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LOC120961748 Sharpr-MPRA regulatory region 13941 [ Homo sapiens (human) ]

Gene ID: 120961748, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120961748
Gene description
Sharpr-MPRA regulatory region 13941
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (42495009..42495303)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (42500448..42500742)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (42722149..42722443)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel modifier subfamily G member 3 Neighboring gene voltage dependent anion channel 1 pseudogene 13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42719309-42720066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42720067-42720824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11406 Neighboring gene ribosomal protein S13 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42752168-42752668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42752669-42753169 Neighboring gene metastasis associated 1 family member 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:42772737-42773623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42774519-42775024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42798824-42799350 Neighboring gene uncharacterized LOC105374555 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42833249-42834000 Neighboring gene MPRA-validated peak3682 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:42881137-42881638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15651 Neighboring gene Sharpr-MPRA regulatory region 10188 Neighboring gene RNA, U6 small nuclear 137, 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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_073965.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    42495009..42495303
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    42500448..42500742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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