LOC130057683 (ATAC-STARR-seq lymphoblastoid silent region 6705) - Rat Genome Database

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Gene: LOC130057683 (ATAC-STARR-seq lymphoblastoid silent region 6705) Homo sapiens
Analyze
Symbol: LOC130057683
Name: ATAC-STARR-seq lymphoblastoid silent region 6705
RGD ID: 329834576
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
GRCh381578,131,150 - 78,131,669 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01575,993,716 - 75,994,235 (+)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 LOC130057683
16 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_006383.4(CIB2):c.4G>A (p.Gly2Arg) single nucleotide variant not provided [RCV001912102] Chr15:78131212 [GRCh38]
Chr15:78423554 [GRCh37]
Chr15:15q25.1		 uncertain significance
NM_006383.4(CIB2):c.40_47del (p.Asp14fs) deletion not provided [RCV001914013] Chr15:78131169..78131176 [GRCh38]
Chr15:78423511..78423518 [GRCh37]
Chr15:15q25.1		 pathogenic
NM_006383.4(CIB2):c.47A>G (p.Tyr16Cys) single nucleotide variant Autosomal recessive nonsyndromic hearing loss 48 [RCV002289439] Chr15:78131169 [GRCh38]
Chr15:78423511 [GRCh37]
Chr15:15q25.1		 uncertain significance
GRCh38/hg38 15q24.3-25.1(chr15:77640317-78459174)x3 copy number gain See cases [RCV000050915] Chr15:77640317..78459174 [GRCh38]
Chr15:77932659..78751516 [GRCh37]
Chr15:75719714..76538571 [NCBI36]
Chr15:15q24.3-25.1		 uncertain significance
NM_006383.4(CIB2):c.44A>G (p.Asn15Ser) single nucleotide variant Inborn genetic diseases [RCV002836655] Chr15:78131172 [GRCh38]
Chr15:78423514 [GRCh37]
Chr15:15q25.1		 uncertain significance
NM_006383.4(CIB2):c.48C>G (p.Tyr16Ter) single nucleotide variant not provided [RCV001222810] Chr15:78131168 [GRCh38]
Chr15:78423510 [GRCh37]
Chr15:15q25.1		 pathogenic
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3 copy number gain See cases [RCV000142915] Chr15:59828460..101920998 [GRCh38]
Chr15:60120659..102461201 [GRCh37]
Chr15:57907951..100278724 [NCBI36]
Chr15:15q22.2-26.3		 pathogenic
GRCh38/hg38 15q23-26.3(chr15:72154949-101920998)x3 copy number gain See cases [RCV000143019] Chr15:72154949..101920998 [GRCh38]
Chr15:72447290..102461201 [GRCh37]
Chr15:70234344..100278724 [NCBI36]
Chr15:15q23-26.3		 pathogenic
GRCh38/hg38 15q24.2-25.1(chr15:76006154-79982417)x1 copy number loss See cases [RCV000137079] Chr15:76006154..79982417 [GRCh38]
Chr15:76298495..80274759 [GRCh37]
Chr15:74085550..78061814 [NCBI36]
Chr15:15q24.2-25.1		 pathogenic|uncertain significance
NM_006383.4(CIB2):c.51+6C>G single nucleotide variant not provided [RCV003024368] Chr15:78131159 [GRCh38]
Chr15:78423501 [GRCh37]
Chr15:15q25.1		 uncertain significance
GRCh38/hg38 15q23-25.1(chr15:70025300-78705993)x1 copy number loss See cases [RCV000141666] Chr15:70025300..78705993 [GRCh38]
Chr15:70317639..78998335 [GRCh37]
Chr15:68104693..76785390 [NCBI36]
Chr15:15q23-25.1		 pathogenic
NM_006383.4(CIB2):c.-39T>A single nucleotide variant not provided [RCV000838288] Chr15:78131254 [GRCh38]
Chr15:78423596 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.27C>G (p.Thr9=) single nucleotide variant not provided [RCV000881849] Chr15:78131189 [GRCh38]
Chr15:78423531 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.9C>G (p.Asn3Lys) single nucleotide variant Autosomal recessive nonsyndromic hearing loss 48 [RCV002463827] Chr15:78131207 [GRCh38]
Chr15:78423549 [GRCh37]
Chr15:15q25.1		 uncertain significance
NM_006383.4(CIB2):c.23T>G (p.Phe8Cys) single nucleotide variant Inborn genetic diseases [RCV003292061] Chr15:78131193 [GRCh38]
Chr15:78423535 [GRCh37]
Chr15:15q25.1		 uncertain significance
NM_006383.4(CIB2):c.39A>G (p.Leu13=) single nucleotide variant not provided [RCV002640233] Chr15:78131177 [GRCh38]
Chr15:78423519 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.28G>A (p.Glu10Lys) single nucleotide variant not provided [RCV002635968] Chr15:78131188 [GRCh38]
Chr15:78423530 [GRCh37]
Chr15:15q25.1		 uncertain significance
NM_006383.4(CIB2):c.24C>T (p.Phe8=) single nucleotide variant not provided [RCV001454923] Chr15:78131192 [GRCh38]
Chr15:78423534 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.-39T>G single nucleotide variant not specified [RCV000606349] Chr15:78131254 [GRCh38]
Chr15:78423596 [GRCh37]
Chr15:15q25.1		 benign
NM_006383.4(CIB2):c.-22G>A single nucleotide variant not specified [RCV000600443] Chr15:78131237 [GRCh38]
Chr15:78423579 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.51+13C>T single nucleotide variant not provided [RCV002653529] Chr15:78131152 [GRCh38]
Chr15:78423494 [GRCh37]
Chr15:15q25.1		 likely benign
NM_006383.4(CIB2):c.-109C>T single nucleotide variant not provided [RCV001639971] Chr15:78131324 [GRCh38]
Chr15:78423666 [GRCh37]
Chr15:15q25.1		 benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130057683 COSMIC
GTEx LOC130057683 GTEx
Human Proteome Map LOC130057683 Human Proteome Map
NCBI Gene LOC130057683 ENTREZGENE