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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
chr1:790009 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
T=0.09857 (1652/16760, 8.3KJPN)
T=0.01797 (276/15360, ALFA)
T=0.0363 (182/5008, 1000G) (+ 9 more)
T=0.0355 (137/3854, ALSPAC)
T=0.0372 (138/3708, TWINSUK)
T=0.036 (36/998, GoNL)
T=0.030 (18/600, NorthernSweden)
T=0.046 (10/216, Qatari)
C=0.50 (24/48, SGDP_PRJ)
T=0.50 (24/48, SGDP_PRJ)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, 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.790009C>A
GRCh38.p13 chr 1 NC_000001.11:g.790009C>T
GRCh37.p13 chr 1 NC_000001.10:g.725389C>A
GRCh37.p13 chr 1 NC_000001.10:g.725389C>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 15360 C=0.98203 A=0.00000, T=0.01797
European Sub 11350 C=0.97577 A=0.00000, T=0.02423
African Sub 2666 C=1.0000 A=0.0000, T=0.0000
African Others Sub 98 C=1.00 A=0.00, T=0.00
African American Sub 2568 C=1.0000 A=0.0000, T=0.0000
Asian Sub 98 C=1.00 A=0.00, T=0.00
East Asian Sub 74 C=1.00 A=0.00, T=0.00
Other Asian Sub 24 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 136 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 584 C=1.000 A=0.000, T=0.000
South Asian Sub 84 C=1.00 A=0.00, T=0.00
Other Sub 442 C=0.998 A=0.000, T=0.002


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
8.3KJPN JAPANESE Study-wide 16760 C=0.90143 T=0.09857
1000Genomes Global Study-wide 5008 C=0.9637 T=0.0363
1000Genomes African Sub 1322 C=0.9728 T=0.0272
1000Genomes East Asian Sub 1008 C=0.9623 T=0.0377
1000Genomes Europe Sub 1006 C=0.9553 T=0.0447
1000Genomes South Asian Sub 978 C=0.956 T=0.044
1000Genomes American Sub 694 C=0.971 T=0.029
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9645 T=0.0355
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9628 T=0.0372
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.964 T=0.036
Northern Sweden ACPOP Study-wide 600 C=0.970 T=0.030
Qatari Global Study-wide 216 C=0.954 T=0.046
SGDP_PRJ Global Study-wide 48 C=0.50 T=0.50
Siberian Global Study-wide 12 C=0.50 T=0.50

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= A T
GRCh38.p13 chr 1 NC_000001.11:g.790009= NC_000001.11:g.790009C>A NC_000001.11:g.790009C>T
GRCh37.p13 chr 1 NC_000001.10:g.725389= NC_000001.10:g.725389C>A NC_000001.10:g.725389C>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#.

19 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSMP ss647515902 Apr 25, 2013 (138)
2 EVA-GONL ss974769100 Aug 21, 2014 (142)
3 1000GENOMES ss1289338146 Aug 21, 2014 (142)
4 EVA_UK10K_ALSPAC ss1599378245 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1642372278 Apr 01, 2015 (144)
6 PADH-LAB_SPU ss1751134732 Sep 08, 2015 (146)
7 WEILL_CORNELL_DGM ss1917959824 Feb 12, 2016 (147)
8 JJLAB ss2019498281 Sep 14, 2016 (149)
9 USC_VALOUEV ss2147483996 Dec 20, 2016 (150)
10 GRF ss2697374180 Nov 08, 2017 (151)
11 GNOMAD ss2750633864 Nov 08, 2017 (151)
12 SWEGEN ss2986147906 Nov 08, 2017 (151)
13 TOPMED ss3066390457 Nov 08, 2017 (151)
14 TOPMED ss3066390458 Nov 08, 2017 (151)
15 CSHL ss3343272254 Nov 08, 2017 (151)
16 ACPOP ss3726716029 Jul 12, 2019 (153)
17 KHV_HUMAN_GENOMES ss3798743165 Jul 12, 2019 (153)
18 SGDP_PRJ ss3847994023 Apr 25, 2020 (154)
19 TOMMO_GENOMICS ss5142049809 Apr 25, 2021 (155)
20 1000Genomes NC_000001.10 - 725389 Oct 11, 2018 (152)
21 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 725389 Oct 11, 2018 (152)
22 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 55509 (NC_000001.11:790008:C:A 1/92478)
Row 55510 (NC_000001.11:790008:C:T 4576/91668)

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

Submission ignored due to conflicting rows:
Row 55509 (NC_000001.11:790008:C:A 1/92478)
Row 55510 (NC_000001.11:790008:C:T 4576/91668)

- Apr 25, 2021 (155)
24 Genome of the Netherlands Release 5 NC_000001.10 - 725389 Apr 25, 2020 (154)
25 Northern Sweden NC_000001.10 - 725389 Jul 12, 2019 (153)
26 Qatari NC_000001.10 - 725389 Apr 25, 2020 (154)
27 SGDP_PRJ NC_000001.10 - 725389 Apr 25, 2020 (154)
28 Siberian NC_000001.10 - 725389 Apr 25, 2020 (154)
29 8.3KJPN NC_000001.10 - 725389 Apr 25, 2021 (155)
30 UK 10K study - Twins NC_000001.10 - 725389 Oct 11, 2018 (152)
31 ALFA NC_000001.11 - 790009 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13334916070, ss3066390457 NC_000001.11:790008:C:A NC_000001.11:790008:C:A (self)
2825, 109, 212, 894, 1754, 11003, 350, 19116, 109, ss647515902, ss974769100, ss1289338146, ss1599378245, ss1642372278, ss1751134732, ss1917959824, ss2019498281, ss2147483996, ss2697374180, ss2750633864, ss2986147906, ss3343272254, ss3726716029, ss3847994023, ss5142049809 NC_000001.10:725388:C:T NC_000001.11:790008:C:T (self)
13334916070, ss3066390458, ss3798743165 NC_000001.11:790008:C:T NC_000001.11:790008:C:T (self)

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

No publications for rs375619475


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