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LOC129995245 ATAC-STARR-seq lymphoblastoid silent region 16610 [ Homo sapiens (human) ]

Gene ID: 129995245, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995245
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16610
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC129995245 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (171419714..171419823)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (171960044..171960153)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (170846718..170846827)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170820663-170821170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170823373-170824094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170824095-170824816 Neighboring gene microRNA 3912 Neighboring gene nucleophosmin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170861243-170861778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170864190-170864698 Neighboring gene fibroblast growth factor 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170872656-170873222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170877967-170878538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170881203-170881704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170888154-170889127 Neighboring gene uncharacterized LOC105377721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170906189-170907025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170907026-170907861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170920637-170921484 Neighboring gene uncharacterized LOC105377720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170946153-170946685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170946686-170947219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170947220-170947752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170949355-170949886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170955957-170956456 Neighboring gene uncharacterized LOC105377722 Neighboring gene uncharacterized LOC107986392

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_174691.1 

    Range
    101..210
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    171419714..171419823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    171960044..171960153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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