40453430 [GRCh37]
Chr15:15q15.1		 benign
NM_001211.6(BUB1B):c.6G>A (p.Ala2=) single nucleotide variant Inborn genetic diseases [RCV002364779]|Mosaic variegated aneuploidy syndrome 1 [RCV003617983] Chr15:40161226 [GRCh38]
Chr15:40453427 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.21A>C (p.Glu7Asp) single nucleotide variant Inborn genetic diseases [RCV002425268]|Mosaic variegated aneuploidy syndrome 1 [RCV001938682] Chr15:40161241 [GRCh38]
Chr15:40453442 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.35+41G>A single nucleotide variant not provided [RCV001641297] Chr15:40161296 [GRCh38]
Chr15:40453497 [GRCh37]
Chr15:15q15.1		 benign
NM_001211.6(BUB1B):c.6G>C (p.Ala2=) single nucleotide variant Inborn genetic diseases [RCV002364783] Chr15:40161226 [GRCh38]
Chr15:40453427 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.8C>T (p.Ala3Val) single nucleotide variant Inborn genetic diseases [RCV002376343] Chr15:40161228 [GRCh38]
Chr15:40453429 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.35+4G>A single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV002241440] Chr15:40161259 [GRCh38]
Chr15:40453460 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.18G>A (p.Lys6=) single nucleotide variant Inborn genetic diseases [RCV002408236] Chr15:40161238 [GRCh38]
Chr15:40453439 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.2dup (p.Met1fs) duplication Mosaic variegated aneuploidy syndrome 1 [RCV002242501] Chr15:40161221..40161222 [GRCh38]
Chr15:40453422..40453423 [GRCh37]
Chr15:15q15.1		 uncertain significance
GRCh38/hg38 15q13.3-15.1(chr15:32635803-40233825)x1 copy number loss See cases [RCV000051617] Chr15:32635803..40233825 [GRCh38]
Chr15:32928004..40526026 [GRCh37]
Chr15:30715296..38313318 [NCBI36]
Chr15:15q13.3-15.1		 pathogenic
NM_001211.6(BUB1B):c.19G>A (p.Glu7Lys) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV002233060] Chr15:40161239 [GRCh38]
Chr15:40453440 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.23G>C (p.Gly8Ala) single nucleotide variant Inborn genetic diseases [RCV002447349]|Mosaic variegated aneuploidy syndrome 1 [RCV002242256] Chr15:40161243 [GRCh38]
Chr15:40453444 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.9G>A (p.Ala3=) single nucleotide variant Inborn genetic diseases [RCV002383148] Chr15:40161229 [GRCh38]
Chr15:40453430 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.35+4G>T single nucleotide variant Inborn genetic diseases [RCV002883991]|Mosaic variegated aneuploidy syndrome 1 [RCV003618046] Chr15:40161259 [GRCh38]
Chr15:40453460 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.22G>T (p.Gly8Trp) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV003029255] Chr15:40161242 [GRCh38]
Chr15:40453443 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.26G>C (p.Gly9Ala) single nucleotide variant Inborn genetic diseases [RCV003163227]|Mosaic variegated aneuploidy syndrome 1 [RCV002233660] Chr15:40161246 [GRCh38]
Chr15:40453447 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.15G>A (p.Lys5=) single nucleotide variant Inborn genetic diseases [RCV002399906]|Mosaic variegated aneuploidy syndrome 1 [RCV000867841]|not provided [RCV003396514] Chr15:40161235 [GRCh38]
Chr15:40453436 [GRCh37]
Chr15:15q15.1		 likely benign
GRCh38/hg38 15q14-15.1(chr15:39710935-40294591)x3 copy number gain See cases [RCV000052105] Chr15:39710935..40294591 [GRCh38]
Chr15:40003136..40586792 [GRCh37]
Chr15:37790428..38374084 [NCBI36]
Chr15:15q14-15.1		 uncertain significance
NC_000015.9:g.(?_40453416)_(40512966_?)dup duplication Mosaic variegated aneuploidy syndrome [RCV000708012] Chr15:40161215..40220765 [GRCh38]
Chr15:40453416..40512966 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.24G>A (p.Gly8=) single nucleotide variant Inborn genetic diseases [RCV002431085] Chr15:40161244 [GRCh38]
Chr15:40453445 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.21A>G (p.Glu7=) single nucleotide variant Inborn genetic diseases [RCV002425681] Chr15:40161241 [GRCh38]
Chr15:40453442 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.7G>A (p.Ala3Thr) single nucleotide variant Inborn genetic diseases [RCV002419172] Chr15:40161227 [GRCh38]
Chr15:40453428 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.27T>A (p.Gly9=) single nucleotide variant Inborn genetic diseases [RCV002441580] Chr15:40161247 [GRCh38]
Chr15:40453448 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.29C>T (p.Ala10Val) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV003828554] Chr15:40161249 [GRCh38]
Chr15:40453450 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.26G>A (p.Gly9Asp) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV003843589] Chr15:40161246 [GRCh38]
Chr15:40453447 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.32T>G (p.Leu11Arg) single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV002574087] Chr15:40161252 [GRCh38]
Chr15:40453453 [GRCh37]
Chr15:15q15.1		 uncertain significance
NM_001211.6(BUB1B):c.35+9G>A single nucleotide variant Mosaic variegated aneuploidy syndrome 1 [RCV000949455] Chr15:40161264 [GRCh38]
Chr15:40453465 [GRCh37]
Chr15:15q15.1		 likely benign
NM_001211.6(BUB1B):c.23G>T (p.Gly8Val) single nucleotide variant Inborn genetic diseases [RCV002430670] Chr15:40161243 [GRCh38]
Chr15:40453444 [GRCh37]
Chr15:15q15.1		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130056830 COSMIC
GTEx LOC130056830 GTEx
Human Proteome Map LOC130056830 Human Proteome Map
NCBI Gene LOC130056830 ENTREZGENE