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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
chr2:144387486 (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
C=0.005391 (1427/264690, TOPMED)
C=0.003216 (451/140256, GnomAD)
C=0.00156 (30/19190, ALFA) (+ 10 more)
C=0.10734 (1799/16760, 8.3KJPN)
C=0.0313 (157/5008, 1000G)
C=0.0002 (1/4480, Estonian)
C=0.0973 (285/2930, KOREAN)
C=0.005 (1/216, Qatari)
C=0.097 (21/216, Vietnamese)
T=0.50 (16/32, SGDP_PRJ)
C=0.50 (16/32, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZEB2 : 3 Prime UTR 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 2 NC_000002.12:g.144387486T>C
GRCh37.p13 chr 2 NC_000002.11:g.145145053T>C
ZEB2 RefSeqGene NG_016431.1:g.137906A>G
Gene: ZEB2, zinc finger E-box binding homeobox 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZEB2 transcript variant 1 NM_014795.4:c.*1965= N/A 3 Prime UTR Variant
ZEB2 transcript variant 2 NM_001171653.2:c.*1965= N/A 3 Prime UTR Variant
ZEB2 transcript variant 3 NR_033258.2:n. N/A Genic Downstream 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 19190 T=0.99844 C=0.00156
European Sub 14286 T=0.99986 C=0.00014
African Sub 2970 T=0.9993 C=0.0007
African Others Sub 114 T=1.000 C=0.000
African American Sub 2856 T=0.9993 C=0.0007
Asian Sub 116 T=0.905 C=0.095
East Asian Sub 88 T=0.91 C=0.09
Other Asian Sub 28 T=0.89 C=0.11
Latin American 1 Sub 154 T=1.000 C=0.000
Latin American 2 Sub 616 T=0.994 C=0.006
South Asian Sub 98 T=0.97 C=0.03
Other Sub 950 T=0.992 C=0.008


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 T=0.994609 C=0.005391
gnomAD - Genomes Global Study-wide 140256 T=0.996784 C=0.003216
gnomAD - Genomes European Sub 75940 T=0.99984 C=0.00016
gnomAD - Genomes African Sub 42052 T=0.99900 C=0.00100
gnomAD - Genomes American Sub 13654 T=0.99744 C=0.00256
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9928 C=0.0072
gnomAD - Genomes East Asian Sub 3134 T=0.8989 C=0.1011
gnomAD - Genomes Other Sub 2152 T=0.9902 C=0.0098
8.3KJPN JAPANESE Study-wide 16760 T=0.89266 C=0.10734
1000Genomes Global Study-wide 5008 T=0.9687 C=0.0313
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=0.8909 C=0.1091
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=0.953 C=0.047
1000Genomes American Sub 694 T=0.999 C=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9998 C=0.0002
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.9027 C=0.0973
Qatari Global Study-wide 216 T=0.995 C=0.005
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.903 C=0.097
SGDP_PRJ Global Study-wide 32 T=0.50 C=0.50
Siberian Global Study-wide 2 T=0.5 C=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 T= C
GRCh38.p13 chr 2 NC_000002.12:g.144387486= NC_000002.12:g.144387486T>C
GRCh37.p13 chr 2 NC_000002.11:g.145145053= NC_000002.11:g.145145053T>C
ZEB2 RefSeqGene NG_016431.1:g.137906= NG_016431.1:g.137906A>G
ZEB2 transcript variant 1 NM_014795.4:c.*1965= NM_014795.4:c.*1965A>G
ZEB2 transcript variant 1 NM_014795.3:c.*1965= NM_014795.3:c.*1965A>G
ZEB2 transcript variant 2 NM_001171653.2:c.*1965= NM_001171653.2:c.*1965A>G
ZEB2 transcript variant 2 NM_001171653.1:c.*1965= NM_001171653.1:c.*1965A>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#.

23 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss238901261 Jul 15, 2010 (132)
2 GMI ss276717661 May 04, 2012 (137)
3 ILLUMINA ss533822049 Sep 08, 2015 (146)
4 SSMP ss649566652 Apr 25, 2013 (138)
5 JMKIDD_LAB ss1069569610 Aug 21, 2014 (142)
6 1000GENOMES ss1299703470 Aug 21, 2014 (142)
7 EVA_DECODE ss1586885682 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1920715984 Feb 12, 2016 (147)
9 USC_VALOUEV ss2148949469 Dec 20, 2016 (150)
10 HUMAN_LONGEVITY ss2235048048 Dec 20, 2016 (150)
11 TOPMED ss2401424058 Dec 20, 2016 (150)
12 GRF ss2703577595 Nov 08, 2017 (151)
13 GNOMAD ss2780721308 Nov 08, 2017 (151)
14 TOPMED ss3325430479 Nov 08, 2017 (151)
15 ILLUMINA ss3628184767 Oct 11, 2018 (152)
16 EGCUT_WGS ss3658427311 Jul 13, 2019 (153)
17 EVA_DECODE ss3705072439 Jul 13, 2019 (153)
18 EVA ss3757498506 Jul 13, 2019 (153)
19 KHV_HUMAN_GENOMES ss3801865077 Jul 13, 2019 (153)
20 SGDP_PRJ ss3853609343 Apr 25, 2020 (154)
21 KRGDB ss3899185959 Apr 25, 2020 (154)
22 TOPMED ss4527218220 Apr 26, 2021 (155)
23 TOMMO_GENOMICS ss5154292481 Apr 26, 2021 (155)
24 1000Genomes NC_000002.11 - 145145053 Oct 11, 2018 (152)
25 Genetic variation in the Estonian population NC_000002.11 - 145145053 Oct 11, 2018 (152)
26 gnomAD - Genomes NC_000002.12 - 144387486 Apr 26, 2021 (155)
27 KOREAN population from KRGDB NC_000002.11 - 145145053 Apr 25, 2020 (154)
28 Qatari NC_000002.11 - 145145053 Apr 25, 2020 (154)
29 SGDP_PRJ NC_000002.11 - 145145053 Apr 25, 2020 (154)
30 Siberian NC_000002.11 - 145145053 Apr 25, 2020 (154)
31 8.3KJPN NC_000002.11 - 145145053 Apr 26, 2021 (155)
32 TopMed NC_000002.12 - 144387486 Apr 26, 2021 (155)
33 A Vietnamese Genetic Variation Database NC_000002.11 - 145145053 Jul 13, 2019 (153)
34 ALFA NC_000002.12 - 144387486 Apr 26, 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
ss276717661, ss1586885682 NC_000002.10:144861522:T:C NC_000002.12:144387485:T:C (self)
10733716, 4165559, 6363353, 2757914, 5626323, 1465823, 12261788, 1282241, ss238901261, ss533822049, ss649566652, ss1069569610, ss1299703470, ss1920715984, ss2148949469, ss2401424058, ss2703577595, ss2780721308, ss3628184767, ss3658427311, ss3757498506, ss3853609343, ss3899185959, ss5154292481 NC_000002.11:145145052:T:C NC_000002.12:144387485:T:C (self)
76483797, 206547088, 331041099, 3965637128, ss2235048048, ss3325430479, ss3705072439, ss3801865077, ss4527218220 NC_000002.12:144387485:T:C NC_000002.12:144387485:T:C (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 rs79710863


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