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LOC129996183 ATAC-STARR-seq lymphoblastoid active region 24368 [ Homo sapiens (human) ]

Gene ID: 129996183, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996183
Gene description
ATAC-STARR-seq lymphoblastoid active region 24368
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 LOC129996183 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 (33711220..33711269)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33532403..33532452)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33678997..33679046)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33602349-33602895 Neighboring gene inositol 1,4,5-trisphosphate receptor type 3 Neighboring gene ITPR3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33618418-33618918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33618919-33619419 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33624122-33624658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33625731-33626265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33626906-33627416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33636045-33636676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33636677-33637307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33641013-33641534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33658493-33659470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33659471-33660446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33660447-33661424 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:33662237-33663436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33665333-33666308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33672165-33672664 Neighboring gene microRNA 3934 Neighboring gene uncharacterized LOC124901304 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33678073-33678970 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 2 Neighboring gene Sharpr-MPRA regulatory region 11056 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:33692274-33693024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33695430-33696209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33696210-33696988 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33703405-33703659 Neighboring gene inositol hexakisphosphate kinase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33710674-33711363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33711622-33712515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33712516-33713408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33713409-33714302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33718585-33719144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33719703-33720261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33728947-33729550 Neighboring gene Sharpr-MPRA regulatory region 8162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33740622-33741320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33747376-33748316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33748317-33749256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33750197-33751135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:33755871-33756420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17057 Neighboring gene LEM domain nuclear envelope protein 2

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_175629.1 

    Range
    101..150
    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
    33711220..33711269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33532403..33532452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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