Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs12729121

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99615561 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.121774 (36181/297116, ALFA)
T=0.103189 (27313/264690, TOPMED)
T=0.102726 (14389/140072, GnomAD) (+ 18 more)
T=0.14773 (2476/16760, 8.3KJPN)
T=0.1224 (613/5008, 1000G)
T=0.0699 (313/4480, Estonian)
T=0.1331 (513/3854, ALSPAC)
T=0.1284 (476/3708, TWINSUK)
T=0.0962 (282/2930, KOREAN)
T=0.1075 (224/2084, HGDP_Stanford)
T=0.1054 (199/1888, HapMap)
T=0.1103 (202/1832, Korea1K)
T=0.121 (121/998, GoNL)
T=0.143 (111/778, PRJEB37584)
T=0.087 (52/600, NorthernSweden)
T=0.093 (20/216, Qatari)
T=0.189 (40/212, Vietnamese)
G=0.441 (45/102, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
T=0.29 (8/28, Ancient Sardinia)
G=0.4 (4/10, 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.99615561G>A
GRCh38.p13 chr 1 NC_000001.11:g.99615561G>T
GRCh37.p13 chr 1 NC_000001.10:g.100081117G>A
GRCh37.p13 chr 1 NC_000001.10:g.100081117G>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

ALFA Allele Frequency (New)
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 297116 G=0.878226 A=0.000000, T=0.121774
European Sub 266984 G=0.876412 A=0.000000, T=0.123588
African Sub 8038 G=0.9485 A=0.0000, T=0.0515
African Others Sub 298 G=0.956 A=0.000, T=0.044
African American Sub 7740 G=0.9482 A=0.0000, T=0.0518
Asian Sub 3894 G=0.8744 A=0.0000, T=0.1256
East Asian Sub 3156 G=0.8824 A=0.0000, T=0.1176
Other Asian Sub 738 G=0.840 A=0.000, T=0.160
Latin American 1 Sub 1042 G=0.8964 A=0.0000, T=0.1036
Latin American 2 Sub 3046 G=0.9274 A=0.0000, T=0.0726
South Asian Sub 5180 G=0.8135 A=0.0000, T=0.1865
Other Sub 8932 G=0.8895 A=0.0000, T=0.1105


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
Allele Frequency Aggregator Total Global 297116 G=0.878226 A=0.000000, T=0.121774
Allele Frequency Aggregator European Sub 266984 G=0.876412 A=0.000000, T=0.123588
Allele Frequency Aggregator Other Sub 8932 G=0.8895 A=0.0000, T=0.1105
Allele Frequency Aggregator African Sub 8038 G=0.9485 A=0.0000, T=0.0515
Allele Frequency Aggregator South Asian Sub 5180 G=0.8135 A=0.0000, T=0.1865
Allele Frequency Aggregator Asian Sub 3894 G=0.8744 A=0.0000, T=0.1256
Allele Frequency Aggregator Latin American 2 Sub 3046 G=0.9274 A=0.0000, T=0.0726
Allele Frequency Aggregator Latin American 1 Sub 1042 G=0.8964 A=0.0000, T=0.1036
TopMed Global Study-wide 264690 G=0.896811 T=0.103189
gnomAD - Genomes Global Study-wide 140072 G=0.897274 T=0.102726
gnomAD - Genomes European Sub 75864 G=0.87942 T=0.12058
gnomAD - Genomes African Sub 41964 G=0.92839 T=0.07161
gnomAD - Genomes American Sub 13646 G=0.90994 T=0.09006
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.8982 T=0.1018
gnomAD - Genomes East Asian Sub 3128 G=0.8613 T=0.1387
gnomAD - Genomes Other Sub 2150 G=0.8907 T=0.1093
8.3KJPN JAPANESE Study-wide 16760 G=0.85227 T=0.14773
1000Genomes Global Study-wide 5008 G=0.8776 T=0.1224
1000Genomes African Sub 1322 G=0.9516 T=0.0484
1000Genomes East Asian Sub 1008 G=0.8472 T=0.1528
1000Genomes Europe Sub 1006 G=0.8648 T=0.1352
1000Genomes South Asian Sub 978 G=0.786 T=0.214
1000Genomes American Sub 694 G=0.928 T=0.072
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9301 T=0.0699
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8669 T=0.1331
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8716 T=0.1284
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.9038 T=0.0962
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8925 T=0.1075
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.913 T=0.087
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.787 T=0.213
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.937 T=0.063
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.828 T=0.172
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.950 T=0.050
HGDP-CEPH-db Supplement 1 America Sub 216 G=1.000 T=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.92 T=0.08
HapMap Global Study-wide 1888 G=0.8946 T=0.1054
HapMap American Sub 768 G=0.867 T=0.133
HapMap African Sub 690 G=0.957 T=0.043
HapMap Asian Sub 254 G=0.854 T=0.146
HapMap Europe Sub 176 G=0.830 T=0.170
Korean Genome Project KOREAN Study-wide 1832 G=0.8897 T=0.1103
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.879 T=0.121
CNV burdens in cranial meningiomas Global Study-wide 778 G=0.857 T=0.143
CNV burdens in cranial meningiomas CRM Sub 778 G=0.857 T=0.143
Northern Sweden ACPOP Study-wide 600 G=0.913 T=0.087
Qatari Global Study-wide 216 G=0.907 T=0.093
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.811 T=0.189
SGDP_PRJ Global Study-wide 102 G=0.441 T=0.559
The Danish reference pan genome Danish Study-wide 40 G=0.97 T=0.03
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 28 G=0.71 T=0.29
Siberian Global Study-wide 10 G=0.4 T=0.6
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 T
GRCh38.p13 chr 1 NC_000001.11:g.99615561= NC_000001.11:g.99615561G>A NC_000001.11:g.99615561G>T
GRCh37.p13 chr 1 NC_000001.10:g.100081117= NC_000001.10:g.100081117G>A NC_000001.10:g.100081117G>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#.

100 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss20460808 Apr 05, 2004 (121)
2 ABI ss41102065 Mar 15, 2006 (126)
3 ILLUMINA ss67036478 Nov 30, 2006 (127)
4 ILLUMINA ss67360444 Nov 30, 2006 (127)
5 ILLUMINA ss68138001 Dec 12, 2006 (127)
6 ILLUMINA ss70583324 May 23, 2008 (130)
7 ILLUMINA ss71125914 May 17, 2007 (127)
8 ILLUMINA ss75448354 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss85268277 Dec 14, 2007 (130)
10 HUMANGENOME_JCVI ss99232676 Feb 03, 2009 (130)
11 1000GENOMES ss108453909 Jan 23, 2009 (130)
12 ENSEMBL ss131830567 Dec 01, 2009 (131)
13 ILLUMINA ss153275904 Dec 01, 2009 (131)
14 ILLUMINA ss159233055 Dec 01, 2009 (131)
15 ILLUMINA ss160297303 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss164869700 Jul 04, 2010 (132)
17 ILLUMINA ss172234612 Jul 04, 2010 (132)
18 1000GENOMES ss218548774 Jul 14, 2010 (132)
19 1000GENOMES ss230656830 Jul 14, 2010 (132)
20 1000GENOMES ss238323787 Jul 15, 2010 (132)
21 GMI ss275945401 May 04, 2012 (137)
22 ILLUMINA ss479813535 May 04, 2012 (137)
23 ILLUMINA ss479820672 May 04, 2012 (137)
24 ILLUMINA ss480405969 Sep 08, 2015 (146)
25 ILLUMINA ss484705257 May 04, 2012 (137)
26 ILLUMINA ss536811182 Sep 08, 2015 (146)
27 TISHKOFF ss554480873 Apr 25, 2013 (138)
28 SSMP ss648254101 Apr 25, 2013 (138)
29 ILLUMINA ss778414911 Sep 08, 2015 (146)
30 ILLUMINA ss782799398 Sep 08, 2015 (146)
31 ILLUMINA ss783764938 Sep 08, 2015 (146)
32 ILLUMINA ss832052354 Sep 08, 2015 (146)
33 ILLUMINA ss832745392 Jul 12, 2019 (153)
34 ILLUMINA ss833870226 Sep 08, 2015 (146)
35 EVA-GONL ss975483224 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1068127874 Aug 21, 2014 (142)
37 1000GENOMES ss1292108560 Aug 21, 2014 (142)
38 EVA_GENOME_DK ss1574271781 Apr 01, 2015 (144)
39 EVA_DECODE ss1584861538 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1600817443 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1643811476 Apr 01, 2015 (144)
42 EVA_SVP ss1712357165 Apr 01, 2015 (144)
43 ILLUMINA ss1751859126 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1918682807 Feb 12, 2016 (147)
45 ILLUMINA ss1946002827 Feb 12, 2016 (147)
46 ILLUMINA ss1958296803 Feb 12, 2016 (147)
47 JJLAB ss2019862928 Sep 14, 2016 (149)
48 USC_VALOUEV ss2147881618 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2165033036 Dec 20, 2016 (150)
50 TOPMED ss2327383842 Dec 20, 2016 (150)
51 TOPMED ss2327383843 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2624442878 Nov 08, 2017 (151)
53 ILLUMINA ss2632553652 Nov 08, 2017 (151)
54 GRF ss2697808967 Nov 08, 2017 (151)
55 ILLUMINA ss2710678280 Nov 08, 2017 (151)
56 GNOMAD ss2758640270 Nov 08, 2017 (151)
57 SWEGEN ss2987306008 Nov 08, 2017 (151)
58 ILLUMINA ss3021113811 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3023695061 Nov 08, 2017 (151)
60 TOPMED ss3084655803 Nov 08, 2017 (151)
61 TOPMED ss3084655804 Nov 08, 2017 (151)
62 CSHL ss3343596038 Nov 08, 2017 (151)
63 ILLUMINA ss3625546139 Oct 11, 2018 (152)
64 ILLUMINA ss3626165330 Oct 11, 2018 (152)
65 ILLUMINA ss3630587828 Oct 11, 2018 (152)
66 ILLUMINA ss3632903295 Oct 11, 2018 (152)
67 ILLUMINA ss3633598294 Oct 11, 2018 (152)
68 ILLUMINA ss3634339268 Oct 11, 2018 (152)
69 ILLUMINA ss3635291903 Oct 11, 2018 (152)
70 ILLUMINA ss3636016823 Oct 11, 2018 (152)
71 ILLUMINA ss3637042360 Oct 11, 2018 (152)
72 ILLUMINA ss3637775465 Oct 11, 2018 (152)
73 ILLUMINA ss3638905841 Oct 11, 2018 (152)
74 ILLUMINA ss3639765065 Oct 11, 2018 (152)
75 ILLUMINA ss3640046628 Oct 11, 2018 (152)
76 ILLUMINA ss3642785650 Oct 11, 2018 (152)
77 ILLUMINA ss3643818615 Oct 11, 2018 (152)
78 ILLUMINA ss3644498789 Oct 11, 2018 (152)
79 URBANLAB ss3646731512 Oct 11, 2018 (152)
80 ILLUMINA ss3651444594 Oct 11, 2018 (152)
81 EGCUT_WGS ss3655391122 Jul 12, 2019 (153)
82 EVA_DECODE ss3687367545 Jul 12, 2019 (153)
83 ILLUMINA ss3725048152 Jul 12, 2019 (153)
84 ACPOP ss3727314266 Jul 12, 2019 (153)
85 ILLUMINA ss3744050999 Jul 12, 2019 (153)
86 ILLUMINA ss3744640237 Jul 12, 2019 (153)
87 EVA ss3746574408 Jul 12, 2019 (153)
88 ILLUMINA ss3772141474 Jul 12, 2019 (153)
89 KHV_HUMAN_GENOMES ss3799575170 Jul 12, 2019 (153)
90 EVA ss3826326704 Apr 25, 2020 (154)
91 EVA ss3836553632 Apr 25, 2020 (154)
92 EVA ss3841961628 Apr 25, 2020 (154)
93 HGDP ss3847343752 Apr 25, 2020 (154)
94 SGDP_PRJ ss3849478030 Apr 25, 2020 (154)
95 KRGDB ss3894556084 Apr 25, 2020 (154)
96 KOGIC ss3945091752 Apr 25, 2020 (154)
97 EVA ss3984461733 Apr 25, 2021 (155)
98 EVA ss3984814990 Apr 25, 2021 (155)
99 TOPMED ss4460705916 Apr 25, 2021 (155)
100 TOMMO_GENOMICS ss5145314185 Apr 25, 2021 (155)
101 1000Genomes NC_000001.10 - 100081117 Oct 11, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100081117 Oct 11, 2018 (152)
103 Genetic variation in the Estonian population NC_000001.10 - 100081117 Oct 11, 2018 (152)
104 The Danish reference pan genome NC_000001.10 - 100081117 Apr 25, 2020 (154)
105 gnomAD - Genomes NC_000001.11 - 99615561 Apr 25, 2021 (155)
106 Genome of the Netherlands Release 5 NC_000001.10 - 100081117 Apr 25, 2020 (154)
107 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99853705 Apr 25, 2020 (154)
108 HapMap NC_000001.11 - 99615561 Apr 25, 2020 (154)
109 KOREAN population from KRGDB NC_000001.10 - 100081117 Apr 25, 2020 (154)
110 Korean Genome Project NC_000001.11 - 99615561 Apr 25, 2020 (154)
111 Northern Sweden NC_000001.10 - 100081117 Jul 12, 2019 (153)
112 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100081117 Apr 25, 2021 (155)
113 CNV burdens in cranial meningiomas NC_000001.10 - 100081117 Apr 25, 2021 (155)
114 Qatari NC_000001.10 - 100081117 Apr 25, 2020 (154)
115 SGDP_PRJ NC_000001.10 - 100081117 Apr 25, 2020 (154)
116 Siberian NC_000001.10 - 100081117 Apr 25, 2020 (154)
117 8.3KJPN NC_000001.10 - 100081117 Apr 25, 2021 (155)
118 TopMed NC_000001.11 - 99615561 Apr 25, 2021 (155)
119 UK 10K study - Twins NC_000001.10 - 100081117 Oct 11, 2018 (152)
120 A Vietnamese Genetic Variation Database NC_000001.10 - 100081117 Jul 12, 2019 (153)
121 ALFA NC_000001.11 - 99615561 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)
rs56839002 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2327383842 NC_000001.10:100081116:G:A NC_000001.11:99615560:G:A (self)
1749874936, ss3084655803 NC_000001.11:99615560:G:A NC_000001.11:99615560:G:A (self)
ss3638905841, ss3639765065, ss3643818615 NC_000001.8:99793137:G:T NC_000001.11:99615560:G:T (self)
21644, ss108453909, ss164869700, ss275945401, ss479813535, ss1584861538, ss1712357165, ss3642785650, ss3847343752 NC_000001.9:99853704:G:T NC_000001.11:99615560:G:T (self)
2872157, 1584410, 1129370, 1629052, 687318, 1733478, 599131, 40917, 11045, 724737, 1495010, 397972, 3283492, 1584410, 341319, ss218548774, ss230656830, ss238323787, ss479820672, ss480405969, ss484705257, ss536811182, ss554480873, ss648254101, ss778414911, ss782799398, ss783764938, ss832052354, ss832745392, ss833870226, ss975483224, ss1068127874, ss1292108560, ss1574271781, ss1600817443, ss1643811476, ss1751859126, ss1918682807, ss1946002827, ss1958296803, ss2019862928, ss2147881618, ss2327383843, ss2624442878, ss2632553652, ss2697808967, ss2710678280, ss2758640270, ss2987306008, ss3021113811, ss3343596038, ss3625546139, ss3626165330, ss3630587828, ss3632903295, ss3633598294, ss3634339268, ss3635291903, ss3636016823, ss3637042360, ss3637775465, ss3640046628, ss3644498789, ss3651444594, ss3655391122, ss3727314266, ss3744050999, ss3744640237, ss3746574408, ss3772141474, ss3826326704, ss3836553632, ss3849478030, ss3894556084, ss3984461733, ss3984814990, ss5145314185 NC_000001.10:100081116:G:T NC_000001.11:99615560:G:T (self)
20303400, 136625, 1469753, 15312585, 24312251, 1749874936, ss2165033036, ss3023695061, ss3084655804, ss3646731512, ss3687367545, ss3725048152, ss3799575170, ss3841961628, ss3945091752, ss4460705916 NC_000001.11:99615560:G:T NC_000001.11:99615560:G:T (self)
ss20460808 NT_028050.13:8270060:G:T NC_000001.11:99615560:G:T (self)
ss41102065, ss67036478, ss67360444, ss68138001, ss70583324, ss71125914, ss75448354, ss85268277, ss99232676, ss131830567, ss153275904, ss159233055, ss160297303, ss172234612 NT_032977.9:70053034:G:T NC_000001.11:99615560:G:T (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 rs12729121

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