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LOC130055821 ATAC-STARR-seq lymphoblastoid active region 8524 [ Homo sapiens (human) ]

Gene ID: 130055821, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130055821
Gene description
ATAC-STARR-seq lymphoblastoid active region 8524
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 LOC130055821 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 (64235144..64235203)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (58442859..58442918)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (64701862..64701921)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene spectrin repeat containing nuclear envelope protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5831 Neighboring gene ribosomal protein S28 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8521 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35084 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:64357721-64358428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:64360139-64360663 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35093 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35095 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:64417577-64418140 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:64418141-64418703 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:64503774-64504468 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:64526989-64527584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:64540907-64541408 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:64581878-64582065 Neighboring gene microRNA 548h-1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:64649031-64649892 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:64652879-64653670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:64663246-64663842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:64691697-64692198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:64692199-64692698 Neighboring gene uncharacterized LOC124903328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8525 Neighboring gene estrogen receptor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8526 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:64805694-64806376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8530 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:64858021-64858754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:64858755-64859488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:64859797-64860574 Neighboring gene testis expressed 21, pseudogene Neighboring gene Sharpr-MPRA regulatory region 9441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8532 Neighboring gene methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 Neighboring gene zinc finger and BTB domain containing 25

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 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_190242.1 

    Range
    101..160
    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
    64235144..64235203
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    58442859..58442918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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