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LOC130063017 ATAC-STARR-seq lymphoblastoid active region 13644 [ Homo sapiens (human) ]

Gene ID: 130063017, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063017
Gene description
ATAC-STARR-seq lymphoblastoid active region 13644
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 LOC130063017 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2071825..2071874)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2044879..2044928)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2071824..2071873)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985278 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:2028556-2029190 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2035637-2036137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2037698-2038472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9759 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2046519-2047019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2047523-2048180 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2048181-2048837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2049495-2050151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9761 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2053416-2053640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2058351-2059250 Neighboring gene MAPK interacting serine/threonine kinase 2 Neighboring gene CRISPRi-validated cis-regulatory element chr19.488 Neighboring gene CRISPRi-validated cis-regulatory element chr19.489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2061953-2062851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2085331-2086056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2089069-2090031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13654 Neighboring gene MOB kinase activator 3A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096431-2096958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096959-2097484 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2104508-2104680 Neighboring gene IZUMO family member 4 Neighboring gene adaptor related protein complex 3 subunit delta 1 Neighboring gene MPRA-validated peak3230 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2141381-2141538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2144918-2145541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2145542-2146164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13657 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2150717-2150878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13658 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2151574-2152011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9770 Neighboring gene DOT1 like histone lysine methyltransferase

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_197434.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    2071825..2071874
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2044879..2044928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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