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LOC129932026 ATAC-STARR-seq lymphoblastoid silent region 1604 [ Homo sapiens (human) ]

Gene ID: 129932026, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932026
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1604
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 LOC129932026 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (181089419..181089638)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (180444478..180444697)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (181058555..181058774)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2170 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:181014030-181014179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:181015297-181015799 Neighboring gene major histocompatibility complex, class I-related Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181046610-181047144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181047145-181047678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1601 Neighboring gene uncharacterized LOC124904465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2173 Neighboring gene Sharpr-MPRA regulatory region 8031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181065969-181066485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:181074489-181075383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1605 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:181080957-181082156 Neighboring gene immediate early response 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2179 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:181103703-181104902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2181 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:181110258-181110758 and GRCh37_chr1:181110759-181111259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1608 Neighboring gene VISTA enhancer hs1862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2184 Neighboring gene Sharpr-MPRA regulatory region 5219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181151125-181151624 Neighboring gene long intergenic non-protein coding RNA 1732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181176185-181177094 Neighboring gene long intergenic non-protein coding RNA 1699

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_165068.1 

    Range
    101..320
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    181089419..181089638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    180444478..180444697
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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