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LOC129933603 ATAC-STARR-seq lymphoblastoid active region 15664 [ Homo sapiens (human) ]

Gene ID: 129933603, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933603
Gene description
ATAC-STARR-seq lymphoblastoid active region 15664
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 LOC129933603 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 (43220161..43220220)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43225528..43225587)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (43447300..43447359)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43360411-43361174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43361175-43361936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367134-43367705 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367706-43368276 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43379975-43380123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43384913-43385431 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43385646-43385841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43394830-43395476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43396769-43397414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43397590-43398275 Neighboring gene uncharacterized LOC124907755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43404972-43405498 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1717 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43407075-43407600 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:43411165-43412364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43412481-43413214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43413949-43414682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43414683-43415416 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43421149-43422068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43437212-43437806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43441787-43442553 Neighboring gene VISTA enhancer hs1909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11423 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43453393-43454356 Neighboring gene ZFP36 ring finger protein like 2 Neighboring gene long intergenic non-protein coding RNA 1126

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_166629.1 

    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
    43220161..43220220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    43225528..43225587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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