LOC129932895 (ATAC-STARR-seq lymphoblastoid silent region 2012) - Rat Genome Database

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Gene: LOC129932895 (ATAC-STARR-seq lymphoblastoid silent region 2012) Homo sapiens
Analyze
Symbol: LOC129932895
Name: ATAC-STARR-seq lymphoblastoid silent region 2012
RGD ID: 329407105
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
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position: No map positions available.


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 1q41-44(chr1:223347693-248918469)x3 copy number gain See cases [RCV000050581] Chr1:223347693..248918469 [GRCh38]
Chr1:223521035..249212668 [GRCh37]
Chr1:221587658..247179291 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q44(chr1:243677224-244923447)x1 copy number loss See cases [RCV000050929] Chr1:243677224..244923447 [GRCh38]
Chr1:243840526..245086749 [GRCh37]
Chr1:241907149..243153372 [NCBI36]
Chr1:1q44		 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 1q43-44(chr1:238351121-248918469)x1 copy number loss See cases [RCV000134172] Chr1:238351121..248918469 [GRCh38]
Chr1:238514421..249212668 [GRCh37]
Chr1:236581044..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238753749-248918467)x1 copy number loss See cases [RCV000134751] Chr1:238753749..248918467 [GRCh38]
Chr1:238917049..249212666 [GRCh37]
Chr1:236983672..247179289 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243264192-244668463)x1 copy number loss See cases [RCV000134045] Chr1:243264192..244668463 [GRCh38]
Chr1:243427494..244831765 [GRCh37]
Chr1:241494117..242898388 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242520315-246857912)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333898] Chr1:242520315..246857912 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241625115-245453782)x3 copy number gain See cases [RCV000136503] Chr1:241625115..245453782 [GRCh38]
Chr1:241788417..245617084 [GRCh37]
Chr1:239855040..243683707 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239907336-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333897] Chr1:239907336..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223815147-248918469)x3 copy number gain See cases [RCV000135839] Chr1:223815147..248918469 [GRCh38]
Chr1:224002849..249212668 [GRCh37]
Chr1:222069472..247179291 [NCBI36]
Chr1:1q41-44		 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 1q43-44(chr1:242932576-248864636)x4 copy number gain See cases [RCV000137155] Chr1:242932576..248864636 [GRCh38]
Chr1:243095878..249158835 [GRCh37]
Chr1:241162501..247125458 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223828500-248891309)x3 copy number gain See cases [RCV000051878] Chr1:223828500..248891309 [GRCh38]
Chr1:224016202..249185508 [GRCh37]
Chr1:222082825..247152131 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q42.13-44(chr1:229022909-248918469)x3 copy number gain See cases [RCV000136666] Chr1:229022909..248918469 [GRCh38]
Chr1:229158656..249212668 [GRCh37]
Chr1:227225279..247179291 [NCBI36]
Chr1:1q42.13-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238192880-248930485)x1 copy number loss See cases [RCV000143374] Chr1:238192880..248930485 [GRCh38]
Chr1:238356180..249224684 [GRCh37]
Chr1:236422803..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.11-44(chr1:224096488-248918469)x3 copy number gain See cases [RCV000051882] Chr1:224096488..248918469 [GRCh38]
Chr1:224284190..249212668 [GRCh37]
Chr1:222350813..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240244444-248891309)x3 copy number gain See cases [RCV000051888] Chr1:240244444..248891309 [GRCh38]
Chr1:240407744..249185508 [GRCh37]
Chr1:238474367..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240465122-248918469)x1 copy number loss See cases [RCV000137260] Chr1:240465122..248918469 [GRCh38]
Chr1:240628422..249212668 [GRCh37]
Chr1:238695045..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223887780-248891309)x3 copy number gain See cases [RCV000051880] Chr1:223887780..248891309 [GRCh38]
Chr1:224075482..249185508 [GRCh37]
Chr1:222142105..247152131 [NCBI36]
Chr1:1q41-44		 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 1q43-44(chr1:238033575-248924534)x1 copy number loss See cases [RCV000140039] Chr1:238033575..248924534 [GRCh38]
Chr1:238196875..249218733 [GRCh37]
Chr1:236263498..247185356 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.11-44(chr1:224022862-248918469)x3 copy number gain See cases [RCV000137769] Chr1:224022862..248918469 [GRCh38]
Chr1:224210564..249212668 [GRCh37]
Chr1:222277187..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242045279-248930485)x1 copy number loss See cases [RCV000139889] Chr1:242045279..248930485 [GRCh38]
Chr1:242208581..249224684 [GRCh37]
Chr1:240275204..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243221458-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327711] Chr1:243221458..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.3-44(chr1:235215476-247005888)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327725] Chr1:235215476..247005888 [GRCh38]
Chr1:1q42.3-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242164274-245299473)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327716] Chr1:242164274..245299473 [GRCh38]
Chr1:1q43-44		 pathogenic
Single allele deletion Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 [RCV000235042] Chr1:242100310..244396371 [GRCh38]
Chr1:242263612..244559673 [GRCh37]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242782194-245138126)x3 copy number gain See cases [RCV000140438] Chr1:242782194..245138126 [GRCh38]
Chr1:242945496..245301428 [GRCh37]
Chr1:241012119..243368051 [NCBI36]
Chr1:1q43-44		 uncertain significance
GRCh38/hg38 1q42.12-44(chr1:225438480-248787200)x3 copy number gain See cases [RCV000142448] Chr1:225438480..248787200 [GRCh38]
Chr1:225626182..249060210 [GRCh37]
Chr1:223692805..247048022 [NCBI36]
Chr1:1q42.12-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:237643281-248918469)x1 copy number loss See cases [RCV000142518] Chr1:237643281..248918469 [GRCh38]
Chr1:237806581..249212668 [GRCh37]
Chr1:235873204..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241967139-245542967)x3 copy number gain See cases [RCV000138233] Chr1:241967139..245542967 [GRCh38]
Chr1:242130441..245706269 [GRCh37]
Chr1:240197064..243772892 [NCBI36]
Chr1:1q43-44		 likely pathogenic
GRCh38/hg38 1q43-44(chr1:242828731-248891309)x3 copy number gain See cases [RCV000053504] Chr1:242828731..248891309 [GRCh38]
Chr1:242992033..249185508 [GRCh37]
Chr1:241058656..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243145749-244433395)x1 copy number loss See cases [RCV000142668] Chr1:243145749..244433395 [GRCh38]
Chr1:243309051..244596697 [GRCh37]
Chr1:241375674..242663320 [NCBI36]
Chr1:1q43-44		 pathogenic|likely benign|uncertain significance
GRCh38/hg38 1q43-44(chr1:239558430-248918469)x1 copy number loss See cases [RCV000054023] Chr1:239558430..248918469 [GRCh38]
Chr1:239721730..249212668 [GRCh37]
Chr1:237788353..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241757249-248891309)x1 copy number loss See cases [RCV000054028] Chr1:241757249..248891309 [GRCh38]
Chr1:241920551..249185508 [GRCh37]
Chr1:239987174..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242240797-245200164)x1 copy number loss See cases [RCV000054030] Chr1:242240797..245200164 [GRCh38]
Chr1:242404099..245363466 [GRCh37]
Chr1:240470722..243430089 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241459440-247704671)x1 copy number loss See cases [RCV000054026] Chr1:241459440..247704671 [GRCh38]
Chr1:241622740..247867973 [GRCh37]
Chr1:239689363..245934596 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q44(chr1:243786629-248918469)x1 copy number loss See cases [RCV000054061] Chr1:243786629..248918469 [GRCh38]
Chr1:243949931..249212668 [GRCh37]
Chr1:242016554..247179291 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241047422-248924593)x1 copy number loss See cases [RCV000054025] Chr1:241047422..248924593 [GRCh38]
Chr1:241210722..249218792 [GRCh37]
Chr1:239277345..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242410569-245413313)x1 copy number loss See cases [RCV000054031] Chr1:242410569..245413313 [GRCh38]
Chr1:242573871..245576615 [GRCh37]
Chr1:240640494..243643238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239629868-248924593)x1 copy number loss See cases [RCV000054024] Chr1:239629868..248924593 [GRCh38]
Chr1:239793168..249218792 [GRCh37]
Chr1:237859791..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243225391-245289313)x1 copy number loss See cases [RCV000054032] Chr1:243225391..245289313 [GRCh38]
Chr1:243388693..245452615 [GRCh37]
Chr1:241455316..243519238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241676908-245647727)x1 copy number loss See cases [RCV000054027] Chr1:241676908..245647727 [GRCh38]
Chr1:241840210..245811029 [GRCh37]
Chr1:239906833..243877652 [NCBI36]
Chr1:1q43-44		 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 1q43-44(chr1:236556082-248918469)x1 copy number loss See cases [RCV000137554] Chr1:236556082..248918469 [GRCh38]
Chr1:236719382..249212668 [GRCh37]
Chr1:234786005..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic

Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_165920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Additional Information

Database Acc Id Source(s)
COSMIC LOC129932895 COSMIC
GTEx LOC129932895 GTEx
Human Proteome Map LOC129932895 Human Proteome Map
NCBI Gene LOC129932895 ENTREZGENE