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LOC129934440 ATAC-STARR-seq lymphoblastoid silent region 11811 [ Homo sapiens (human) ]

Gene ID: 129934440, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934440
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11811
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 LOC129934440 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 (99489642..99489741)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (99948298..99948397)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (100106104..100106203)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99952564-99953104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99953733-99954234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99954235-99954734 Neighboring gene thioredoxin domain containing 9 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:100019841-100021040 Neighboring gene eukaryotic translation initiation factor 5B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11809 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:100056357-100057026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:100092059-100092722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:100106417-100107302 Neighboring gene REV1 DNA directed polymerase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100146131-100146758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100170377-100170925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100170926-100171473 Neighboring gene NANOG hESC enhancer GRCh37_chr2:100171857-100172363 Neighboring gene NANOG hESC enhancer GRCh37_chr2:100188674-100189175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100218069-100218631 Neighboring gene ALF transcription elongation factor 3 Neighboring gene uncharacterized LOC124906051 Neighboring gene uncharacterized LOC105373504

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_167457.1 

    Range
    101..200
    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
    99489642..99489741
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    99948298..99948397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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