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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.

rs2392039

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99597526 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.328108 (86847/264690, TOPMED)
G=0.314440 (44397/141194, ALFA)
G=0.311265 (43523/139826, GnomAD) (+ 15 more)
A=0.35626 (5971/16760, 8.3KJPN)
G=0.4213 (2110/5008, 1000G)
G=0.2857 (1280/4480, Estonian)
G=0.3033 (1169/3854, ALSPAC)
G=0.3101 (1150/3708, TWINSUK)
A=0.3215 (942/2930, KOREAN)
A=0.3302 (605/1832, Korea1K)
G=0.304 (303/998, GoNL)
G=0.275 (165/600, NorthernSweden)
G=0.292 (124/424, SGDP_PRJ)
G=0.370 (122/330, HapMap)
G=0.440 (95/216, Qatari)
A=0.322 (69/214, Vietnamese)
G=0.30 (14/46, Siberian)
G=0.40 (16/40, 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.99597526G>A
GRCh38.p13 chr 1 NC_000001.11:g.99597526G>C
GRCh37.p13 chr 1 NC_000001.10:g.100063082G>A
GRCh37.p13 chr 1 NC_000001.10:g.100063082G>C
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
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 141194 G=0.314440 A=0.685560, C=0.000000
European Sub 122188 G=0.306593 A=0.693407, C=0.000000
African Sub 5062 G=0.3161 A=0.6839, C=0.0000
African Others Sub 186 G=0.285 A=0.715, C=0.000
African American Sub 4876 G=0.3173 A=0.6827, C=0.0000
Asian Sub 622 G=0.616 A=0.384, C=0.000
East Asian Sub 490 G=0.639 A=0.361, C=0.000
Other Asian Sub 132 G=0.530 A=0.470, C=0.000
Latin American 1 Sub 736 G=0.334 A=0.666, C=0.000
Latin American 2 Sub 6272 G=0.4176 A=0.5824, C=0.0000
South Asian Sub 184 G=0.565 A=0.435, C=0.000
Other Sub 6130 G=0.3235 A=0.6765, C=0.0000


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=0.328108 A=0.671892
gnomAD - Genomes Global Study-wide 139826 G=0.311265 A=0.688735
gnomAD - Genomes European Sub 75800 G=0.29449 A=0.70551
gnomAD - Genomes African Sub 41844 G=0.29232 A=0.70768
gnomAD - Genomes American Sub 13602 G=0.38958 A=0.61042
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.2877 A=0.7123
gnomAD - Genomes East Asian Sub 3112 G=0.6478 A=0.3522
gnomAD - Genomes Other Sub 2148 G=0.3254 A=0.6746
8.3KJPN JAPANESE Study-wide 16760 G=0.64374 A=0.35626
1000Genomes Global Study-wide 5008 G=0.4213 A=0.5787
1000Genomes African Sub 1322 G=0.2648 A=0.7352
1000Genomes East Asian Sub 1008 G=0.6220 A=0.3780
1000Genomes Europe Sub 1006 G=0.3022 A=0.6978
1000Genomes South Asian Sub 978 G=0.571 A=0.429
1000Genomes American Sub 694 G=0.390 A=0.610
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2857 A=0.7143
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3033 A=0.6967
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3101 A=0.6899
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6785 A=0.3215
Korean Genome Project KOREAN Study-wide 1832 G=0.6698 A=0.3302
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.304 A=0.696
Northern Sweden ACPOP Study-wide 600 G=0.275 A=0.725
SGDP_PRJ Global Study-wide 424 G=0.292 A=0.708
HapMap Global Study-wide 330 G=0.370 A=0.630
HapMap African Sub 120 G=0.258 A=0.742
HapMap American Sub 120 G=0.292 A=0.708
HapMap Asian Sub 90 G=0.62 A=0.38
Qatari Global Study-wide 216 G=0.440 A=0.560
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.678 A=0.322
Siberian Global Study-wide 46 G=0.30 A=0.70
The Danish reference pan genome Danish Study-wide 40 G=0.40 A=0.60
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 C
GRCh38.p13 chr 1 NC_000001.11:g.99597526= NC_000001.11:g.99597526G>A NC_000001.11:g.99597526G>C
GRCh37.p13 chr 1 NC_000001.10:g.100063082= NC_000001.10:g.100063082G>A NC_000001.10:g.100063082G>C
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#.

90 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3354061 Sep 28, 2001 (100)
2 CSHL-HAPMAP ss19830812 Feb 27, 2004 (120)
3 SSAHASNP ss20451873 Apr 05, 2004 (121)
4 ABI ss44020172 Mar 15, 2006 (126)
5 HGSV ss86050915 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss87656594 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss97961357 Feb 06, 2009 (130)
8 BGI ss102767837 Dec 01, 2009 (131)
9 1000GENOMES ss108453767 Jan 23, 2009 (130)
10 1000GENOMES ss110891168 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118919261 Feb 15, 2009 (130)
12 ENSEMBL ss138842440 Dec 01, 2009 (131)
13 GMI ss155415698 Dec 01, 2009 (131)
14 ILLUMINA ss160543140 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss163739296 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss164869296 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss166904839 Jul 04, 2010 (132)
18 BUSHMAN ss198832848 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss205102655 Jul 04, 2010 (132)
20 1000GENOMES ss218548692 Jul 14, 2010 (132)
21 1000GENOMES ss230656774 Jul 14, 2010 (132)
22 1000GENOMES ss238323742 Jul 15, 2010 (132)
23 BL ss253316028 May 09, 2011 (134)
24 GMI ss275945350 May 04, 2012 (137)
25 GMI ss284105698 Apr 25, 2013 (138)
26 PJP ss290580516 May 09, 2011 (134)
27 ILLUMINA ss480555406 May 04, 2012 (137)
28 ILLUMINA ss480569646 May 04, 2012 (137)
29 ILLUMINA ss481386941 Sep 08, 2015 (146)
30 ILLUMINA ss485073360 May 04, 2012 (137)
31 ILLUMINA ss537085709 Sep 08, 2015 (146)
32 TISHKOFF ss554480733 Apr 25, 2013 (138)
33 SSMP ss648253999 Apr 25, 2013 (138)
34 ILLUMINA ss778867760 Aug 21, 2014 (142)
35 ILLUMINA ss782982950 Aug 21, 2014 (142)
36 ILLUMINA ss783943933 Aug 21, 2014 (142)
37 ILLUMINA ss832239546 Apr 01, 2015 (144)
38 ILLUMINA ss834328625 Aug 21, 2014 (142)
39 EVA-GONL ss975483098 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1068127773 Aug 21, 2014 (142)
41 1000GENOMES ss1292108081 Aug 21, 2014 (142)
42 DDI ss1425911019 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1574271669 Apr 01, 2015 (144)
44 EVA_DECODE ss1584861408 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1600817180 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1643811213 Apr 01, 2015 (144)
47 ILLUMINA ss1751859119 Sep 08, 2015 (146)
48 HAMMER_LAB ss1794807789 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1918682687 Feb 12, 2016 (147)
50 GENOMED ss1966820808 Jul 19, 2016 (147)
51 JJLAB ss2019862856 Sep 14, 2016 (149)
52 USC_VALOUEV ss2147881555 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2165031978 Dec 20, 2016 (150)
54 TOPMED ss2327382781 Dec 20, 2016 (150)
55 ILLUMINA ss2632553631 Nov 08, 2017 (151)
56 GRF ss2697808885 Nov 08, 2017 (151)
57 GNOMAD ss2758638878 Nov 08, 2017 (151)
58 SWEGEN ss2987305820 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3023695017 Nov 08, 2017 (151)
60 TOPMED ss3084652630 Nov 08, 2017 (151)
61 TOPMED ss3084652631 Nov 08, 2017 (151)
62 CSHL ss3343595979 Nov 08, 2017 (151)
63 ILLUMINA ss3626165304 Oct 11, 2018 (152)
64 ILLUMINA ss3630587805 Oct 11, 2018 (152)
65 ILLUMINA ss3632903288 Oct 11, 2018 (152)
66 ILLUMINA ss3633598286 Oct 11, 2018 (152)
67 ILLUMINA ss3634339261 Oct 11, 2018 (152)
68 ILLUMINA ss3635291897 Oct 11, 2018 (152)
69 ILLUMINA ss3636016815 Oct 11, 2018 (152)
70 ILLUMINA ss3637042353 Oct 11, 2018 (152)
71 ILLUMINA ss3640046621 Oct 11, 2018 (152)
72 URBANLAB ss3646731472 Oct 11, 2018 (152)
73 EGCUT_WGS ss3655390933 Jul 12, 2019 (153)
74 EVA_DECODE ss3687367329 Jul 12, 2019 (153)
75 ACPOP ss3727314163 Jul 12, 2019 (153)
76 ILLUMINA ss3744640230 Jul 12, 2019 (153)
77 EVA ss3746574252 Jul 12, 2019 (153)
78 ILLUMINA ss3772141467 Jul 12, 2019 (153)
79 PACBIO ss3783495924 Jul 12, 2019 (153)
80 PACBIO ss3789140959 Jul 12, 2019 (153)
81 PACBIO ss3794013803 Jul 12, 2019 (153)
82 KHV_HUMAN_GENOMES ss3799575011 Jul 12, 2019 (153)
83 EVA ss3826326636 Apr 25, 2020 (154)
84 EVA ss3836553592 Apr 25, 2020 (154)
85 EVA ss3841961589 Apr 25, 2020 (154)
86 SGDP_PRJ ss3849477780 Apr 25, 2020 (154)
87 KRGDB ss3894555835 Apr 25, 2020 (154)
88 KOGIC ss3945091525 Apr 25, 2020 (154)
89 TOPMED ss4460701528 Apr 25, 2021 (155)
90 TOMMO_GENOMICS ss5145313680 Apr 25, 2021 (155)
91 1000Genomes NC_000001.10 - 100063082 Oct 11, 2018 (152)
92 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100063082 Oct 11, 2018 (152)
93 Genetic variation in the Estonian population NC_000001.10 - 100063082 Oct 11, 2018 (152)
94 The Danish reference pan genome NC_000001.10 - 100063082 Apr 25, 2020 (154)
95 gnomAD - Genomes NC_000001.11 - 99597526 Apr 25, 2021 (155)
96 Genome of the Netherlands Release 5 NC_000001.10 - 100063082 Apr 25, 2020 (154)
97 HapMap NC_000001.11 - 99597526 Apr 25, 2020 (154)
98 KOREAN population from KRGDB NC_000001.10 - 100063082 Apr 25, 2020 (154)
99 Korean Genome Project NC_000001.11 - 99597526 Apr 25, 2020 (154)
100 Northern Sweden NC_000001.10 - 100063082 Jul 12, 2019 (153)
101 Qatari NC_000001.10 - 100063082 Apr 25, 2020 (154)
102 SGDP_PRJ NC_000001.10 - 100063082 Apr 25, 2020 (154)
103 Siberian NC_000001.10 - 100063082 Apr 25, 2020 (154)
104 8.3KJPN NC_000001.10 - 100063082 Apr 25, 2021 (155)
105 TopMed NC_000001.11 - 99597526 Apr 25, 2021 (155)
106 UK 10K study - Twins NC_000001.10 - 100063082 Oct 11, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000001.10 - 100063082 Jul 12, 2019 (153)
108 ALFA NC_000001.11 - 99597526 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)
rs60179223 May 25, 2008 (130)
rs386566340 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss86050915 NC_000001.8:99775102:G:A NC_000001.11:99597525:G:A (self)
ss87656594, ss108453767, ss110891168, ss118919261, ss163739296, ss164869296, ss166904839, ss198832848, ss205102655, ss253316028, ss275945350, ss284105698, ss290580516, ss480555406, ss1584861408 NC_000001.9:99835669:G:A NC_000001.11:99597525:G:A (self)
2871660, 1584124, 1129181, 1628992, 687195, 1733229, 599028, 724617, 1494760, 397909, 3282987, 1584124, 341245, ss218548692, ss230656774, ss238323742, ss480569646, ss481386941, ss485073360, ss537085709, ss554480733, ss648253999, ss778867760, ss782982950, ss783943933, ss832239546, ss834328625, ss975483098, ss1068127773, ss1292108081, ss1425911019, ss1574271669, ss1600817180, ss1643811213, ss1751859119, ss1794807789, ss1918682687, ss1966820808, ss2019862856, ss2147881555, ss2327382781, ss2632553631, ss2697808885, ss2758638878, ss2987305820, ss3343595979, ss3626165304, ss3630587805, ss3632903288, ss3633598286, ss3634339261, ss3635291897, ss3636016815, ss3637042353, ss3640046621, ss3655390933, ss3727314163, ss3744640230, ss3746574252, ss3772141467, ss3783495924, ss3789140959, ss3794013803, ss3826326636, ss3836553592, ss3849477780, ss3894555835, ss5145313680 NC_000001.10:100063081:G:A NC_000001.11:99597525:G:A (self)
20299886, 136587, 1469526, 15309751, 24307863, 9174731534, ss2165031978, ss3023695017, ss3084652630, ss3646731472, ss3687367329, ss3799575011, ss3841961589, ss3945091525, ss4460701528 NC_000001.11:99597525:G:A NC_000001.11:99597525:G:A (self)
ss19830812, ss20451873 NT_028050.13:8252025:G:A NC_000001.11:99597525:G:A (self)
ss3354061, ss44020172, ss97961357, ss102767837, ss138842440, ss155415698, ss160543140 NT_032977.9:70034999:G:A NC_000001.11:99597525:G:A (self)
9174731534, ss3084652631 NC_000001.11:99597525:G:C NC_000001.11:99597525:G:C (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 rs2392039

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