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LOC130061569 ATAC-STARR-seq lymphoblastoid active region 12683 [ Homo sapiens (human) ]

Gene ID: 130061569, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061569
Gene description
ATAC-STARR-seq lymphoblastoid active region 12683
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 LOC130061569 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72992867..72992956)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (73880700..73880789)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70989006..70989095)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:70662937-70663580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70663581-70664223 Neighboring gene solute carrier family 39 member 11 Neighboring gene RN7SK pseudogene 180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:70682597-70683097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70715406-70716084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70716085-70716762 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:70717445-70717660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8917 Neighboring gene Sharpr-MPRA regulatory region 3582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70738945-70739482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70739483-70740019 Neighboring gene small Cajal body-specific RNA 24 Neighboring gene Sharpr-MPRA regulatory region 3335 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:70943638-70944837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70947920-70948848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70948849-70949777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70950549-70951109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70949987-70950548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70974043-70974543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12684 Neighboring gene Sharpr-MPRA regulatory region 7306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71085784-71086284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71086285-71086785 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:71087756-71087987 Neighboring gene autophagy related 12 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:71128061-71128610 Neighboring gene MPRA-validated peak2987 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12687 Neighboring gene RNA polymerase III subunit K 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

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_196718.1 

    Range
    101..190
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    72992867..72992956
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    73880700..73880789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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