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LOC129934201 ATAC-STARR-seq lymphoblastoid active region 16117 [ Homo sapiens (human) ]

Gene ID: 129934201, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934201
Gene description
ATAC-STARR-seq lymphoblastoid active region 16117
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 LOC129934201 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 (85327002..85327181)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (85328993..85329172)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85554125..85554304)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene transcription factor 7 like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85440681-85441182 Neighboring gene uncharacterized LOC102724579 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85442025-85442959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85461879-85462384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85464915-85465420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85465421-85465924 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85482618-85483340 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85483341-85484064 Neighboring gene Sharpr-MPRA regulatory region 427 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85486956-85487677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85489661-85490588 Neighboring gene SNRPE pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85517073-85517573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85521502-85522173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85533336-85533836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85536759-85537642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85540508-85541008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85561675-85562174 Neighboring gene trans-golgi network protein 2 Neighboring gene phosphatidylethanolamine binding protein 1 pseudogene 2 Neighboring gene retinol saturase

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_167224.1 

    Range
    101..280
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    85327002..85327181
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791763.1 Reference GRCh38.p14 PATCHES

    Range
    253240..253419
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    85328993..85329172
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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