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LOC130056241 ATAC-STARR-seq lymphoblastoid active region 8850 [ Homo sapiens (human) ]

Gene ID: 130056241, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056241
Gene description
ATAC-STARR-seq lymphoblastoid active region 8850
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 LOC130056241 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 (89303716..89303785)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (83527359..83527428)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (89770060..89770129)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903357 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89605771-89606692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89631335-89632266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89641541-89642042 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:89654698-89654882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8848 Neighboring gene forkhead box N3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89671451-89671952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89718876-89719531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8849 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760189-89760856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760857-89761524 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762398-89762960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762961-89763522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89763523-89764084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775236-89775736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775737-89776237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8856 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8858 Neighboring gene Sharpr-MPRA regulatory region 10244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89807187-89807686 Neighboring gene uncharacterized LOC101928817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89818959-89819674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89858093-89858593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89865667-89866237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89869264-89869764 Neighboring gene Sharpr-MPRA regulatory region 4092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89882738-89883271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89883272-89883804 Neighboring gene FOXN3 antisense RNA 1

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_190662.1 

    Range
    101..170
    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
    89303716..89303785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    83527359..83527428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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