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LOC129932318 ATAC-STARR-seq lymphoblastoid active region 2384 [ Homo sapiens (human) ]

Gene ID: 129932318, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932318
Gene description
ATAC-STARR-seq lymphoblastoid active region 2384
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 LOC129932318 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 (205631059..205631478)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (204895694..204896117)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (205600187..205600606)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene major facilitator superfamily domain containing 4A Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:205569093-205570292 Neighboring gene RNA, U6 small nuclear 418, pseudogene Neighboring gene GABA type A receptor-associated protein pseudogene Neighboring gene ETS transcription factor ELK4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205629205-205629793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205631113-205631667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205631668-205632223 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:205633133-205634332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2387 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205639145-205639706 Neighboring gene solute carrier family 45 member 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205644516-205645016 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205645017-205645517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1747 Neighboring gene uncharacterized LOC105371701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205657475-205658431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205662277-205662826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205670015-205670516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205670517-205671016 Neighboring gene nuclear casein kinase and cyclin dependent kinase substrate 1 Neighboring gene small nucleolar RNA SNORA72

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_171363.1 

    Range
    101..520
    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
    205631059..205631478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    204895694..204896117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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