LOC130004506 (ATAC-STARR-seq lymphoblastoid active region 3872) - Rat Genome Database

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Gene: LOC130004506 (ATAC-STARR-seq lymphoblastoid active region 3872) Homo sapiens
Analyze
Symbol: LOC130004506
Name: ATAC-STARR-seq lymphoblastoid active region 3872
RGD ID: 329819753
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
GRCh381099,731,829 - 99,732,048 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.010100,614,819 - 100,615,038 (+)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

Variants

.
Variants in LOC130004506
36 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_078470.6(COX15):c.27G>C (p.Leu9Phe) single nucleotide variant not provided [RCV001983649] Chr10:99732023 [GRCh38]
Chr10:101491780 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.84A>G (p.Arg28=) single nucleotide variant Leigh syndrome [RCV001103674]|not provided [RCV002555014] Chr10:99731966 [GRCh38]
Chr10:101491723 [GRCh37]
Chr10:10q24.2		 likely benign|uncertain significance
NM_078470.6(COX15):c.79_90+3delinsGACT indel Leigh syndrome [RCV002282872] Chr10:99731957..99731971 [GRCh38]
Chr10:101491714..101491728 [GRCh37]
Chr10:10q24.2		 likely pathogenic
GRCh38/hg38 10q23.33-25.3(chr10:95112607-116776637)x3 copy number gain See cases [RCV000050747] Chr10:95112607..116776637 [GRCh38]
Chr10:96872364..118383651 [GRCh37]
Chr10:96862354..118526138 [NCBI36]
Chr10:10q23.33-25.3		 pathogenic
NM_078470.6(COX15):c.90+20T>C single nucleotide variant not provided [RCV002085163] Chr10:99731940 [GRCh38]
Chr10:101491697 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.36G>C (p.Leu12Phe) single nucleotide variant not provided [RCV001981670] Chr10:99732014 [GRCh38]
Chr10:101491771 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.47A>G (p.Gln16Arg) single nucleotide variant not provided [RCV001983181] Chr10:99732003 [GRCh38]
Chr10:101491760 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.53T>G (p.Leu18Arg) single nucleotide variant not provided [RCV001908135] Chr10:99731997 [GRCh38]
Chr10:101491754 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.90+16G>A single nucleotide variant not provided [RCV002055514]|not specified [RCV000124577] Chr10:99731944 [GRCh38]
Chr10:101491701 [GRCh37]
Chr10:10q24.2		 benign
GRCh38/hg38 10q24.2(chr10:99716324-99999957)x3 copy number gain See cases [RCV000051649] Chr10:99716324..99999957 [GRCh38]
Chr10:101476081..101759714 [GRCh37]
Chr10:101466071..101749704 [NCBI36]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.73G>A (p.Ala25Thr) single nucleotide variant not provided [RCV002861439] Chr10:99731977 [GRCh38]
Chr10:101491734 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.73G>T (p.Ala25Ser) single nucleotide variant Inborn genetic diseases [RCV002805516]|not provided [RCV002805515] Chr10:99731977 [GRCh38]
Chr10:101491734 [GRCh37]
Chr10:10q24.2		 uncertain significance
GRCh38/hg38 10q24.2-24.31(chr10:99333940-100475567)x3 copy number gain See cases [RCV000051647] Chr10:99333940..100475567 [GRCh38]
Chr10:101093697..102235324 [GRCh37]
Chr10:101083687..102225314 [NCBI36]
Chr10:10q24.2-24.31		 uncertain significance
NM_078470.6(COX15):c.90+15C>T single nucleotide variant not provided [RCV002834900] Chr10:99731945 [GRCh38]
Chr10:101491702 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.83G>C (p.Arg28Thr) single nucleotide variant Inborn genetic diseases [RCV003243016]|not provided [RCV001853174]|not specified [RCV000199425] Chr10:99731967 [GRCh38]
Chr10:101491724 [GRCh37]
Chr10:10q24.2		 likely benign|uncertain significance
NM_078470.6(COX15):c.59T>A (p.Leu20His) single nucleotide variant not provided [RCV003078665] Chr10:99731991 [GRCh38]
Chr10:101491748 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.90+27C>A single nucleotide variant not provided [RCV000833887] Chr10:99731933 [GRCh38]
Chr10:101491690 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+13A>G single nucleotide variant not provided [RCV002626421] Chr10:99731947 [GRCh38]
Chr10:101491704 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+1G>A single nucleotide variant not provided [RCV002603581] Chr10:99731959 [GRCh38]
Chr10:101491716 [GRCh37]
Chr10:10q24.2		 likely pathogenic
NM_078470.6(COX15):c.41G>C (p.Gly14Ala) single nucleotide variant not provided [RCV000596802] Chr10:99732009 [GRCh38]
Chr10:101491766 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.90+8A>T single nucleotide variant not provided [RCV003660816]|not specified [RCV000612928] Chr10:99731952 [GRCh38]
Chr10:101491709 [GRCh37]
Chr10:10q24.2		 likely benign
GRCh38/hg38 10q23.33-24.32(chr10:93181201-101356779)x1 copy number loss See cases [RCV000052565] Chr10:93181201..101356779 [GRCh38]
Chr10:94940958..103116536 [GRCh37]
Chr10:94930948..103106526 [NCBI36]
Chr10:10q23.33-24.32		 pathogenic
NM_078470.6(COX15):c.87A>G (p.Ala29=) single nucleotide variant not provided [RCV003874705] Chr10:99731963 [GRCh38]
Chr10:101491720 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.4C>T (p.Gln2Ter) single nucleotide variant not provided [RCV003546954] Chr10:99732046 [GRCh38]
Chr10:101491803 [GRCh37]
Chr10:10q24.2		 pathogenic
NM_078470.6(COX15):c.90+19_90+24del deletion not provided [RCV003662760] Chr10:99731936..99731941 [GRCh38]
Chr10:101491693..101491698 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+1G>C single nucleotide variant not provided [RCV003688722] Chr10:99731959 [GRCh38]
Chr10:101491716 [GRCh37]
Chr10:10q24.2		 likely pathogenic
NM_078470.6(COX15):c.33C>G (p.Ala11=) single nucleotide variant not provided [RCV003544545] Chr10:99732017 [GRCh38]
Chr10:101491774 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+16G>T single nucleotide variant not provided [RCV003662761] Chr10:99731944 [GRCh38]
Chr10:101491701 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.34T>C (p.Leu12=) single nucleotide variant not provided [RCV003690639] Chr10:99732016 [GRCh38]
Chr10:101491773 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.15C>T (p.Leu5=) single nucleotide variant not provided [RCV003849994] Chr10:99732035 [GRCh38]
Chr10:101491792 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+19C>T single nucleotide variant not provided [RCV003840219] Chr10:99731941 [GRCh38]
Chr10:101491698 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.90+11G>A single nucleotide variant not provided [RCV003558186] Chr10:99731949 [GRCh38]
Chr10:101491706 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.30G>A (p.Arg10=) single nucleotide variant not provided [RCV003856259] Chr10:99732020 [GRCh38]
Chr10:101491777 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.78G>T (p.Ala26=) single nucleotide variant not provided [RCV003701261] Chr10:99731972 [GRCh38]
Chr10:101491729 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.42G>C (p.Gly14=) single nucleotide variant not provided [RCV003557333] Chr10:99732008 [GRCh38]
Chr10:101491765 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.52C>T (p.Leu18=) single nucleotide variant not provided [RCV003553547] Chr10:99731998 [GRCh38]
Chr10:101491755 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.33C>T (p.Ala11=) single nucleotide variant not provided [RCV003819400] Chr10:99732017 [GRCh38]
Chr10:101491774 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.60C>T (p.Leu20=) single nucleotide variant not provided [RCV003848022] Chr10:99731990 [GRCh38]
Chr10:101491747 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.51T>C (p.Tyr17=) single nucleotide variant not provided [RCV003706643] Chr10:99731999 [GRCh38]
Chr10:101491756 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.10T>C (p.Leu4=) single nucleotide variant not provided [RCV003566718] Chr10:99732040 [GRCh38]
Chr10:101491797 [GRCh37]
Chr10:10q24.2		 likely benign
NM_078470.6(COX15):c.55C>T (p.Pro19Ser) single nucleotide variant not provided [RCV003073940] Chr10:99731995 [GRCh38]
Chr10:101491752 [GRCh37]
Chr10:10q24.2		 uncertain significance
NM_078470.6(COX15):c.50A>G (p.Tyr17Cys) single nucleotide variant Inborn genetic diseases [RCV002786206]|not provided [RCV002805517] Chr10:99732000 [GRCh38]
Chr10:101491757 [GRCh37]
Chr10:10q24.2		 likely benign|uncertain significance
GRCh38/hg38 10q24.2-24.31(chr10:99386632-100648221)x3 copy number gain See cases [RCV000135650] Chr10:99386632..100648221 [GRCh38]
Chr10:101146389..102407978 [GRCh37]
Chr10:101136379..102397968 [NCBI36]
Chr10:10q24.2-24.31		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130004506 COSMIC
GTEx LOC130004506 GTEx
Human Proteome Map LOC130004506 Human Proteome Map
NCBI Gene LOC130004506 ENTREZGENE