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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.

rs10432782

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:31664078 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.204186 (54046/264690, TOPMED)
G=0.189980 (26606/140046, GnomAD)
T=0.48369 (13668/28258, 14KJPN) (+ 16 more)
T=0.48317 (8098/16760, 8.3KJPN)
G=0.07220 (1131/15664, ALFA)
G=0.2887 (1849/6404, 1000G_30x)
G=0.2949 (1477/5008, 1000G)
G=0.1315 (589/4480, Estonian)
G=0.1092 (421/3854, ALSPAC)
G=0.1046 (388/3708, TWINSUK)
T=0.4959 (1453/2930, KOREAN)
G=0.115 (115/998, GoNL)
G=0.135 (81/600, NorthernSweden)
G=0.245 (80/326, HapMap)
T=0.355 (100/282, SGDP_PRJ)
G=0.102 (22/216, Qatari)
T=0.481 (102/212, Vietnamese)
G=0.12 (5/40, GENOME_DK)
T=0.45 (10/22, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SOD1 : Intron Variant
LOC124900469 : 2KB Upstream Variant
Publications
12 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 15664 T=0.92780 C=0.00000, G=0.07220
European Sub 12796 T=0.92701 C=0.00000, G=0.07299
African Sub 1878 T=0.9164 C=0.0000, G=0.0836
African Others Sub 56 T=0.91 C=0.00, G=0.09
African American Sub 1822 T=0.9166 C=0.0000, G=0.0834
Asian Sub 32 T=0.94 C=0.00, G=0.06
East Asian Sub 18 T=0.94 C=0.00, G=0.06
Other Asian Sub 14 T=0.93 C=0.00, G=0.07
Latin American 1 Sub 114 T=1.000 C=0.000, G=0.000
Latin American 2 Sub 278 T=1.000 C=0.000, G=0.000
South Asian Sub 66 T=0.97 C=0.00, G=0.03
Other Sub 500 T=0.928 C=0.000, G=0.072


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 T=0.795814 G=0.204186
gnomAD - Genomes Global Study-wide 140046 T=0.810020 G=0.189980
gnomAD - Genomes European Sub 75896 T=0.87584 G=0.12416
gnomAD - Genomes African Sub 41914 T=0.72238 G=0.27762
gnomAD - Genomes American Sub 13644 T=0.76554 G=0.23446
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9031 G=0.0969
gnomAD - Genomes East Asian Sub 3120 T=0.4724 G=0.5276
gnomAD - Genomes Other Sub 2150 T=0.8233 G=0.1767
14KJPN JAPANESE Study-wide 28258 T=0.48369 G=0.51631
8.3KJPN JAPANESE Study-wide 16760 T=0.48317 G=0.51683
Allele Frequency Aggregator Total Global 15664 T=0.92780 C=0.00000, G=0.07220
Allele Frequency Aggregator European Sub 12796 T=0.92701 C=0.00000, G=0.07299
Allele Frequency Aggregator African Sub 1878 T=0.9164 C=0.0000, G=0.0836
Allele Frequency Aggregator Other Sub 500 T=0.928 C=0.000, G=0.072
Allele Frequency Aggregator Latin American 2 Sub 278 T=1.000 C=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 114 T=1.000 C=0.000, G=0.000
Allele Frequency Aggregator South Asian Sub 66 T=0.97 C=0.00, G=0.03
Allele Frequency Aggregator Asian Sub 32 T=0.94 C=0.00, G=0.06
1000Genomes_30x Global Study-wide 6404 T=0.7113 G=0.2887
1000Genomes_30x African Sub 1786 T=0.6937 G=0.3063
1000Genomes_30x Europe Sub 1266 T=0.8689 G=0.1311
1000Genomes_30x South Asian Sub 1202 T=0.7671 G=0.2329
1000Genomes_30x East Asian Sub 1170 T=0.4812 G=0.5188
1000Genomes_30x American Sub 980 T=0.746 G=0.254
1000Genomes Global Study-wide 5008 T=0.7051 G=0.2949
1000Genomes African Sub 1322 T=0.6899 G=0.3101
1000Genomes East Asian Sub 1008 T=0.4821 G=0.5179
1000Genomes Europe Sub 1006 T=0.8678 G=0.1322
1000Genomes South Asian Sub 978 T=0.760 G=0.240
1000Genomes American Sub 694 T=0.745 G=0.255
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8685 G=0.1315
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8908 G=0.1092
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8954 G=0.1046
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4959 G=0.5041
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.885 G=0.115
Northern Sweden ACPOP Study-wide 600 T=0.865 G=0.135
HapMap Global Study-wide 326 T=0.755 G=0.245
HapMap African Sub 120 T=0.733 G=0.267
HapMap American Sub 118 T=0.881 G=0.119
HapMap Asian Sub 88 T=0.61 G=0.39
SGDP_PRJ Global Study-wide 282 T=0.355 G=0.645
Qatari Global Study-wide 216 T=0.898 G=0.102
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.481 G=0.519
The Danish reference pan genome Danish Study-wide 40 T=0.88 G=0.12
Siberian Global Study-wide 22 T=0.45 G=0.55
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 21 NC_000021.9:g.31664078T>C
GRCh38.p14 chr 21 NC_000021.9:g.31664078T>G
GRCh37.p13 chr 21 NC_000021.8:g.33036391T>C
GRCh37.p13 chr 21 NC_000021.8:g.33036391T>G
SOD1 RefSeqGene (LRG_652) NG_008689.1:g.9457T>C
SOD1 RefSeqGene (LRG_652) NG_008689.1:g.9457T>G
Gene: SOD1, superoxide dismutase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SOD1 transcript NM_000454.5:c.169+192T>C N/A Intron Variant
Gene: LOC124900469, uncharacterized LOC124900469 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC124900469 transcript XR_007067939.1:n. N/A Upstream Transcript Variant
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.

Allele: G (allele ID: 1213682 )
ClinVar Accession Disease Names Clinical Significance
RCV001595938.3 not provided Benign
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 T= C G
GRCh38.p14 chr 21 NC_000021.9:g.31664078= NC_000021.9:g.31664078T>C NC_000021.9:g.31664078T>G
GRCh37.p13 chr 21 NC_000021.8:g.33036391= NC_000021.8:g.33036391T>C NC_000021.8:g.33036391T>G
SOD1 RefSeqGene (LRG_652) NG_008689.1:g.9457= NG_008689.1:g.9457T>C NG_008689.1:g.9457T>G
SOD1 transcript NM_000454.4:c.169+192= NM_000454.4:c.169+192T>C NM_000454.4:c.169+192T>G
SOD1 transcript NM_000454.5:c.169+192= NM_000454.5:c.169+192T>C NM_000454.5:c.169+192T>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#.

57 SubSNP, 19 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14742912 Dec 05, 2003 (119)
2 HGRG-RIK ss16338423 Feb 28, 2004 (126)
3 EGP_SNPS ss32469355 Dec 02, 2004 (126)
4 HGSV ss83279926 Dec 15, 2007 (130)
5 SNP500CANCER ss105440365 Feb 05, 2009 (130)
6 1000GENOMES ss112432910 Jan 25, 2009 (130)
7 GMI ss156850572 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss167916216 Jul 04, 2010 (132)
9 BUSHMAN ss204002164 Jul 04, 2010 (132)
10 1000GENOMES ss228538510 Jul 14, 2010 (132)
11 1000GENOMES ss237963549 Jul 15, 2010 (132)
12 1000GENOMES ss244106365 Jul 15, 2010 (132)
13 GMI ss283524200 May 04, 2012 (137)
14 TISHKOFF ss566464649 Apr 25, 2013 (138)
15 SSMP ss662375366 Apr 25, 2013 (138)
16 EVA-GONL ss995070839 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1082463921 Aug 21, 2014 (142)
18 1000GENOMES ss1366113116 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1579644524 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1639464973 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1682459006 Apr 01, 2015 (144)
22 EVA_DECODE ss1699140091 Apr 01, 2015 (144)
23 HAMMER_LAB ss1809664347 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1938622664 Feb 12, 2016 (147)
25 GENOMED ss1969214291 Jul 19, 2016 (147)
26 JJLAB ss2030082323 Sep 14, 2016 (149)
27 USC_VALOUEV ss2158685285 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2245424597 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2629539567 Nov 08, 2017 (151)
30 GRF ss2704414461 Nov 08, 2017 (151)
31 GNOMAD ss2971309978 Nov 08, 2017 (151)
32 SWEGEN ss3018819283 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3028879376 Nov 08, 2017 (151)
34 CSHL ss3352697212 Nov 08, 2017 (151)
35 EGCUT_WGS ss3685396606 Jul 13, 2019 (153)
36 EVA_DECODE ss3707643310 Jul 13, 2019 (153)
37 ACPOP ss3743692151 Jul 13, 2019 (153)
38 EVA ss3759052838 Jul 13, 2019 (153)
39 KHV_HUMAN_GENOMES ss3822220481 Jul 13, 2019 (153)
40 EVA ss3835850668 Apr 27, 2020 (154)
41 EVA ss3841552335 Apr 27, 2020 (154)
42 EVA ss3847065879 Apr 27, 2020 (154)
43 SGDP_PRJ ss3889909920 Apr 27, 2020 (154)
44 KRGDB ss3940260244 Apr 27, 2020 (154)
45 TOPMED ss5100151575 Apr 27, 2021 (155)
46 TOMMO_GENOMICS ss5231335116 Apr 27, 2021 (155)
47 1000G_HIGH_COVERAGE ss5310067479 Oct 13, 2022 (156)
48 EVA ss5439608163 Oct 13, 2022 (156)
49 HUGCELL_USP ss5502127995 Oct 13, 2022 (156)
50 1000G_HIGH_COVERAGE ss5617140133 Oct 13, 2022 (156)
51 SANFORD_IMAGENETICS ss5663926040 Oct 13, 2022 (156)
52 TOMMO_GENOMICS ss5791793095 Oct 13, 2022 (156)
53 YY_MCH ss5818407702 Oct 13, 2022 (156)
54 EVA ss5838979271 Oct 13, 2022 (156)
55 EVA ss5853285878 Oct 13, 2022 (156)
56 EVA ss5892181226 Oct 13, 2022 (156)
57 EVA ss5958817970 Oct 13, 2022 (156)
58 1000Genomes NC_000021.8 - 33036391 Oct 12, 2018 (152)
59 1000Genomes_30x NC_000021.9 - 31664078 Oct 13, 2022 (156)
60 The Avon Longitudinal Study of Parents and Children NC_000021.8 - 33036391 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000021.8 - 33036391 Oct 12, 2018 (152)
62 The Danish reference pan genome NC_000021.8 - 33036391 Apr 27, 2020 (154)
63 gnomAD - Genomes NC_000021.9 - 31664078 Apr 27, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000021.8 - 33036391 Apr 27, 2020 (154)
65 HapMap NC_000021.9 - 31664078 Apr 27, 2020 (154)
66 KOREAN population from KRGDB NC_000021.8 - 33036391 Apr 27, 2020 (154)
67 Northern Sweden NC_000021.8 - 33036391 Jul 13, 2019 (153)
68 Qatari NC_000021.8 - 33036391 Apr 27, 2020 (154)
69 SGDP_PRJ NC_000021.8 - 33036391 Apr 27, 2020 (154)
70 Siberian NC_000021.8 - 33036391 Apr 27, 2020 (154)
71 8.3KJPN NC_000021.8 - 33036391 Apr 27, 2021 (155)
72 14KJPN NC_000021.9 - 31664078 Oct 13, 2022 (156)
73 TopMed NC_000021.9 - 31664078 Apr 27, 2021 (155)
74 UK 10K study - Twins NC_000021.8 - 33036391 Oct 12, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000021.8 - 33036391 Jul 13, 2019 (153)
76 ALFA NC_000021.9 - 31664078 Apr 27, 2021 (155)
77 ClinVar RCV001595938.3 Oct 13, 2022 (156)
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)
rs11567844 Mar 11, 2006 (126)
rs17883726 Mar 11, 2006 (126)
rs59567187 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10996089389 NC_000021.9:31664077:T:C NC_000021.9:31664077:T:C (self)
ss83279926, ss112432910, ss167916216, ss204002164, ss283524200, ss1699140091 NC_000021.7:31958261:T:G NC_000021.9:31664077:T:G (self)
79625987, 44062077, 31134854, 5809463, 19630028, 47437638, 16977016, 20664586, 41926900, 11201639, 89304423, 44062077, 9723570, ss228538510, ss237963549, ss244106365, ss566464649, ss662375366, ss995070839, ss1082463921, ss1366113116, ss1579644524, ss1639464973, ss1682459006, ss1809664347, ss1938622664, ss1969214291, ss2030082323, ss2158685285, ss2629539567, ss2704414461, ss2971309978, ss3018819283, ss3352697212, ss3685396606, ss3743692151, ss3759052838, ss3835850668, ss3841552335, ss3889909920, ss3940260244, ss5231335116, ss5439608163, ss5663926040, ss5838979271, ss5958817970 NC_000021.8:33036390:T:G NC_000021.9:31664077:T:G (self)
RCV001595938.3, 104666068, 561987135, 2200717, 125630199, 375260521, 10996089389, ss2245424597, ss3028879376, ss3707643310, ss3822220481, ss3847065879, ss5100151575, ss5310067479, ss5502127995, ss5617140133, ss5791793095, ss5818407702, ss5853285878, ss5892181226 NC_000021.9:31664077:T:G NC_000021.9:31664077:T:G (self)
ss14742912 NT_011512.9:18696787:T:G NC_000021.9:31664077:T:G (self)
ss16338423, ss32469355, ss105440365, ss156850572 NT_011512.11:18698261:T:G NC_000021.9:31664077:T:G (self)
Help

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

12 citations for rs10432782
PMID Title Author Year Journal
19423521 Genetic polymorphisms in nitric oxide synthase genes modify the relationship between vegetable and fruit intake and risk of non-Hodgkin lymphoma. Han X et al. 2009 Cancer epidemiology, biomarkers & prevention
19895330 Association between polymorphisms in SOD1 and noise-induced hearing loss in Chinese workers. Liu YM et al. 2010 Acta oto-laryngologica
20477822 Single-nucleotide polymorphisms within the antioxidant defence system and associations with aggressive prostate cancer. Abe M et al. 2011 BJU international
21940907 Joint effects of alcohol consumption and polymorphisms in alcohol and oxidative stress metabolism genes on risk of head and neck cancer. Hakenewerth AM et al. 2011 Cancer epidemiology, biomarkers & prevention
22608880 Allelic variations in superoxide dismutase-1 (SOD1) gene and renal and cardiovascular morbidity and mortality in type 2 diabetic subjects. Neves AL et al. 2012 Molecular genetics and metabolism
25315963 Oxidative stress-related genetic variants, pro- and antioxidant intake and status, and advanced prostate cancer risk. Geybels MS et al. 2015 Cancer epidemiology, biomarkers & prevention
25463281 Association between maternal micronutrient status, oxidative stress, and common genetic variants in antioxidant enzymes at 15 weeks׳ gestation in nulliparous women who subsequently develop preeclampsia. Mistry HD et al. 2015 Free radical biology & medicine
27713515 The influence of single nucleotide polymorphisms on the association between dietary acrylamide intake and endometrial cancer risk. Hogervorst JG et al. 2016 Scientific reports
31647334 Impact of oxidative stress SNPs and dietary antioxidant quality score on prostate cancer. Pascual-Geler M et al. 2020 International journal of food sciences and nutrition
32388358 Genetic variants in xenobiotic detoxification enzymes, antioxidant defenses and hormonal pathways as biomarkers of susceptibility to prostate cancer. Martinez-Gonzalez LJ et al. 2020 The Science of the total environment
32991532 Influence of Oxidative Stress-Related Genes on Susceptibility to Fibromyalgia. Rus A et al. 2021 Nursing research
35764155 Genetic variants of antioxidant enzymes and environmental exposures as molecular biomarkers associated with the risk and aggressiveness of bladder cancer. Martin-Way D et al. 2022 The Science of the total environment
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