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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.

rs12136809

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99586244 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.031811 (8420/264690, TOPMED)
G=0.046452 (8519/183394, ALFA)
G=0.034940 (4902/140296, GnomAD) (+ 14 more)
G=0.0204 (102/5008, 1000G)
G=0.0643 (288/4480, Estonian)
G=0.0558 (215/3854, ALSPAC)
G=0.0507 (188/3708, TWINSUK)
G=0.0149 (31/2084, HGDP_Stanford)
G=0.057 (57/998, GoNL)
G=0.033 (32/982, HapMap)
G=0.062 (37/600, NorthernSweden)
G=0.042 (9/216, Qatari)
G=0.03 (1/40, GENOME_DK)
G=0.00 (0/38, Ancient Sardinia)
A=0.46 (13/28, SGDP_PRJ)
A=0.5 (3/6, Siberian)
G=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.99586244A>G
GRCh37.p13 chr 1 NC_000001.10:g.100051800A>G
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 183394 A=0.953548 G=0.046452
European Sub 161416 A=0.950798 G=0.049202
African Sub 6550 A=0.9921 G=0.0079
African Others Sub 254 A=1.000 G=0.000
African American Sub 6296 A=0.9917 G=0.0083
Asian Sub 414 A=1.000 G=0.000
East Asian Sub 300 A=1.000 G=0.000
Other Asian Sub 114 A=1.000 G=0.000
Latin American 1 Sub 752 A=0.976 G=0.024
Latin American 2 Sub 2664 A=0.9816 G=0.0184
South Asian Sub 5024 A=0.9658 G=0.0342
Other Sub 6574 A=0.9565 G=0.0435


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 A=0.968189 G=0.031811
gnomAD - Genomes Global Study-wide 140296 A=0.965060 G=0.034940
gnomAD - Genomes European Sub 75956 A=0.94905 G=0.05095
gnomAD - Genomes African Sub 42068 A=0.99094 G=0.00906
gnomAD - Genomes American Sub 13664 A=0.97497 G=0.02503
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9269 G=0.0731
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9693 G=0.0307
1000Genomes Global Study-wide 5008 A=0.9796 G=0.0204
1000Genomes African Sub 1322 A=0.9970 G=0.0030
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9563 G=0.0437
1000Genomes South Asian Sub 978 A=0.957 G=0.043
1000Genomes American Sub 694 A=0.983 G=0.017
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9357 G=0.0643
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9442 G=0.0558
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9493 G=0.0507
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.9851 G=0.0149
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.978 G=0.022
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.980 G=0.020
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.956 G=0.044
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 A=0.995 G=0.005
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.943 G=0.057
HapMap Global Study-wide 982 A=0.967 G=0.033
HapMap American Sub 600 A=0.953 G=0.047
HapMap Europe Sub 176 A=0.977 G=0.023
HapMap African Sub 118 A=1.000 G=0.000
HapMap Asian Sub 88 A=1.00 G=0.00
Northern Sweden ACPOP Study-wide 600 A=0.938 G=0.062
Qatari Global Study-wide 216 A=0.958 G=0.042
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 38 A=1.00 G=0.00
SGDP_PRJ Global Study-wide 28 A=0.46 G=0.54
Siberian Global Study-wide 6 A=0.5 G=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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.99586244= NC_000001.11:g.99586244A>G
GRCh37.p13 chr 1 NC_000001.10:g.100051800= NC_000001.10:g.100051800A>G
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#.

81 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18281286 Feb 28, 2004 (120)
2 PERLEGEN ss24244055 Sep 20, 2004 (123)
3 ILLUMINA ss66766786 Nov 30, 2006 (127)
4 ILLUMINA ss66984881 Nov 30, 2006 (127)
5 ILLUMINA ss67158823 Nov 30, 2006 (127)
6 ILLUMINA ss70405453 May 17, 2007 (127)
7 ILLUMINA ss70556972 May 23, 2008 (130)
8 ILLUMINA ss71094413 May 17, 2007 (127)
9 ILLUMINA ss75792033 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss85187990 Dec 14, 2007 (130)
11 ILLUMINA ss121539218 Dec 01, 2009 (131)
12 ILLUMINA ss153139343 Dec 01, 2009 (131)
13 ILLUMINA ss159205237 Dec 01, 2009 (131)
14 ILLUMINA ss160036472 Dec 01, 2009 (131)
15 ILLUMINA ss170053282 Jul 04, 2010 (132)
16 ILLUMINA ss171885939 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss205441468 Jul 04, 2010 (132)
18 1000GENOMES ss230656734 Jul 14, 2010 (132)
19 GMI ss284105674 Apr 25, 2013 (138)
20 ILLUMINA ss479679966 May 04, 2012 (137)
21 ILLUMINA ss479685458 May 04, 2012 (137)
22 ILLUMINA ss480211562 Sep 08, 2015 (146)
23 ILLUMINA ss484638532 May 04, 2012 (137)
24 ILLUMINA ss536758018 Sep 08, 2015 (146)
25 SSMP ss648253936 Apr 25, 2013 (138)
26 ILLUMINA ss778775148 Aug 21, 2014 (142)
27 ILLUMINA ss782766105 Aug 21, 2014 (142)
28 ILLUMINA ss783732393 Aug 21, 2014 (142)
29 ILLUMINA ss825374727 Jul 19, 2016 (147)
30 ILLUMINA ss832018451 Apr 01, 2015 (144)
31 ILLUMINA ss832717672 Aug 21, 2014 (142)
32 ILLUMINA ss833308502 Aug 21, 2014 (142)
33 ILLUMINA ss834235036 Aug 21, 2014 (142)
34 EVA-GONL ss975483008 Aug 21, 2014 (142)
35 1000GENOMES ss1292107765 Aug 21, 2014 (142)
36 DDI ss1425910988 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1574271575 Apr 01, 2015 (144)
38 EVA_DECODE ss1584861321 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1600816980 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1643811013 Apr 01, 2015 (144)
41 EVA_SVP ss1712357149 Apr 01, 2015 (144)
42 ILLUMINA ss1751859115 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1918682612 Feb 12, 2016 (147)
44 JJLAB ss2019862796 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147881499 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2165031307 Dec 20, 2016 (150)
47 TOPMED ss2327382105 Dec 20, 2016 (150)
48 ILLUMINA ss2632553624 Nov 08, 2017 (151)
49 GNOMAD ss2758637995 Nov 08, 2017 (151)
50 SWEGEN ss2987305713 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3023694989 Nov 08, 2017 (151)
52 TOPMED ss3084650614 Nov 08, 2017 (151)
53 CSHL ss3343595926 Nov 08, 2017 (151)
54 ILLUMINA ss3626165290 Oct 11, 2018 (152)
55 ILLUMINA ss3630587798 Oct 11, 2018 (152)
56 ILLUMINA ss3632903284 Oct 11, 2018 (152)
57 ILLUMINA ss3633598282 Oct 11, 2018 (152)
58 ILLUMINA ss3634339257 Oct 11, 2018 (152)
59 ILLUMINA ss3635291893 Oct 11, 2018 (152)
60 ILLUMINA ss3636016812 Oct 11, 2018 (152)
61 ILLUMINA ss3637042349 Oct 11, 2018 (152)
62 ILLUMINA ss3637775456 Oct 11, 2018 (152)
63 ILLUMINA ss3638905835 Oct 11, 2018 (152)
64 ILLUMINA ss3639450876 Oct 11, 2018 (152)
65 ILLUMINA ss3640046617 Oct 11, 2018 (152)
66 ILLUMINA ss3640984524 Oct 11, 2018 (152)
67 ILLUMINA ss3641278512 Oct 11, 2018 (152)
68 ILLUMINA ss3642785641 Oct 11, 2018 (152)
69 EGCUT_WGS ss3655390794 Jul 12, 2019 (153)
70 EVA_DECODE ss3687367199 Jul 12, 2019 (153)
71 ACPOP ss3727314087 Jul 12, 2019 (153)
72 ILLUMINA ss3744640226 Jul 12, 2019 (153)
73 EVA ss3746574139 Jul 12, 2019 (153)
74 ILLUMINA ss3772141463 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3799574916 Jul 12, 2019 (153)
76 EVA ss3826326578 Apr 25, 2020 (154)
77 HGDP ss3847343744 Apr 25, 2020 (154)
78 SGDP_PRJ ss3849477630 Apr 25, 2020 (154)
79 EVA ss3984814971 Apr 25, 2021 (155)
80 EVA ss4016927694 Apr 25, 2021 (155)
81 TOPMED ss4460698739 Apr 25, 2021 (155)
82 1000Genomes NC_000001.10 - 100051800 Oct 11, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100051800 Oct 11, 2018 (152)
84 Genetic variation in the Estonian population NC_000001.10 - 100051800 Oct 11, 2018 (152)
85 The Danish reference pan genome NC_000001.10 - 100051800 Apr 25, 2020 (154)
86 gnomAD - Genomes NC_000001.11 - 99586244 Apr 25, 2021 (155)
87 Genome of the Netherlands Release 5 NC_000001.10 - 100051800 Apr 25, 2020 (154)
88 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99824388 Apr 25, 2020 (154)
89 HapMap NC_000001.11 - 99586244 Apr 25, 2020 (154)
90 Northern Sweden NC_000001.10 - 100051800 Jul 12, 2019 (153)
91 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100051800 Apr 25, 2021 (155)
92 Qatari NC_000001.10 - 100051800 Apr 25, 2020 (154)
93 SGDP_PRJ NC_000001.10 - 100051800 Apr 25, 2020 (154)
94 Siberian NC_000001.10 - 100051800 Apr 25, 2020 (154)
95 TopMed NC_000001.11 - 99586244 Apr 25, 2021 (155)
96 UK 10K study - Twins NC_000001.10 - 100051800 Oct 11, 2018 (152)
97 ALFA NC_000001.11 - 99586244 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)
rs17413479 Oct 07, 2004 (123)
rs57083274 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638905835, ss3639450876 NC_000001.8:99763820:A:G NC_000001.11:99586243:A:G (self)
21636, ss160036472, ss205441468, ss284105674, ss479679966, ss825374727, ss1584861321, ss1712357149, ss3642785641, ss3847343744 NC_000001.9:99824387:A:G NC_000001.11:99586243:A:G (self)
2871334, 1583920, 1129042, 1628956, 687105, 598952, 40898, 724542, 1494610, 397853, 1583920, ss230656734, ss479685458, ss480211562, ss484638532, ss536758018, ss648253936, ss778775148, ss782766105, ss783732393, ss832018451, ss832717672, ss833308502, ss834235036, ss975483008, ss1292107765, ss1425910988, ss1574271575, ss1600816980, ss1643811013, ss1751859115, ss1918682612, ss2019862796, ss2147881499, ss2327382105, ss2632553624, ss2758637995, ss2987305713, ss3343595926, ss3626165290, ss3630587798, ss3632903284, ss3633598282, ss3634339257, ss3635291893, ss3636016812, ss3637042349, ss3637775456, ss3640046617, ss3640984524, ss3641278512, ss3655390794, ss3727314087, ss3744640226, ss3746574139, ss3772141463, ss3826326578, ss3849477630, ss3984814971, ss4016927694 NC_000001.10:100051799:A:G NC_000001.11:99586243:A:G (self)
20297661, 136561, 15307946, 24305074, 4363456709, ss2165031307, ss3023694989, ss3084650614, ss3687367199, ss3799574916, ss4460698739 NC_000001.11:99586243:A:G NC_000001.11:99586243:A:G (self)
ss18281286 NT_028050.13:8240743:A:G NC_000001.11:99586243:A:G (self)
ss24244055, ss66766786, ss66984881, ss67158823, ss70405453, ss70556972, ss71094413, ss75792033, ss85187990, ss121539218, ss153139343, ss159205237, ss170053282, ss171885939 NT_032977.9:70023717:A:G NC_000001.11:99586243:A:G (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 rs12136809

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