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LOC130066748 ATAC-STARR-seq lymphoblastoid active region 18521 [ Homo sapiens (human) ]

Gene ID: 130066748, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066748
Gene description
ATAC-STARR-seq lymphoblastoid active region 18521
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 LOC130066748 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42478465..42478534)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40868180..40868249)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43898575..43898644)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43792792-43793740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43796799-43797369 Neighboring gene transmembrane serine protease 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43808797-43809682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18513 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:43814254-43815453 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:43834765-43835964 Neighboring gene ubiquitin associated and SH3 domain containing A Neighboring gene RNA, U6 small nuclear 1149, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43857898-43858585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43858586-43859272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43883987-43884498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18518 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:43887967-43889166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18520 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43912470-43913669 Neighboring gene radial spoke head component 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43919416-43919916 Neighboring gene RSPH1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43932366-43933088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43933089-43933811 Neighboring gene solute carrier family 37 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43940701-43941202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43941203-43941702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18523 Neighboring gene uncharacterized LOC107987299

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_201164.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    42478465..42478534
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    40868180..40868249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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