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LOC130007623 ATAC-STARR-seq lymphoblastoid active region 6158 [ Homo sapiens (human) ]

Gene ID: 130007623, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007623
Gene description
ATAC-STARR-seq lymphoblastoid active region 6158
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 LOC130007623 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (30695759..30696258)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (30570422..30570921)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (30848693..30849192)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene transmembrane O-mannosyltransferase targeting cadherins 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30637986-30638520 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28085 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28118 Neighboring gene uncharacterized LOC105369719 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30756793-30757482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30757483-30758172 Neighboring gene importin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4321 Neighboring gene caprin family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4322 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:30909210-30909413 Neighboring gene uncharacterized LOC645485

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_188245.1 

    Range
    101..600
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    30695759..30696258
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    30570422..30570921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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