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LOC130059569 ATAC-STARR-seq lymphoblastoid active region 11235 [ Homo sapiens (human) ]

Gene ID: 130059569, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059569
Gene description
ATAC-STARR-seq lymphoblastoid active region 11235
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 LOC130059569 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84511246..84511295)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90577563..90577612)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84544852..84544901)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:84512589-84513788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84516869-84517370 Neighboring gene MTOR associated protein, eak-7 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84537675-84538175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84538296-84539243 Neighboring gene uncharacterized LOC124903736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7783 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84540344-84540580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84540853-84541353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84543104-84543903 Neighboring gene uncharacterized LOC124903735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84547599-84548206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84557586-84558169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84558170-84558754 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84565033-84565246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84565360-84566037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84566038-84566716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84566717-84567393 Neighboring gene Sharpr-MPRA regulatory region 4738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84577753-84578254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84578255-84578754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84580244-84580995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84580996-84581746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84582498-84583247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84589034-84589534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84593245-84593762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84594827-84595594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84595595-84596362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84605929-84606461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84617304-84617809 Neighboring gene coactosin like F-actin binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84623933-84624432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631141-84631642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631643-84632142 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84632885-84633706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11245 Neighboring gene Sharpr-MPRA regulatory region 4329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84637045-84637609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647291-84647792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647793-84648292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84674539-84675097 Neighboring gene uncharacterized LOC105371376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7789 Neighboring gene kelch like family member 36

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_193990.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    84511246..84511295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90577563..90577612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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