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LOC129934418 ATAC-STARR-seq lymphoblastoid active region 16268 [ Homo sapiens (human) ]

Gene ID: 129934418, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934418
Gene description
ATAC-STARR-seq lymphoblastoid active region 16268
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 LOC129934418 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (98549075..98549164)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (99007382..99007471)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (99165538..99165627)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene von Willebrand factor A domain containing 3B Neighboring gene ATP synthase F1 subunit beta pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98896664-98897164 Neighboring gene NANOG hESC enhancer GRCh37_chr2:98933593-98934329 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:98950857-98951787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98963419-98963930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98993983-98994750 Neighboring gene Sharpr-MPRA regulatory region 13649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98998693-98999270 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:98999847-99000424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99000425-99001000 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99004561-99004748 Neighboring gene cyclic nucleotide gated channel subunit alpha 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16257 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:99051832-99053031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16260 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99079757-99080272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99082317-99082881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16265 Neighboring gene inositol polyphosphate-4-phosphatase type I A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136086-99136586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136587-99137087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99170837-99171337 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99176784-99176955 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99190711-99190893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99200423-99200924 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99209219-99209372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16269 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99224127-99225116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11802 Neighboring gene cytochrome c oxidase assembly factor 5 Neighboring gene unc-50 inner nuclear membrane RNA binding protein

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_167435.1 

    Range
    101..190
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    98549075..98549164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    99007382..99007471
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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