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LOC130001554 ATAC-STARR-seq lymphoblastoid active region 28209 [ Homo sapiens (human) ]

Gene ID: 130001554, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001554
Gene description
ATAC-STARR-seq lymphoblastoid active region 28209
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 LOC130001554 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (6917363..6917442)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (6913671..6913750)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (6917363..6917442)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28205 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6756064-6756775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:6761325-6762007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6766791-6767436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6767437-6768080 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6771154-6772127 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:6775214-6775806 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:6776991-6777582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6776399-6776990 Neighboring gene lysine demethylase 4C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6789083-6789798 Neighboring gene SNRPE pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:6808287-6808846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:6834601-6835322 Neighboring gene actin gamma 1 pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19772 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:6940065-6940565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:7147699-7148200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:7148201-7148700 Neighboring gene NANOG hESC enhancer GRCh37_chr9:7185598-7186113 Neighboring gene uncharacterized LOC105375969 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:7240589-7241138 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:7284400-7285015 Neighboring gene uncharacterized LOC105375970 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:7319761-7320960 Neighboring gene uncharacterized LOC102723994

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_181000.1 

    Range
    101..180
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    6917363..6917442
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    6913671..6913750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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