LOC130002129 (ATAC-STARR-seq lymphoblastoid silent region 20065) - Rat Genome Database

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Gene: LOC130002129 (ATAC-STARR-seq lymphoblastoid silent region 20065) Homo sapiens
Analyze
Symbol: LOC130002129
Name: ATAC-STARR-seq lymphoblastoid silent region 20065
RGD ID: 329833308
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
GRCh38995,426,698 - 95,427,087 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.09107,596,206 - 107,596,595 (+)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


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9q22.32-31.3(chr9:95061030-108695569)x1 copy number loss See cases [RCV000134375] Chr9:95061030..108695569 [GRCh38]
Chr9:97823312..111457849 [GRCh37]
Chr9:96863133..110497670 [NCBI36]
Chr9:9q22.32-31.3		 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 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 9q22.32-22.33(chr9:94713892-98121186)x1 copy number loss See cases [RCV000135303] Chr9:94713892..98121186 [GRCh38]
Chr9:97476174..100883468 [GRCh37]
Chr9:96515995..99923289 [NCBI36]
Chr9:9q22.32-22.33		 pathogenic
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(chr9:193412-138124524)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(chr9:193412-138159073)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 9q21.11-31.2(chr9:68420430-106579493)x3 copy number gain See cases [RCV000136788] Chr9:68420430..106579493 [GRCh38]
Chr9:71130848..109341774 [GRCh37]
Chr9:70225166..108381595 [NCBI36]
Chr9:9q21.11-31.2		 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
GRCh38/hg38 9q21.12-31.3(chr9:69627642-111454304)x3 copy number gain See cases [RCV000139789] Chr9:69627642..111454304 [GRCh38]
Chr9:72242558..114216584 [GRCh37]
Chr9:71432378..113256405 [NCBI36]
Chr9:9q21.12-31.3		 pathogenic
NC_000009.11:g.(?_97863983)_(98270649_?)dup duplication Fanconi anemia [RCV000708140] Chr9:95101701..95508367 [GRCh38]
Chr9:97863983..98270649 [GRCh37]
Chr9:9q22.32		 uncertain significance
NC_000009.12:g.(?_95101697)_(95508371_?)del deletion Gorlin syndrome [RCV000813978] Chr9:95101697..95508371 [GRCh38]
Chr9:97863979..98270653 [GRCh37]
Chr9:9q22.32		 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 9q22.32(chr9:95046229-96111163)x1 copy number loss See cases [RCV000052918] Chr9:95046229..96111163 [GRCh38]
Chr9:97808511..98873445 [GRCh37]
Chr9:96848332..97913266 [NCBI36]
Chr9:9q22.32		 pathogenic
GRCh38/hg38 9q22.31-22.33(chr9:92561720-98122580)x3 copy number gain See cases [RCV000053773] Chr9:92561720..98122580 [GRCh38]
Chr9:95324002..100884862 [GRCh37]
Chr9:94363823..99924683 [NCBI36]
Chr9:9q22.31-22.33		 pathogenic
GRCh38/hg38 9q22.31-22.33(chr9:91596533-97018746)x1 copy number loss See cases [RCV000052916] Chr9:91596533..97018746 [GRCh38]
Chr9:94358815..99781028 [GRCh37]
Chr9:93398636..98820849 [NCBI36]
Chr9:9q22.31-22.33		 pathogenic
GRCh38/hg38 9q22.32(chr9:95316018-95668838)x1 copy number loss See cases [RCV000052919] Chr9:95316018..95668838 [GRCh38]
Chr9:98078300..98431120 [GRCh37]
Chr9:97118121..97470941 [NCBI36]
Chr9:9q22.32		 pathogenic
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
GRCh37/hg19 9q22.32(97579146-99280739)x1 copy number loss Gorlin syndrome [RCV000201243] Chr9:94816864..96518457 [GRCh38]
Chr9:97579146..99280739 [GRCh37]
Chr9:9q22.32-22.33		 pathogenic
NC_000009.12:g.(?_95101700)_(95508367_?)del deletion Fanconi anemia [RCV000553847]|Gorlin syndrome [RCV001381802] Chr9:95101700..95508367 [GRCh38]
Chr9:97863982..98270649 [GRCh37]
Chr9:9q22.32		 pathogenic
GRCh38/hg38 9q22.1-32(chr9:88522292-113687796)x3 copy number gain See cases [RCV000053752] Chr9:88522292..113687796 [GRCh38]
Chr9:91137207..116450076 [GRCh37]
Chr9:90327027..115489897 [NCBI36]
Chr9:9q22.1-32		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130002129 COSMIC
GTEx LOC130002129 GTEx
Human Proteome Map LOC130002129 Human Proteome Map
NCBI Gene LOC130002129 ENTREZGENE