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LOC129934262 ATAC-STARR-seq lymphoblastoid active region 16165 [ Homo sapiens (human) ]

Gene ID: 129934262, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934262
Gene description
ATAC-STARR-seq lymphoblastoid active region 16165
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 LOC129934262 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86784193..86784292)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86786092..86786191)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (87011316..87011415)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNF103-CHMP3 readthrough Neighboring gene uncharacterized LOC124907853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86859935-86860458 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:86921806-86923005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:86946607-86947140 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86947334-86947492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952106-86952606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952607-86953107 Neighboring gene required for meiotic nuclear division 5 homolog A Neighboring gene CD8A intronic regulatory region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:87016737-87017571 Neighboring gene uncharacterized LOC105374846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11721 Neighboring gene MPRA-validated peak3783 silencer Neighboring gene CD8 subunit alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87066785-87067341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083199-87083700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083701-87084200 Neighboring gene CD8 subunit beta Neighboring gene ANAPC1 pseudogene 1

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 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_167282.1 

    Range
    101..200
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    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
    86784193..86784292
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86786092..86786191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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