LOC130065089 (ATAC-STARR-seq lymphoblastoid active region 15077) - Rat Genome Database

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Gene: LOC130065089 (ATAC-STARR-seq lymphoblastoid active region 15077) Homo sapiens
Analyze
Symbol: LOC130065089
Name: ATAC-STARR-seq lymphoblastoid active region 15077
RGD ID: 329841715
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
GRCh381955,141,272 - 55,141,331 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01958,235,273 - 58,235,332 (+)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
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130065089
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_003283.6(TNNT1):c.193-24A>C single nucleotide variant not provided [RCV001581328] Chr19:55141326 [GRCh38]
Chr19:55652694 [GRCh37]
Chr19:19q13.42		 likely benign
GRCh38/hg38 19q13.33-13.43(chr19:50191219-58535818)x3 copy number gain See cases [RCV000050883] Chr19:50191219..58535818 [GRCh38]
Chr19:50694476..59047185 [GRCh37]
Chr19:55386288..63738997 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
NM_003283.6(TNNT1):c.199C>T (p.His67Tyr) single nucleotide variant not provided [RCV001756332] Chr19:55141296 [GRCh38]
Chr19:55652664 [GRCh37]
Chr19:19q13.42		 uncertain significance
GRCh38/hg38 19q13.41-13.43(chr19:52612432-58581203)x3 copy number gain See cases [RCV000134174] Chr19:52612432..58581203 [GRCh38]
Chr19:53115685..59092570 [GRCh37]
Chr19:57807497..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52955056-58581203)x3 copy number gain See cases [RCV000134139] Chr19:52955056..58581203 [GRCh38]
Chr19:53458309..59092570 [GRCh37]
Chr19:58150121..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50152520-58581203)x3 copy number gain See cases [RCV000135843] Chr19:50152520..58581203 [GRCh38]
Chr19:50655777..59092570 [GRCh37]
Chr19:55347589..63784382 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
NM_003283.6(TNNT1):c.193-6C>T single nucleotide variant Nemaline myopathy 5 [RCV002169720] Chr19:55141308 [GRCh38]
Chr19:55652676 [GRCh37]
Chr19:19q13.42		 likely benign
GRCh38/hg38 19q13.42-13.43(chr19:55048514-56972458)x3 copy number gain See cases [RCV000138139] Chr19:55048514..56972458 [GRCh38]
Chr19:55595687..57483826 [GRCh37]
Chr19:60251694..62175638 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52143873-58445521)x3 copy number gain See cases [RCV000142008] Chr19:52143873..58445521 [GRCh38]
Chr19:52647126..58956888 [GRCh37]
Chr19:57338938..63648700 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
NM_003283.6(TNNT1):c.193-3C>T single nucleotide variant Nemaline myopathy 5 [RCV002663043] Chr19:55141305 [GRCh38]
Chr19:55652673 [GRCh37]
Chr19:19q13.42		 uncertain significance
NC_000019.9:g.(?_55644273)_(55768277_?)dup duplication Hypertrophic cardiomyopathy [RCV000803281]|Nemaline myopathy 5 [RCV001319583] Chr19:55132905..55256909 [GRCh38]
Chr19:55644273..55768277 [GRCh37]
Chr19:19q13.42		 uncertain significance
NC_000019.10:g.(?_55140863)_(55147177_?)del deletion Nemaline myopathy 5 [RCV000708173] Chr19:55140863..55147177 [GRCh38]
Chr19:55652231..55658545 [GRCh37]
Chr19:19q13.42		 pathogenic
GRCh38/hg38 19q13.42(chr19:55066790-55789870)x3 copy number gain See cases [RCV000142067] Chr19:55066790..55789870 [GRCh38]
Chr19:55578158..56301236 [GRCh37]
Chr19:60269970..60993048 [NCBI36]
Chr19:19q13.42		 uncertain significance
NC_000019.10:g.(?_55140863)_(55151937_?)del deletion Nemaline myopathy 5 [RCV000806573] Chr19:55140863..55151937 [GRCh38]
Chr19:55652231..55663305 [GRCh37]
Chr19:19q13.42		 pathogenic
NC_000019.10:g.(?_55140873)_(55147167_?)del deletion Nemaline myopathy 5 [RCV000817940] Chr19:55140873..55147167 [GRCh38]
Chr19:55652241..55658535 [GRCh37]
Chr19:19q13.42		 pathogenic
NM_003283.6(TNNT1):c.200A>C (p.His67Pro) single nucleotide variant Nemaline myopathy 5 [RCV000791771] Chr19:55141295 [GRCh38]
Chr19:55652663 [GRCh37]
Chr19:19q13.42		 uncertain significance
GRCh38/hg38 19q13.41-13.43(chr19:51141518-58539965)x3 copy number gain See cases [RCV000052926] Chr19:51141518..58539965 [GRCh38]
Chr19:51644775..59051332 [GRCh37]
Chr19:56336587..63743144 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
NC_000019.10:g.(?_55140863)_(55141322_?)del deletion Nemaline myopathy 5 [RCV000641955] Chr19:55140863..55141322 [GRCh38]
Chr19:55652231..55652690 [GRCh37]
Chr19:19q13.42		 uncertain significance
NM_003283.6(TNNT1):c.200A>G (p.His67Arg) single nucleotide variant Nemaline myopathy 5 [RCV000539592] Chr19:55141295 [GRCh38]
Chr19:55652663 [GRCh37]
Chr19:19q13.42		 uncertain significance
GRCh38/hg38 19q13.42-13.43(chr19:55037146-56982033)x3 copy number gain See cases [RCV000142245] Chr19:55037146..56982033 [GRCh38]
Chr19:55548514..57493401 [GRCh37]
Chr19:60240326..62185213 [NCBI36]
Chr19:19q13.42-13.43		 uncertain significance
NM_003283.6(TNNT1):c.193-14C>T single nucleotide variant Nemaline myopathy 5 [RCV002637782] Chr19:55141316 [GRCh38]
Chr19:55652684 [GRCh37]
Chr19:19q13.42		 likely benign
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
NM_003283.6(TNNT1):c.202C>T (p.Arg68Cys) single nucleotide variant Nemaline myopathy 5 [RCV001230480]|not provided [RCV003487281] Chr19:55141293 [GRCh38]
Chr19:55652661 [GRCh37]
Chr19:19q13.42		 uncertain significance
NM_003283.6(TNNT1):c.219A>G (p.Lys73=) single nucleotide variant Nemaline myopathy 5 [RCV001455722] Chr19:55141276 [GRCh38]
Chr19:55652644 [GRCh37]
Chr19:19q13.42		 likely benign
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
NM_003283.6(TNNT1):c.194A>C (p.Asp65Ala) single nucleotide variant Nemaline myopathy 5C, autosomal dominant [RCV003230316] Chr19:55141301 [GRCh38]
Chr19:55652669 [GRCh37]
Chr19:19q13.42		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:49907832-58557889)x3 copy number gain See cases [RCV000052925] Chr19:49907832..58557889 [GRCh38]
Chr19:50411089..59069256 [GRCh37]
Chr19:55102901..63761068 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
NM_003283.6(TNNT1):c.207G>T (p.Lys69Asn) single nucleotide variant Nemaline myopathy 5 [RCV001307668] Chr19:55141288 [GRCh38]
Chr19:55652656 [GRCh37]
Chr19:19q13.42		 uncertain significance
NM_003283.6(TNNT1):c.211A>T (p.Met71Leu) single nucleotide variant Inborn genetic diseases [RCV004475419] Chr19:55141284 [GRCh38]
Chr19:55652652 [GRCh37]
Chr19:19q13.42		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130065089 COSMIC
GTEx LOC130065089 GTEx
Human Proteome Map LOC130065089 Human Proteome Map
NCBI Gene LOC130065089 ENTREZGENE