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LOC130001222 ATAC-STARR-seq lymphoblastoid active region 28001 [ Homo sapiens (human) ]

Gene ID: 130001222, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001222
Gene description
ATAC-STARR-seq lymphoblastoid active region 28001
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 LOC130001222 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (133500761..133500850)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (134624605..134624694)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (134513004..134513093)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:134420089-134420640 Neighboring gene DPPA3 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:134434961-134435460 Neighboring gene ST13, Hsp70 interacting protein pseudogene 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:134461533-134461691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:134465210-134465710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:134465711-134466211 Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:134500724-134501507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:134502985-134503530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:134512049-134512574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:134513872-134514372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_101228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28003 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:134544558-134545408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_101271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:134581917-134582770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19566 Neighboring gene ST3GAL1 divergent transcript Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_101278 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:134643666-134643864 Neighboring gene small nucleolar RNA SNORA40

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_180668.1 

    Range
    101..190
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    133500761..133500850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    134624605..134624694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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