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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
chr1:782207 (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.

G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
A=0.013926 (3686/264690, TOPMED)
A=0.00239 (44/18440, ALFA)
A=0.0046 (23/5008, 1000G) (+ 9 more)
A=0.0150 (58/3854, ALSPAC)
A=0.0200 (74/3708, TWINSUK)
A=0.0007 (2/2922, KOREAN)
A=0.021 (21/998, GoNL)
A=0.017 (10/600, NorthernSweden)
A=0.017 (9/534, MGP)
A=0.079 (17/216, Qatari)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
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.782207G>A
GRCh38.p13 chr 1 NC_000001.11:g.782207G>C
GRCh38.p13 chr 1 NC_000001.11:g.782207G>T
GRCh37.p13 chr 1 NC_000001.10:g.717587G>A
GRCh37.p13 chr 1 NC_000001.10:g.717587G>C
GRCh37.p13 chr 1 NC_000001.10:g.717587G>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 (New)
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 18440 G=0.99761 A=0.00239, T=0.00000
European Sub 13898 G=0.99712 A=0.00288, T=0.00000
African Sub 2916 G=1.0000 A=0.0000, T=0.0000
African Others Sub 112 G=1.000 A=0.000, T=0.000
African American Sub 2804 G=1.0000 A=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 134 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 598 G=1.000 A=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, T=0.00
Other Sub 684 G=0.994 A=0.006, T=0.000


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
TopMed Global Study-wide 264690 G=0.986074 A=0.013926
1000Genomes Global Study-wide 5008 G=0.9954 A=0.0046
1000Genomes African Sub 1322 G=0.9962 A=0.0038
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9911 A=0.0089
1000Genomes South Asian Sub 978 G=0.998 A=0.002
1000Genomes American Sub 694 G=0.990 A=0.010
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9850 A=0.0150
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9800 A=0.0200
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9993 A=0.0007
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.979 A=0.021
Northern Sweden ACPOP Study-wide 600 G=0.983 A=0.017
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.983 A=0.017
Qatari Global Study-wide 216 G=0.921 A=0.079
SGDP_PRJ Global Study-wide 6 G=0.5 A=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 G= A C T
GRCh38.p13 chr 1 NC_000001.11:g.782207= NC_000001.11:g.782207G>A NC_000001.11:g.782207G>C NC_000001.11:g.782207G>T
GRCh37.p13 chr 1 NC_000001.10:g.717587= NC_000001.10:g.717587G>A NC_000001.10:g.717587G>C NC_000001.10:g.717587G>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#.

21 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328357089 May 09, 2011 (134)
2 EVA-GONL ss974769056 Aug 21, 2014 (142)
3 1000GENOMES ss1289337962 Aug 21, 2014 (142)
4 DDI ss1425684725 Apr 01, 2015 (144)
5 EVA_DECODE ss1584129334 Apr 01, 2015 (144)
6 EVA_UK10K_ALSPAC ss1599378232 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1642372265 Apr 01, 2015 (144)
8 EVA_MGP ss1710883330 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1917959732 Feb 12, 2016 (147)
10 JJLAB ss2019498269 Sep 14, 2016 (149)
11 TOPMED ss2321501075 Dec 20, 2016 (150)
12 GNOMAD ss2750633042 Nov 08, 2017 (151)
13 SWEGEN ss2986147726 Nov 08, 2017 (151)
14 TOPMED ss3066388850 Nov 08, 2017 (151)
15 TOPMED ss3066388851 Nov 08, 2017 (151)
16 CSHL ss3343272182 Nov 08, 2017 (151)
17 EVA_DECODE ss3685991632 Jul 12, 2019 (153)
18 ACPOP ss3726715985 Jul 12, 2019 (153)
19 SGDP_PRJ ss3847993829 Apr 25, 2020 (154)
20 KRGDB ss3892833274 Apr 25, 2020 (154)
21 TOPMED ss4436422448 Apr 25, 2021 (155)
22 1000Genomes NC_000001.10 - 717587 Oct 11, 2018 (152)
23 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 717587 Oct 11, 2018 (152)
24 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 53830 (NC_000001.11:782206:G:A 1892/140114)
Row 53831 (NC_000001.11:782206:G:C 1/140116)
Row 53832 (NC_000001.11:782206:G:T 1/140116)

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

Submission ignored due to conflicting rows:
Row 53830 (NC_000001.11:782206:G:A 1892/140114)
Row 53831 (NC_000001.11:782206:G:C 1/140116)
Row 53832 (NC_000001.11:782206:G:T 1/140116)

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

Submission ignored due to conflicting rows:
Row 53830 (NC_000001.11:782206:G:A 1892/140114)
Row 53831 (NC_000001.11:782206:G:C 1/140116)
Row 53832 (NC_000001.11:782206:G:T 1/140116)

- Apr 25, 2021 (155)
27 Genome of the Netherlands Release 5 NC_000001.10 - 717587 Apr 25, 2020 (154)
28 KOREAN population from KRGDB NC_000001.10 - 717587 Apr 25, 2020 (154)
29 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 717587 Apr 25, 2020 (154)
30 Northern Sweden NC_000001.10 - 717587 Jul 12, 2019 (153)
31 Qatari NC_000001.10 - 717587 Apr 25, 2020 (154)
32 SGDP_PRJ NC_000001.10 - 717587 Apr 25, 2020 (154)
33 TopMed NC_000001.11 - 782207 Apr 25, 2021 (155)
34 UK 10K study - Twins NC_000001.10 - 717587 Oct 11, 2018 (152)
35 ALFA NC_000001.11 - 782207 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
ss1584129334 NC_000001.9:707449:G:A NC_000001.11:782206:G:A (self)
2628, 77, 174, 10668, 82, 850, 1662, 10809, 77, ss328357089, ss974769056, ss1289337962, ss1425684725, ss1599378232, ss1642372265, ss1710883330, ss1917959732, ss2019498269, ss2321501075, ss2750633042, ss2986147726, ss3343272182, ss3726715985, ss3847993829, ss3892833274 NC_000001.10:717586:G:A NC_000001.11:782206:G:A (self)
10728, 28783, 4912454407, ss3066388850, ss3685991632, ss4436422448 NC_000001.11:782206:G:A NC_000001.11:782206:G:A (self)
NC_000001.11:782206:G:C NC_000001.11:782206:G:C
10728, 4912454407, ss3066388851 NC_000001.11:782206:G:T NC_000001.11:782206:G: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 rs144155419


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