LOC130005598 (ATAC-STARR-seq lymphoblastoid silent region 3272) - Rat Genome Database

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Gene: LOC130005598 (ATAC-STARR-seq lymphoblastoid silent region 3272) Homo sapiens
Analyze
Symbol: LOC130005598
Name: ATAC-STARR-seq lymphoblastoid silent region 3272
RGD ID: 329826938
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress 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
GRCh381144,095,545 - 44,096,164 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01144,250,892 - 44,251,511 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130005598
12 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11p12-11.2(chr11:41118322-48643003)x1 copy number loss See cases [RCV000135405] Chr11:41118322..48643003 [GRCh38]
Chr11:41139872..48664555 [GRCh37]
Chr11:41096448..48621131 [NCBI36]
Chr11:11p12-11.2		 pathogenic
NM_207122.1(EXT2):c.-242G>T single nucleotide variant Exostoses, multiple, type 2 [RCV001104140] Chr11:44095641 [GRCh38]
Chr11:44117191 [GRCh37]
Chr11:11p11.2		 uncertain significance
NM_207122.2(EXT2):c.-45G>T single nucleotide variant Exostoses, multiple, type 2 [RCV001104445] Chr11:44095838 [GRCh38]
Chr11:44117388 [GRCh37]
Chr11:11p11.2		 uncertain significance
NM_207122.2(EXT2):c.-31+7G>T single nucleotide variant Exostoses, multiple, type 2 [RCV000356448]|not provided [RCV001597056]|not specified [RCV001731473] Chr11:44095859 [GRCh38]
Chr11:44117409 [GRCh37]
Chr11:11p11.2		 benign
Single allele duplication not specified [RCV002286377] Chr11:42871836..44852545 [GRCh38]
Chr11:11p12-11.2		 uncertain significance
GRCh38/hg38 11p12-11.2(chr11:40688674-44913409)x3 copy number gain See cases [RCV000133775] Chr11:40688674..44913409 [GRCh38]
Chr11:40710224..44934960 [GRCh37]
Chr11:40666800..44891536 [NCBI36]
Chr11:11p12-11.2		 uncertain significance
NM_207122.2(EXT2):c.-31+106C>T single nucleotide variant not provided [RCV001779909] Chr11:44095958 [GRCh38]
Chr11:44117508 [GRCh37]
Chr11:11p11.2		 likely benign
NM_207122.2(EXT2):c.-31+42A>G single nucleotide variant not provided [RCV001639417] Chr11:44095894 [GRCh38]
Chr11:44117444 [GRCh37]
Chr11:11p11.2		 benign
GRCh38/hg38 11p12-11.12(chr11:39179252-49135735)x1 copy number loss See cases [RCV000137391] Chr11:39179252..49135735 [GRCh38]
Chr11:39200802..49157287 [GRCh37]
Chr11:39157378..49113863 [NCBI36]
Chr11:11p12-11.12		 pathogenic
GRCh38/hg38 11p12-11.2(chr11:40688674-44184136)x3 copy number gain See cases [RCV000138110] Chr11:40688674..44184136 [GRCh38]
Chr11:40710224..44205686 [GRCh37]
Chr11:40666800..44162262 [NCBI36]
Chr11:11p12-11.2		 likely pathogenic
GRCh38/hg38 11p12-11.12(chr11:42727555-49135735)x3 copy number gain See cases [RCV000139422] Chr11:42727555..49135735 [GRCh38]
Chr11:42749105..49157287 [GRCh37]
Chr11:42705681..49113863 [NCBI36]
Chr11:11p12-11.12		 likely pathogenic
GRCh38/hg38 11p12-11.2(chr11:42553659-46114792)x1 copy number loss See cases [RCV000142289] Chr11:42553659..46114792 [GRCh38]
Chr11:42575209..46136343 [GRCh37]
Chr11:42531785..46092919 [NCBI36]
Chr11:11p12-11.2		 pathogenic
GRCh38/hg38 11p12-11.2(chr11:39684826-44845260)x1 copy number loss See cases [RCV000142439] Chr11:39684826..44845260 [GRCh38]
Chr11:39706376..44866811 [GRCh37]
Chr11:39662952..44823387 [NCBI36]
Chr11:11p12-11.2		 pathogenic
NM_207122.1(EXT2):c.-307G>T single nucleotide variant Exostoses, multiple, type 2 [RCV000302488] Chr11:44095576 [GRCh38]
Chr11:44117126 [GRCh37]
Chr11:11p11.2		 likely benign|uncertain significance
NM_207122.2(EXT2):c.-61C>G single nucleotide variant Exostoses, multiple, type 2 [RCV000296956] Chr11:44095822 [GRCh38]
Chr11:44117372 [GRCh37]
Chr11:11p11.2		 benign|likely benign
NM_207122.1(EXT2):c.-311G>A single nucleotide variant Exostoses, multiple, type 2 [RCV000400767] Chr11:44095572 [GRCh38]
Chr11:44117122 [GRCh37]
Chr11:11p11.2		 benign
GRCh38/hg38 11p13-11.2(chr11:35663578-46959820)x1 copy number loss See cases [RCV000052679] Chr11:35663578..46959820 [GRCh38]
Chr11:35685126..46981371 [GRCh37]
Chr11:35641702..46937947 [NCBI36]
Chr11:11p13-11.2		 pathogenic
NM_207122.1(EXT2):c.-331T>C single nucleotide variant Exostoses, multiple, type 2 [RCV000342075] Chr11:44095552 [GRCh38]
Chr11:44117102 [GRCh37]
Chr11:11p11.2		 benign
NM_207122.2(EXT2):c.-197C>G single nucleotide variant Exostoses, multiple, type 2 [RCV000341020] Chr11:44095686 [GRCh38]
Chr11:44117236 [GRCh37]
Chr11:11p11.2		 benign
NM_207122.2(EXT2):c.-148G>A single nucleotide variant Exostoses, multiple, type 2 [RCV000408028] Chr11:44095735 [GRCh38]
Chr11:44117285 [GRCh37]
Chr11:11p11.2		 benign|likely benign
NM_207122.2(EXT2):c.-31+22G>A single nucleotide variant not provided [RCV001654716] Chr11:44095874 [GRCh38]
Chr11:44117424 [GRCh37]
Chr11:11p11.2		 benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130005598 COSMIC
GTEx LOC130005598 GTEx
Human Proteome Map LOC130005598 Human Proteome Map
NCBI Gene LOC130005598 ENTREZGENE