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LOC129995660 ATAC-STARR-seq lymphoblastoid active region 23898 [ Homo sapiens (human) ]

Gene ID: 129995660, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995660
Gene description
ATAC-STARR-seq lymphoblastoid active region 23898
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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (4906680..4906739)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4775673..4775732)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:4719503-4720314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4725821-4726368 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4732250-4733140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4733141-4734030 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4735211-4735409 Neighboring gene chromodomain Y like Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:4772853-4773404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4775329-4775982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16862 Neighboring gene NANOG hESC enhancer GRCh37_chr6:4787179-4787707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4788958-4789502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23897 Neighboring gene CDYL antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:4864691-4865890 Neighboring gene uncharacterized LOC105374897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4903364-4903864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16863 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:4922310-4922536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4922523-4923034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:4923035-4923546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4924846-4925614 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4925615-4926383 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:4932371-4933089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4947173-4947916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4971812-4972338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:4972339-4972863 Neighboring gene MPRA-validated peak5629 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16865 Neighboring gene ribosomal protein S18 pseudogene 8 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene ribonuclease P/MRP subunit p40

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

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_175106.1 

    Range
    101..160
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    4906680..4906739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    4775673..4775732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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