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LOC130066122 ATAC-STARR-seq lymphoblastoid active region 18081 [ Homo sapiens (human) ]

Gene ID: 130066122, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066122
Gene description
ATAC-STARR-seq lymphoblastoid active region 18081
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 LOC130066122 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 (50041395..50041594)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (51811013..51811212)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (48657932..48658131)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48606199-48606951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18079 Neighboring gene snail family transcriptional repressor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48632321-48633048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48643875-48644714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48644715-48645552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48646392-48647229 Neighboring gene SNAI1 cis-regulatory eRNA expressed in monocytes 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48660109-48661056 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48666284-48667078 Neighboring gene translation regulatory long non-coding RNA 1 Neighboring gene uncharacterized LOC105372655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48671143-48671728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18082 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:48681498-48681675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48689593-48690102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48690103-48690612 Neighboring gene PEDS1-UBE2V1 readthrough Neighboring gene ubiquitin conjugating enzyme E2 V1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:48715799-48716462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18083 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:48730039-48730606 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:48732458-48732614

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_200539.1 

    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
    50041395..50041594
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    51811013..51811212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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