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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
chr1:858567 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.159779 (20252/126750, GnomAD)
G=0.19685 (3298/16754, 8.3KJPN)
G=0.16309 (2724/16702, ALFA) (+ 6 more)
G=0.0086 (43/5008, 1000G)
G=0.2228 (650/2918, KOREAN)
G=0.1912 (260/1360, HapMap)
G=0.088 (53/600, NorthernSweden)
G=0.009 (2/212, Qatari)
A=0.443 (86/194, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : Non Coding Transcript Variant
LOC107984850 : 2KB Upstream 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.858567A>G
GRCh37.p13 chr 1 NC_000001.10:g.793947A>G
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n.5897A>G N/A Non Coding Transcript Variant
LINC01128 transcript variant 3 NR_047521.1:n.5744A>G N/A Non Coding Transcript Variant
LINC01128 transcript variant 5 NR_047523.1:n.5648A>G N/A Non Coding Transcript Variant
LINC01128 transcript variant 7 NR_047524.1:n.5560A>G N/A Non Coding Transcript Variant
LINC01128 transcript variant 8 NR_047525.1:n.5611A>G N/A Non Coding Transcript Variant
LINC01128 transcript variant 9 NR_047526.1:n. N/A Genic Downstream Transcript Variant
Gene: LOC107984850, uncharacterized LOC107984850 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107984850 transcript variant X1 XR_001737607.2:n. N/A Upstream Transcript Variant
LOC107984850 transcript variant X2 XR_001737608.2:n. N/A 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 A=0.83691 G=0.16309
European Sub 12214 A=0.89168 G=0.10832
African Sub 2864 A=0.6159 G=0.3841
African Others Sub 108 A=0.602 G=0.398
African American Sub 2756 A=0.6165 G=0.3835
Asian Sub 108 A=0.769 G=0.231
East Asian Sub 84 A=0.75 G=0.25
Other Asian Sub 24 A=0.83 G=0.17
Latin American 1 Sub 146 A=0.788 G=0.212
Latin American 2 Sub 610 A=0.766 G=0.234
South Asian Sub 94 A=0.94 G=0.06
Other Sub 666 A=0.856 G=0.144


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
gnomAD - Genomes Global Study-wide 126750 A=0.840221 G=0.159779
gnomAD - Genomes European Sub 72662 A=0.90576 G=0.09424
gnomAD - Genomes African Sub 33532 A=0.69289 G=0.30711
gnomAD - Genomes American Sub 12632 A=0.81753 G=0.18247
gnomAD - Genomes Ashkenazi Jewish Sub 3262 A=0.9672 G=0.0328
gnomAD - Genomes East Asian Sub 2714 A=0.8475 G=0.1525
gnomAD - Genomes Other Sub 1948 A=0.8563 G=0.1437
8.3KJPN JAPANESE Study-wide 16754 A=0.80315 G=0.19685
1000Genomes Global Study-wide 5008 A=0.9914 G=0.0086
1000Genomes African Sub 1322 A=0.9781 G=0.0219
1000Genomes East Asian Sub 1008 A=0.9980 G=0.0020
1000Genomes Europe Sub 1006 A=0.9920 G=0.0080
1000Genomes South Asian Sub 978 A=0.997 G=0.003
1000Genomes American Sub 694 A=0.999 G=0.001
KOREAN population from KRGDB KOREAN Study-wide 2918 A=0.7772 G=0.2228
HapMap Global Study-wide 1360 A=0.8088 G=0.1912
HapMap American Sub 762 A=0.841 G=0.159
HapMap Asian Sub 246 A=0.829 G=0.171
HapMap African Sub 176 A=0.517 G=0.483
HapMap Europe Sub 176 A=0.932 G=0.068
Northern Sweden ACPOP Study-wide 600 A=0.912 G=0.088
Qatari Global Study-wide 212 A=0.991 G=0.009
SGDP_PRJ Global Study-wide 194 A=0.443 G=0.557

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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.858567= NC_000001.11:g.858567A>G
GRCh37.p13 chr 1 NC_000001.10:g.793947= NC_000001.10:g.793947A>G
LINC01128 transcript variant 6 NR_015368.2:n.5603= NR_015368.2:n.5603A>G
LINC01128 transcript variant 1 NR_047519.1:n.5897= NR_047519.1:n.5897A>G
LINC01128 transcript variant 2 NR_047520.1:n.5848= NR_047520.1:n.5848A>G
LINC01128 transcript variant 3 NR_047521.1:n.5744= NR_047521.1:n.5744A>G
LINC01128 transcript variant 4 NR_047522.1:n.5695= NR_047522.1:n.5695A>G
LINC01128 transcript variant 5 NR_047523.1:n.5648= NR_047523.1:n.5648A>G
LINC01128 transcript variant 8 NR_047525.1:n.5611= NR_047525.1:n.5611A>G
LINC01128 transcript variant 7 NR_047524.1:n.5560= NR_047524.1:n.5560A>G

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#.

26 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3530634 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss9809768 Jul 11, 2003 (117)
3 ILLUMINA ss75321774 Dec 06, 2007 (129)
4 ILLUMINA ss123455488 Dec 01, 2009 (131)
5 ILLUMINA ss153917683 Dec 01, 2009 (131)
6 ILLUMINA ss171289300 Jul 04, 2010 (132)
7 ILLUMINA ss173379232 Jul 04, 2010 (132)
8 1000GENOMES ss230395493 Jul 14, 2010 (132)
9 SSMP ss647516401 Apr 25, 2013 (138)
10 ILLUMINA ss825677114 Apr 01, 2015 (144)
11 1000GENOMES ss1289340091 Aug 21, 2014 (142)
12 WEILL_CORNELL_DGM ss1917960698 Feb 12, 2016 (147)
13 JJLAB ss2019498475 Sep 14, 2016 (149)
14 GNOMAD ss2750641112 Nov 08, 2017 (151)
15 SWEGEN ss2986149394 Nov 08, 2017 (151)
16 TOPMED ss3066404893 Nov 08, 2017 (151)
17 ILLUMINA ss3637732369 Oct 11, 2018 (152)
18 ILLUMINA ss3642746673 Oct 11, 2018 (152)
19 ACPOP ss3726716494 Jul 12, 2019 (153)
20 EVA ss3745721156 Jul 12, 2019 (153)
21 KHV_HUMAN_GENOMES ss3798743830 Jul 12, 2019 (153)
22 EVA ss3836378460 Apr 25, 2020 (154)
23 EVA ss3841782462 Apr 25, 2020 (154)
24 SGDP_PRJ ss3847996033 Apr 25, 2020 (154)
25 KRGDB ss3892836275 Apr 25, 2020 (154)
26 TOMMO_GENOMICS ss5142053062 Apr 25, 2021 (155)
27 1000Genomes NC_000001.10 - 793947 Oct 11, 2018 (152)
28 gnomAD - Genomes NC_000001.11 - 858567 Apr 25, 2021 (155)
29 HapMap NC_000001.11 - 858567 Apr 25, 2020 (154)
30 KOREAN population from KRGDB NC_000001.10 - 793947 Apr 25, 2020 (154)
31 Northern Sweden NC_000001.10 - 793947 Jul 12, 2019 (153)
32 Qatari NC_000001.10 - 793947 Apr 25, 2020 (154)
33 SGDP_PRJ NC_000001.10 - 793947 Apr 25, 2020 (154)
34 8.3KJPN NC_000001.10 - 793947 Apr 25, 2021 (155)
35 ALFA NC_000001.11 - 858567 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)
rs3812319 Oct 09, 2002 (108)
rs6657149 Aug 27, 2003 (117)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss825677114, ss3642746673 NC_000001.9:783809:A:G NC_000001.11:858566:A:G (self)
4856, 13669, 1359, 2628, 13013, 22369, ss230395493, ss647516401, ss1289340091, ss1917960698, ss2019498475, ss2750641112, ss2986149394, ss3637732369, ss3726716494, ss3745721156, ss3836378460, ss3847996033, ss3892836275, ss5142053062 NC_000001.10:793946:A:G NC_000001.11:858566:A:G (self)
70084, 81, 8177163237, ss3066404893, ss3798743830, ss3841782462 NC_000001.11:858566:A:G NC_000001.11:858566:A:G (self)
ss3530634, ss75321774, ss123455488, ss153917683, ss171289300, ss173379232 NT_004350.19:272578:A:G NC_000001.11:858566:A:G (self)
ss9809768 NT_034471.3:272578:A:G NC_000001.11:858566:A:G (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 rs2519031


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