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LOC130007780 ATAC-STARR-seq lymphoblastoid active region 6273 [ Homo sapiens (human) ]

Gene ID: 130007780, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007780
Gene description
ATAC-STARR-seq lymphoblastoid active region 6273
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 LOC130007780 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 (47883191..47883300)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47844589..47844698)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48276974..48277083)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902926 Neighboring gene histone deacetylase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48211237-48211897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48212615-48213188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4403 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48214527-48215448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6269 Neighboring gene long intergenic non-protein coding RNA 2354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48236992-48237565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48237566-48238138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48239663-48240164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48262276-48262776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6271 Neighboring gene vitamin D receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48276324-48276836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48329073-48329573 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:48353651-48354181 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:48367908-48368120 Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48375074-48375619 Neighboring gene collagen type II alpha 1 chain

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_188374.1 

    Range
    101..210
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    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
    47883191..47883300
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    47844589..47844698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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