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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.

rs1339856

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99578233 (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.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.327919 (86797/264690, TOPMED)
A=0.322992 (78841/244096, ALFA)
A=0.314732 (44021/139868, GnomAD) (+ 17 more)
A=0.36957 (28900/78200, PAGE_STUDY)
G=0.35686 (5981/16760, 8.3KJPN)
A=0.4189 (2098/5008, 1000G)
A=0.2960 (1326/4480, Estonian)
A=0.3101 (1195/3854, ALSPAC)
A=0.3166 (1174/3708, TWINSUK)
G=0.3208 (940/2930, KOREAN)
G=0.3297 (604/1832, Korea1K)
A=0.314 (313/998, GoNL)
G=0.380 (291/766, PRJEB37584)
A=0.282 (169/600, NorthernSweden)
A=0.285 (119/418, SGDP_PRJ)
A=0.351 (108/308, HapMap)
A=0.444 (96/216, Qatari)
G=0.313 (67/214, Vietnamese)
A=0.30 (14/46, Siberian)
A=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.99578233A>G
GRCh37.p13 chr 1 NC_000001.10:g.100043789A>G
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

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 244096 A=0.322992 G=0.677008
European Sub 216974 A=0.313756 G=0.686244
African Sub 6818 A=0.2807 G=0.7193
African Others Sub 260 A=0.227 G=0.773
African American Sub 6558 A=0.2829 G=0.7171
Asian Sub 3846 A=0.6456 G=0.3544
East Asian Sub 3116 A=0.6621 G=0.3379
Other Asian Sub 730 A=0.575 G=0.425
Latin American 1 Sub 1028 A=0.3337 G=0.6663
Latin American 2 Sub 6586 A=0.4189 G=0.5811
South Asian Sub 366 A=0.566 G=0.434
Other Sub 8478 A=0.3607 G=0.6393


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 A=0.327919 G=0.672081
gnomAD - Genomes Global Study-wide 139868 A=0.314732 G=0.685268
gnomAD - Genomes European Sub 75766 A=0.30613 G=0.69387
gnomAD - Genomes African Sub 41936 A=0.27728 G=0.72272
gnomAD - Genomes American Sub 13578 A=0.39299 G=0.60701
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.3427 G=0.6573
gnomAD - Genomes East Asian Sub 3122 A=0.6477 G=0.3523
gnomAD - Genomes Other Sub 2148 A=0.3277 G=0.6723
The PAGE Study Global Study-wide 78200 A=0.36957 G=0.63043
The PAGE Study AfricanAmerican Sub 32328 A=0.27923 G=0.72077
The PAGE Study Mexican Sub 10734 A=0.41364 G=0.58636
The PAGE Study Asian Sub 8260 A=0.6229 G=0.3771
The PAGE Study PuertoRican Sub 7862 A=0.3313 G=0.6687
The PAGE Study NativeHawaiian Sub 4502 A=0.5355 G=0.4645
The PAGE Study Cuban Sub 4206 A=0.3307 G=0.6693
The PAGE Study Dominican Sub 3808 A=0.2994 G=0.7006
The PAGE Study CentralAmerican Sub 2432 A=0.4100 G=0.5900
The PAGE Study SouthAmerican Sub 1968 A=0.4278 G=0.5722
The PAGE Study NativeAmerican Sub 1252 A=0.3530 G=0.6470
The PAGE Study SouthAsian Sub 848 A=0.542 G=0.458
8.3KJPN JAPANESE Study-wide 16760 A=0.64314 G=0.35686
1000Genomes Global Study-wide 5008 A=0.4189 G=0.5811
1000Genomes African Sub 1322 A=0.2489 G=0.7511
1000Genomes East Asian Sub 1008 A=0.6210 G=0.3790
1000Genomes Europe Sub 1006 A=0.3151 G=0.6849
1000Genomes South Asian Sub 978 A=0.570 G=0.430
1000Genomes American Sub 694 A=0.388 G=0.612
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2960 G=0.7040
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3101 G=0.6899
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3166 G=0.6834
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6792 G=0.3208
Korean Genome Project KOREAN Study-wide 1832 A=0.6703 G=0.3297
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.314 G=0.686
CNV burdens in cranial meningiomas Global Study-wide 766 A=0.620 G=0.380
CNV burdens in cranial meningiomas CRM Sub 766 A=0.620 G=0.380
Northern Sweden ACPOP Study-wide 600 A=0.282 G=0.718
SGDP_PRJ Global Study-wide 418 A=0.285 G=0.715
HapMap Global Study-wide 308 A=0.351 G=0.649
HapMap American Sub 116 A=0.302 G=0.698
HapMap African Sub 112 A=0.205 G=0.795
HapMap Asian Sub 80 A=0.62 G=0.38
Qatari Global Study-wide 216 A=0.444 G=0.556
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.687 G=0.313
Siberian Global Study-wide 46 A=0.30 G=0.70
The Danish reference pan genome Danish Study-wide 40 A=0.42 G=0.57
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.99578233= NC_000001.11:g.99578233A>G
GRCh37.p13 chr 1 NC_000001.10:g.100043789= NC_000001.10:g.100043789A>G
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#.

99 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2115164 Oct 23, 2000 (88)
2 CSHL-HAPMAP ss16430738 Feb 27, 2004 (120)
3 SSAHASNP ss20496838 Apr 05, 2004 (121)
4 ABI ss41068515 Mar 15, 2006 (126)
5 HGSV ss78491959 Dec 07, 2007 (129)
6 HGSV ss85805101 Dec 16, 2007 (130)
7 HUMANGENOME_JCVI ss97961317 Feb 06, 2009 (130)
8 BGI ss102767802 Dec 01, 2009 (131)
9 1000GENOMES ss108453536 Jan 23, 2009 (130)
10 1000GENOMES ss110890760 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118919080 Feb 15, 2009 (130)
12 ENSEMBL ss138842551 Dec 01, 2009 (131)
13 GMI ss155415373 Dec 01, 2009 (131)
14 ILLUMINA ss160335477 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss163738777 Jul 04, 2010 (132)
16 BUSHMAN ss198832592 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss205090579 Jul 04, 2010 (132)
18 1000GENOMES ss218548612 Jul 14, 2010 (132)
19 1000GENOMES ss230656712 Jul 14, 2010 (132)
20 1000GENOMES ss238323680 Jul 15, 2010 (132)
21 GMI ss275945298 May 04, 2012 (137)
22 GMI ss284105665 Apr 25, 2013 (138)
23 PJP ss290580476 May 09, 2011 (134)
24 ILLUMINA ss479922489 May 04, 2012 (137)
25 ILLUMINA ss479930382 May 04, 2012 (137)
26 ILLUMINA ss480560430 Sep 08, 2015 (146)
27 ILLUMINA ss484759440 May 04, 2012 (137)
28 ILLUMINA ss536851757 Sep 08, 2015 (146)
29 SSMP ss648253889 Apr 25, 2013 (138)
30 ILLUMINA ss778693699 Sep 08, 2015 (146)
31 ILLUMINA ss782826448 Sep 08, 2015 (146)
32 ILLUMINA ss783791322 Sep 08, 2015 (146)
33 ILLUMINA ss832079861 Sep 08, 2015 (146)
34 ILLUMINA ss834152489 Sep 08, 2015 (146)
35 EVA-GONL ss975482952 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1068127640 Aug 21, 2014 (142)
37 1000GENOMES ss1292107500 Aug 21, 2014 (142)
38 DDI ss1425910974 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1574271510 Apr 01, 2015 (144)
40 EVA_DECODE ss1584861250 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1600816833 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1643810866 Apr 01, 2015 (144)
43 ILLUMINA ss1751859109 Sep 08, 2015 (146)
44 HAMMER_LAB ss1794807575 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1918682563 Feb 12, 2016 (147)
46 ILLUMINA ss1946002821 Feb 12, 2016 (147)
47 ILLUMINA ss1958296786 Feb 12, 2016 (147)
48 GENOMED ss1966820766 Jul 19, 2016 (147)
49 JJLAB ss2019862756 Sep 14, 2016 (149)
50 USC_VALOUEV ss2147881468 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2165030817 Dec 20, 2016 (150)
52 TOPMED ss2327381622 Dec 20, 2016 (150)
53 ILLUMINA ss2632553616 Nov 08, 2017 (151)
54 GRF ss2697808800 Nov 08, 2017 (151)
55 ILLUMINA ss2710678272 Nov 08, 2017 (151)
56 GNOMAD ss2758637392 Nov 08, 2017 (151)
57 SWEGEN ss2987305638 Nov 08, 2017 (151)
58 ILLUMINA ss3021113791 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3023694972 Nov 08, 2017 (151)
60 TOPMED ss3084649205 Nov 08, 2017 (151)
61 CSHL ss3343595899 Nov 08, 2017 (151)
62 ILLUMINA ss3625546133 Oct 11, 2018 (152)
63 ILLUMINA ss3626165274 Oct 11, 2018 (152)
64 ILLUMINA ss3630587790 Oct 11, 2018 (152)
65 ILLUMINA ss3632903279 Oct 11, 2018 (152)
66 ILLUMINA ss3633598277 Oct 11, 2018 (152)
67 ILLUMINA ss3634339251 Oct 11, 2018 (152)
68 ILLUMINA ss3635291888 Oct 11, 2018 (152)
69 ILLUMINA ss3636016807 Oct 11, 2018 (152)
70 ILLUMINA ss3637042344 Oct 11, 2018 (152)
71 ILLUMINA ss3640046611 Oct 11, 2018 (152)
72 ILLUMINA ss3640984522 Oct 11, 2018 (152)
73 ILLUMINA ss3641278510 Oct 11, 2018 (152)
74 ILLUMINA ss3644498783 Oct 11, 2018 (152)
75 URBANLAB ss3646731427 Oct 11, 2018 (152)
76 ILLUMINA ss3651444572 Oct 11, 2018 (152)
77 EGCUT_WGS ss3655390707 Jul 12, 2019 (153)
78 EVA_DECODE ss3687367090 Jul 12, 2019 (153)
79 ILLUMINA ss3725048131 Jul 12, 2019 (153)
80 ACPOP ss3727314039 Jul 12, 2019 (153)
81 ILLUMINA ss3744050994 Jul 12, 2019 (153)
82 ILLUMINA ss3744640220 Jul 12, 2019 (153)
83 EVA ss3746574064 Jul 12, 2019 (153)
84 PAGE_CC ss3770827996 Jul 12, 2019 (153)
85 ILLUMINA ss3772141457 Jul 12, 2019 (153)
86 PACBIO ss3783495874 Jul 12, 2019 (153)
87 PACBIO ss3789140915 Jul 12, 2019 (153)
88 PACBIO ss3794013759 Jul 12, 2019 (153)
89 KHV_HUMAN_GENOMES ss3799574847 Jul 12, 2019 (153)
90 EVA ss3826326545 Apr 25, 2020 (154)
91 EVA ss3836553553 Apr 25, 2020 (154)
92 EVA ss3841961550 Apr 25, 2020 (154)
93 SGDP_PRJ ss3849477513 Apr 25, 2020 (154)
94 KRGDB ss3894555534 Apr 25, 2020 (154)
95 KOGIC ss3945091286 Apr 25, 2020 (154)
96 EVA ss3984461729 Apr 25, 2021 (155)
97 EVA ss4016927689 Apr 25, 2021 (155)
98 TOPMED ss4460696725 Apr 25, 2021 (155)
99 TOMMO_GENOMICS ss5145313150 Apr 25, 2021 (155)
100 1000Genomes NC_000001.10 - 100043789 Oct 11, 2018 (152)
101 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100043789 Oct 11, 2018 (152)
102 Genetic variation in the Estonian population NC_000001.10 - 100043789 Oct 11, 2018 (152)
103 The Danish reference pan genome NC_000001.10 - 100043789 Apr 25, 2020 (154)
104 gnomAD - Genomes NC_000001.11 - 99578233 Apr 25, 2021 (155)
105 Genome of the Netherlands Release 5 NC_000001.10 - 100043789 Apr 25, 2020 (154)
106 HapMap NC_000001.11 - 99578233 Apr 25, 2020 (154)
107 KOREAN population from KRGDB NC_000001.10 - 100043789 Apr 25, 2020 (154)
108 Korean Genome Project NC_000001.11 - 99578233 Apr 25, 2020 (154)
109 Northern Sweden NC_000001.10 - 100043789 Jul 12, 2019 (153)
110 The PAGE Study NC_000001.11 - 99578233 Jul 12, 2019 (153)
111 CNV burdens in cranial meningiomas NC_000001.10 - 100043789 Apr 25, 2021 (155)
112 Qatari NC_000001.10 - 100043789 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000001.10 - 100043789 Apr 25, 2020 (154)
114 Siberian NC_000001.10 - 100043789 Apr 25, 2020 (154)
115 8.3KJPN NC_000001.10 - 100043789 Apr 25, 2021 (155)
116 TopMed NC_000001.11 - 99578233 Apr 25, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 100043789 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000001.10 - 100043789 Jul 12, 2019 (153)
119 ALFA NC_000001.11 - 99578233 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)
rs61613821 May 27, 2008 (130)
rs386528478 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78491959, ss85805101 NC_000001.8:99755809:A:G NC_000001.11:99578232:A:G (self)
ss108453536, ss110890760, ss118919080, ss163738777, ss198832592, ss205090579, ss275945298, ss284105665, ss290580476, ss479922489, ss1584861250 NC_000001.9:99816376:A:G NC_000001.11:99578232:A:G (self)
2871067, 1583762, 1128955, 1628932, 687049, 1732928, 598904, 11041, 724493, 1494493, 397822, 3282457, 1583762, 341154, ss218548612, ss230656712, ss238323680, ss479930382, ss480560430, ss484759440, ss536851757, ss648253889, ss778693699, ss782826448, ss783791322, ss832079861, ss834152489, ss975482952, ss1068127640, ss1292107500, ss1425910974, ss1574271510, ss1600816833, ss1643810866, ss1751859109, ss1794807575, ss1918682563, ss1946002821, ss1958296786, ss1966820766, ss2019862756, ss2147881468, ss2327381622, ss2632553616, ss2697808800, ss2710678272, ss2758637392, ss2987305638, ss3021113791, ss3343595899, ss3625546133, ss3626165274, ss3630587790, ss3632903279, ss3633598277, ss3634339251, ss3635291888, ss3636016807, ss3637042344, ss3640046611, ss3640984522, ss3641278510, ss3644498783, ss3651444572, ss3655390707, ss3727314039, ss3744050994, ss3744640220, ss3746574064, ss3772141457, ss3783495874, ss3789140915, ss3794013759, ss3826326545, ss3836553553, ss3849477513, ss3894555534, ss3984461729, ss4016927689, ss5145313150 NC_000001.10:100043788:A:G NC_000001.11:99578232:A:G (self)
20296116, 136546, 1469287, 49465, 15306673, 24303060, 6457964075, ss2165030817, ss3023694972, ss3084649205, ss3646731427, ss3687367090, ss3725048131, ss3770827996, ss3799574847, ss3841961550, ss3945091286, ss4460696725 NC_000001.11:99578232:A:G NC_000001.11:99578232:A:G (self)
ss16430738, ss20496838 NT_028050.13:8232732:A:G NC_000001.11:99578232:A:G (self)
ss2115164, ss41068515, ss97961317, ss102767802, ss138842551, ss155415373, ss160335477 NT_032977.9:70015706:A:G NC_000001.11:99578232:A:G (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 rs1339856

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.post596+ae089ad