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LOC130001383 ATAC-STARR-seq lymphoblastoid active region 28093 [ Homo sapiens (human) ]

Gene ID: 130001383, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001383
Gene description
ATAC-STARR-seq lymphoblastoid active region 28093
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 LOC130001383 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 (144317264..144317513)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145485899..145486148)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145540927..145541176)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145321725-145322492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145322493-145323258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145494989-145495632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145495633-145496276 Neighboring gene BOP1 ribosomal biogenesis factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145498855-145499497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19669 Neighboring gene scleraxis bHLH transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145515765-145516421 Neighboring gene heat shock transcription factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145536471-145537002 Neighboring gene uncharacterized LOC124902050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145543593-145544435 Neighboring gene diacylglycerol O-acyltransferase 1 Neighboring gene microRNA 6848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145555531-145556238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145556239-145556947 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145556948-145557655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145558559-145559174 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145559298-145559484 Neighboring gene scratch family transcriptional repressor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145566939-145567080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19675 Neighboring gene transmembrane protein 249

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_180829.1 

    Range
    101..350
    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
    144317264..144317513
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p14 PATCHES

    Range
    47867..48116
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145485899..145486148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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