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LOC129994996 ATAC-STARR-seq lymphoblastoid active region 23409 [ Homo sapiens (human) ]

Gene ID: 129994996, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994996
Gene description
ATAC-STARR-seq lymphoblastoid active region 23409
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 LOC129994996 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150406209..150406258)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150942750..150942799)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149785772..149785821)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378226 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16509 Neighboring gene treacle ribosome biogenesis factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149755228-149755750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149756274-149756796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149792263-149792832 Neighboring gene CD74 molecule Neighboring gene uncharacterized LOC124901106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149807381-149807882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149807883-149808382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23416 Neighboring gene MPRA-validated peak5536 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149820554-149821093 Neighboring gene MPRA-validated peak5537 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149828819-149829757 Neighboring gene ribosomal protein S14

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_174442.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    150406209..150406258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150942750..150942799
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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