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LOC129931876 ATAC-STARR-seq lymphoblastoid active region 2055 [ Homo sapiens (human) ]

Gene ID: 129931876, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129931876
Gene description
ATAC-STARR-seq lymphoblastoid active region 2055
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 LOC129931876 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (167936259..167936568)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (167287725..167288034)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:167691547-167692047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167697263-167697762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2053 Neighboring gene myelin protein zero like 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:167739237-167739808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167740743-167741244 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:167761820-167761968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1538 Neighboring gene adenylate cyclase 10 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:167830579-167831095 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:167831096-167831613 Neighboring gene Sharpr-MPRA regulatory region 4419 Neighboring gene DDB1 and CUL4 associated factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:167882400-167883076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:167883077-167883753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1541 Neighboring gene mitochondrial pyruvate carrier 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:167956130-167957329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2056 Neighboring gene microRNA 1255b-2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:168025104-168025604 Neighboring gene GCSH pseudogene 5

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_164919.1 

    Range
    101..410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    167936259..167936568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    167287725..167288034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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