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LOC130057420 ATAC-STARR-seq lymphoblastoid active region 9672 [ Homo sapiens (human) ]

Gene ID: 130057420, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057420
Gene description
ATAC-STARR-seq lymphoblastoid active region 9672
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 LOC130057420 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (70125795..70125844)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (67948010..67948059)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (70418134..70418183)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70324572-70325184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70325185-70325795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70349697-70350197 Neighboring gene TLE family member 3, transcriptional corepressor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70359676-70360176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70360177-70360677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70363742-70364242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70370658-70371264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70371265-70371871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:70374946-70375494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70380981-70381568 Neighboring gene microRNA 629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6603 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:70390514-70391488 Neighboring gene VISTA enhancer hs359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70402651-70403162 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:70403675-70404186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70404187-70404696 Neighboring gene Sharpr-MPRA regulatory region 6929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9671 Neighboring gene uncharacterized LOC107984734 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:70432131-70432636 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:70433141-70433644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70472929-70473512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70473513-70474096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70479256-70479756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:70482961-70483463 Neighboring gene RNA, U6 small nuclear 745, pseudogene

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_191841.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    70125795..70125844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    67948010..67948059
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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