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LOC129997585 ATAC-STARR-seq lymphoblastoid silent region 17744 [ Homo sapiens (human) ]

Gene ID: 129997585, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997585
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17744
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 LOC129997585 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 (158818212..158818411)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (160063656..160063855)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (159239244..159239443)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene synaptotagmin like 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159151193-159152392 Neighboring gene AMZ2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159176343-159176927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159180075-159180750 Neighboring gene Sharpr-MPRA regulatory region 4567 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159192487-159192693 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:159193631-159194830 Neighboring gene microRNA 3918 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159205226-159206425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25363 Neighboring gene ezrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159245802-159246776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256297-159256987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256988-159257678 Neighboring gene EZR antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159273679-159274204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274205-159274730 Neighboring gene uncharacterized LOC124901448 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274731-159275254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159275781-159276305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159276306-159276830 Neighboring gene oligosaccharyltransferase complex subunit pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159289820-159290492 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159290493-159291165 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:159291166-159291839 Neighboring gene long intergenic non-protein coding RNA 2901 Neighboring gene MPRA-validated peak6275 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159314985-159315685 Neighboring gene MPRA-validated peak6276 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159331041-159331834

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_177031.1 

    Range
    101..300
    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
    158818212..158818411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    160063656..160063855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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