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LOC129995007 ATAC-STARR-seq lymphoblastoid active region 23421 [ Homo sapiens (human) ]

Gene ID: 129995007, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129995007
Gene description
ATAC-STARR-seq lymphoblastoid active region 23421
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 LOC129995007 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150557108..150557277)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151093654..151093823)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82371 Neighboring gene NDST1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149865131-149865786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149872150-149872771 Neighboring gene Sharpr-MPRA regulatory region 285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149881034-149881594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149881595-149882153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149889677-149890250 Neighboring gene Sharpr-MPRA regulatory region 361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149891552-149892205 Neighboring gene N-deacetylase and N-sulfotransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149902065-149902942 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149905099-149905839 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149916701-149917473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149919751-149920250 Neighboring gene Sharpr-MPRA regulatory region 2793 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149926039-149926554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149953456-149954442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149956181-149956887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149969781-149970280 Neighboring gene synaptopodin Neighboring gene uncharacterized LOC124901108 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149995691-149995878 Neighboring gene uncharacterized LOC124901107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23423 Neighboring gene Sharpr-MPRA regulatory region 14746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150003601-150004100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150005713-150006428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150006429-150007142

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_174453.1 

    Range
    101..270
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    150557108..150557277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151093654..151093823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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