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LOC129935102 ATAC-STARR-seq lymphoblastoid active region 16756 [ Homo sapiens (human) ]

Gene ID: 129935102, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129935102
Gene description
ATAC-STARR-seq lymphoblastoid active region 16756
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 LOC129935102 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (171433224..171433393)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (171910364..171910533)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373737 Neighboring gene small integral membrane protein 26-like Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:172172370-172173192 Neighboring gene Sharpr-MPRA regulatory region 707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16746 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:172174870-172175072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16747 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172175660-172176482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16748 Neighboring gene Sharpr-MPRA regulatory region 8774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16750 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:172183340-172183864 Neighboring gene methyltransferase 8, tRNA N3-cytidine Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172242874-172243458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172243459-172244043 Neighboring gene ribosomal protein S26 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16755 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr2:172289881-172290441 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172291003-172291562 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:172303768-172303972 Neighboring gene DDB1 and CUL4 associated factor 17 Neighboring gene death associated protein 3 pseudogene 2

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

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_168118.1 

    Range
    101..270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    171433224..171433393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    171910364..171910533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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