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LOC130065561 ATAC-STARR-seq lymphoblastoid active region 17653 [ Homo sapiens (human) ]

Gene ID: 130065561, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065561
Gene description
ATAC-STARR-seq lymphoblastoid active region 17653
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 LOC130065561 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 (24955248..24955377)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25019362..25019491)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (24935884..24936013)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes 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 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17652 Neighboring gene cystatin F Neighboring gene RNA, U6 small nuclear 1257, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24960021-24960521 Neighboring gene adipocyte plasma membrane associated protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:24961283-24961783 Neighboring gene H3K27ac hESC enhancers GRCh37_chr20:24972940-24973440 and GRCh37_chr20:24973441-24973941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17657 Neighboring gene acyl-CoA synthetase short chain family member 1 Neighboring gene Sharpr-MPRA regulatory region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25038651-25039256

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_199978.1 

    Range
    101..230
    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
    24955248..24955377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    25019362..25019491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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