LOC130058571 (ATAC-STARR-seq lymphoblastoid silent region 7236) - Rat Genome Database

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Gene: LOC130058571 (ATAC-STARR-seq lymphoblastoid silent region 7236) Homo sapiens
Analyze
Symbol: LOC130058571
Name: ATAC-STARR-seq lymphoblastoid silent region 7236
RGD ID: 329833626
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
GRCh381617,376,026 - 17,376,095 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01617,383,038 - 17,383,107 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16p13.11-12.3(chr16:14816348-18047194)x1 copy number loss See cases [RCV000050818] Chr16:14816348..18047194 [GRCh38]
Chr16:14910205..18141051 [GRCh37]
Chr16:14817706..18048552 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:14816348-18658403)x1 copy number loss See cases [RCV000050970] Chr16:14816348..18658403 [GRCh38]
Chr16:14910205..18669725 [GRCh37]
Chr16:14817706..18577226 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15457445-18047194)x3 copy number gain See cases [RCV000050377] Chr16:15457445..18047194 [GRCh38]
Chr16:15551302..18141051 [GRCh37]
Chr16:15458803..18048552 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15310595-18212997)x3 copy number gain See cases [RCV000050601] Chr16:15310595..18212997 [GRCh38]
Chr16:15404452..18306854 [GRCh37]
Chr16:15311953..18214355 [NCBI36]
Chr16:16p13.11-12.3		 likely pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 16p13.3-11.2(chr16:4644892-29170820)x3 copy number gain See cases [RCV000133809] Chr16:4644892..29170820 [GRCh38]
Chr16:4694893..29182141 [GRCh37]
Chr16:4634894..29089642 [NCBI36]
Chr16:16p13.3-11.2		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15050263-18212997)x3 copy number gain See cases [RCV000051399] Chr16:15050263..18212997 [GRCh38]
Chr16:15144120..18306854 [GRCh37]
Chr16:15051621..18214355 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.1(chr16:14954894-28306843)x3 copy number gain See cases [RCV000051828] Chr16:14954894..28306843 [GRCh38]
Chr16:15048751..28318164 [GRCh37]
Chr16:14956252..28225665 [NCBI36]
Chr16:16p13.11-12.1		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15140576-18658403)x1 copy number loss See cases [RCV000051057] Chr16:15140576..18658403 [GRCh38]
Chr16:15234433..18669725 [GRCh37]
Chr16:15141934..18577226 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.12-12.3(chr16:14609647-18765817)x3 copy number gain See cases [RCV000051353] Chr16:14609647..18765817 [GRCh38]
Chr16:14703504..18777139 [GRCh37]
Chr16:14611005..18684640 [NCBI36]
Chr16:16p13.12-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15310595-18212997)x1 copy number loss See cases [RCV000135502] Chr16:15310595..18212997 [GRCh38]
Chr16:15404452..18306854 [GRCh37]
Chr16:15311953..18214355 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15457445-18658403)x3 copy number gain See cases [RCV000051141] Chr16:15457445..18658403 [GRCh38]
Chr16:15551302..18669725 [GRCh37]
Chr16:15458803..18577226 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15222856-18148856)x3 copy number gain See cases [RCV000143165] Chr16:15222856..18148856 [GRCh38]
Chr16:15316713..18242713 [GRCh37]
Chr16:15224214..18150214 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15184811-18535419)x3 copy number gain See cases [RCV000139051] Chr16:15184811..18535419 [GRCh38]
Chr16:15278668..18546741 [GRCh37]
Chr16:15186169..18454242 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p12.3(chr16:17228304-17601077)x1 copy number loss See cases [RCV000139115] Chr16:17228304..17601077 [GRCh38]
Chr16:17322161..17694934 [GRCh37]
Chr16:17229662..17602435 [NCBI36]
Chr16:16p12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:14783830-18536926)x3 copy number gain See cases [RCV000143143] Chr16:14783830..18536926 [GRCh38]
Chr16:14877687..18548248 [GRCh37]
Chr16:14785188..18455749 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15398450-18272881)x1 copy number loss See cases [RCV000143204] Chr16:15398450..18272881 [GRCh38]
Chr16:15492307..18366738 [GRCh37]
Chr16:15399808..18274239 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic|likely pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15457205-18212984)x1 copy number loss See cases [RCV000138825] Chr16:15457205..18212984 [GRCh38]
Chr16:15551062..18306841 [GRCh37]
Chr16:15458563..18214342 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:16541781-18768479)x3 copy number gain See cases [RCV000137333] Chr16:16541781..18768479 [GRCh38]
Chr16:16635638..18779801 [GRCh37]
Chr16:16543139..18687302 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic|uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15060830-18535437)x3 copy number gain See cases [RCV000136807] Chr16:15060830..18535437 [GRCh38]
Chr16:15154687..18546759 [GRCh37]
Chr16:15062188..18454260 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15398450-18068310)x1 copy number loss See cases [RCV000139649] Chr16:15398450..18068310 [GRCh38]
Chr16:15492307..18162167 [GRCh37]
Chr16:15399808..18069668 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15194583-18236409)x3 copy number gain See cases [RCV000138003] Chr16:15194583..18236409 [GRCh38]
Chr16:15288440..18330266 [GRCh37]
Chr16:15195941..18237767 [NCBI36]
Chr16:16p13.11-12.3		 likely pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15223052-18148856)x3 copy number gain See cases [RCV000143416] Chr16:15223052..18148856 [GRCh38]
Chr16:15316909..18242713 [GRCh37]
Chr16:15224410..18150214 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15186140-18783183)x3 copy number gain See cases [RCV000137700] Chr16:15186140..18783183 [GRCh38]
Chr16:15279997..18794505 [GRCh37]
Chr16:15187498..18702006 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15194583-18170423)x3 copy number gain See cases [RCV000137491] Chr16:15194583..18170423 [GRCh38]
Chr16:15288440..18264280 [GRCh37]
Chr16:15195941..18171781 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15261472-18768479)x3 copy number gain See cases [RCV000137451] Chr16:15261472..18768479 [GRCh38]
Chr16:15355329..18779801 [GRCh37]
Chr16:15262830..18687302 [NCBI36]
Chr16:16p13.11-12.3		 likely pathogenic|uncertain significance
GRCh38/hg38 16p12.3(chr16:17169800-17966460)x3 copy number gain See cases [RCV000137907] Chr16:17169800..17966460 [GRCh38]
Chr16:17263657..18060317 [GRCh37]
Chr16:17171158..17967818 [NCBI36]
Chr16:16p12.3		 likely benign
GRCh38/hg38 16p13.11-12.3(chr16:14783830-18680735)x3 copy number gain See cases [RCV000137543] Chr16:14783830..18680735 [GRCh38]
Chr16:14877687..18692057 [GRCh37]
Chr16:14785188..18599558 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15398450-18212997)x1 copy number loss See cases [RCV000138168] Chr16:15398450..18212997 [GRCh38]
Chr16:15492307..18306854 [GRCh37]
Chr16:15399808..18214355 [NCBI36]
Chr16:16p13.11-12.3		 likely pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15186140-18768479)x3 copy number gain See cases [RCV000138546] Chr16:15186140..18768479 [GRCh38]
Chr16:15279997..18779801 [GRCh37]
Chr16:15187498..18687302 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15310595-18212997)x3 copy number gain See cases [RCV000148208] Chr16:15310595..18212997 [GRCh38]
Chr16:15404452..18306854 [GRCh37]
Chr16:15311953..18214355 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15457445-18047194)x1 copy number loss See cases [RCV000142529] Chr16:15457445..18047194 [GRCh38]
Chr16:15551302..18141051 [GRCh37]
Chr16:15458803..18048552 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic|likely pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15128213-18577521)x3 copy number gain See cases [RCV000140646] Chr16:15128213..18577521 [GRCh38]
Chr16:15222070..18588843 [GRCh37]
Chr16:15129571..18496344 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15218552-18148856)x3 copy number gain See cases [RCV000142135] Chr16:15218552..18148856 [GRCh38]
Chr16:15312409..18242713 [GRCh37]
Chr16:15219910..18150214 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15186140-18068310)x3 copy number gain See cases [RCV000140664] Chr16:15186140..18068310 [GRCh38]
Chr16:15279997..18162167 [GRCh37]
Chr16:15187498..18069668 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:14783830-18768479)x3 copy number gain See cases [RCV000138254] Chr16:14783830..18768479 [GRCh38]
Chr16:14877687..18779801 [GRCh37]
Chr16:14785188..18687302 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p12.3(chr16:16753846-18768479)x3 copy number gain See cases [RCV000138195] Chr16:16753846..18768479 [GRCh38]
Chr16:16847703..18779801 [GRCh37]
Chr16:16755204..18687302 [NCBI36]
Chr16:16p12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15325296-18078611)x3 copy number gain See cases [RCV000141667] Chr16:15325296..18078611 [GRCh38]
Chr16:15419153..18172468 [GRCh37]
Chr16:15326654..18079969 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15060830-18212997)x3 copy number gain See cases [RCV000053093] Chr16:15060830..18212997 [GRCh38]
Chr16:15154687..18306854 [GRCh37]
Chr16:15062188..18214355 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
NC_000016.10:g.(?_17108675)_(17470816_?)del deletion Desbuquois dysplasia 1 [RCV000652128] Chr16:17108675..17470816 [GRCh38]
Chr16:17202532..17564673 [GRCh37]
Chr16:16p12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15310595-18620659)x3 copy number gain See cases [RCV000053099] Chr16:15310595..18620659 [GRCh38]
Chr16:15404452..18631981 [GRCh37]
Chr16:15311953..18539482 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15398460-18047194)x3 copy number gain See cases [RCV000053102] Chr16:15398460..18047194 [GRCh38]
Chr16:15492317..18141051 [GRCh37]
Chr16:15399818..18048552 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15299037-18267893)x3 copy number gain See cases [RCV000053098] Chr16:15299037..18267893 [GRCh38]
Chr16:15392894..18361750 [GRCh37]
Chr16:15300395..18269251 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15186140-18658403)x3 copy number gain See cases [RCV000053095] Chr16:15186140..18658403 [GRCh38]
Chr16:15279997..18669725 [GRCh37]
Chr16:15187498..18577226 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance|conflicting data from submitters
Single allele duplication Schizophrenia [RCV000754173] Chr16:15085515..18775195 [GRCh38]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15186140-18620659)x3 copy number gain See cases [RCV000053096] Chr16:15186140..18620659 [GRCh38]
Chr16:15279997..18631981 [GRCh37]
Chr16:15187498..18539482 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance|conflicting data from submitters
Single allele duplication Schizophrenia [RCV000754174] Chr16:15279737..18291544 [GRCh38]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15434653-18055828)x3 copy number gain See cases [RCV000052515] Chr16:15434653..18055828 [GRCh38]
Chr16:15528510..18149685 [GRCh37]
Chr16:15436011..18057186 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:16450841-18203371)x1 copy number loss See cases [RCV000052518] Chr16:16450841..18203371 [GRCh38]
Chr16:16544698..18297228 [GRCh37]
Chr16:16452199..18204729 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15434653-18055828)x1 copy number loss See cases [RCV000052516] Chr16:15434653..18055828 [GRCh38]
Chr16:15528510..18149685 [GRCh37]
Chr16:15436011..18057186 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:14823949-18055828)x1 copy number loss See cases [RCV000052487] Chr16:14823949..18055828 [GRCh38]
Chr16:14917806..18149685 [GRCh37]
Chr16:14825307..18057186 [NCBI36]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15184811-18708191) copy number loss Autism spectrum disorder [RCV003883423] Chr16:15184811..18708191 [GRCh38]
Chr16:16p13.11-12.3		 pathogenic
GRCh38/hg38 16p13.11-12.3(chr16:15194583-18726698)x3 copy number gain See cases [RCV000137588] Chr16:15194583..18726698 [GRCh38]
Chr16:15288440..18738020 [GRCh37]
Chr16:15195941..18645521 [NCBI36]
Chr16:16p13.11-12.3		 likely pathogenic|uncertain significance
GRCh38/hg38 16p13.11-12.3(chr16:15194583-18214016)x3 copy number gain See cases [RCV000137336] Chr16:15194583..18214016 [GRCh38]
Chr16:15288440..18307873 [GRCh37]
Chr16:15195941..18215374 [NCBI36]
Chr16:16p13.11-12.3		 uncertain significance|conflicting data from submitters

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130058571 COSMIC
GTEx LOC130058571 GTEx
Human Proteome Map LOC130058571 Human Proteome Map
NCBI Gene LOC130058571 ENTREZGENE