LOC129932510 (ATAC-STARR-seq lymphoblastoid active region 2539) - Rat Genome Database

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Gene: LOC129932510 (ATAC-STARR-seq lymphoblastoid active region 2539) Homo sapiens
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Symbol: LOC129932510
Name: ATAC-STARR-seq lymphoblastoid active region 2539
RGD ID: 329406701
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
GRCh381218,284,671 - 218,284,740 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371218,458,013 - 218,458,082 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01217,519,436 - 217,519,505 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC129932510HumanUsher syndrome  IAGPRGD:134354448554872ClinVar Annotator: match by term: Usher syndromeClinVarPMID:28041643

PMID:35858748  



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Variants in LOC129932510
1 total Variants

1 to 10 of 14 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000050298] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3 copy number gain See cases [RCV000142054] Chr1:204764914..225408698 [GRCh38]
Chr1:204734042..225596400 [GRCh37]
Chr1:203000665..223663023 [NCBI36]
Chr1:1q32.1-42.12		 pathogenic
Single allele deletion Usher syndrome [RCV000505151] Chr1:216066818..222607612 [GRCh38]
Chr1:216240159..222780953 [GRCh37]
Chr1:1q41		 likely pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000148255] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q41(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41		 pathogenic
1 to 10 of 14 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
597486405GWAS1582479_HBMI-adjusted hip circumference QTL GWAS1582479 (human)3e-08BMI-adjusted hip circumferencehip circumference (CMO:0000014)1218284716218284717Human
RefSeq Transcripts NG_165537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC099337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC129932510 COSMIC
GTEx LOC129932510 GTEx
Human Proteome Map LOC129932510 Human Proteome Map
NCBI Gene LOC129932510 ENTREZGENE