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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs17127999

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:65788190 (GRCh38.p14) 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.

Alleles
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.087499 (23160/264690, TOPMED)
A=0.075940 (10621/139860, GnomAD)
A=0.03173 (2018/63608, ALFA) (+ 17 more)
A=0.14491 (4095/28258, 14KJPN)
A=0.14469 (2425/16760, 8.3KJPN)
A=0.1277 (818/6404, 1000G_30x)
A=0.1266 (634/5008, 1000G)
A=0.0087 (39/4480, Estonian)
A=0.0127 (49/3854, ALSPAC)
A=0.0146 (54/3708, TWINSUK)
A=0.1663 (486/2922, KOREAN)
A=0.1094 (228/2084, HGDP_Stanford)
A=0.1425 (244/1712, HapMap)
A=0.008 (8/998, GoNL)
A=0.168 (105/626, Chileans)
A=0.015 (9/600, NorthernSweden)
A=0.060 (13/216, Qatari)
A=0.204 (44/216, Vietnamese)
G=0.432 (57/132, SGDP_PRJ)
A=0.11 (2/18, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 63608 G=0.96827 A=0.03173
European Sub 51100 G=0.98679 A=0.01321
African Sub 4526 G=0.8285 A=0.1715
African Others Sub 170 G=0.782 A=0.218
African American Sub 4356 G=0.8303 A=0.1697
Asian Sub 190 G=0.863 A=0.137
East Asian Sub 148 G=0.872 A=0.128
Other Asian Sub 42 G=0.83 A=0.17
Latin American 1 Sub 254 G=0.902 A=0.098
Latin American 2 Sub 1232 G=0.8847 A=0.1153
South Asian Sub 4940 G=0.9393 A=0.0607
Other Sub 1366 G=0.9458 A=0.0542


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.912501 A=0.087499
gnomAD - Genomes Global Study-wide 139860 G=0.924060 A=0.075940
gnomAD - Genomes European Sub 75740 G=0.98871 A=0.01129
gnomAD - Genomes African Sub 41914 G=0.81312 A=0.18688
gnomAD - Genomes American Sub 13616 G=0.90871 A=0.09129
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9934 A=0.0066
gnomAD - Genomes East Asian Sub 3124 G=0.8431 A=0.1569
gnomAD - Genomes Other Sub 2144 G=0.9170 A=0.0830
Allele Frequency Aggregator Total Global 63608 G=0.96827 A=0.03173
Allele Frequency Aggregator European Sub 51100 G=0.98679 A=0.01321
Allele Frequency Aggregator South Asian Sub 4940 G=0.9393 A=0.0607
Allele Frequency Aggregator African Sub 4526 G=0.8285 A=0.1715
Allele Frequency Aggregator Other Sub 1366 G=0.9458 A=0.0542
Allele Frequency Aggregator Latin American 2 Sub 1232 G=0.8847 A=0.1153
Allele Frequency Aggregator Latin American 1 Sub 254 G=0.902 A=0.098
Allele Frequency Aggregator Asian Sub 190 G=0.863 A=0.137
14KJPN JAPANESE Study-wide 28258 G=0.85509 A=0.14491
8.3KJPN JAPANESE Study-wide 16760 G=0.85531 A=0.14469
1000Genomes_30x Global Study-wide 6404 G=0.8723 A=0.1277
1000Genomes_30x African Sub 1786 G=0.7979 A=0.2021
1000Genomes_30x Europe Sub 1266 G=0.9897 A=0.0103
1000Genomes_30x South Asian Sub 1202 G=0.9118 A=0.0882
1000Genomes_30x East Asian Sub 1170 G=0.8385 A=0.1615
1000Genomes_30x American Sub 980 G=0.848 A=0.152
1000Genomes Global Study-wide 5008 G=0.8734 A=0.1266
1000Genomes African Sub 1322 G=0.7943 A=0.2057
1000Genomes East Asian Sub 1008 G=0.8403 A=0.1597
1000Genomes Europe Sub 1006 G=0.9920 A=0.0080
1000Genomes South Asian Sub 978 G=0.904 A=0.096
1000Genomes American Sub 694 G=0.857 A=0.143
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9913 A=0.0087
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9873 A=0.0127
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9854 A=0.0146
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.8337 A=0.1663
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8906 A=0.1094
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.862 A=0.138
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.944 A=0.056
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.960 A=0.040
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.997 A=0.003
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.764 A=0.236
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.745 A=0.255
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.82 A=0.18
HapMap Global Study-wide 1712 G=0.8575 A=0.1425
HapMap American Sub 768 G=0.908 A=0.092
HapMap African Sub 690 G=0.806 A=0.194
HapMap Asian Sub 254 G=0.846 A=0.154
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.992 A=0.008
Chileans Chilean Study-wide 626 G=0.832 A=0.168
Northern Sweden ACPOP Study-wide 600 G=0.985 A=0.015
Qatari Global Study-wide 216 G=0.940 A=0.060
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.796 A=0.204
SGDP_PRJ Global Study-wide 132 G=0.432 A=0.568
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 18 G=0.89 A=0.11
Help

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.p14 chr 1 NC_000001.11:g.65788190G>A
GRCh37.p13 chr 1 NC_000001.10:g.66253873G>A
PDE4B RefSeqGene NG_029038.1:g.681G>A
Help

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
Help

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
GRCh38.p14 chr 1 NC_000001.11:g.65788190= NC_000001.11:g.65788190G>A
GRCh37.p13 chr 1 NC_000001.10:g.66253873= NC_000001.10:g.66253873G>A
PDE4B RefSeqGene NG_029038.1:g.681= NG_029038.1:g.681G>A
Help

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#.

72 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23160170 Sep 20, 2004 (123)
2 ILLUMINA ss67178131 Dec 01, 2006 (127)
3 ILLUMINA ss67540850 Dec 01, 2006 (127)
4 ILLUMINA ss68175152 Dec 12, 2006 (127)
5 ILLUMINA ss70656155 May 25, 2008 (130)
6 ILLUMINA ss71216005 May 18, 2007 (127)
7 ILLUMINA ss75575096 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss85367307 Dec 15, 2007 (130)
9 HGSV ss85435794 Dec 15, 2007 (130)
10 ILLUMINA-UK ss118762508 Feb 14, 2009 (130)
11 ILLUMINA ss153633978 Dec 01, 2009 (131)
12 GMI ss155107704 Dec 01, 2009 (131)
13 ILLUMINA ss159309824 Dec 01, 2009 (131)
14 ILLUMINA ss172757964 Jul 04, 2010 (132)
15 1000GENOMES ss210543557 Jul 14, 2010 (132)
16 1000GENOMES ss218426793 Jul 14, 2010 (132)
17 1000GENOMES ss230565281 Jul 14, 2010 (132)
18 1000GENOMES ss238253795 Jul 15, 2010 (132)
19 GMI ss275856177 May 04, 2012 (137)
20 ILLUMINA ss410912072 Sep 17, 2011 (135)
21 ILLUMINA ss536950856 Sep 08, 2015 (146)
22 TISHKOFF ss554199109 Apr 25, 2013 (138)
23 SSMP ss648067026 Apr 25, 2013 (138)
24 ILLUMINA ss832821886 Jul 12, 2019 (153)
25 EVA-GONL ss975239171 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1067947686 Aug 21, 2014 (142)
27 1000GENOMES ss1291191895 Aug 21, 2014 (142)
28 EVA_DECODE ss1584608209 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1600333495 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1643327528 Apr 01, 2015 (144)
31 EVA_SVP ss1712339524 Apr 01, 2015 (144)
32 HAMMER_LAB ss1794485943 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1918447104 Feb 12, 2016 (147)
34 GENOMED ss1966764425 Jul 19, 2016 (147)
35 JJLAB ss2019740637 Sep 14, 2016 (149)
36 CSHL ss2136653568 Nov 08, 2017 (151)
37 HUMAN_LONGEVITY ss2163128521 Dec 20, 2016 (150)
38 GRF ss2697673406 Nov 08, 2017 (151)
39 GNOMAD ss2755992887 Nov 08, 2017 (151)
40 SWEGEN ss2986936977 Nov 08, 2017 (151)
41 CSHL ss3343489190 Nov 08, 2017 (151)
42 ILLUMINA ss3626115747 Oct 11, 2018 (152)
43 ILLUMINA ss3637761610 Oct 11, 2018 (152)
44 ILLUMINA ss3638899725 Oct 11, 2018 (152)
45 ILLUMINA ss3639762155 Oct 11, 2018 (152)
46 ILLUMINA ss3642773294 Oct 11, 2018 (152)
47 ILLUMINA ss3643815845 Oct 11, 2018 (152)
48 EGCUT_WGS ss3655006632 Jul 12, 2019 (153)
49 EVA_DECODE ss3686919578 Jul 12, 2019 (153)
50 ACPOP ss3727112764 Jul 12, 2019 (153)
51 EVA ss3746297397 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3799304591 Jul 12, 2019 (153)
53 EVA ss3826211010 Apr 25, 2020 (154)
54 HGDP ss3847336211 Apr 25, 2020 (154)
55 SGDP_PRJ ss3849004313 Apr 25, 2020 (154)
56 KRGDB ss3894029798 Apr 25, 2020 (154)
57 EVA ss3984801634 Apr 25, 2021 (155)
58 EVA ss4016914868 Apr 25, 2021 (155)
59 TOPMED ss4452372671 Apr 25, 2021 (155)
60 TOMMO_GENOMICS ss5144286043 Apr 25, 2021 (155)
61 1000G_HIGH_COVERAGE ss5242529830 Oct 12, 2022 (156)
62 EVA ss5319206047 Oct 12, 2022 (156)
63 HUGCELL_USP ss5443566890 Oct 12, 2022 (156)
64 EVA ss5505876649 Oct 12, 2022 (156)
65 1000G_HIGH_COVERAGE ss5514936210 Oct 12, 2022 (156)
66 SANFORD_IMAGENETICS ss5625678367 Oct 12, 2022 (156)
67 TOMMO_GENOMICS ss5669154294 Oct 12, 2022 (156)
68 YY_MCH ss5800661584 Oct 12, 2022 (156)
69 EVA ss5832060604 Oct 12, 2022 (156)
70 EVA ss5848938223 Oct 12, 2022 (156)
71 EVA ss5908561031 Oct 12, 2022 (156)
72 EVA ss5937516254 Oct 12, 2022 (156)
73 1000Genomes NC_000001.10 - 66253873 Oct 11, 2018 (152)
74 1000Genomes_30x NC_000001.11 - 65788190 Oct 12, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 66253873 Oct 11, 2018 (152)
76 Chileans NC_000001.10 - 66253873 Apr 25, 2020 (154)
77 Genetic variation in the Estonian population NC_000001.10 - 66253873 Oct 11, 2018 (152)
78 gnomAD - Genomes NC_000001.11 - 65788190 Apr 25, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000001.10 - 66253873 Apr 25, 2020 (154)
80 HGDP-CEPH-db Supplement 1 NC_000001.9 - 66026461 Apr 25, 2020 (154)
81 HapMap NC_000001.11 - 65788190 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000001.10 - 66253873 Apr 25, 2020 (154)
83 Northern Sweden NC_000001.10 - 66253873 Jul 12, 2019 (153)
84 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 66253873 Apr 25, 2021 (155)
85 Qatari NC_000001.10 - 66253873 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 66253873 Apr 25, 2020 (154)
87 8.3KJPN NC_000001.10 - 66253873 Apr 25, 2021 (155)
88 14KJPN NC_000001.11 - 65788190 Oct 12, 2022 (156)
89 TopMed NC_000001.11 - 65788190 Apr 25, 2021 (155)
90 UK 10K study - Twins NC_000001.10 - 66253873 Oct 11, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000001.10 - 66253873 Jul 12, 2019 (153)
92 ALFA NC_000001.11 - 65788190 Apr 25, 2021 (155)
Help

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)
rs56452303 May 25, 2008 (130)
rs59155658 May 25, 2008 (130)
rs111189783 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85435794, ss3638899725, ss3639762155, ss3643815845 NC_000001.8:65965893:G:A NC_000001.11:65788189:G:A (self)
14103, ss118762508, ss210543557, ss275856177, ss1584608209, ss1712339524, ss2136653568, ss3642773294, ss3847336211 NC_000001.9:66026460:G:A NC_000001.11:65788189:G:A (self)
1920979, 1051866, 10711, 744880, 448849, 1207192, 397629, 27561, 489034, 1021293, 2255350, 1051866, 219600, ss218426793, ss230565281, ss238253795, ss536950856, ss554199109, ss648067026, ss832821886, ss975239171, ss1067947686, ss1291191895, ss1600333495, ss1643327528, ss1794485943, ss1918447104, ss1966764425, ss2019740637, ss2697673406, ss2755992887, ss2986936977, ss3343489190, ss3626115747, ss3637761610, ss3655006632, ss3727112764, ss3746297397, ss3826211010, ss3849004313, ss3894029798, ss3984801634, ss4016914868, ss5144286043, ss5319206047, ss5505876649, ss5625678367, ss5832060604, ss5937516254 NC_000001.10:66253872:G:A NC_000001.11:65788189:G:A (self)
2462145, 13549717, 85772, 2991398, 15979006, 719416603, ss2163128521, ss3686919578, ss3799304591, ss4452372671, ss5242529830, ss5443566890, ss5514936210, ss5669154294, ss5800661584, ss5848938223, ss5908561031 NC_000001.11:65788189:G:A NC_000001.11:65788189:G:A (self)
ss23160170, ss67178131, ss67540850, ss68175152, ss70656155, ss71216005, ss75575096, ss85367307, ss153633978, ss155107704, ss159309824, ss172757964, ss410912072 NT_032977.9:36225790:G:A NC_000001.11:65788189:G:A (self)
Help

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

No publications for rs17127999

Help

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.post761+d5e8e07