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LOC130000197 ATAC-STARR-seq lymphoblastoid active region 27225 [ Homo sapiens (human) ]

Gene ID: 130000197, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000197
Gene description
ATAC-STARR-seq lymphoblastoid active region 27225
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 LOC130000197 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 (37416855..37416934)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (37692183..37692262)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (37274373..37274452)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100507403 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:37188590-37189789 Neighboring gene uncharacterized LOC124901930 Neighboring gene VISTA enhancer hs302 Neighboring gene long intergenic non-protein coding RNA 1605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37310647-37311224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37374880-37375400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37375401-37375919 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:37378682-37379881 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37387319-37387531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37400987-37401487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37404685-37405219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37405335-37405836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37405837-37406336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37413320-37413920 Neighboring gene uncharacterized LOC105379379 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37417549-37418050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37418051-37418550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37438583-37439182 Neighboring gene uncharacterized LOC105379378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37439183-37439782

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_179643.1 

    Range
    101..180
    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
    37416855..37416934
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    37692183..37692262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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