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LOC130065923 ATAC-STARR-seq lymphoblastoid active region 17918 [ Homo sapiens (human) ]

Gene ID: 130065923, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065923
Gene description
ATAC-STARR-seq lymphoblastoid active region 17918
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 LOC130065923 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 (43950575..43950664)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45683741..45683830)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42579215..42579304)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904908 Neighboring gene long intergenic non-protein coding RNA 1728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543229-42543946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543947-42544664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42564724-42565224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42565225-42565725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42571264-42571764 Neighboring gene TOX high mobility group box family member 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:42583279-42584478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42584612-42585246 Neighboring gene Sharpr-MPRA regulatory region 6747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42634840-42635340 Neighboring gene RNA, 7SL, cytoplasmic 443, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42696545-42697061 Neighboring gene Sharpr-MPRA regulatory region 7745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42739928-42740441 Neighboring gene Sharpr-MPRA regulatory region 3924 Neighboring gene junctophilin 2 Neighboring gene uncharacterized LOC124904909 Neighboring gene JPH2 intron CAGE-defined T cell enhancer

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_200340.1 

    Range
    101..190
    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
    43950575..43950664
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    45683741..45683830
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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