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LOC129933074 ATAC-STARR-seq lymphoblastoid silent region 11141 [ Homo sapiens (human) ]

Gene ID: 129933074, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933074
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11141
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 LOC129933074 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 (9778028..9778157)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (9805936..9806065)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (9918157..9918286)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15293 Neighboring gene RNA, U4 small nuclear 73, pseudogene Neighboring gene uncharacterized LOC124905969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9893196-9893982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9893983-9894769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9896844-9897366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9897367-9897889 Neighboring gene uncharacterized LOC100996549 Neighboring gene Sharpr-MPRA regulatory region 12215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9905902-9906452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9910317-9911245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9911246-9912173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:9939945-9940780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9940781-9941616 Neighboring gene uncharacterized LOC105373421 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:9949571-9950071 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:9959896-9961095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:9970201-9970740 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:9974742-9974950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11144 Neighboring gene TATA-box binding protein associated factor, RNA polymerase I subunit B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10057557-10058058 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10073172-10073377

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_166099.1 

    Range
    101..230
    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
    9778028..9778157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    9805936..9806065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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