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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:791414 (GRCh38.p13) 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.

C>G / C>T
Variation Type
SNV Single Nucleotide Variation
G=0.04514 (754/16702, ALFA)
G=0.0280 (140/5008, 1000G)
G=0.0355 (137/3854, ALSPAC) (+ 10 more)
G=0.0380 (141/3708, TWINSUK)
G=0.0005 (1/1832, Korea1K)
G=0.033 (33/998, GoNL)
G=0.030 (18/600, NorthernSweden)
G=0.046 (10/216, Qatari)
G=0.03 (1/40, GENOME_DK)
C=0.50 (18/36, SGDP_PRJ)
G=0.50 (18/36, SGDP_PRJ)
C=0.5 (2/4, Siberian)
G=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Intron Variant
0 citations
Genomic View
See rs on genome

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.p13 chr 1 NC_000001.11:g.791414C>G
GRCh38.p13 chr 1 NC_000001.11:g.791414C>T
GRCh37.p13 chr 1 NC_000001.10:g.726794C>G
GRCh37.p13 chr 1 NC_000001.10:g.726794C>T
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Intron Variant
LINC01409 transcript variant X5 XR_002958525.1:n. N/A Intron Variant
LINC01409 transcript variant X4 XR_946806.3:n. N/A Intron Variant
LINC01409 transcript variant X2 XR_002958523.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X3 XR_002958524.1:n. N/A Genic Upstream Transcript Variant

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

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 16702 C=0.95486 G=0.04514
European Sub 12214 C=0.94801 G=0.05199
African Sub 2864 C=0.9738 G=0.0262
African Others Sub 108 C=0.954 G=0.046
African American Sub 2756 C=0.9746 G=0.0254
Asian Sub 108 C=0.981 G=0.019
East Asian Sub 84 C=0.98 G=0.02
Other Asian Sub 24 C=1.00 G=0.00
Latin American 1 Sub 146 C=0.966 G=0.034
Latin American 2 Sub 610 C=0.982 G=0.018
South Asian Sub 94 C=0.95 G=0.05
Other Sub 666 C=0.968 G=0.032


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").

Study Population Group Sample Size Ref Allele Alt Allele
1000Genomes Global Study-wide 5008 C=0.9720 G=0.0280
1000Genomes African Sub 1322 C=0.9735 G=0.0265
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=0.9563 G=0.0437
1000Genomes South Asian Sub 978 C=0.958 G=0.042
1000Genomes American Sub 694 C=0.971 G=0.029
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9645 G=0.0355
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9620 G=0.0380
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 G=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.967 G=0.033
Northern Sweden ACPOP Study-wide 600 C=0.970 G=0.030
Qatari Global Study-wide 216 C=0.954 G=0.046
The Danish reference pan genome Danish Study-wide 40 C=0.97 G=0.03
SGDP_PRJ Global Study-wide 36 C=0.50 G=0.50
Siberian Global Study-wide 4 C=0.5 G=0.5

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 C= G T
GRCh38.p13 chr 1 NC_000001.11:g.791414= NC_000001.11:g.791414C>G NC_000001.11:g.791414C>T
GRCh37.p13 chr 1 NC_000001.10:g.726794= NC_000001.10:g.726794C>G NC_000001.10:g.726794C>T

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#.

24 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35191878 May 24, 2005 (125)
2 1000GENOMES ss328357211 May 09, 2011 (134)
3 ILLUMINA ss481568668 Sep 08, 2015 (146)
4 SSMP ss647515921 Apr 25, 2013 (138)
5 ILLUMINA ss832928552 Aug 21, 2014 (142)
6 ILLUMINA ss833519382 Aug 21, 2014 (142)
7 EVA-GONL ss974769107 Aug 21, 2014 (142)
8 1000GENOMES ss1289338191 Aug 21, 2014 (142)
9 EVA_GENOME_DK ss1573851072 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1599378247 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1642372280 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1917959849 Feb 12, 2016 (147)
13 USC_VALOUEV ss2147484170 Dec 20, 2016 (150)
14 GNOMAD ss2750634233 Nov 08, 2017 (151)
15 SWEGEN ss2986148067 Nov 08, 2017 (151)
16 TOPMED ss3066391007 Nov 08, 2017 (151)
17 CSHL ss3343272280 Nov 08, 2017 (151)
18 ILLUMINA ss3635978591 Oct 11, 2018 (152)
19 EVA_DECODE ss3685991750 Jul 12, 2019 (153)
20 ACPOP ss3726716039 Jul 12, 2019 (153)
21 EVA ss3745720735 Jul 12, 2019 (153)
22 KHV_HUMAN_GENOMES ss3798743180 Jul 12, 2019 (153)
23 SGDP_PRJ ss3847994128 Apr 25, 2020 (154)
24 KOGIC ss3943628637 Apr 25, 2020 (154)
25 1000Genomes NC_000001.10 - 726794 Oct 11, 2018 (152)
26 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 726794 Oct 11, 2018 (152)
27 The Danish reference pan genome NC_000001.10 - 726794 Apr 25, 2020 (154)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56120 (NC_000001.11:791413:C:G 4813/117410)
Row 56121 (NC_000001.11:791413:C:T 2/117720)

- Apr 25, 2021 (155)
29 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56120 (NC_000001.11:791413:C:G 4813/117410)
Row 56121 (NC_000001.11:791413:C:T 2/117720)

- Apr 25, 2021 (155)
30 Genome of the Netherlands Release 5 NC_000001.10 - 726794 Apr 25, 2020 (154)
31 Korean Genome Project NC_000001.11 - 791414 Apr 25, 2020 (154)
32 Northern Sweden NC_000001.10 - 726794 Jul 12, 2019 (153)
33 Qatari NC_000001.10 - 726794 Apr 25, 2020 (154)
34 SGDP_PRJ NC_000001.10 - 726794 Apr 25, 2020 (154)
35 Siberian NC_000001.10 - 726794 Apr 25, 2020 (154)
36 UK 10K study - Twins NC_000001.10 - 726794 Oct 11, 2018 (152)
37 ALFA NC_000001.11 - 791414 Apr 25, 2021 (155)

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).

Associated ID History Updated (Build)
rs111153806 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35191878 NC_000001.8:766656:C:G NC_000001.11:791413:C:G (self)
2872, 113, 1358306, 219, 904, 1779, 11108, 524, 113, ss328357211, ss481568668, ss647515921, ss832928552, ss833519382, ss974769107, ss1289338191, ss1573851072, ss1599378247, ss1642372280, ss1917959849, ss2147484170, ss2750634233, ss2986148067, ss3343272280, ss3635978591, ss3726716039, ss3745720735, ss3847994128 NC_000001.10:726793:C:G NC_000001.11:791413:C:G (self)
6638, 6403500915, ss3066391007, ss3685991750, ss3798743180, ss3943628637 NC_000001.11:791413:C:G NC_000001.11:791413:C:G (self)
NC_000001.11:791413:C:T NC_000001.11:791413:C:T

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

No publications for rs28454925


The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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: 2.0.1.post596+ae089ad