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LOC130066851 ATAC-STARR-seq lymphoblastoid active region 18590 [ Homo sapiens (human) ]

Gene ID: 130066851, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066851
Gene description
ATAC-STARR-seq lymphoblastoid active region 18590
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 LOC130066851 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 (45470836..45471055)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43836560..43836785)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46890750..46890969)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene collagen type XVIII alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839219-46839973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839974-46840729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46841485-46842239 Neighboring gene COL18A1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844008-46844605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844606-46845204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46847276-46847948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46850948-46851946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46851947-46852943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46854143-46854992 Neighboring gene uncharacterized LOC124905042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46858777-46859506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46859507-46860236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46860237-46860966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46862147-46862656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46870853-46871354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46871355-46871854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46874827-46875383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885176-46885740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885741-46886304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46894762-46895262 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46908672-46909202 Neighboring gene microRNA 6815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46912122-46912622 Neighboring gene solute carrier family 19 member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46934825-46935332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46935840-46936346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18591 Neighboring gene Sharpr-MPRA regulatory region 1559 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46948644-46948814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46954106-46954980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46962482-46962994 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46970045-46970201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46975660-46976554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46980259-46980968

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_201266.1 

    Range
    101..320
    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
    45470836..45471055
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791815.1 Reference GRCh38.p14 PATCHES

    Range
    88071..88290
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43836560..43836785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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