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LOC129932831 ATAC-STARR-seq lymphoblastoid active region 2780 [ Homo sapiens (human) ]

Gene ID: 129932831, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932831
Gene description
ATAC-STARR-seq lymphoblastoid active region 2780
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 LOC129932831 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 (235006237..235006296)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234397012..234397071)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235141984..235142043)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:235098512-235099711 Neighboring gene long intergenic non-protein coding RNA 2971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2779 Neighboring gene lncRNA negative regulator of antiviral signaling Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235115282-235115785 Neighboring gene long intergenic non-protein coding RNA 3108 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:235122747-235123286 and GRCh37_chr1:235122207-235122746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235123287-235123826 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:235133684-235134883 Neighboring gene Sharpr-MPRA regulatory region 4658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2788 Neighboring gene Sharpr-MPRA regulatory region 5019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235191005-235191504 Neighboring gene long intergenic non-protein coding RNA 1348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2790 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235245875-235246397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235256647-235257230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2792 Neighboring gene translocase of outer mitochondrial membrane 20 Neighboring gene uncharacterized LOC105379283 Neighboring gene small nucleolar RNA, H/ACA box 14B

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_165856.1 

    Range
    101..160
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    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
    235006237..235006296
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    234397012..234397071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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