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LOC129995685 ATAC-STARR-seq lymphoblastoid active region 23914 [ Homo sapiens (human) ]

Gene ID: 129995685, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995685
Gene description
ATAC-STARR-seq lymphoblastoid active region 23914
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: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5778518..5778707)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (5647904..5648093)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene phenylalanyl-tRNA synthetase 2, mitochondrial Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23910 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:5639236-5640099 Neighboring gene uncharacterized LOC101927950 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5665450-5666649 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5672975-5673971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:5737751-5738252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5783313-5783996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5783997-5784680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5804076-5804576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5804577-5805077 Neighboring gene uncharacterized LOC124901250 Neighboring gene ribosomal protein L34 pseudogene 16

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_175131.1 

    Range
    101..290
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    5778518..5778707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    5647904..5648093
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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