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LOC130067755 ATAC-STARR-seq lymphoblastoid active region 19270 [ Homo sapiens (human) ]

Gene ID: 130067755, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067755
Gene description
ATAC-STARR-seq lymphoblastoid active region 19270
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 LOC130067755 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (48090254..48090333)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (48582770..48582849)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (48486071..48486150)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:48055109-48055612 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:48055613-48056116 Neighboring gene Sharpr-MPRA regulatory region 4711 Neighboring gene epigenetically induced MYC interacting lncRNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr22:48123351-48123882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48135325-48135934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48171821-48172322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48172323-48172822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48209585-48210084 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:48260220-48260392 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:48268308-48269507 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:48279628-48280827 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:48363686-48363861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48438360-48438860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48438861-48439361 Neighboring gene uncharacterized LOC124905150 Neighboring gene MPRA-validated peak4509 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:48479499-48480083 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:48480084-48480668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19274 Neighboring gene uncharacterized LOC107985536 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:48498183-48498415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48541592-48542324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48548671-48549462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:48552617-48553118 Neighboring gene uncharacterized LOC107985581 Neighboring gene MPRA-validated peak4510 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr22:48580642-48580843

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_202170.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    48090254..48090333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    48582770..48582849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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