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LOC130002600 ATAC-STARR-seq lymphoblastoid active region 29008 [ Homo sapiens (human) ]

Gene ID: 130002600, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002600
Gene description
ATAC-STARR-seq lymphoblastoid active region 29008
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 LOC130002600 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125530231..125530390)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137729880..137730039)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128194217-128194791 Neighboring gene RNA, U5B small nuclear 5, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128207109-128207610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128207611-128208110 Neighboring gene NANOG hESC enhancer GRCh37_chr9:128208606-128209135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128209344-128209872 Neighboring gene MAPK associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128242575-128243076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128243077-128243576 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128243732-128243912 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128246700-128246866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128257291-128258078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29005 Neighboring gene Sharpr-MPRA regulatory region 1305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29007 Neighboring gene RNA, 7SL, cytoplasmic 30, pseudogene Neighboring gene uncharacterized LOC124902270 Neighboring gene uncharacterized LOC105376272

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

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_182046.1 

    Range
    101..260
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    125530231..125530390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137729880..137730039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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