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LOC130065554 ATAC-STARR-seq lymphoblastoid active region 17647 [ Homo sapiens (human) ]

Gene ID: 130065554, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065554
Gene description
ATAC-STARR-seq lymphoblastoid active region 17647
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 LOC130065554 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (24843356..24843555)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (24907486..24907685)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (24823992..24824191)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24460095-24460596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24470679-24471340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24471341-24472000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24472001-24472660 Neighboring gene synapse differentiation inducing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24484347-24484848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24484849-24485348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24492633-24493134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24493135-24493634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24565613-24566113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24570298-24570888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24570889-24571480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24590903-24591802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24596611-24597428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24614353-24615005 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:24615089-24616288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24619223-24619724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24619725-24620224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24715421-24716327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24717937-24718763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:24723033-24723933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24728165-24728664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24727663-24728164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24743840-24744340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24770113-24770614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24789476-24789976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24796263-24796764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24796765-24797264 Neighboring gene uncharacterized LOC107985402 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:24806238-24806412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24849215-24849714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:24855486-24855986 Neighboring gene uncharacterized LOC124904881 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:24881363-24881542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24899137-24899770 Neighboring gene long intergenic non-protein coding RNA 2967

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_199971.1 

    Range
    101..300
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    24843356..24843555
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    24907486..24907685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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