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LOC129995807 ATAC-STARR-seq lymphoblastoid silent region 16928 [ Homo sapiens (human) ]

Gene ID: 129995807, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995807
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16928
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 LOC129995807 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (13355616..13355705)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13228856..13228945)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (13355848..13355937)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901261 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13328608-13329114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16927 Neighboring gene uncharacterized LOC105374936 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16929 Neighboring gene MPRA-validated peak5665 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24025 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:13422205-13422994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13461923-13462595 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:13462671-13463323 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:13463324-13463975 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:13466168-13467367 Neighboring gene Sharpr-MPRA regulatory region 12646 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:13479720-13480919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24032 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:13487020-13487183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16931 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24034 Neighboring gene GFOD1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24035 Neighboring gene ribosomal protein S4X pseudogene 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_175253.1 

    Range
    101..190
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    13355616..13355705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13228856..13228945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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