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LOC129929211 ATAC-STARR-seq lymphoblastoid active region 69 [ Homo sapiens (human) ]

Gene ID: 129929211, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929211
Gene description
ATAC-STARR-seq lymphoblastoid active region 69
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 LOC129929211 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (4652600..4652649)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (4166324..4166373)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (4712660..4712709)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904578 Neighboring gene long intergenic non-protein coding RNA 1646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4659710-4660493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4660494-4661276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4673757-4674270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4696215-4696828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4697441-4698052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4698053-4698664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4750784-4751735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4753674-4754174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4754175-4754675 Neighboring gene adherens junctions associated protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4761588-4762504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4762505-4763419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4763460-4763971 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:4766013-4766207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4769069-4769981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4770432-4771050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4771051-4771667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4793939-4794439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4804152-4804652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4804653-4805153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4811516-4812353 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4814461-4815322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4822523-4823023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4842233-4842751 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:4881125-4881715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4929251-4929752 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:4957340-4957510 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:5025208-5026407 Neighboring gene long intergenic non-protein coding RNA 2781

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_162268.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    4652600..4652649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    4166324..4166373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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