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LOC129994980 ATAC-STARR-seq lymphoblastoid active region 23396 [ Homo sapiens (human) ]

Gene ID: 129994980, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994980
Gene description
ATAC-STARR-seq lymphoblastoid active region 23396
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 LOC129994980 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 (150035387..150035596)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150571933..150572142)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149414950..149415159)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene HMG-box containing 3 Neighboring gene small nucleolar RNA U13 Neighboring gene ribosomal protein S20 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23395 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149439174-149439376 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149444398-149444573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149447500-149448210 Neighboring gene colony stimulating factor 1 receptor Neighboring gene RORalpha allelically-responsive CSF1R enhancer Neighboring gene CSF1R promoter/intronic regulatory region Neighboring gene LTR-CSF1R promoter Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 12786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149490949-149491461 Neighboring gene CSF1R promoter E1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149497723-149498310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149499971-149500878 Neighboring gene platelet derived growth factor receptor beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149507353-149507854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149509491-149510101 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149515109-149515620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149515621-149516130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149516131-149516642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149517153-149517664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149526270-149526796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532128-149532648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532649-149533168

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_174426.1 

    Range
    101..310
    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
    150035387..150035596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150571933..150572142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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