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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.

rs8177406

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr5:151020073 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.148578 (39327/264690, TOPMED)
C=0.131789 (23358/177238, ALFA)
C=0.149664 (20973/140134, GnomAD) (+ 19 more)
C=0.11444 (1918/16760, 8.3KJPN)
C=0.1565 (784/5008, 1000G)
C=0.1529 (685/4480, Estonian)
C=0.1310 (505/3854, ALSPAC)
C=0.1195 (443/3708, TWINSUK)
C=0.1612 (471/2922, KOREAN)
C=0.1799 (375/2084, HGDP_Stanford)
C=0.1691 (320/1892, HapMap)
C=0.1425 (261/1832, Korea1K)
C=0.133 (133/998, GoNL)
C=0.128 (101/788, PRJEB37584)
C=0.082 (49/600, NorthernSweden)
C=0.264 (57/216, Qatari)
C=0.107 (23/214, Vietnamese)
T=0.473 (71/150, SGDP_PRJ)
C=0.09 (8/86, Ancient Sardinia)
C=0.28 (11/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPX3 : 2KB Upstream Variant
LOC105378228 : Non Coding Transcript Variant
Publications
4 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 177238 T=0.868211 C=0.131789
European Sub 150124 T=0.869961 C=0.130039
African Sub 7062 T=0.7951 C=0.2049
African Others Sub 264 T=0.773 C=0.227
African American Sub 6798 T=0.7960 C=0.2040
Asian Sub 700 T=0.857 C=0.143
East Asian Sub 554 T=0.866 C=0.134
Other Asian Sub 146 T=0.822 C=0.178
Latin American 1 Sub 840 T=0.836 C=0.164
Latin American 2 Sub 6888 T=0.9294 C=0.0706
South Asian Sub 5042 T=0.8445 C=0.1555
Other Sub 6582 T=0.8662 C=0.1338


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=0.851422 C=0.148578
Allele Frequency Aggregator Total Global 177238 T=0.868211 C=0.131789
Allele Frequency Aggregator European Sub 150124 T=0.869961 C=0.130039
Allele Frequency Aggregator African Sub 7062 T=0.7951 C=0.2049
Allele Frequency Aggregator Latin American 2 Sub 6888 T=0.9294 C=0.0706
Allele Frequency Aggregator Other Sub 6582 T=0.8662 C=0.1338
Allele Frequency Aggregator South Asian Sub 5042 T=0.8445 C=0.1555
Allele Frequency Aggregator Latin American 1 Sub 840 T=0.836 C=0.164
Allele Frequency Aggregator Asian Sub 700 T=0.857 C=0.143
gnomAD - Genomes Global Study-wide 140134 T=0.850336 C=0.149664
gnomAD - Genomes European Sub 75924 T=0.86974 C=0.13026
gnomAD - Genomes African Sub 41960 T=0.79521 C=0.20479
gnomAD - Genomes American Sub 13650 T=0.90462 C=0.09538
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.8721 C=0.1279
gnomAD - Genomes East Asian Sub 3128 T=0.8440 C=0.1560
gnomAD - Genomes Other Sub 2148 T=0.8720 C=0.1280
8.3KJPN JAPANESE Study-wide 16760 T=0.88556 C=0.11444
1000Genomes Global Study-wide 5008 T=0.8435 C=0.1565
1000Genomes African Sub 1322 T=0.7632 C=0.2368
1000Genomes East Asian Sub 1008 T=0.8482 C=0.1518
1000Genomes Europe Sub 1006 T=0.8847 C=0.1153
1000Genomes South Asian Sub 978 T=0.855 C=0.145
1000Genomes American Sub 694 T=0.914 C=0.086
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8471 C=0.1529
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8690 C=0.1310
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8805 C=0.1195
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.8388 C=0.1612, G=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.8201 C=0.1799
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.819 C=0.181
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.754 C=0.246
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.789 C=0.211
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.856 C=0.144
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.731 C=0.269
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.991 C=0.009
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.99 C=0.01
HapMap Global Study-wide 1892 T=0.8309 C=0.1691
HapMap American Sub 770 T=0.884 C=0.116
HapMap African Sub 692 T=0.753 C=0.247
HapMap Asian Sub 254 T=0.862 C=0.138
HapMap Europe Sub 176 T=0.858 C=0.142
Korean Genome Project KOREAN Study-wide 1832 T=0.8575 C=0.1425
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.867 C=0.133
CNV burdens in cranial meningiomas Global Study-wide 788 T=0.872 C=0.128
CNV burdens in cranial meningiomas CRM Sub 788 T=0.872 C=0.128
Northern Sweden ACPOP Study-wide 600 T=0.918 C=0.082
Qatari Global Study-wide 216 T=0.736 C=0.264
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.893 C=0.107
SGDP_PRJ Global Study-wide 150 T=0.473 C=0.527
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 86 T=0.91 C=0.09
The Danish reference pan genome Danish Study-wide 40 T=0.72 C=0.28
Siberian Global Study-wide 6 T=0.5 C=0.5
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 5 NC_000005.10:g.151020073T>C
GRCh38.p13 chr 5 NC_000005.10:g.151020073T>G
GRCh37.p13 chr 5 NC_000005.9:g.150399634T>C
GRCh37.p13 chr 5 NC_000005.9:g.150399634T>G
Gene: GPX3, glutathione peroxidase 3 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
GPX3 transcript variant 2 NM_001329790.2:c. N/A Upstream Transcript Variant
GPX3 transcript variant 1 NM_002084.5:c. N/A Upstream Transcript Variant
Gene: LOC105378228, uncharacterized LOC105378228 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378228 transcript XR_944410.2:n.257A>G N/A Non Coding Transcript Variant
LOC105378228 transcript XR_944410.2:n.257A>C N/A Non Coding 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.

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 T= C G
GRCh38.p13 chr 5 NC_000005.10:g.151020073= NC_000005.10:g.151020073T>C NC_000005.10:g.151020073T>G
GRCh37.p13 chr 5 NC_000005.9:g.150399634= NC_000005.9:g.150399634T>C NC_000005.9:g.150399634T>G
LOC105378228 transcript XR_944410.2:n.257= XR_944410.2:n.257A>G XR_944410.2:n.257A>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#.

96 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss8820582 Aug 27, 2003 (117)
2 KYUGEN ss28476799 Sep 20, 2004 (126)
3 STEJUSTINE-REGGEN ss51853755 Mar 16, 2006 (126)
4 ILLUMINA ss65753869 Oct 13, 2006 (127)
5 EGP_SNPS ss66859803 Nov 29, 2006 (127)
6 ILLUMINA ss67875574 Nov 29, 2006 (127)
7 ILLUMINA ss68018886 Nov 29, 2006 (127)
8 ILLUMINA ss68296414 Dec 12, 2006 (127)
9 PERLEGEN ss68953756 May 16, 2007 (127)
10 ILLUMINA ss70972424 May 25, 2008 (130)
11 ILLUMINA ss71583521 May 16, 2007 (127)
12 ILLUMINA ss75608129 Dec 06, 2007 (129)
13 KRIBB_YJKIM ss84791587 Dec 15, 2007 (130)
14 BGI ss104251122 Dec 01, 2009 (131)
15 SNP500CANCER ss105435093 Feb 05, 2009 (130)
16 1000GENOMES ss109511965 Jan 24, 2009 (130)
17 ILLUMINA ss154471184 Dec 01, 2009 (131)
18 ILLUMINA ss159102403 Dec 01, 2009 (131)
19 ILLUMINA ss159645719 Dec 01, 2009 (131)
20 ILLUMINA ss160953654 Dec 01, 2009 (131)
21 ILLUMINA ss174732840 Jul 04, 2010 (132)
22 1000GENOMES ss222037456 Jul 14, 2010 (132)
23 1000GENOMES ss233198302 Jul 14, 2010 (132)
24 1000GENOMES ss240311455 Jul 15, 2010 (132)
25 BL ss253884601 May 09, 2011 (134)
26 GMI ss278531088 May 04, 2012 (137)
27 ILLUMINA ss481795817 May 04, 2012 (137)
28 ILLUMINA ss481828164 May 04, 2012 (137)
29 ILLUMINA ss482789605 Sep 08, 2015 (146)
30 ILLUMINA ss485692545 May 04, 2012 (137)
31 ILLUMINA ss537560050 Sep 08, 2015 (146)
32 TISHKOFF ss558795495 Apr 25, 2013 (138)
33 SSMP ss652699664 Apr 25, 2013 (138)
34 ILLUMINA ss778999151 Sep 08, 2015 (146)
35 ILLUMINA ss783291856 Sep 08, 2015 (146)
36 ILLUMINA ss784244450 Sep 08, 2015 (146)
37 ILLUMINA ss832553111 Sep 08, 2015 (146)
38 ILLUMINA ss833156551 Jul 13, 2019 (153)
39 ILLUMINA ss834461489 Sep 08, 2015 (146)
40 EVA-GONL ss982260330 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1073142162 Aug 21, 2014 (142)
42 1000GENOMES ss1317755425 Aug 21, 2014 (142)
43 EVA_GENOME_DK ss1581402236 Apr 01, 2015 (144)
44 EVA_DECODE ss1591793634 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1614301845 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1657295878 Apr 01, 2015 (144)
47 EVA_SVP ss1712810491 Apr 01, 2015 (144)
48 ILLUMINA ss1752556495 Sep 08, 2015 (146)
49 HAMMER_LAB ss1804139389 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1925514384 Feb 12, 2016 (147)
51 JJLAB ss2023365302 Sep 14, 2016 (149)
52 USC_VALOUEV ss2151523892 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2279285191 Dec 20, 2016 (150)
54 TOPMED ss2447603990 Dec 20, 2016 (150)
55 ILLUMINA ss2634356994 Nov 08, 2017 (151)
56 GRF ss2707093965 Nov 08, 2017 (151)
57 GNOMAD ss2832320155 Nov 08, 2017 (151)
58 SWEGEN ss2998006976 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3025464129 Nov 08, 2017 (151)
60 CSHL ss3346685411 Nov 08, 2017 (151)
61 TOPMED ss3482221293 Nov 08, 2017 (151)
62 ILLUMINA ss3629372177 Oct 12, 2018 (152)
63 ILLUMINA ss3632279877 Oct 12, 2018 (152)
64 ILLUMINA ss3633394425 Oct 12, 2018 (152)
65 ILLUMINA ss3634115831 Oct 12, 2018 (152)
66 ILLUMINA ss3635029153 Oct 12, 2018 (152)
67 ILLUMINA ss3636742144 Oct 12, 2018 (152)
68 ILLUMINA ss3637550122 Oct 12, 2018 (152)
69 ILLUMINA ss3638588759 Oct 12, 2018 (152)
70 ILLUMINA ss3639296602 Oct 12, 2018 (152)
71 ILLUMINA ss3639945179 Oct 12, 2018 (152)
72 ILLUMINA ss3640736447 Oct 12, 2018 (152)
73 ILLUMINA ss3643532102 Oct 12, 2018 (152)
74 ILLUMINA ss3643990449 Oct 12, 2018 (152)
75 EGCUT_WGS ss3665928176 Jul 13, 2019 (153)
76 EVA_DECODE ss3715961686 Jul 13, 2019 (153)
77 ACPOP ss3732929318 Jul 13, 2019 (153)
78 ILLUMINA ss3745329332 Jul 13, 2019 (153)
79 EVA ss3764227046 Jul 13, 2019 (153)
80 ILLUMINA ss3772823257 Jul 13, 2019 (153)
81 PACBIO ss3785284297 Jul 13, 2019 (153)
82 PACBIO ss3790661603 Jul 13, 2019 (153)
83 PACBIO ss3795538651 Jul 13, 2019 (153)
84 KHV_HUMAN_GENOMES ss3807395406 Jul 13, 2019 (153)
85 EVA ss3829569161 Apr 26, 2020 (154)
86 EVA ss3838257839 Apr 26, 2020 (154)
87 EVA ss3843700950 Apr 26, 2020 (154)
88 HGDP ss3847811350 Apr 26, 2020 (154)
89 SGDP_PRJ ss3863251947 Apr 26, 2020 (154)
90 KRGDB ss3909929984 Apr 26, 2020 (154)
91 KOGIC ss3957902563 Apr 26, 2020 (154)
92 EVA ss3984556406 Apr 26, 2021 (155)
93 EVA ss3985178556 Apr 26, 2021 (155)
94 EVA ss4017238533 Apr 26, 2021 (155)
95 TOPMED ss4683423746 Apr 26, 2021 (155)
96 TOMMO_GENOMICS ss5174752480 Apr 26, 2021 (155)
97 1000Genomes NC_000005.9 - 150399634 Oct 12, 2018 (152)
98 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 150399634 Oct 12, 2018 (152)
99 Genetic variation in the Estonian population NC_000005.9 - 150399634 Oct 12, 2018 (152)
100 The Danish reference pan genome NC_000005.9 - 150399634 Apr 26, 2020 (154)
101 gnomAD - Genomes NC_000005.10 - 151020073 Apr 26, 2021 (155)
102 Genome of the Netherlands Release 5 NC_000005.9 - 150399634 Apr 26, 2020 (154)
103 HGDP-CEPH-db Supplement 1 NC_000005.8 - 150379827 Apr 26, 2020 (154)
104 HapMap NC_000005.10 - 151020073 Apr 26, 2020 (154)
105 KOREAN population from KRGDB NC_000005.9 - 150399634 Apr 26, 2020 (154)
106 Korean Genome Project NC_000005.10 - 151020073 Apr 26, 2020 (154)
107 Northern Sweden NC_000005.9 - 150399634 Jul 13, 2019 (153)
108 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000005.9 - 150399634 Apr 26, 2021 (155)
109 CNV burdens in cranial meningiomas NC_000005.9 - 150399634 Apr 26, 2021 (155)
110 Qatari NC_000005.9 - 150399634 Apr 26, 2020 (154)
111 SGDP_PRJ NC_000005.9 - 150399634 Apr 26, 2020 (154)
112 Siberian NC_000005.9 - 150399634 Apr 26, 2020 (154)
113 8.3KJPN NC_000005.9 - 150399634 Apr 26, 2021 (155)
114 TopMed NC_000005.10 - 151020073 Apr 26, 2021 (155)
115 UK 10K study - Twins NC_000005.9 - 150399634 Oct 12, 2018 (152)
116 A Vietnamese Genetic Variation Database NC_000005.9 - 150399634 Jul 13, 2019 (153)
117 ALFA NC_000005.10 - 151020073 Apr 26, 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)
rs17550829 Mar 11, 2006 (126)
rs36206980 Oct 25, 2006 (127)
rs59242567 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
489242, ss109511965, ss253884601, ss278531088, ss481795817, ss1591793634, ss1712810491, ss3639296602, ss3639945179, ss3643532102, ss3643990449, ss3847811350 NC_000005.8:150379826:T:C NC_000005.10:151020072:T:C (self)
29453151, 16388668, 11666424, 7567175, 7275716, 17107378, 6214183, 404483, 105779, 7556314, 15268927, 4040246, 32721787, 16388668, 3631937, ss222037456, ss233198302, ss240311455, ss481828164, ss482789605, ss485692545, ss537560050, ss558795495, ss652699664, ss778999151, ss783291856, ss784244450, ss832553111, ss833156551, ss834461489, ss982260330, ss1073142162, ss1317755425, ss1581402236, ss1614301845, ss1657295878, ss1752556495, ss1804139389, ss1925514384, ss2023365302, ss2151523892, ss2447603990, ss2634356994, ss2707093965, ss2832320155, ss2998006976, ss3346685411, ss3629372177, ss3632279877, ss3633394425, ss3634115831, ss3635029153, ss3636742144, ss3637550122, ss3638588759, ss3640736447, ss3665928176, ss3732929318, ss3745329332, ss3764227046, ss3772823257, ss3785284297, ss3790661603, ss3795538651, ss3829569161, ss3838257839, ss3863251947, ss3909929984, ss3984556406, ss3985178556, ss4017238533, ss5174752480 NC_000005.9:150399633:T:C NC_000005.10:151020072:T:C (self)
208324350, 2995576, 14280564, 325667742, 520801303, 11277437839, ss2279285191, ss3025464129, ss3482221293, ss3715961686, ss3807395406, ss3843700950, ss3957902563, ss4683423746 NC_000005.10:151020072:T:C NC_000005.10:151020072:T:C (self)
ss8820582, ss28476799, ss51853755, ss65753869, ss66859803, ss67875574, ss68018886, ss68296414, ss68953756, ss70972424, ss71583521, ss75608129, ss84791587, ss104251122, ss105435093, ss154471184, ss159102403, ss159645719, ss160953654, ss174732840 NT_029289.11:11562560:T:C NC_000005.10:151020072:T:C (self)
17107378, ss3909929984 NC_000005.9:150399633:T:G NC_000005.10:151020072: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.

4 citations for rs8177406
PMID Title Author Year Journal
22259188 Genetic variation in GPX1 is associated with GPX1 activity in a comprehensive analysis of genetic variations in selenoenzyme genes and their activity and oxidative stress in humans. Takata Y et al. 2012 The Journal of nutrition
22715394 Selenium, selenoenzymes, oxidative stress and risk of neoplastic progression from Barrett's esophagus: results from biomarkers and genetic variants. Takata Y et al. 2012 PloS one
24819036 Glutathione peroxidase 3 serum levels and GPX3 gene polymorphisms in subjects with metabolic syndrome. Baez-Duarte BG et al. 2014 Archives of medical research
32344219 Evaluation of oxidative stress-related genetic variants for predicting stroke in patients with sickle cell anemia. Domingos IF et al. 2020 Journal of the neurological sciences
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.post676+237644a