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LOC129995047 ATAC-STARR-seq lymphoblastoid active region 23458 [ Homo sapiens (human) ]

Gene ID: 129995047, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995047
Gene description
ATAC-STARR-seq lymphoblastoid active region 23458
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 LOC129995047 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 (151569383..151569472)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152108371..152108460)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (150948944..150949033)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 36 member 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82529 Neighboring gene RNA, 5S ribosomal pseudogene 197 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:150875552-150876101 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150877439-150878100 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82543 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82555 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82563 Neighboring gene FAT atypical cadherin 2 Neighboring gene microRNA 6499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150950930-150951442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150974668-150975189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150998970-150999648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150999649-151000325 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:151003759-151004958 Neighboring gene uncharacterized LOC105378231 Neighboring gene uncharacterized LOC124901116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23460 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:151042798-151043997 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151063929-151064758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151065587-151066416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:151066417-151067244 Neighboring gene secreted protein acidic and cysteine rich Neighboring gene colorectal liver metastasis associated transcript 3

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_174493.1 

    Range
    101..190
    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
    151569383..151569472
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    152108371..152108460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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