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LOC128559983 MPRA functional variant 6:109625879:G:A red blood cell enhancer [ Homo sapiens (human) ]

Gene ID: 128559983, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128559983
Gene description
MPRA functional variant 6:109625879:G:A red blood cell enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents a red blood cell enhancer that was functionally validated by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. It includes rs1546723, an MPRA functional variant (MFV) that affects enhancer activity. Deletions encompassing the MFV, which were obtained by CRISPR/Cas9 editing, indicate this region is a positively-acting cis-regulatory element for the CD164 (CD164 molecule), FIG4 (FIG4 phosphoinositide 5-phosphatase) and FOXO3 (forkhead box O3) genes in K562 cells. [provided by RefSeq, Feb 2023]
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Genomic context

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See LOC128559983 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109304580..109304724)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110482617..110482761)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:109612245-109613444 Neighboring gene small nucleolar RNA U13 Neighboring gene patched domain containing 3 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109625443-109625633 Neighboring gene RNY3 pseudogene 11 Neighboring gene ribosomal protein L7 pseudogene 28

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. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Ulirsch JC, et al. Cell, 2016 Jun 2. PMID 27259154, Free PMC Article
  2. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, 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

General gene information

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Other Names

  • CRISPRi-validated CD164, FIG4 and FOXO3 regulatory element

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_149607.1 

    Range
    101..245
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    109304580..109304724
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    110482617..110482761
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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