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LOC130056529 ATAC-STARR-seq lymphoblastoid active region 9075 [ Homo sapiens (human) ]

Gene ID: 130056529, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056529
Gene description
ATAC-STARR-seq lymphoblastoid active region 9075
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 LOC130056529 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (102590921..102590970)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (96827146..96827195)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (103057258..103057307)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103022683-103023183 Neighboring gene MPRA-validated peak2254 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103036323-103036892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103039389-103040275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103040276-103041163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103045898-103046584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103046585-103047269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103050544-103051072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103057589-103058404 Neighboring gene RNA, 7SL, cytoplasmic 546, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9076 Neighboring gene REST corepressor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:103119605-103120104 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103129073-103129810 Neighboring gene ribosomal protein L23a pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9077 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:103174038-103175237 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:103188411-103189610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103204471-103204972 Neighboring gene uncharacterized LOC124903390 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103213106-103213279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103216089-103216923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103224133-103224633

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_190950.1 

    Range
    101..150
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    102590921..102590970
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    96827146..96827195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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