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LOC129991959 ATAC-STARR-seq lymphoblastoid active region 21135 [ Homo sapiens (human) ]

Gene ID: 129991959, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129991959
Gene description
ATAC-STARR-seq lymphoblastoid active region 21135
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 LOC129991959 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (794382..794501)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (792138..792257)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (788170..788289)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene polycomb group ring finger 3 Neighboring gene uncharacterized LOC124900644 Neighboring gene chloride intracellular channel protein 6-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:759135-759682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:762535-763476 Neighboring gene PCGF3 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:774752-775469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:775470-776186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:776187-776904 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:778899-779770 Neighboring gene uncharacterized LOC105374339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:781743-782244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:782245-782744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:783251-783750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:784983-785792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:793259-793758 Neighboring gene complexin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:823745-824262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:824263-824778 Neighboring gene uncharacterized LOC105374340 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:860125-861324 Neighboring gene uncharacterized LOC105374341 Neighboring gene cyclin G associated kinase

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_171405.1 

    Range
    101..220
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    794382..794501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    792138..792257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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