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LOC130007233 ATAC-STARR-seq lymphoblastoid active region 5850 [ Homo sapiens (human) ]

Gene ID: 130007233, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007233
Gene description
ATAC-STARR-seq lymphoblastoid active region 5850
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 LOC130007233 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6341879..6341978)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6351264..6351363)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6451045..6451144)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369625 Neighboring gene ATP synthase membrane subunit f pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4158 Neighboring gene Sharpr-MPRA regulatory region 10601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6390295-6390794 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:6402555-6402765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6404819-6405319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6418662-6419382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6427837-6428456 Neighboring gene pleckstrin homology and RhoGEF domain containing G6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6432098-6432639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433181-6433722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433723-6434262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6443488-6444358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6446101-6446970 Neighboring gene TNF receptor superfamily member 1A Neighboring gene uncharacterized LOC112268088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6455043-6455543 Neighboring gene RNA, 7SL, cytoplasmic 391, pseudogene Neighboring gene sodium channel epithelial 1 subunit alpha

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_187899.1 

    Range
    101..200
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6341879..6341978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6351264..6351363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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