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LOC130059779 ATAC-STARR-seq lymphoblastoid active region 11382 [ Homo sapiens (human) ]

Gene ID: 130059779, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059779
Gene description
ATAC-STARR-seq lymphoblastoid active region 11382
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 LOC130059779 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88973231..88973390)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95050604..95050763)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88991210-88992117 Neighboring gene cadmium/zinc-transporting ATPase HMA2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88993027-88993933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11376 Neighboring gene uncharacterized LOC107984871 Neighboring gene uncharacterized LOC100129697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7889 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89023211-89023356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89035421-89036276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89041740-89042284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11384 Neighboring gene uncharacterized LOC124903756 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89048580-89048782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89049867-89050367 Neighboring gene VISTA enhancer hs1854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89067412-89067972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11386 Neighboring gene GATA motif-containing MPRA enhancer 137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89100847-89101733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89103856-89104363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11391 Neighboring gene uncharacterized LOC105371411

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

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_194200.1 

    Range
    101..260
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    88973231..88973390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    95050604..95050763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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