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LOC129934748 ATAC-STARR-seq lymphoblastoid silent region 11948 [ Homo sapiens (human) ]

Gene ID: 129934748, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934748
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11948
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 LOC129934748 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (128317877..128318106)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (128753826..128754055)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (129075451..129075680)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128994251-128994793 Neighboring gene ribosomal protein L21 pseudogene 34 Neighboring gene NANOG hESC enhancer GRCh37_chr2:128999497-129000000 Neighboring gene uncharacterized LOC124907886 Neighboring gene Sharpr-MPRA regulatory region 14953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129019563-129020132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129020147-129020648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129028169-129028830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129028831-129029492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129042083-129042912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129045407-129046236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129052695-129053244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129057516-129058114 Neighboring gene heparan sulfate 6-O-sulfotransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129058115-129058712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129058713-129059311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16511 Neighboring gene Sharpr-MPRA regulatory region 5144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129067670-129068650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129068651-129069632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129080477-129081409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129102864-129103364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129119009-129119548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129119549-129120087 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129120088-129120626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129124244-129124934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129125695-129126536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129132078-129132952 Neighboring gene uncharacterized LOC105373610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129142763-129143262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129146579-129147236 Neighboring gene uncharacterized LOC105373611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129165673-129166670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129166671-129167666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129195850-129196350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129196351-129196851 Neighboring gene RNA, 5S ribosomal pseudogene 103

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_167765.1 

    Range
    101..330
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    128317877..128318106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    128753826..128754055
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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