LOC129995627 (ATAC-STARR-seq lymphoblastoid active region 23882) - 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: LOC129995627 (ATAC-STARR-seq lymphoblastoid active region 23882) Homo sapiens
Analyze
Symbol: LOC129995627
Name: ATAC-STARR-seq lymphoblastoid active region 23882
RGD ID: 329838375
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
GRCh3863,026,958 - 3,027,117 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3763,027,192 - 3,027,351 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.062,895,860 - 2,896,019 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


PMID:35858748  



.

1 to 10 of 28 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 6p25.3-25.1(chr6:163083-6062800)x1 copy number loss See cases [RCV000050686] Chr6:163083..6062800 [GRCh38]
Chr6:163083..6063033 [GRCh37]
Chr6:108083..6008032 [NCBI36]
Chr6:6p25.3-25.1		 pathogenic
GRCh38/hg38 6p25.3-24.1(chr6:164360-13339881)x3 copy number gain See cases [RCV000134022] Chr6:164360..13339881 [GRCh38]
Chr6:164360..13340113 [GRCh37]
Chr6:109360..13448092 [NCBI36]
Chr6:6p25.3-24.1		 pathogenic
GRCh38/hg38 6p25.2(chr6:2380066-3313353)x3 copy number gain See cases [RCV000134886] Chr6:2380066..3313353 [GRCh38]
Chr6:2380300..3313587 [GRCh37]
Chr6:2325299..3258586 [NCBI36]
Chr6:6p25.2		 uncertain significance
GRCh38/hg38 6p25.3-24.3(chr6:163083-9525496)x3 copy number gain See cases [RCV000136567] Chr6:163083..9525496 [GRCh38]
Chr6:163083..9525729 [GRCh37]
Chr6:108083..9633715 [NCBI36]
Chr6:6p25.3-24.3		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:106431-18360595)x3 copy number gain See cases [RCV000051869] Chr6:106431..18360595 [GRCh38]
Chr6:106431..18360826 [GRCh37]
Chr6:51431..18468805 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:152634-6027547)x1 copy number loss See cases [RCV000138717] Chr6:152634..6027547 [GRCh38]
Chr6:152634..6027780 [GRCh37]
Chr6:97634..5972779 [NCBI36]
Chr6:6p25.3-25.1		 pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:152634-6289804)x1 copy number loss See cases [RCV000142916] Chr6:152634..6289804 [GRCh38]
Chr6:152634..6290037 [GRCh37]
Chr6:97634..6235036 [NCBI36]
Chr6:6p25.3-25.1		 pathogenic
GRCh38/hg38 6p25.3-23(chr6:152634-14417003)x3 copy number gain See cases [RCV000143334] Chr6:152634..14417003 [GRCh38]
Chr6:152634..14417234 [GRCh37]
Chr6:97634..14525213 [NCBI36]
Chr6:6p25.3-23		 pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:152634-6027547)x3 copy number gain See cases [RCV000138716] Chr6:152634..6027547 [GRCh38]
Chr6:152634..6027780 [GRCh37]
Chr6:97634..5972779 [NCBI36]
Chr6:6p25.3-25.1		 likely pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:156974-4946857)x3 copy number gain See cases [RCV000143375] Chr6:156974..4946857 [GRCh38]
Chr6:156974..4947091 [GRCh37]
Chr6:101974..4892090 [NCBI36]
Chr6:6p25.3-25.1		 uncertain significance
1 to 10 of 28 rows

The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
2289408BW324_HBody weight QTL 324 (human)3.150.0001Body fat amount6120803913Human
1643418BW282_HBody Weight QTL 282 (human)2.070.001Body weight6119321359Human
2289435BMD4_HBone mineral density QTL 4 (human)3.150.0001Bone mineral density6120803913Human
2292824PRSTS5_HProstate tumor susceptibility QTL 5 (human)Prostate tumor susceptibility6119232373Human
2289320BW390_HBody weight QTL 390 (human)2.13Body weightBMI6119321359Human
1643495BW291_HBody Weight QTL 291 (human)2.13Body weightBMI6119321359Human
RefSeq Transcripts NG_175073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL133351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC129995627 COSMIC
GTEx LOC129995627 GTEx
Human Proteome Map LOC129995627 Human Proteome Map
NCBI Gene LOC129995627 ENTREZGENE