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LOC130009277 ATAC-STARR-seq lymphoblastoid active region 7392 [ Homo sapiens (human) ]

Gene ID: 130009277, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130009277
Gene description
ATAC-STARR-seq lymphoblastoid active region 7392
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 LOC130009277 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (132828957..132829096)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (132879742..132879881)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and LEM domain containing 2 Neighboring gene TPD52 like 2 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr12:133334029-133334208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:133337764-133338632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7389 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7390 Neighboring gene golgin A3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133365291-133365792 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5129 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5130 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:133412143-133413342 Neighboring gene ribosomal protein S11 pseudogene 5 Neighboring gene RNA, U6 small nuclear 327, pseudogene Neighboring gene checkpoint with forkhead and ring finger domains Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133428785-133429286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133429287-133429786 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:133433141-133434340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133449077-133449774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:133449775-133450470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:133450471-133451166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:133451167-133451862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7393 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:133464984-133465786 Neighboring gene CHFR divergent transcript

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_188911.1 

    Range
    101..240
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    132828957..132829096
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    132879742..132879881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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