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LOC129935698 ATAC-STARR-seq lymphoblastoid active region 17180 [ Homo sapiens (human) ]

Gene ID: 129935698, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935698
Gene description
ATAC-STARR-seq lymphoblastoid active region 17180
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: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (223896759..223896818)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (224380005..224380064)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (224761476..224761535)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17172 Neighboring gene adaptor related protein complex 1 subunit sigma 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17175 Neighboring gene uncharacterized LOC124907988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746345-224746846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746847-224747346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17176 Neighboring gene WD repeat and FYVE domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:224786671-224787171 Neighboring gene general transcription factor IIIA pseudogene 3 Neighboring gene uncharacterized LOC124907989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12378

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_168709.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    223896759..223896818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    224380005..224380064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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