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LOC130066509 ATAC-STARR-seq lymphoblastoid active region 18330 [ Homo sapiens (human) ]

Gene ID: 130066509, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066509
Gene description
ATAC-STARR-seq lymphoblastoid active region 18330
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 LOC130066509 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (29065183..29065292)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (27428624..27428733)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (30437504..30437613)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18327 Neighboring gene RWD domain containing 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18328 Neighboring gene ubiquitin specific peptidase 16 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:30416252-30416450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18329 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:30445041-30445952 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:30445953-30446864 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:30447741-30448940 Neighboring gene chaperonin containing TCP1 subunit 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18333 Neighboring gene MAP3K7 C-terminal like Neighboring gene Sharpr-MPRA regulatory region 4059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13237 Neighboring gene NANOG hESC enhancer GRCh37_chr21:30506062-30506608 Neighboring gene ribosomal protein L12 pseudogene 9 Neighboring gene Sharpr-MPRA regulatory region 14833 Neighboring gene uncharacterized LOC105372767 Neighboring gene small nucleolar RNA U3

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_200926.1 

    Range
    101..210
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    29065183..29065292
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791813.1 Reference GRCh38.p14 PATCHES

    Range
    155917..156026
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    27428624..27428733
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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