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LOC129997429 ATAC-STARR-seq lymphoblastoid silent region 17661 [ Homo sapiens (human) ]

Gene ID: 129997429, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997429
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17661
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 LOC129997429 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 (149474628..149474727)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (150674335..150674434)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (149795764..149795863)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25253 Neighboring gene fatty acid binding protein 12 pseudogene 1 Neighboring gene MPRA-validated peak6211 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25254 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:149699707-149700906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149746425-149746924 Neighboring gene small ubiquitin like modifier 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:149753111-149753397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149761776-149762690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149772303-149772854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149772855-149773406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25256 Neighboring gene zinc finger CCCH-type containing 12D Neighboring gene ReSE screen-validated silencer GRCh37_chr6:149794343-149794528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149802875-149803730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149805477-149806341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149817836-149818336 Neighboring gene coiled-coil domain containing 59 pseudogene Neighboring gene peptidylprolyl isomerase like 4 Neighboring gene RNA, U7 small nuclear 3 pseudogene

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_176875.1 

    Range
    101..200
    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
    149474628..149474727
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    150674335..150674434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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