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LOC130058755 ATAC-STARR-seq lymphoblastoid active region 10656 [ Homo sapiens (human) ]

Gene ID: 130058755, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058755
Gene description
ATAC-STARR-seq lymphoblastoid active region 10656
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
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Genomic context

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See LOC130058755 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29335673..29335722)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29617721..29617770)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29346994..29347043)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903676 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:29276626-29276788 Neighboring gene uncharacterized LOC105371159 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29296048-29296841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29296842-29297634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29297988-29298594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29298595-29299200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29324515-29325223 Neighboring gene sorting nexin 29 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29330917-29331417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29339867-29340728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29340729-29341590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29393253-29393874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29393875-29394494 Neighboring gene nuclear pore complex interacting protein family member B11 Neighboring gene small nucleolar RNA U13 Neighboring gene SMG1 pseudogene 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_193176.1 

    Range
    101..150
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29335673..29335722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29617721..29617770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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