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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.

rs17120680

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99566018 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.075821 (20069/264690, TOPMED)
C=0.059134 (8988/151994, ALFA)
C=0.078626 (11018/140132, GnomAD) (+ 18 more)
C=0.02834 (475/16758, 8.3KJPN)
C=0.0815 (408/5008, 1000G)
C=0.0757 (339/4480, Estonian)
C=0.0436 (168/3854, ALSPAC)
C=0.0421 (156/3708, TWINSUK)
C=0.0243 (71/2920, KOREAN)
C=0.0677 (141/2084, HGDP_Stanford)
C=0.0926 (175/1890, HapMap)
C=0.0493 (56/1136, Daghestan)
C=0.064 (64/998, GoNL)
C=0.112 (67/600, NorthernSweden)
C=0.069 (15/216, Qatari)
C=0.042 (9/214, Vietnamese)
T=0.46 (32/70, SGDP_PRJ)
C=0.17 (8/46, Ancient Sardinia)
C=0.05 (2/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
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.99566018T>C
GRCh37.p13 chr 1 NC_000001.10:g.100031574T>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 151994 T=0.940866 C=0.059134
European Sub 128528 T=0.945024 C=0.054976
African Sub 9308 T=0.8653 C=0.1347
African Others Sub 326 T=0.880 C=0.120
African American Sub 8982 T=0.8647 C=0.1353
Asian Sub 632 T=0.937 C=0.063
East Asian Sub 500 T=0.938 C=0.062
Other Asian Sub 132 T=0.932 C=0.068
Latin American 1 Sub 748 T=0.936 C=0.064
Latin American 2 Sub 6302 T=0.9695 C=0.0305
South Asian Sub 186 T=0.935 C=0.065
Other Sub 6290 T=0.9402 C=0.0598


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=0.924179 C=0.075821
gnomAD - Genomes Global Study-wide 140132 T=0.921374 C=0.078626
gnomAD - Genomes European Sub 75894 T=0.94267 C=0.05733
gnomAD - Genomes African Sub 42000 T=0.87155 C=0.12845
gnomAD - Genomes American Sub 13636 T=0.94749 C=0.05251
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9398 C=0.0602
gnomAD - Genomes East Asian Sub 3130 T=0.9351 C=0.0649
gnomAD - Genomes Other Sub 2150 T=0.9288 C=0.0712
8.3KJPN JAPANESE Study-wide 16758 T=0.97166 C=0.02834
1000Genomes Global Study-wide 5008 T=0.9185 C=0.0815
1000Genomes African Sub 1322 T=0.8563 C=0.1437
1000Genomes East Asian Sub 1008 T=0.9375 C=0.0625
1000Genomes Europe Sub 1006 T=0.9443 C=0.0557
1000Genomes South Asian Sub 978 T=0.948 C=0.052
1000Genomes American Sub 694 T=0.931 C=0.069
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9243 C=0.0757
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9564 C=0.0436
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9579 C=0.0421
KOREAN population from KRGDB KOREAN Study-wide 2920 T=0.9757 C=0.0243
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.9323 C=0.0677
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.947 C=0.053
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.911 C=0.089
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.940 C=0.060
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.934 C=0.066
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.860 C=0.140
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 1890 T=0.9074 C=0.0926
HapMap American Sub 768 T=0.953 C=0.047
HapMap African Sub 692 T=0.831 C=0.169
HapMap Asian Sub 254 T=0.965 C=0.035
HapMap Europe Sub 176 T=0.926 C=0.074
Genome-wide autozygosity in Daghestan Global Study-wide 1136 T=0.9507 C=0.0493
Genome-wide autozygosity in Daghestan Daghestan Sub 628 T=0.951 C=0.049
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.938 C=0.062
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.992 C=0.008
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.954 C=0.046
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=0.92 C=0.08
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.94 C=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.936 C=0.064
Northern Sweden ACPOP Study-wide 600 T=0.888 C=0.112
Qatari Global Study-wide 216 T=0.931 C=0.069
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.958 C=0.042
SGDP_PRJ Global Study-wide 70 T=0.46 C=0.54
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 46 T=0.83 C=0.17
The Danish reference pan genome Danish Study-wide 40 T=0.95 C=0.05
Siberian Global Study-wide 6 T=0.5 C=0.5
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
GRCh38.p13 chr 1 NC_000001.11:g.99566018= NC_000001.11:g.99566018T>C
GRCh37.p13 chr 1 NC_000001.10:g.100031574= NC_000001.10:g.100031574T>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#.

71 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23158163 Sep 20, 2004 (123)
2 ILLUMINA ss67539504 Nov 30, 2006 (127)
3 ILLUMINA ss71215377 May 17, 2007 (127)
4 ILLUMINA ss75380452 Dec 06, 2007 (129)
5 KRIBB_YJKIM ss119876239 Dec 01, 2009 (131)
6 ILLUMINA ss160426392 Dec 01, 2009 (131)
7 ILLUMINA ss172754570 Jul 04, 2010 (132)
8 1000GENOMES ss218548559 Jul 14, 2010 (132)
9 1000GENOMES ss230656673 Jul 14, 2010 (132)
10 1000GENOMES ss238323657 Jul 15, 2010 (132)
11 ILLUMINA ss480189440 May 04, 2012 (137)
12 ILLUMINA ss480199356 May 04, 2012 (137)
13 ILLUMINA ss480921862 Sep 08, 2015 (146)
14 ILLUMINA ss484892798 May 04, 2012 (137)
15 ILLUMINA ss536949734 Sep 08, 2015 (146)
16 TISHKOFF ss554480384 Apr 25, 2013 (138)
17 SSMP ss648253826 Apr 25, 2013 (138)
18 ILLUMINA ss779035612 Aug 21, 2014 (142)
19 ILLUMINA ss782892717 Aug 21, 2014 (142)
20 ILLUMINA ss783856236 Aug 21, 2014 (142)
21 ILLUMINA ss832147278 Apr 01, 2015 (144)
22 ILLUMINA ss834498385 Aug 21, 2014 (142)
23 EVA-GONL ss975482856 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1068127564 Aug 21, 2014 (142)
25 1000GENOMES ss1292107172 Aug 21, 2014 (142)
26 HAMMER_LAB ss1397255144 Sep 08, 2015 (146)
27 EVA_GENOME_DK ss1574271410 Apr 01, 2015 (144)
28 EVA_DECODE ss1584861155 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1600816644 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1643810677 Apr 01, 2015 (144)
31 EVA_SVP ss1712357130 Apr 01, 2015 (144)
32 ILLUMINA ss1751859104 Sep 08, 2015 (146)
33 HAMMER_LAB ss1794807465 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1918682477 Feb 12, 2016 (147)
35 JJLAB ss2019862702 Sep 14, 2016 (149)
36 USC_VALOUEV ss2147881412 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2165030140 Dec 20, 2016 (150)
38 TOPMED ss2327380947 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624442838 Nov 08, 2017 (151)
40 ILLUMINA ss2632553607 Nov 08, 2017 (151)
41 GRF ss2697808760 Nov 08, 2017 (151)
42 GNOMAD ss2758636505 Nov 08, 2017 (151)
43 SWEGEN ss2987305522 Nov 08, 2017 (151)
44 TOPMED ss3084647097 Nov 08, 2017 (151)
45 CSHL ss3343595857 Nov 08, 2017 (151)
46 ILLUMINA ss3626165260 Oct 11, 2018 (152)
47 ILLUMINA ss3630587781 Oct 11, 2018 (152)
48 ILLUMINA ss3632903276 Oct 11, 2018 (152)
49 ILLUMINA ss3633598274 Oct 11, 2018 (152)
50 ILLUMINA ss3634339248 Oct 11, 2018 (152)
51 ILLUMINA ss3635291885 Oct 11, 2018 (152)
52 ILLUMINA ss3636016804 Oct 11, 2018 (152)
53 ILLUMINA ss3637042341 Oct 11, 2018 (152)
54 ILLUMINA ss3637775446 Oct 11, 2018 (152)
55 ILLUMINA ss3640046608 Oct 11, 2018 (152)
56 ILLUMINA ss3642785631 Oct 11, 2018 (152)
57 EGCUT_WGS ss3655390573 Jul 12, 2019 (153)
58 EVA_DECODE ss3687366901 Jul 12, 2019 (153)
59 ACPOP ss3727313949 Jul 12, 2019 (153)
60 ILLUMINA ss3744640217 Jul 12, 2019 (153)
61 EVA ss3746573976 Jul 12, 2019 (153)
62 ILLUMINA ss3772141454 Jul 12, 2019 (153)
63 KHV_HUMAN_GENOMES ss3799574735 Jul 12, 2019 (153)
64 EVA ss3826326485 Apr 25, 2020 (154)
65 HGDP ss3847343736 Apr 25, 2020 (154)
66 SGDP_PRJ ss3849477323 Apr 25, 2020 (154)
67 KRGDB ss3894555351 Apr 25, 2020 (154)
68 EVA ss3984814958 Apr 25, 2021 (155)
69 EVA ss4016927685 Apr 25, 2021 (155)
70 TOPMED ss4460693843 Apr 25, 2021 (155)
71 TOMMO_GENOMICS ss5145312791 Apr 25, 2021 (155)
72 1000Genomes NC_000001.10 - 100031574 Oct 11, 2018 (152)
73 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100031574 Oct 11, 2018 (152)
74 Genome-wide autozygosity in Daghestan NC_000001.9 - 99804162 Apr 25, 2020 (154)
75 Genetic variation in the Estonian population NC_000001.10 - 100031574 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000001.10 - 100031574 Apr 25, 2020 (154)
77 gnomAD - Genomes NC_000001.11 - 99566018 Apr 25, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000001.10 - 100031574 Apr 25, 2020 (154)
79 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99804162 Apr 25, 2020 (154)
80 HapMap NC_000001.11 - 99566018 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000001.10 - 100031574 Apr 25, 2020 (154)
82 Northern Sweden NC_000001.10 - 100031574 Jul 12, 2019 (153)
83 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100031574 Apr 25, 2021 (155)
84 Qatari NC_000001.10 - 100031574 Apr 25, 2020 (154)
85 SGDP_PRJ NC_000001.10 - 100031574 Apr 25, 2020 (154)
86 Siberian NC_000001.10 - 100031574 Apr 25, 2020 (154)
87 8.3KJPN NC_000001.10 - 100031574 Apr 25, 2021 (155)
88 TopMed NC_000001.11 - 99566018 Apr 25, 2021 (155)
89 UK 10K study - Twins NC_000001.10 - 100031574 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000001.10 - 100031574 Jul 12, 2019 (153)
91 ALFA NC_000001.11 - 99566018 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
16446, 21628, ss160426392, ss480189440, ss1397255144, ss1584861155, ss1712357130, ss3642785631, ss3847343736 NC_000001.9:99804161:T:C NC_000001.11:99566017:T:C (self)
2870727, 1583555, 1128821, 1628895, 686953, 1732745, 598814, 40885, 724407, 1494303, 397766, 3282098, 1583555, 341111, ss218548559, ss230656673, ss238323657, ss480199356, ss480921862, ss484892798, ss536949734, ss554480384, ss648253826, ss779035612, ss782892717, ss783856236, ss832147278, ss834498385, ss975482856, ss1068127564, ss1292107172, ss1574271410, ss1600816644, ss1643810677, ss1751859104, ss1794807465, ss1918682477, ss2019862702, ss2147881412, ss2327380947, ss2624442838, ss2632553607, ss2697808760, ss2758636505, ss2987305522, ss3343595857, ss3626165260, ss3630587781, ss3632903276, ss3633598274, ss3634339248, ss3635291885, ss3636016804, ss3637042341, ss3637775446, ss3640046608, ss3655390573, ss3727313949, ss3744640217, ss3746573976, ss3772141454, ss3826326485, ss3849477323, ss3894555351, ss3984814958, ss4016927685, ss5145312791 NC_000001.10:100031573:T:C NC_000001.11:99566017:T:C (self)
20293734, 136512, 15304892, 24300178, 10077909714, ss2165030140, ss3084647097, ss3687366901, ss3799574735, ss4460693843 NC_000001.11:99566017:T:C NC_000001.11:99566017:T:C (self)
ss23158163, ss67539504, ss71215377, ss75380452, ss119876239, ss172754570 NT_032977.9:70003491:T:C NC_000001.11:99566017:T: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 rs17120680

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