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LOC129996357 ATAC-STARR-seq lymphoblastoid silent region 17153 [ Homo sapiens (human) ]

Gene ID: 129996357, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996357
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17153
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 LOC129996357 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 (37705576..37705835)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37530591..37530850)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37673352..37673611)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37551989-37552662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37552663-37553335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17144 Neighboring gene MAM domain containing glycosylphosphatidylinositol anchor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37663553-37664282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37664283-37665012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37695835-37696335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37717757-37718578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37730195-37730696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37744227-37744777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37744845-37745776 Neighboring gene Sharpr-MPRA regulatory regions 13021 and 15353 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24480 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37787069-37787871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17156 Neighboring gene ZFAND3 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 285, pseudogene Neighboring gene zinc finger AN1-type containing 3

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_175803.1 

    Range
    101..360
    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
    37705576..37705835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    37530591..37530850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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