LOC130062624 (ATAC-STARR-seq lymphoblastoid active region 13429) - Rat Genome Database

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Gene: LOC130062624 (ATAC-STARR-seq lymphoblastoid active region 13429) Homo sapiens
Analyze
Symbol: LOC130062624
Name: ATAC-STARR-seq lymphoblastoid active region 13429
RGD ID: 329832436
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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
GRCh381862,187,361 - 62,187,570 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01862,390,171 - 62,390,380 (+)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
Single allele deletion Deletion of long arm of chromosome 18 [RCV002280357] Chr18:61490305..80247612 [GRCh38]
Chr18:18q21.33-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:149089-80234391)x3 copy number gain See cases [RCV000134110] Chr18:149089..80234391 [GRCh38]
Chr18:149089..77992274 [GRCh37]
Chr18:139089..76093265 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q21.1-23(chr18:50068129-80252149)x3 copy number gain See cases [RCV000050989] Chr18:50068129..80252149 [GRCh38]
Chr18:47594499..78010032 [GRCh37]
Chr18:45848497..76111023 [NCBI36]
Chr18:18q21.1-23		 pathogenic
GRCh38/hg38 18q21.32-23(chr18:59567681-80252149)x1 copy number loss See cases [RCV000133689] Chr18:59567681..80252149 [GRCh38]
Chr18:57234913..78010032 [GRCh37]
Chr18:55385893..76111023 [NCBI36]
Chr18:18q21.32-23		 pathogenic
GRCh38/hg38 18q21.2-23(chr18:51190429-80252149)x1 copy number loss See cases [RCV000135413] Chr18:51190429..80252149 [GRCh38]
Chr18:48716799..78010032 [GRCh37]
Chr18:46970797..76111023 [NCBI36]
Chr18:18q21.2-23		 pathogenic
GRCh38/hg38 18q21.33-23(chr18:61827111-80252149)x1 copy number loss See cases [RCV000135567] Chr18:61827111..80252149 [GRCh38]
Chr18:59494344..78010032 [GRCh37]
Chr18:57645324..76111023 [NCBI36]
Chr18:18q21.33-23		 pathogenic|uncertain significance
GRCh38/hg38 18q21.31-23(chr18:56618038-80252149)x1 copy number loss See cases [RCV000051032] Chr18:56618038..80252149 [GRCh38]
Chr18:54285269..78010032 [GRCh37]
Chr18:52436267..76111023 [NCBI36]
Chr18:18q21.31-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136226-80256240)x3 copy number gain See cases [RCV000143218] Chr18:136226..80256240 [GRCh38]
Chr18:136226..78014123 [GRCh37]
Chr18:126226..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q21.32-22.3(chr18:59909593-72609801)x3 copy number gain See cases [RCV000143195] Chr18:59909593..72609801 [GRCh38]
Chr18:57576825..70277036 [GRCh37]
Chr18:55727805..68428016 [NCBI36]
Chr18:18q21.32-22.3		 likely pathogenic
GRCh38/hg38 18q12.2-22.1(chr18:38794728-65632804)x3 copy number gain See cases [RCV000136910] Chr18:38794728..65632804 [GRCh38]
Chr18:36374692..63300040 [GRCh37]
Chr18:34628690..61451020 [NCBI36]
Chr18:18q12.2-22.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000051048] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q21.33-23(chr18:61576009-80252149)x1 copy number loss See cases [RCV000135616] Chr18:61576009..80252149 [GRCh38]
Chr18:59243242..78010032 [GRCh37]
Chr18:57394222..76111023 [NCBI36]
Chr18:18q21.33-23		 pathogenic
GRCh38/hg38 18q12.1-23(chr18:32123105-80252149)x3 copy number gain See cases [RCV000136890] Chr18:32123105..80252149 [GRCh38]
Chr18:29703068..78010032 [GRCh37]
Chr18:27957066..76111023 [NCBI36]
Chr18:18q12.1-23		 pathogenic
GRCh38/hg38 18q21.2-23(chr18:55179364-80254946)x1 copy number loss See cases [RCV000137375] Chr18:55179364..80254946 [GRCh38]
Chr18:52846595..78012829 [GRCh37]
Chr18:50997593..76113817 [NCBI36]
Chr18:18q21.2-23		 pathogenic
GRCh38/hg38 18q21.2-23(chr18:52421052-80254946)x1 copy number loss See cases [RCV000139134] Chr18:52421052..80254946 [GRCh38]
Chr18:49947422..78012829 [GRCh37]
Chr18:48201420..76113817 [NCBI36]
Chr18:18q21.2-23		 pathogenic
GRCh38/hg38 18q21.2-23(chr18:53865057-80252149)x1 copy number loss See cases [RCV000136674] Chr18:53865057..80252149 [GRCh38]
Chr18:51391427..78010032 [GRCh37]
Chr18:49645425..76111023 [NCBI36]
Chr18:18q21.2-23		 pathogenic
GRCh38/hg38 18q21.1-23(chr18:49199411-80254946)x3 copy number gain See cases [RCV000137342] Chr18:49199411..80254946 [GRCh38]
Chr18:46725781..78012829 [GRCh37]
Chr18:44979779..76113817 [NCBI36]
Chr18:18q21.1-23		 pathogenic
GRCh38/hg38 18q11.1-22.3(chr18:20962119-74691446)x3 copy number gain See cases [RCV000143057] Chr18:20962119..74691446 [GRCh38]
Chr18:18542080..72403402 [GRCh37]
Chr18:16796078..70532390 [NCBI36]
Chr18:18q11.1-22.3		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:149089-80254936)x3 copy number gain See cases [RCV000139397] Chr18:149089..80254936 [GRCh38]
Chr18:149089..78012819 [GRCh37]
Chr18:139089..76113807 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.3-23(chr18:42651392-80254946)x3 copy number gain See cases [RCV000138034] Chr18:42651392..80254946 [GRCh38]
Chr18:40231357..78012829 [GRCh37]
Chr18:38485355..76113817 [NCBI36]
Chr18:18q12.3-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000148072] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q21.32-23(chr18:59996934-80254946)x1 copy number loss See cases [RCV000139669] Chr18:59996934..80254946 [GRCh38]
Chr18:57664166..78012829 [GRCh37]
Chr18:55815146..76113817 [NCBI36]
Chr18:18q21.32-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:118760-80254946)x3 copy number gain See cases [RCV000138656] Chr18:118760..80254946 [GRCh38]
Chr18:118760..78012829 [GRCh37]
Chr18:108760..76113817 [NCBI36]
Chr18:18p11.32-q23		 pathogenic|conflicting data from submitters
NC_000018.9:g.(?_59713069)_(60131307_?)dup duplication Multiple congenital anomalies-hypotonia-seizures syndrome 1 [RCV000803267] Chr18:62045836..62464074 [GRCh38]
Chr18:59713069..60131307 [GRCh37]
Chr18:18q21.33		 uncertain significance
GRCh38/hg38 18p11.32-q23(chr18:136227-80256240)x3 copy number gain See cases [RCV000142244] Chr18:136227..80256240 [GRCh38]
Chr18:136227..78014123 [GRCh37]
Chr18:126227..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.3-23(chr18:40367455-80256240)x3 copy number gain See cases [RCV000142227] Chr18:40367455..80256240 [GRCh38]
Chr18:37947419..78014123 [GRCh37]
Chr18:36201417..76115097 [NCBI36]
Chr18:18q12.3-23		 pathogenic
GRCh38/hg38 18q21.33-23(chr18:61613338-80252090)x1 copy number loss See cases [RCV000141429] Chr18:61613338..80252090 [GRCh38]
Chr18:59280571..78009973 [GRCh37]
Chr18:57431551..76110964 [NCBI36]
Chr18:18q21.33-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:53345-80209986)x3 copy number gain See cases [RCV000052501] Chr18:53345..80209986 [GRCh38]
Chr18:53345..77967869 [GRCh37]
Chr18:43345..76068860 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20960320-80234429)x3 copy number gain See cases [RCV000052543] Chr18:20960320..80234429 [GRCh38]
Chr18:18540281..77992312 [GRCh37]
Chr18:16794279..76093303 [NCBI36]
Chr18:18q11.1-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80244381)x3 copy number gain See cases [RCV000052514] Chr18:148963..80244381 [GRCh38]
Chr18:148963..78002264 [GRCh37]
Chr18:138963..76103255 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20989762-80209986)x3 copy number gain See cases [RCV000052549] Chr18:20989762..80209986 [GRCh38]
Chr18:18569723..77967869 [GRCh37]
Chr18:16823721..76068860 [NCBI36]
Chr18:18q11.1-23		 pathogenic
GRCh38/hg38 18q21.2-22.1(chr18:52156899-65408762)x1 copy number loss See cases [RCV000053836] Chr18:52156899..65408762 [GRCh38]
Chr18:49683269..63075998 [GRCh37]
Chr18:47937267..61226978 [NCBI36]
Chr18:18q21.2-22.1		 pathogenic
GRCh38/hg38 18q21.31-23(chr18:56353040-80209986)x1 copy number loss See cases [RCV000053873] Chr18:56353040..80209986 [GRCh38]
Chr18:54020271..77967869 [GRCh37]
Chr18:52171269..76068860 [NCBI36]
Chr18:18q21.31-23		 pathogenic
NM_001346231.2(RELCH):c.32G>A (p.Ser11Asn) single nucleotide variant not specified [RCV004443841] Chr18:62187537 [GRCh38]
Chr18:59854770 [GRCh37]
Chr18:18q21.33		 uncertain significance
NM_001346231.2(RELCH):c.31A>C (p.Ser11Arg) single nucleotide variant not specified [RCV004443839] Chr18:62187536 [GRCh38]
Chr18:59854769 [GRCh37]
Chr18:18q21.33		 uncertain significance
GRCh38/hg38 18q21.2-23(chr18:51167159-80256240)x1 copy number loss See cases [RCV000140925] Chr18:51167159..80256240 [GRCh38]
Chr18:48693529..78014123 [GRCh37]
Chr18:46947527..76115097 [NCBI36]
Chr18:18q21.2-23		 pathogenic
GRCh38/hg38 18q21.2-23(chr18:53959828-80254936)x3 copy number gain See cases [RCV000139496] Chr18:53959828..80254936 [GRCh38]
Chr18:51486198..78012819 [GRCh37]
Chr18:49740196..76113807 [NCBI36]
Chr18:18q21.2-23		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130062624 COSMIC
GTEx LOC130062624 GTEx
Human Proteome Map LOC130062624 Human Proteome Map
NCBI Gene LOC130062624 ENTREZGENE