LOC130002663 (ATAC-STARR-seq lymphoblastoid silent region 20313) - Rat Genome Database

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Gene: LOC130002663 (ATAC-STARR-seq lymphoblastoid silent region 20313) Homo sapiens
Analyze
Symbol: LOC130002663
Name: ATAC-STARR-seq lymphoblastoid silent region 20313
RGD ID: 329819786
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
GRCh389127,802,719 - 127,803,118 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.09140,010,138 - 140,010,537 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130002663
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121112395-138075224)x3 copy number gain See cases [RCV000051009] Chr9:121112395..138075224 [GRCh38]
Chr9:123874673..140969676 [GRCh37]
Chr9:122914494..140089497 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q33.3-34.11(chr9:125993583-129682375)x1 copy number loss See cases [RCV000052923] Chr9:125993583..129682375 [GRCh38]
Chr9:128755862..132444654 [GRCh37]
Chr9:127795683..131484475 [NCBI36]
Chr9:9q33.3-34.11		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:122792658-138124532)x3 copy number gain See cases [RCV000051040] Chr9:122792658..138124532 [GRCh38]
Chr9:125554937..141018984 [GRCh37]
Chr9:124594758..140138805 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121073102-138179445)x3 copy number gain See cases [RCV000134920] Chr9:121073102..138179445 [GRCh38]
Chr9:123835380..141073897 [GRCh37]
Chr9:122875201..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q33.3-34.11(chr9:125055865-128637946)x1 copy number loss See cases [RCV000137787] Chr9:125055865..128637946 [GRCh38]
Chr9:127818144..131400225 [GRCh37]
Chr9:126857965..130440046 [NCBI36]
Chr9:9q33.3-34.11		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
NC_000009.12:g.(?_127612384)_(128566997_?)del deletion Early infantile epileptic encephalopathy with suppression bursts [RCV000819894]|Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome [RCV001387712] Chr9:127612384..128566997 [GRCh38]
Chr9:130374663..131329276 [GRCh37]
Chr9:9q34.11		 pathogenic|uncertain significance
NC_000009.11:g.(?_130216797)_(130953151_?)dup duplication Congenital muscular dystrophy with intellectual disability and severe epilepsy [RCV000821291] Chr9:127454518..128190872 [GRCh38]
Chr9:130216797..130953151 [GRCh37]
Chr9:9q33.3-34.11		 uncertain significance
NM_004957.6(FPGS):c.64A>G (p.Ile22Val) single nucleotide variant not provided [RCV001612770] Chr9:127802988 [GRCh38]
Chr9:130565267 [GRCh37]
Chr9:9q34.11		 benign
NM_004957.6(FPGS):c.77T>G (p.Val26Gly) single nucleotide variant not specified [RCV004080685] Chr9:127803001 [GRCh38]
Chr9:130565280 [GRCh37]
Chr9:9q34.11		 uncertain significance
NM_004957.6(FPGS):c.88C>T (p.Arg30Trp) single nucleotide variant not specified [RCV004222794] Chr9:127803012 [GRCh38]
Chr9:130565291 [GRCh37]
Chr9:9q34.11		 uncertain significance
NM_004957.6(FPGS):c.89G>A (p.Arg30Gln) single nucleotide variant not specified [RCV004212843] Chr9:127803013 [GRCh38]
Chr9:130565292 [GRCh37]
Chr9:9q34.11		 uncertain significance
NM_004957.6(FPGS):c.11C>T (p.Ala4Val) single nucleotide variant not specified [RCV004222403] Chr9:127802935 [GRCh38]
Chr9:130565214 [GRCh37]
Chr9:9q34.11		 uncertain significance
NM_004957.6(FPGS):c.13C>T (p.Arg5Trp) single nucleotide variant not specified [RCV004260923] Chr9:127802937 [GRCh38]
Chr9:130565216 [GRCh37]
Chr9:9q34.11		 uncertain significance
NM_004957.6(FPGS):c.19C>T (p.His7Tyr) single nucleotide variant not specified [RCV004394490] Chr9:127802943 [GRCh38]
Chr9:130565222 [GRCh37]
Chr9:9q34.11		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130002663 COSMIC
GTEx LOC130002663 GTEx
Human Proteome Map LOC130002663 Human Proteome Map
NCBI Gene LOC130002663 ENTREZGENE