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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.

rs17120729

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99586024 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.041315 (12395/300014, ALFA)
A=0.093226 (24676/264690, TOPMED)
A=0.092683 (12992/140176, GnomAD) (+ 19 more)
A=0.12443 (9792/78698, PAGE_STUDY)
A=0.04302 (721/16760, 8.3KJPN)
A=0.0960 (481/5008, 1000G)
A=0.0460 (206/4480, Estonian)
A=0.0353 (136/3854, ALSPAC)
A=0.0283 (105/3708, TWINSUK)
A=0.0332 (97/2922, KOREAN)
A=0.0591 (123/2082, HGDP_Stanford)
A=0.1173 (222/1892, HapMap)
A=0.0349 (64/1832, Korea1K)
A=0.045 (45/998, GoNL)
A=0.029 (23/788, PRJEB37584)
A=0.068 (41/600, NorthernSweden)
A=0.060 (13/216, Qatari)
A=0.046 (10/216, Vietnamese)
A=0.05 (4/78, Ancient Sardinia)
G=0.49 (34/70, SGDP_PRJ)
G=0.5 (3/6, Siberian)
A=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.99586024G>A
GRCh37.p13 chr 1 NC_000001.10:g.100051580G>A
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 300014 G=0.958685 A=0.041315
European Sub 265084 G=0.964336 A=0.035664
African Sub 8382 G=0.7890 A=0.2110
African Others Sub 318 G=0.745 A=0.255
African American Sub 8064 G=0.7907 A=0.2093
Asian Sub 3942 G=0.9447 A=0.0553
East Asian Sub 3196 G=0.9628 A=0.0372
Other Asian Sub 746 G=0.867 A=0.133
Latin American 1 Sub 1134 G=0.9162 A=0.0838
Latin American 2 Sub 7228 G=0.9736 A=0.0264
South Asian Sub 5224 G=0.9675 A=0.0325
Other Sub 9020 G=0.9448 A=0.0552


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=0.906774 A=0.093226
gnomAD - Genomes Global Study-wide 140176 G=0.907317 A=0.092683
gnomAD - Genomes European Sub 75938 G=0.96268 A=0.03732
gnomAD - Genomes African Sub 41988 G=0.78415 A=0.21585
gnomAD - Genomes American Sub 13646 G=0.95742 A=0.04258
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9489 A=0.0511
gnomAD - Genomes East Asian Sub 3130 G=0.9412 A=0.0588
gnomAD - Genomes Other Sub 2150 G=0.9256 A=0.0744
The PAGE Study Global Study-wide 78698 G=0.87557 A=0.12443
The PAGE Study AfricanAmerican Sub 32512 G=0.78872 A=0.21128
The PAGE Study Mexican Sub 10810 G=0.97077 A=0.02923
The PAGE Study Asian Sub 8318 G=0.9517 A=0.0483
The PAGE Study PuertoRican Sub 7918 G=0.9206 A=0.0794
The PAGE Study NativeHawaiian Sub 4534 G=0.8913 A=0.1087
The PAGE Study Cuban Sub 4230 G=0.9366 A=0.0634
The PAGE Study Dominican Sub 3828 G=0.8558 A=0.1442
The PAGE Study CentralAmerican Sub 2450 G=0.9559 A=0.0441
The PAGE Study SouthAmerican Sub 1982 G=0.9632 A=0.0368
The PAGE Study NativeAmerican Sub 1260 G=0.9556 A=0.0444
The PAGE Study SouthAsian Sub 856 G=0.970 A=0.030
8.3KJPN JAPANESE Study-wide 16760 G=0.95698 A=0.04302
1000Genomes Global Study-wide 5008 G=0.9040 A=0.0960
1000Genomes African Sub 1322 G=0.7504 A=0.2496
1000Genomes East Asian Sub 1008 G=0.9415 A=0.0585
1000Genomes Europe Sub 1006 G=0.9592 A=0.0408
1000Genomes South Asian Sub 978 G=0.974 A=0.026
1000Genomes American Sub 694 G=0.963 A=0.037
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9540 A=0.0460
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9647 A=0.0353
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9717 A=0.0283
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9668 A=0.0332
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 G=0.9409 A=0.0591
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.953 A=0.047
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.935 A=0.065
HGDP-CEPH-db Supplement 1 Middle_Est Sub 348 G=0.966 A=0.034
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.953 A=0.047
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.847 A=0.153
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.991 A=0.009
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.89 A=0.11
HapMap Global Study-wide 1892 G=0.8827 A=0.1173
HapMap American Sub 770 G=0.943 A=0.057
HapMap African Sub 692 G=0.769 A=0.231
HapMap Asian Sub 254 G=0.957 A=0.043
HapMap Europe Sub 176 G=0.960 A=0.040
Korean Genome Project KOREAN Study-wide 1832 G=0.9651 A=0.0349
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.955 A=0.045
CNV burdens in cranial meningiomas Global Study-wide 788 G=0.971 A=0.029
CNV burdens in cranial meningiomas CRM Sub 788 G=0.971 A=0.029
Northern Sweden ACPOP Study-wide 600 G=0.932 A=0.068
Qatari Global Study-wide 216 G=0.940 A=0.060
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.954 A=0.046
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 78 G=0.95 A=0.05
SGDP_PRJ Global Study-wide 70 G=0.49 A=0.51
Siberian Global Study-wide 6 G=0.5 A=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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.99586024= NC_000001.11:g.99586024G>A
GRCh37.p13 chr 1 NC_000001.10:g.100051580= NC_000001.10:g.100051580G>A
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#.

95 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23158362 Sep 20, 2004 (123)
2 ILLUMINA ss67177700 Dec 02, 2006 (127)
3 ILLUMINA ss67539520 Dec 02, 2006 (127)
4 ILLUMINA ss68174787 Dec 12, 2006 (127)
5 ILLUMINA ss70655722 May 23, 2008 (130)
6 ILLUMINA ss71215384 May 18, 2007 (127)
7 ILLUMINA ss75543883 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss85366152 Dec 14, 2007 (130)
9 1000GENOMES ss108453607 Jan 23, 2009 (130)
10 1000GENOMES ss110890900 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118919142 Feb 15, 2009 (130)
12 ILLUMINA ss153631686 Dec 01, 2009 (131)
13 ILLUMINA ss159309373 Dec 01, 2009 (131)
14 ILLUMINA ss160426399 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss163738952 Jul 04, 2010 (132)
16 ILLUMINA ss172754600 Jul 04, 2010 (132)
17 BUSHMAN ss198832680 Jul 04, 2010 (132)
18 1000GENOMES ss218548639 Jul 14, 2010 (132)
19 1000GENOMES ss238323698 Jul 15, 2010 (132)
20 ILLUMINA ss480189468 May 04, 2012 (137)
21 ILLUMINA ss480199384 May 04, 2012 (137)
22 ILLUMINA ss480921888 Sep 08, 2015 (146)
23 ILLUMINA ss484892812 May 04, 2012 (137)
24 ILLUMINA ss536949742 Sep 08, 2015 (146)
25 TISHKOFF ss554480585 Apr 25, 2013 (138)
26 SSMP ss648253934 Apr 25, 2013 (138)
27 ILLUMINA ss778829749 Sep 08, 2015 (146)
28 ILLUMINA ss782892724 Sep 08, 2015 (146)
29 ILLUMINA ss783856243 Sep 08, 2015 (146)
30 ILLUMINA ss832147285 Sep 08, 2015 (146)
31 ILLUMINA ss832821435 Jul 12, 2019 (153)
32 ILLUMINA ss834290189 Sep 08, 2015 (146)
33 EVA-GONL ss975483005 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1068127691 Aug 21, 2014 (142)
35 1000GENOMES ss1292107755 Aug 21, 2014 (142)
36 EVA_DECODE ss1584861317 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1600816976 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1643811009 Apr 01, 2015 (144)
39 EVA_SVP ss1712357147 Apr 01, 2015 (144)
40 ILLUMINA ss1751859113 Sep 08, 2015 (146)
41 HAMMER_LAB ss1794807645 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1918682610 Feb 12, 2016 (147)
43 ILLUMINA ss1946002824 Feb 12, 2016 (147)
44 ILLUMINA ss1958296792 Feb 12, 2016 (147)
45 JJLAB ss2019862793 Sep 14, 2016 (149)
46 USC_VALOUEV ss2147881497 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2165031293 Dec 20, 2016 (150)
48 TOPMED ss2327382090 Dec 20, 2016 (150)
49 ILLUMINA ss2632553622 Nov 08, 2017 (151)
50 ILLUMINA ss2635001582 Nov 08, 2017 (151)
51 GRF ss2697808833 Nov 08, 2017 (151)
52 ILLUMINA ss2710678275 Nov 08, 2017 (151)
53 GNOMAD ss2758637976 Nov 08, 2017 (151)
54 SWEGEN ss2987305709 Nov 08, 2017 (151)
55 ILLUMINA ss3021113796 Nov 08, 2017 (151)
56 TOPMED ss3084650581 Nov 08, 2017 (151)
57 CSHL ss3343595924 Nov 08, 2017 (151)
58 ILLUMINA ss3625546135 Oct 11, 2018 (152)
59 ILLUMINA ss3626165288 Oct 11, 2018 (152)
60 ILLUMINA ss3630587796 Oct 11, 2018 (152)
61 ILLUMINA ss3632903282 Oct 11, 2018 (152)
62 ILLUMINA ss3633598280 Oct 11, 2018 (152)
63 ILLUMINA ss3634339255 Oct 11, 2018 (152)
64 ILLUMINA ss3635291891 Oct 11, 2018 (152)
65 ILLUMINA ss3636016810 Oct 11, 2018 (152)
66 ILLUMINA ss3637042347 Oct 11, 2018 (152)
67 ILLUMINA ss3637775454 Oct 11, 2018 (152)
68 ILLUMINA ss3638905833 Oct 11, 2018 (152)
69 ILLUMINA ss3639765063 Oct 11, 2018 (152)
70 ILLUMINA ss3640046615 Oct 11, 2018 (152)
71 ILLUMINA ss3642785639 Oct 11, 2018 (152)
72 ILLUMINA ss3643818613 Oct 11, 2018 (152)
73 ILLUMINA ss3644498786 Oct 11, 2018 (152)
74 ILLUMINA ss3651444577 Oct 11, 2018 (152)
75 EGCUT_WGS ss3655390791 Jul 12, 2019 (153)
76 EVA_DECODE ss3687367195 Jul 12, 2019 (153)
77 ILLUMINA ss3725048137 Jul 12, 2019 (153)
78 ACPOP ss3727314084 Jul 12, 2019 (153)
79 ILLUMINA ss3744050996 Jul 12, 2019 (153)
80 ILLUMINA ss3744640224 Jul 12, 2019 (153)
81 EVA ss3746574136 Jul 12, 2019 (153)
82 PAGE_CC ss3770828000 Jul 12, 2019 (153)
83 ILLUMINA ss3772141461 Jul 12, 2019 (153)
84 KHV_HUMAN_GENOMES ss3799574913 Jul 12, 2019 (153)
85 EVA ss3826326575 Apr 25, 2020 (154)
86 HGDP ss3847343742 Apr 25, 2020 (154)
87 SGDP_PRJ ss3849477627 Apr 25, 2020 (154)
88 KRGDB ss3894555653 Apr 25, 2020 (154)
89 KOGIC ss3945091380 Apr 25, 2020 (154)
90 EVA ss3984461730 Apr 25, 2021 (155)
91 EVA ss3984814969 Apr 25, 2021 (155)
92 EVA ss4016927692 Apr 25, 2021 (155)
93 TOPMED ss4460698686 Apr 25, 2021 (155)
94 TOMMO_GENOMICS ss5145313344 Apr 25, 2021 (155)
95 EVA ss5237270829 Apr 25, 2021 (155)
96 1000Genomes NC_000001.10 - 100051580 Oct 11, 2018 (152)
97 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100051580 Oct 11, 2018 (152)
98 Genetic variation in the Estonian population NC_000001.10 - 100051580 Oct 11, 2018 (152)
99 gnomAD - Genomes NC_000001.11 - 99586024 Apr 25, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000001.10 - 100051580 Apr 25, 2020 (154)
101 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99824168 Apr 25, 2020 (154)
102 HapMap NC_000001.11 - 99586024 Apr 25, 2020 (154)
103 KOREAN population from KRGDB NC_000001.10 - 100051580 Apr 25, 2020 (154)
104 Korean Genome Project NC_000001.11 - 99586024 Apr 25, 2020 (154)
105 Northern Sweden NC_000001.10 - 100051580 Jul 12, 2019 (153)
106 The PAGE Study NC_000001.11 - 99586024 Jul 12, 2019 (153)
107 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100051580 Apr 25, 2021 (155)
108 CNV burdens in cranial meningiomas NC_000001.10 - 100051580 Apr 25, 2021 (155)
109 Qatari NC_000001.10 - 100051580 Apr 25, 2020 (154)
110 SGDP_PRJ NC_000001.10 - 100051580 Apr 25, 2020 (154)
111 Siberian NC_000001.10 - 100051580 Apr 25, 2020 (154)
112 8.3KJPN NC_000001.10 - 100051580 Apr 25, 2021 (155)
113 TopMed NC_000001.11 - 99586024 Apr 25, 2021 (155)
114 UK 10K study - Twins NC_000001.10 - 100051580 Oct 11, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000001.10 - 100051580 Jul 12, 2019 (153)
116 ALFA NC_000001.11 - 99586024 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)
rs56871929 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638905833, ss3639765063, ss3643818613 NC_000001.8:99763600:G:A NC_000001.11:99586023:G:A (self)
21634, ss108453607, ss110890900, ss118919142, ss163738952, ss198832680, ss480189468, ss1584861317, ss1712357147, ss2635001582, ss3642785639, ss3847343742 NC_000001.9:99824167:G:A NC_000001.11:99586023:G:A (self)
2871324, 1583916, 1129039, 687102, 1733047, 598949, 40896, 11042, 724540, 1494607, 397851, 3282651, 1583916, 341186, ss218548639, ss238323698, ss480199384, ss480921888, ss484892812, ss536949742, ss554480585, ss648253934, ss778829749, ss782892724, ss783856243, ss832147285, ss832821435, ss834290189, ss975483005, ss1068127691, ss1292107755, ss1600816976, ss1643811009, ss1751859113, ss1794807645, ss1918682610, ss1946002824, ss1958296792, ss2019862793, ss2147881497, ss2327382090, ss2632553622, ss2697808833, ss2710678275, ss2758637976, ss2987305709, ss3021113796, ss3343595924, ss3625546135, ss3626165288, ss3630587796, ss3632903282, ss3633598280, ss3634339255, ss3635291891, ss3636016810, ss3637042347, ss3637775454, ss3640046615, ss3644498786, ss3651444577, ss3655390791, ss3727314084, ss3744050996, ss3744640224, ss3746574136, ss3772141461, ss3826326575, ss3849477627, ss3894555653, ss3984461730, ss3984814969, ss4016927692, ss5145313344, ss5237270829 NC_000001.10:100051579:G:A NC_000001.11:99586023:G:A (self)
20297619, 136558, 1469381, 49469, 15307914, 24305021, 4368449870, ss2165031293, ss3084650581, ss3687367195, ss3725048137, ss3770828000, ss3799574913, ss3945091380, ss4460698686 NC_000001.11:99586023:G:A NC_000001.11:99586023:G:A (self)
ss23158362, ss67177700, ss67539520, ss68174787, ss70655722, ss71215384, ss75543883, ss85366152, ss153631686, ss159309373, ss160426399, ss172754600 NT_032977.9:70023497:G:A NC_000001.11:99586023:G:A (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 rs17120729

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