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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.

rs1320754

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:189960217 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.484057 (128125/264690, TOPMED)
G=0.466395 (65175/139742, GnomAD)
A=0.40508 (11446/28256, 14KJPN) (+ 16 more)
A=0.40388 (6769/16760, 8.3KJPN)
A=0.4375 (4255/9726, ALFA)
A=0.4642 (2973/6404, 1000G_30x)
A=0.4601 (2304/5008, 1000G)
G=0.3607 (1616/4480, Estonian)
G=0.4603 (1774/3854, ALSPAC)
G=0.4571 (1695/3708, TWINSUK)
A=0.3809 (1116/2930, KOREAN)
A=0.4023 (737/1832, Korea1K)
G=0.445 (444/998, GoNL)
A=0.488 (293/600, NorthernSweden)
G=0.328 (116/354, SGDP_PRJ)
G=0.495 (107/216, Qatari)
G=0.458 (55/120, HapMap)
G=0.25 (11/44, Siberian)
G=0.47 (19/40, GENOME_DK)
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 9726 G=0.5625 A=0.4375, T=0.0000
European Sub 8246 G=0.5057 A=0.4943, T=0.0000
African Sub 878 G=0.924 A=0.076, T=0.000
African Others Sub 40 G=0.95 A=0.05, T=0.00
African American Sub 838 G=0.922 A=0.078, T=0.000
Asian Sub 36 G=0.97 A=0.03, T=0.00
East Asian Sub 28 G=1.00 A=0.00, T=0.00
Other Asian Sub 8 G=0.9 A=0.1, T=0.0
Latin American 1 Sub 38 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 160 G=1.000 A=0.000, T=0.000
South Asian Sub 38 G=0.95 A=0.05, T=0.00
Other Sub 330 G=0.670 A=0.330, T=0.000


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=0.484057 A=0.515943
gnomAD - Genomes Global Study-wide 139742 G=0.466395 A=0.533605
gnomAD - Genomes European Sub 75722 G=0.43854 A=0.56146
gnomAD - Genomes African Sub 41864 G=0.49071 A=0.50929
gnomAD - Genomes American Sub 13582 G=0.50368 A=0.49632
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.4704 A=0.5296
gnomAD - Genomes East Asian Sub 3112 G=0.6150 A=0.3850
gnomAD - Genomes Other Sub 2146 G=0.5172 A=0.4828
14KJPN JAPANESE Study-wide 28256 G=0.59492 A=0.40508
8.3KJPN JAPANESE Study-wide 16760 G=0.59612 A=0.40388
Allele Frequency Aggregator Total Global 9726 G=0.5625 A=0.4375, T=0.0000
Allele Frequency Aggregator European Sub 8246 G=0.5057 A=0.4943, T=0.0000
Allele Frequency Aggregator African Sub 878 G=0.924 A=0.076, T=0.000
Allele Frequency Aggregator Other Sub 330 G=0.670 A=0.330, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 160 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 38 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 38 G=0.95 A=0.05, T=0.00
Allele Frequency Aggregator Asian Sub 36 G=0.97 A=0.03, T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.5358 A=0.4642
1000Genomes_30x African Sub 1786 G=0.4787 A=0.5213
1000Genomes_30x Europe Sub 1266 G=0.4526 A=0.5474
1000Genomes_30x South Asian Sub 1202 G=0.5699 A=0.4301
1000Genomes_30x East Asian Sub 1170 G=0.6256 A=0.3744
1000Genomes_30x American Sub 980 G=0.598 A=0.402
1000Genomes Global Study-wide 5008 G=0.5399 A=0.4601
1000Genomes African Sub 1322 G=0.4705 A=0.5295
1000Genomes East Asian Sub 1008 G=0.6240 A=0.3760
1000Genomes Europe Sub 1006 G=0.4573 A=0.5427
1000Genomes South Asian Sub 978 G=0.586 A=0.414
1000Genomes American Sub 694 G=0.605 A=0.395
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3607 A=0.6393
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4603 A=0.5397
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4571 A=0.5429
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6191 A=0.3809
Korean Genome Project KOREAN Study-wide 1832 G=0.5977 A=0.4023
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.445 A=0.555
Northern Sweden ACPOP Study-wide 600 G=0.512 A=0.488
SGDP_PRJ Global Study-wide 354 G=0.328 A=0.672
Qatari Global Study-wide 216 G=0.495 A=0.505
HapMap Global Study-wide 120 G=0.458 A=0.542
HapMap American Sub 120 G=0.458 A=0.542
Siberian Global Study-wide 44 G=0.25 A=0.75
The Danish reference pan genome Danish Study-wide 40 G=0.47 A=0.53
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.189960217G>A
GRCh38.p14 chr 1 NC_000001.11:g.189960217G>T
GRCh37.p13 chr 1 NC_000001.10:g.189929347G>A
GRCh37.p13 chr 1 NC_000001.10:g.189929347G>T
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 T
GRCh38.p14 chr 1 NC_000001.11:g.189960217= NC_000001.11:g.189960217G>A NC_000001.11:g.189960217G>T
GRCh37.p13 chr 1 NC_000001.10:g.189929347= NC_000001.10:g.189929347G>A NC_000001.10:g.189929347G>T
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#.

66 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2089183 Oct 23, 2000 (88)
2 BCMHGSC_JDW ss87909732 Mar 23, 2008 (129)
3 HUMANGENOME_JCVI ss99271617 Feb 05, 2009 (130)
4 BGI ss102806728 Dec 01, 2009 (131)
5 1000GENOMES ss108796318 Jan 23, 2009 (130)
6 ILLUMINA-UK ss119147492 Feb 15, 2009 (130)
7 ENSEMBL ss138123896 Dec 01, 2009 (131)
8 ENSEMBL ss143778835 Dec 01, 2009 (131)
9 GMI ss156061392 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss165589764 Jul 04, 2010 (132)
11 BUSHMAN ss199391512 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss205320733 Jul 04, 2010 (132)
13 1000GENOMES ss218784823 Jul 14, 2010 (132)
14 1000GENOMES ss230828686 Jul 14, 2010 (132)
15 1000GENOMES ss238455459 Jul 15, 2010 (132)
16 GMI ss276145056 May 04, 2012 (137)
17 PJP ss290687562 May 09, 2011 (134)
18 SSMP ss648576483 Apr 25, 2013 (138)
19 EVA-GONL ss975942321 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1068459493 Aug 21, 2014 (142)
21 1000GENOMES ss1293908099 Aug 21, 2014 (142)
22 DDI ss1426054752 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1574555370 Apr 01, 2015 (144)
24 EVA_DECODE ss1585335560 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1601738609 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1644732642 Apr 01, 2015 (144)
27 HAMMER_LAB ss1795459605 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1919177238 Feb 12, 2016 (147)
29 GENOMED ss1966926863 Jul 19, 2016 (147)
30 JJLAB ss2020105864 Sep 14, 2016 (149)
31 USC_VALOUEV ss2148132982 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2168557033 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624560894 Nov 08, 2017 (151)
34 GRF ss2698118729 Nov 08, 2017 (151)
35 GNOMAD ss2764098501 Nov 08, 2017 (151)
36 SWEGEN ss2988146757 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3023812339 Nov 08, 2017 (151)
38 CSHL ss3343825409 Nov 08, 2017 (151)
39 URBANLAB ss3646845428 Oct 11, 2018 (152)
40 EGCUT_WGS ss3656100647 Jul 12, 2019 (153)
41 EVA_DECODE ss3688259878 Jul 12, 2019 (153)
42 ACPOP ss3727698169 Jul 12, 2019 (153)
43 EVA ss3747107386 Jul 12, 2019 (153)
44 PACBIO ss3783636414 Jul 12, 2019 (153)
45 PACBIO ss3789256579 Jul 12, 2019 (153)
46 PACBIO ss3794128733 Jul 12, 2019 (153)
47 KHV_HUMAN_GENOMES ss3800112016 Jul 12, 2019 (153)
48 EVA ss3826551296 Apr 25, 2020 (154)
49 EVA ss3836672771 Apr 25, 2020 (154)
50 EVA ss3842083396 Apr 25, 2020 (154)
51 SGDP_PRJ ss3850513529 Apr 25, 2020 (154)
52 KRGDB ss3895782235 Apr 25, 2020 (154)
53 KOGIC ss3946128474 Apr 25, 2020 (154)
54 TOPMED ss4476970079 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5147585582 Apr 25, 2021 (155)
56 1000G_HIGH_COVERAGE ss5245146319 Oct 12, 2022 (156)
57 HUGCELL_USP ss5445646026 Oct 12, 2022 (156)
58 EVA ss5506120588 Oct 12, 2022 (156)
59 1000G_HIGH_COVERAGE ss5518909498 Oct 12, 2022 (156)
60 SANFORD_IMAGENETICS ss5627078693 Oct 12, 2022 (156)
61 TOMMO_GENOMICS ss5675101235 Oct 12, 2022 (156)
62 YY_MCH ss5801473899 Oct 12, 2022 (156)
63 EVA ss5833001629 Oct 12, 2022 (156)
64 EVA ss5849207006 Oct 12, 2022 (156)
65 EVA ss5911227379 Oct 12, 2022 (156)
66 EVA ss5938898263 Oct 12, 2022 (156)
67 1000Genomes NC_000001.10 - 189929347 Oct 11, 2018 (152)
68 1000Genomes_30x NC_000001.11 - 189960217 Oct 12, 2022 (156)
69 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 189929347 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population NC_000001.10 - 189929347 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000001.10 - 189929347 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000001.11 - 189960217 Apr 25, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000001.10 - 189929347 Apr 25, 2020 (154)
74 HapMap NC_000001.11 - 189960217 Apr 25, 2020 (154)
75 KOREAN population from KRGDB NC_000001.10 - 189929347 Apr 25, 2020 (154)
76 Korean Genome Project NC_000001.11 - 189960217 Apr 25, 2020 (154)
77 Northern Sweden NC_000001.10 - 189929347 Jul 12, 2019 (153)
78 Qatari NC_000001.10 - 189929347 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000001.10 - 189929347 Apr 25, 2020 (154)
80 Siberian NC_000001.10 - 189929347 Apr 25, 2020 (154)
81 8.3KJPN NC_000001.10 - 189929347 Apr 25, 2021 (155)
82 14KJPN NC_000001.11 - 189960217 Oct 12, 2022 (156)
83 TopMed NC_000001.11 - 189960217 Apr 25, 2021 (155)
84 UK 10K study - Twins NC_000001.10 - 189929347 Oct 11, 2018 (152)
85 ALFA NC_000001.11 - 189960217 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87909732, ss108796318, ss119147492, ss165589764, ss199391512, ss205320733, ss276145056, ss290687562, ss1585335560 NC_000001.9:188195969:G:A NC_000001.11:189960216:G:A (self)
4735336, 2597313, 1838895, 1809217, 1131155, 2959629, 983034, 1219168, 2530509, 649336, 5554889, 2597313, ss218784823, ss230828686, ss238455459, ss648576483, ss975942321, ss1068459493, ss1293908099, ss1426054752, ss1574555370, ss1601738609, ss1644732642, ss1795459605, ss1919177238, ss1966926863, ss2020105864, ss2148132982, ss2624560894, ss2698118729, ss2764098501, ss2988146757, ss3343825409, ss3656100647, ss3727698169, ss3747107386, ss3783636414, ss3789256579, ss3794128733, ss3826551296, ss3836672771, ss3850513529, ss3895782235, ss5147585582, ss5506120588, ss5627078693, ss5833001629, ss5938898263 NC_000001.10:189929346:G:A NC_000001.11:189960216:G:A (self)
6435433, 34138945, 227865, 2506475, 8938339, 40576414, 4510335042, ss2168557033, ss3023812339, ss3646845428, ss3688259878, ss3800112016, ss3842083396, ss3946128474, ss4476970079, ss5245146319, ss5445646026, ss5518909498, ss5675101235, ss5801473899, ss5849207006, ss5911227379 NC_000001.11:189960216:G:A NC_000001.11:189960216:G:A (self)
ss2089183, ss99271617, ss102806728, ss138123896, ss143778835, ss156061392 NT_004487.19:41417988:G:A NC_000001.11:189960216:G:A (self)
4510335042 NC_000001.11:189960216:G:T NC_000001.11:189960216:G:T (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 rs1320754

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