LOC129999452 (ATAC-STARR-seq lymphoblastoid silent region 18687) - Rat Genome Database

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Gene: LOC129999452 (ATAC-STARR-seq lymphoblastoid silent region 18687) Homo sapiens
Analyze
Symbol: LOC129999452
Name: ATAC-STARR-seq lymphoblastoid silent region 18687
RGD ID: 329826452
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
GRCh387138,460,651 - 138,461,130 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.07139,770,345 - 139,770,824 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
ovarian cancer  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129999452
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7q32.1-36.3(chr7:129310166-159282390)x3 copy number gain See cases [RCV000050876] Chr7:129310166..159282390 [GRCh38]
Chr7:128950007..159075079 [GRCh37]
Chr7:128737243..158767840 [NCBI36]
Chr7:7q32.1-36.3		 pathogenic
GRCh38/hg38 7q33-36.2(chr7:137751200-154815582)x3 copy number gain See cases [RCV000136592] Chr7:137751200..154815582 [GRCh38]
Chr7:137435946..154607292 [GRCh37]
Chr7:137086486..154238225 [NCBI36]
Chr7:7q33-36.2		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
NM_015905.3(TRIM24):c.341G>T (p.Gly114Val) single nucleotide variant not specified [RCV004238721] Chr7:138460889 [GRCh38]
Chr7:138145634 [GRCh37]
Chr7:7q33		 uncertain significance
NM_015905.3(TRIM24):c.290G>C (p.Gly97Ala) single nucleotide variant not specified [RCV004223512] Chr7:138460838 [GRCh38]
Chr7:138145583 [GRCh37]
Chr7:7q33		 uncertain significance
GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 copy number gain See cases [RCV000051101] Chr7:132850196..159325876 [GRCh38]
Chr7:132534956..159118566 [GRCh37]
Chr7:132185496..158811327 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q33-36.1(chr7:135017687-148807400)x1 copy number loss See cases [RCV000138903] Chr7:135017687..148807400 [GRCh38]
Chr7:134702438..148504492 [GRCh37]
Chr7:134352978..148135425 [NCBI36]
Chr7:7q33-36.1		 pathogenic
GRCh38/hg38 7q31.32-36.3(chr7:121863759-159335865)x3 copy number gain See cases [RCV000138847] Chr7:121863759..159335865 [GRCh38]
Chr7:121503813..159128555 [GRCh37]
Chr7:121291049..158821316 [NCBI36]
Chr7:7q31.32-36.3		 pathogenic
NM_015905.3(TRIM24):c.257A>T (p.Gln86Leu) single nucleotide variant not specified [RCV004169569] Chr7:138460805 [GRCh38]
Chr7:138145550 [GRCh37]
Chr7:7q33		 uncertain significance
GRCh38/hg38 7q21.3-36.3(chr7:97419852-158923762)x3 copy number gain See cases [RCV000136717] Chr7:97419852..158923762 [GRCh38]
Chr7:97049164..158716453 [GRCh37]
Chr7:96887100..158409214 [NCBI36]
Chr7:7q21.3-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:131171478-159327017)x3 copy number gain See cases [RCV000143754] Chr7:131171478..159327017 [GRCh38]
Chr7:130856237..159119707 [GRCh37]
Chr7:130506777..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132444095-159335866)x3 copy number gain See cases [RCV000139654] Chr7:132444095..159335866 [GRCh38]
Chr7:132128854..159128556 [GRCh37]
Chr7:131779394..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132438072-159327017)x3 copy number gain See cases [RCV000143707] Chr7:132438072..159327017 [GRCh38]
Chr7:132122831..159119707 [GRCh37]
Chr7:131773371..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
NM_015905.3(TRIM24):c.259C>T (p.Arg87Cys) single nucleotide variant Ovarian cancer [RCV003154706] Chr7:138460807 [GRCh38]
Chr7:138145552 [GRCh37]
Chr7:7q33		 benign
NM_015905.3(TRIM24):c.133G>A (p.Gly45Ser) single nucleotide variant not specified [RCV004312668] Chr7:138460681 [GRCh38]
Chr7:138145426 [GRCh37]
Chr7:7q33		 uncertain significance
NM_015905.3(TRIM24):c.296C>G (p.Ala99Gly) single nucleotide variant not specified [RCV004312669] Chr7:138460844 [GRCh38]
Chr7:138145589 [GRCh37]
Chr7:7q33		 uncertain significance
GRCh38/hg38 7q33-36.3(chr7:136309982-159307523)x3 copy number gain See cases [RCV000053576] Chr7:136309982..159307523 [GRCh38]
Chr7:135994730..159100212 [GRCh37]
Chr7:135645270..158792973 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:131228764-159335866)x3 copy number gain See cases [RCV000142802] Chr7:131228764..159335866 [GRCh38]
Chr7:130913523..159128556 [GRCh37]
Chr7:130564063..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q33-35(chr7:135414108-144140219)x1 copy number loss See cases [RCV000054173] Chr7:135414108..144140219 [GRCh38]
Chr7:135098857..143837312 [GRCh37]
Chr7:134749397..143468245 [NCBI36]
Chr7:7q33-35		 pathogenic
NM_015905.3(TRIM24):c.193A>T (p.Ser65Cys) single nucleotide variant not specified [RCV004082435] Chr7:138460741 [GRCh38]
Chr7:138145486 [GRCh37]
Chr7:7q33		 uncertain significance
GRCh38/hg38 7q33-34(chr7:137741740-139688885)x1 copy number loss See cases [RCV000054174] Chr7:137741740..139688885 [GRCh38]
Chr7:137426486..139373631 [GRCh37]
Chr7:137077026..139024171 [NCBI36]
Chr7:7q33-34		 pathogenic
NM_015905.3(TRIM24):c.352T>G (p.Phe118Val) single nucleotide variant not specified [RCV004473718] Chr7:138460900 [GRCh38]
Chr7:138145645 [GRCh37]
Chr7:7q33		 uncertain significance
GRCh38/hg38 7q31.2-36.3(chr7:115459015-159325817)x3 copy number gain See cases [RCV000141413] Chr7:115459015..159325817 [GRCh38]
Chr7:115099069..159118507 [GRCh37]
Chr7:114886305..158811268 [NCBI36]
Chr7:7q31.2-36.3		 pathogenic
GRCh38/hg38 7q33-36.3(chr7:134666829-158591882)x1 copy number loss See cases [RCV000138120] Chr7:134666829..158591882 [GRCh38]
Chr7:134351581..158384574 [GRCh37]
Chr7:134002121..158077335 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q33-36.3(chr7:137463392-159345973)x3 copy number gain Neurodevelopmental disorder [RCV003327609] Chr7:137463392..159345973 [GRCh38]
Chr7:7q33-36.3		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129999452 COSMIC
GTEx LOC129999452 GTEx
Human Proteome Map LOC129999452 Human Proteome Map
NCBI Gene LOC129999452 ENTREZGENE