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LOC129933059 ATAC-STARR-seq lymphoblastoid active region 15282 [ Homo sapiens (human) ]

Gene ID: 129933059, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933059
Gene description
ATAC-STARR-seq lymphoblastoid active region 15282
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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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (9608166..9608215)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (9633173..9633222)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (9748295..9748344)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ADAM metallopeptidase domain 17 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15279 Neighboring gene Sharpr-MPRA regulatory region 4047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11136 Neighboring gene Sharpr-MPRA regulatory region 1969 Neighboring gene uncharacterized LOC101929643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15281 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:9769712-9770614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11138 Neighboring gene uncharacterized LOC105373418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9789200-9789709 Neighboring gene NANOG hESC enhancer GRCh37_chr2:9790441-9791022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15287 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:9796459-9796960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15288 Neighboring gene NANOG hESC enhancer GRCh37_chr2:9797816-9798376 Neighboring gene uncharacterized LOC105373419 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:9832275-9833074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15290 Neighboring gene RNA, U4 small nuclear 73, pseudogene

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_166084.1 

    Range
    101..150
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    9608166..9608215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    9633173..9633222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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