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LOC130004843 ATAC-STARR-seq lymphoblastoid active region 4120 [ Homo sapiens (human) ]

Gene ID: 130004843, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004843
Gene description
ATAC-STARR-seq lymphoblastoid active region 4120
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 LOC130004843 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (119478074..119478143)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (120373656..120373725)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (121237586..121237655)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor kinase 5 Neighboring gene uncharacterized LOC105378511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121100806-121101398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121100212-121100805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121108919-121109420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121150987-121151487 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:121160908-121162107 Neighboring gene microRNA 4681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121164620-121165120 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121203591-121204381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121210069-121210568 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:121211884-121212060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121214023-121214544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121225296-121225796 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:121239005-121239584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121269325-121269826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:121269827-121270326 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:121274963-121275176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121275942-121276524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4123 Neighboring gene regulator of G protein signaling 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4125 Neighboring gene NANOG hESC enhancer GRCh37_chr10:121303486-121303994 Neighboring gene uncharacterized LOC105378512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121355707-121356705 Neighboring gene TIA1 cytotoxic granule associated RNA binding protein like 1

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_184288.1 

    Range
    101..170
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    119478074..119478143
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    120373656..120373725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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