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LOC129995905 ATAC-STARR-seq lymphoblastoid active region 24100 [ Homo sapiens (human) ]

Gene ID: 129995905, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995905
Gene description
ATAC-STARR-seq lymphoblastoid active region 24100
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 LOC129995905 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16305580..16305699)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (16178135..16178254)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (16305811..16305930)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24098 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16215087-16215263 Neighboring gene CRISPRi-validated cis-regulatory element chr6.847 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16217722-16217944 Neighboring gene RNA, U6 small nuclear 1114, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16957 Neighboring gene NANOG hESC enhancer GRCh37_chr6:16259269-16259823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16262581-16263080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:16264120-16264690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16264691-16265260 Neighboring gene Sharpr-MPRA regulatory region 9524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24099 Neighboring gene guanosine monophosphate reductase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16303323-16303902 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16310151-16310359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16320601-16321434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16327606-16328166 Neighboring gene ataxin 1 repeat instability region Neighboring gene uncharacterized LOC127903862 Neighboring gene Sharpr-MPRA regulatory region 3581 Neighboring gene ataxin 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16387334-16387547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24111 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16603501-16603686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16672541-16673042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16723974-16724586 Neighboring gene HNF1 motif-containing MPRA enhancer 207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16962 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16761792-16762007 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:16762145-16763344 Neighboring gene ATXN1 antisense RNA 1

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_175351.1 

    Range
    101..220
    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
    16305580..16305699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    16178135..16178254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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