LOC130003663 (ATAC-STARR-seq lymphoblastoid active region 3255) - 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: LOC130003663 (ATAC-STARR-seq lymphoblastoid active region 3255) Homo sapiens
Analyze
Symbol: LOC130003663
Name: ATAC-STARR-seq lymphoblastoid active region 3255
RGD ID: 329827450
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
GRCh381034,649,254 - 34,649,353 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371034,938,182 - 34,938,281 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01034,677,737 - 34,677,836 (+)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
References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 10p11.22-11.1(chr10:31999920-38119681)x3 copy number gain See cases [RCV000135414] Chr10:31999920..38119681 [GRCh38]
Chr10:32288848..38408609 [GRCh37]
Chr10:32328854..38448615 [NCBI36]
Chr10:10p11.22-11.1		 pathogenic
GRCh38/hg38 10p11.22-11.21(chr10:34121283-34690759)x1 copy number loss See cases [RCV000143638] Chr10:34121283..34690759 [GRCh38]
Chr10:34410211..34979687 [GRCh37]
Chr10:34450217..35019693 [NCBI36]
Chr10:10p11.22-11.21		 uncertain significance
GRCh38/hg38 10p11.22-11.21(chr10:34149753-34733161)x1 copy number loss See cases [RCV000137641] Chr10:34149753..34733161 [GRCh38]
Chr10:34438681..35022089 [GRCh37]
Chr10:34478687..35062095 [NCBI36]
Chr10:10p11.22-11.21		 likely benign|uncertain significance
NC_000010.10:g.34835589_34975192del139604 deletion Neural tube defect [RCV000490783] Chr10:34546661..34686264 [GRCh38]
Chr10:34835589..34975192 [GRCh37]
Chr10:10p11.21		 pathogenic
GRCh38/hg38 10p15.1-q11.22(chr10:4604734-48074662)x3 copy number gain See cases [RCV000141497] Chr10:4604734..48074662 [GRCh38]
Chr10:4646926..47531169 [GRCh37]
Chr10:4636926..47125152 [NCBI36]
Chr10:10p15.1-q11.22		 benign
GRCh38/hg38 10p11.21(chr10:34239065-34655264)x1 copy number loss See cases [RCV000138286] Chr10:34239065..34655264 [GRCh38]
Chr10:34527993..34944192 [GRCh37]
Chr10:34567999..34984198 [NCBI36]
Chr10:10p11.21		 uncertain significance
GRCh38/hg38 10p11.21(chr10:34460387-35130934)x3 copy number gain See cases [RCV000142120] Chr10:34460387..35130934 [GRCh38]
Chr10:34749315..35419862 [GRCh37]
Chr10:34789321..35459868 [NCBI36]
Chr10:10p11.21		 uncertain significance
Single allele deletion not provided [RCV000677961] Chr10:33254302..35641435 [GRCh38]
Chr10:33543230..35930363 [GRCh37]
Chr10:10p11.22-11.21		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1643515BW287_HBody Weight QTL 287 (human)2.450.0004Body weightBMI101842411044424110Human
1300009BW22_HBody weight QTL 22 (human)2.32Body weightbody mass index101842411044424110Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130003663 COSMIC
GTEx LOC130003663 GTEx
Human Proteome Map LOC130003663 Human Proteome Map
NCBI Gene LOC130003663 ENTREZGENE