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LOC129995777 ATAC-STARR-seq lymphoblastoid active region 23999 [ Homo sapiens (human) ]

Gene ID: 129995777, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995777
Gene description
ATAC-STARR-seq lymphoblastoid active region 23999
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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (11938553..11938612)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (11806687..11806746)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986567 Neighboring gene uncharacterized LOC124901257 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11834142-11834332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23994 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11838380-11838562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23997 Neighboring gene uncharacterized LOC102724379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23998 Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 316 Neighboring gene uncharacterized LOC107986570 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11935862-11936084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24000 Neighboring gene uncharacterized LOC101928253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12010596-12011140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16921 Neighboring gene Sharpr-MPRA regulatory region 4667 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12036533-12037034 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12037035-12037534 Neighboring gene HIVEP zinc finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12099563-12100062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24008 Neighboring gene Sharpr-MPRA regulatory region 8641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12164419-12164919

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

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_175223.1 

    Range
    101..160
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    11938553..11938612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    11806687..11806746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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