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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.

rs12602084

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:42559751 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.358397 (94864/264690, TOPMED)
T=0.353080 (49422/139974, GnomAD)
T=0.32787 (16376/49946, ALFA) (+ 20 more)
C=0.46015 (13003/28258, 14KJPN)
C=0.46163 (7737/16760, 8.3KJPN)
T=0.3545 (2270/6404, 1000G_30x)
T=0.3614 (1810/5008, 1000G)
T=0.4074 (1825/4480, Estonian)
T=0.3825 (1474/3854, ALSPAC)
T=0.3892 (1443/3708, TWINSUK)
C=0.3874 (1135/2930, KOREAN)
T=0.3921 (814/2076, HGDP_Stanford)
C=0.4023 (737/1832, Korea1K)
T=0.3201 (571/1784, HapMap)
T=0.374 (373/998, GoNL)
C=0.441 (347/786, PRJEB37584)
T=0.363 (218/600, NorthernSweden)
C=0.369 (118/320, SGDP_PRJ)
T=0.449 (97/216, Qatari)
C=0.443 (94/212, Vietnamese)
T=0.35 (30/86, Ancient Sardinia)
T=0.35 (14/40, GENOME_DK)
C=0.36 (13/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 49946 C=0.67213 G=0.00000, T=0.32787
European Sub 40748 C=0.65505 G=0.00000, T=0.34495
African Sub 2498 C=0.9091 G=0.0000, T=0.0909
African Others Sub 102 C=0.941 G=0.000, T=0.059
African American Sub 2396 C=0.9078 G=0.0000, T=0.0922
Asian Sub 92 C=0.55 G=0.00, T=0.45
East Asian Sub 72 C=0.54 G=0.00, T=0.46
Other Asian Sub 20 C=0.60 G=0.00, T=0.40
Latin American 1 Sub 146 C=0.842 G=0.000, T=0.158
Latin American 2 Sub 768 C=0.707 G=0.000, T=0.293
South Asian Sub 4888 C=0.6784 G=0.0000, T=0.3216
Other Sub 806 C=0.712 G=0.000, T=0.288


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 C=0.641603 T=0.358397
gnomAD - Genomes Global Study-wide 139974 C=0.646920 T=0.353080
gnomAD - Genomes European Sub 75798 C=0.60614 T=0.39386
gnomAD - Genomes African Sub 41938 C=0.78506 T=0.21494
gnomAD - Genomes American Sub 13638 C=0.55301 T=0.44699
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.4555 T=0.5445
gnomAD - Genomes East Asian Sub 3130 C=0.4211 T=0.5789
gnomAD - Genomes Other Sub 2146 C=0.6104 T=0.3896
Allele Frequency Aggregator Total Global 49946 C=0.67213 G=0.00000, T=0.32787
Allele Frequency Aggregator European Sub 40748 C=0.65505 G=0.00000, T=0.34495
Allele Frequency Aggregator South Asian Sub 4888 C=0.6784 G=0.0000, T=0.3216
Allele Frequency Aggregator African Sub 2498 C=0.9091 G=0.0000, T=0.0909
Allele Frequency Aggregator Other Sub 806 C=0.712 G=0.000, T=0.288
Allele Frequency Aggregator Latin American 2 Sub 768 C=0.707 G=0.000, T=0.293
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.842 G=0.000, T=0.158
Allele Frequency Aggregator Asian Sub 92 C=0.55 G=0.00, T=0.45
14KJPN JAPANESE Study-wide 28258 C=0.46015 T=0.53985
8.3KJPN JAPANESE Study-wide 16760 C=0.46163 T=0.53837
1000Genomes_30x Global Study-wide 6404 C=0.6455 T=0.3545
1000Genomes_30x African Sub 1786 C=0.8275 T=0.1725
1000Genomes_30x Europe Sub 1266 C=0.5845 T=0.4155
1000Genomes_30x South Asian Sub 1202 C=0.6972 T=0.3028
1000Genomes_30x East Asian Sub 1170 C=0.4598 T=0.5402
1000Genomes_30x American Sub 980 C=0.551 T=0.449
1000Genomes Global Study-wide 5008 C=0.6386 T=0.3614
1000Genomes African Sub 1322 C=0.8306 T=0.1694
1000Genomes East Asian Sub 1008 C=0.4544 T=0.5456
1000Genomes Europe Sub 1006 C=0.5736 T=0.4264
1000Genomes South Asian Sub 978 C=0.694 T=0.306
1000Genomes American Sub 694 C=0.556 T=0.444
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5926 T=0.4074
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6175 T=0.3825
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6108 T=0.3892
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3874 T=0.6126
HGDP-CEPH-db Supplement 1 Global Study-wide 2076 C=0.6079 T=0.3921
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.468 T=0.532
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.606 T=0.394
HGDP-CEPH-db Supplement 1 Middle_Est Sub 348 C=0.586 T=0.414
HGDP-CEPH-db Supplement 1 Europe Sub 314 C=0.634 T=0.366
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.785 T=0.215
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.620 T=0.380
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.89 T=0.11
Korean Genome Project KOREAN Study-wide 1832 C=0.4023 T=0.5977
HapMap Global Study-wide 1784 C=0.6799 T=0.3201
HapMap African Sub 688 C=0.882 T=0.118
HapMap American Sub 666 C=0.613 T=0.387
HapMap Asian Sub 254 C=0.441 T=0.559
HapMap Europe Sub 176 C=0.489 T=0.511
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.626 T=0.374
CNV burdens in cranial meningiomas Global Study-wide 786 C=0.441 T=0.559
CNV burdens in cranial meningiomas CRM Sub 786 C=0.441 T=0.559
Northern Sweden ACPOP Study-wide 600 C=0.637 T=0.363
SGDP_PRJ Global Study-wide 320 C=0.369 T=0.631
Qatari Global Study-wide 216 C=0.551 T=0.449
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.443 T=0.557
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 86 C=0.65 T=0.35
The Danish reference pan genome Danish Study-wide 40 C=0.65 T=0.35
Siberian Global Study-wide 36 C=0.36 T=0.64
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 17 NC_000017.11:g.42559751C>G
GRCh38.p14 chr 17 NC_000017.11:g.42559751C>T
GRCh37.p13 chr 17 NC_000017.10:g.40711769C>G
GRCh37.p13 chr 17 NC_000017.10:g.40711769C>T
COASY RefSeqGene NG_034110.1:g.2678C>G
COASY RefSeqGene NG_034110.1:g.2678C>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 C= G T
GRCh38.p14 chr 17 NC_000017.11:g.42559751= NC_000017.11:g.42559751C>G NC_000017.11:g.42559751C>T
GRCh37.p13 chr 17 NC_000017.10:g.40711769= NC_000017.10:g.40711769C>G NC_000017.10:g.40711769C>T
COASY RefSeqGene NG_034110.1:g.2678= NG_034110.1:g.2678C>G NG_034110.1:g.2678C>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#.

91 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss20037638 Feb 28, 2004 (120)
2 PERLEGEN ss24118667 Sep 20, 2004 (123)
3 ABI ss40854851 Mar 15, 2006 (126)
4 ILLUMINA ss67024147 Nov 30, 2006 (127)
5 ILLUMINA ss67346066 Nov 30, 2006 (127)
6 ILLUMINA ss68134346 Dec 12, 2006 (127)
7 PERLEGEN ss69196448 May 17, 2007 (127)
8 ILLUMINA ss70577028 May 26, 2008 (130)
9 ILLUMINA ss71118652 May 17, 2007 (127)
10 ILLUMINA ss75619884 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss85248070 Dec 16, 2007 (130)
12 BCMHGSC_JDW ss90590160 Mar 24, 2008 (129)
13 1000GENOMES ss109768000 Jan 24, 2009 (130)
14 ENSEMBL ss137073337 Dec 01, 2009 (131)
15 ILLUMINA ss153243922 Dec 01, 2009 (131)
16 GMI ss158036769 Dec 01, 2009 (131)
17 ILLUMINA ss159226495 Dec 01, 2009 (131)
18 ILLUMINA ss160286473 Dec 01, 2009 (131)
19 ENSEMBL ss161830946 Dec 01, 2009 (131)
20 ILLUMINA ss172178991 Jul 04, 2010 (132)
21 BUSHMAN ss202518288 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss207856601 Jul 04, 2010 (132)
23 1000GENOMES ss211798670 Jul 14, 2010 (132)
24 1000GENOMES ss227548768 Jul 14, 2010 (132)
25 1000GENOMES ss237243979 Jul 15, 2010 (132)
26 1000GENOMES ss243542395 Jul 15, 2010 (132)
27 GMI ss282766745 May 04, 2012 (137)
28 ILLUMINA ss480362687 Sep 08, 2015 (146)
29 ILLUMINA ss536799021 Sep 08, 2015 (146)
30 TISHKOFF ss565274057 Apr 25, 2013 (138)
31 SSMP ss661076728 Apr 25, 2013 (138)
32 ILLUMINA ss832738860 Jul 13, 2019 (153)
33 EVA-GONL ss993109062 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1081059675 Aug 21, 2014 (142)
35 1000GENOMES ss1358659146 Aug 21, 2014 (142)
36 DDI ss1428034006 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1578157938 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1635654891 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1678648924 Apr 01, 2015 (144)
40 EVA_DECODE ss1697151856 Apr 01, 2015 (144)
41 EVA_SVP ss1713582662 Apr 01, 2015 (144)
42 HAMMER_LAB ss1808783616 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1936569332 Feb 12, 2016 (147)
44 GENOMED ss1968390233 Jul 19, 2016 (147)
45 JJLAB ss2029062164 Sep 14, 2016 (149)
46 USC_VALOUEV ss2157531974 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2216850338 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2629027091 Nov 08, 2017 (151)
49 GRF ss2702094124 Nov 08, 2017 (151)
50 GNOMAD ss2949878681 Nov 08, 2017 (151)
51 SWEGEN ss3015535762 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3028351183 Nov 08, 2017 (151)
53 CSHL ss3351747191 Nov 08, 2017 (151)
54 ILLUMINA ss3627669928 Oct 12, 2018 (152)
55 ILLUMINA ss3636365179 Oct 12, 2018 (152)
56 ILLUMINA ss3638161452 Oct 12, 2018 (152)
57 ILLUMINA ss3639090071 Oct 12, 2018 (152)
58 ILLUMINA ss3639853553 Oct 12, 2018 (152)
59 ILLUMINA ss3641080792 Oct 12, 2018 (152)
60 ILLUMINA ss3641376280 Oct 12, 2018 (152)
61 ILLUMINA ss3643139852 Oct 12, 2018 (152)
62 ILLUMINA ss3643902979 Oct 12, 2018 (152)
63 EGCUT_WGS ss3682424173 Jul 13, 2019 (153)
64 EVA_DECODE ss3700467798 Jul 13, 2019 (153)
65 ACPOP ss3742027235 Jul 13, 2019 (153)
66 EVA ss3754668699 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3819938230 Jul 13, 2019 (153)
68 EVA ss3834868351 Apr 27, 2020 (154)
69 EVA ss3841044059 Apr 27, 2020 (154)
70 EVA ss3846540920 Apr 27, 2020 (154)
71 HGDP ss3847564118 Apr 27, 2020 (154)
72 SGDP_PRJ ss3885751759 Apr 27, 2020 (154)
73 KRGDB ss3935436703 Apr 27, 2020 (154)
74 KOGIC ss3978844759 Apr 27, 2020 (154)
75 EVA ss3984723212 Apr 27, 2021 (155)
76 EVA ss3985791197 Apr 27, 2021 (155)
77 EVA ss4017766916 Apr 27, 2021 (155)
78 TOPMED ss5036014610 Apr 27, 2021 (155)
79 TOMMO_GENOMICS ss5222418750 Apr 27, 2021 (155)
80 1000G_HIGH_COVERAGE ss5303136405 Oct 16, 2022 (156)
81 EVA ss5427601504 Oct 16, 2022 (156)
82 HUGCELL_USP ss5496192089 Oct 16, 2022 (156)
83 EVA ss5511766594 Oct 16, 2022 (156)
84 1000G_HIGH_COVERAGE ss5606858478 Oct 16, 2022 (156)
85 SANFORD_IMAGENETICS ss5660105943 Oct 16, 2022 (156)
86 TOMMO_GENOMICS ss5778627551 Oct 16, 2022 (156)
87 YY_MCH ss5816544031 Oct 16, 2022 (156)
88 EVA ss5833985042 Oct 16, 2022 (156)
89 EVA ss5851809305 Oct 16, 2022 (156)
90 EVA ss5913962656 Oct 16, 2022 (156)
91 EVA ss5951499359 Oct 16, 2022 (156)
92 1000Genomes NC_000017.10 - 40711769 Oct 12, 2018 (152)
93 1000Genomes_30x NC_000017.11 - 42559751 Oct 16, 2022 (156)
94 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 40711769 Oct 12, 2018 (152)
95 Genetic variation in the Estonian population NC_000017.10 - 40711769 Oct 12, 2018 (152)
96 The Danish reference pan genome NC_000017.10 - 40711769 Apr 27, 2020 (154)
97 gnomAD - Genomes NC_000017.11 - 42559751 Apr 27, 2021 (155)
98 Genome of the Netherlands Release 5 NC_000017.10 - 40711769 Apr 27, 2020 (154)
99 HGDP-CEPH-db Supplement 1 NC_000017.9 - 37965295 Apr 27, 2020 (154)
100 HapMap NC_000017.11 - 42559751 Apr 27, 2020 (154)
101 KOREAN population from KRGDB NC_000017.10 - 40711769 Apr 27, 2020 (154)
102 Korean Genome Project NC_000017.11 - 42559751 Apr 27, 2020 (154)
103 Northern Sweden NC_000017.10 - 40711769 Jul 13, 2019 (153)
104 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000017.10 - 40711769 Apr 27, 2021 (155)
105 CNV burdens in cranial meningiomas NC_000017.10 - 40711769 Apr 27, 2021 (155)
106 Qatari NC_000017.10 - 40711769 Apr 27, 2020 (154)
107 SGDP_PRJ NC_000017.10 - 40711769 Apr 27, 2020 (154)
108 Siberian NC_000017.10 - 40711769 Apr 27, 2020 (154)
109 8.3KJPN NC_000017.10 - 40711769 Apr 27, 2021 (155)
110 14KJPN NC_000017.11 - 42559751 Oct 16, 2022 (156)
111 TopMed NC_000017.11 - 42559751 Apr 27, 2021 (155)
112 UK 10K study - Twins NC_000017.10 - 40711769 Oct 12, 2018 (152)
113 A Vietnamese Genetic Variation Database NC_000017.10 - 40711769 Jul 13, 2019 (153)
114 ALFA NC_000017.11 - 42559751 Apr 27, 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)
rs61135894 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10735274377 NC_000017.11:42559750:C:G NC_000017.11:42559750:C:G (self)
242010, ss90590160, ss109768000, ss202518288, ss207856601, ss211798670, ss282766745, ss1697151856, ss1713582662, ss3639090071, ss3639853553, ss3643139852, ss3643902979, ss3847564118 NC_000017.9:37965294:C:T NC_000017.11:42559750:C:T (self)
71900968, 39850775, 28162421, 4360310, 17761139, 42614097, 15312100, 1017124, 272758, 18611254, 37768739, 10048328, 80388057, 39850775, 8818642, ss227548768, ss237243979, ss243542395, ss480362687, ss536799021, ss565274057, ss661076728, ss832738860, ss993109062, ss1081059675, ss1358659146, ss1428034006, ss1578157938, ss1635654891, ss1678648924, ss1808783616, ss1936569332, ss1968390233, ss2029062164, ss2157531974, ss2629027091, ss2702094124, ss2949878681, ss3015535762, ss3351747191, ss3627669928, ss3636365179, ss3638161452, ss3641080792, ss3641376280, ss3682424173, ss3742027235, ss3754668699, ss3834868351, ss3841044059, ss3885751759, ss3935436703, ss3984723212, ss3985791197, ss4017766916, ss5222418750, ss5427601504, ss5511766594, ss5660105943, ss5833985042, ss5951499359 NC_000017.10:40711768:C:T NC_000017.11:42559750:C:T (self)
94384413, 507264833, 1488419, 35222760, 112464655, 251560272, 10735274377, ss2216850338, ss3028351183, ss3700467798, ss3819938230, ss3846540920, ss3978844759, ss5036014610, ss5303136405, ss5496192089, ss5606858478, ss5778627551, ss5816544031, ss5851809305, ss5913962656 NC_000017.11:42559750:C:T NC_000017.11:42559750:C:T (self)
ss20037638 NT_010755.14:4434266:C:T NC_000017.11:42559750:C:T (self)
ss24118667, ss40854851, ss67024147, ss67346066, ss68134346, ss69196448, ss70577028, ss71118652, ss75619884, ss85248070, ss137073337, ss153243922, ss158036769, ss159226495, ss160286473, ss161830946, ss172178991 NT_010783.15:5985920:C:T NC_000017.11:42559750:C:T (self)
Help

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

1 citation for rs12602084
PMID Title Author Year Journal
21900597 The impact of common genetic variations in genes of the sex hormone metabolic pathways on steroid hormone levels and prostate cancer aggressiveness. Sun T et al. 2011 Cancer prevention research (Philadelphia, Pa.)
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