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LOC130000238 ATAC-STARR-seq lymphoblastoid active region 27255 [ Homo sapiens (human) ]

Gene ID: 130000238, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000238
Gene description
ATAC-STARR-seq lymphoblastoid active region 27255
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 LOC130000238 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38721307..38721356)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38998281..38998330)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38578825..38578874)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38508026-38508628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38508629-38509230 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:38546721-38547014 Neighboring gene uncharacterized LOC124901936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38558842-38559342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38577151-38577672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38591927-38592426 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38593007-38593506 Neighboring gene Sharpr-MPRA regulatory region 10821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19135 Neighboring gene transforming acidic coiled-coil containing protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27258 Neighboring gene Sharpr-MPRA regulatory region 13542 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:38654374-38654912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27262 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:38664233-38664424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38692400-38693183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27263 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38718798-38719298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38719299-38719799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38721554-38722054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38722055-38722555 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:38724712-38725911 Neighboring gene uncharacterized LOC124901937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19138 Neighboring gene pleckstrin homology domain containing A2

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_179684.1 

    Range
    101..150
    Download
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    38721307..38721356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    38998281..38998330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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