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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1048456

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr5:141641152 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FCHSD1 : Non Coding Transcript Variant
RELL2 : 500B Downstream Variant
Publications
3 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 5 NC_000005.10:g.141641152T>G
GRCh37.p13 chr 5 NC_000005.9:g.141020719T>G
HDAC3 RefSeqGene NG_029678.1:g.705A>C
Gene: FCHSD1, FCH and double SH3 domains 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FCHSD1 transcript NM_033449.2:c. N/A 3 Prime UTR Variant
FCHSD1 transcript variant X1 XM_005268524.4:c. N/A 3 Prime UTR Variant
FCHSD1 transcript variant X3 XM_006714803.3:c. N/A 3 Prime UTR Variant
FCHSD1 transcript variant X4 XM_011537698.2:c. N/A 3 Prime UTR Variant
FCHSD1 transcript variant X7 XM_011537700.2:c. N/A Genic Downstream Transcript Variant
FCHSD1 transcript variant X10 XM_011537701.2:c. N/A Genic Downstream Transcript Variant
FCHSD1 transcript variant X2 XM_017010013.1:c. N/A Genic Downstream Transcript Variant
FCHSD1 transcript variant X9 XR_001742323.1:n....

XR_001742323.1:n.2821A>C

N/A Non Coding Transcript Variant
FCHSD1 transcript variant X8 XR_427781.3:n. N/A Genic Downstream Transcript Variant
FCHSD1 transcript variant X5 XR_944338.2:n. N/A Genic Downstream Transcript Variant
FCHSD1 transcript variant X6 XR_944339.2:n. N/A Genic Downstream Transcript Variant
Gene: RELL2, RELT like 2 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
RELL2 transcript variant 2 NM_001130029.1:c. N/A Downstream Transcript Variant
RELL2 transcript variant 1 NM_173828.4:c. N/A Downstream Transcript Variant
RELL2 transcript variant X1 XM_005268414.3:c. N/A Downstream Transcript Variant
RELL2 transcript variant X2 XM_011537624.1:c. N/A Downstream Transcript Variant
RELL2 transcript variant X3 XM_011537625.2:c. N/A Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= G Note
GRCh38.p7 chr 5 NC_000005.10:g.141641152T= NC_000005.10:g.14164115...

NC_000005.10:g.141641152T>G

GRCh37.p13 chr 5 NC_000005.9:g.141020719T= NC_000005.9:g.141020719T>G
HDAC3 RefSeqGene NG_029678.1:g.705A= NG_029678.1:g.705A>C
FCHSD1 transcript variant X1 XM_005268524.4:c.*346A= XM_005268524.4:c.*346A>C
FCHSD1 transcript variant X1 XM_005268524.1:c.*346A= XM_005268524.1:c.*346A>C
FCHSD1 transcript variant X3 XM_006714803.3:c.*346A= XM_006714803.3:c.*346A>C
FCHSD1 transcript NM_033449.2:c.*346A= NM_033449.2:c.*346A>C
FCHSD1 transcript variant X4 XM_011537698.2:c.*432A= XM_011537698.2:c.*432A>C
FCHSD1 transcript variant X9 XR_001742323.1:n.2821A= XR_001742323.1:n.2821A>C
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 LEE ss1521381 Oct 05, 2000 (86)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss1521381 NT_029289.11:2183645:T= NC_000005.10:141641151:T= (self)
ss1521381 NT_029289.11:2183645:T>G NC_000005.10:141641151:T>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs1048456
PMID Title Author Year Journal
21533074 GWAS of follicular lymphoma reveals allelic heterogeneity at 6p21.32 and suggests shared genetic susceptibility with diffuse large B-cell lymphoma. Smedby KE et al. 2011 PLoS genetics
21658613 Host genetics in follicular lymphoma. Cerhan JR et al. 2011 Best practice & research. Clinical haematology
24707947 Genetic markers in a multi-ethnic sample for childhood acute lymphoblastic leukemia risk. Kennedy AE et al. 2015 Leukemia & lymphoma

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e