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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.

rs12145826

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1130649 (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=0.047637 (12609/264690, TOPMED)
A=0.050131 (7030/140232, GnomAD)
A=0.02561 (2015/78694, PAGE_STUDY) (+ 17 more)
A=0.06707 (4833/72054, ALFA)
A=0.0258 (129/5008, 1000G)
A=0.0674 (302/4480, Estonian)
A=0.0776 (299/3854, ALSPAC)
A=0.0690 (256/3708, TWINSUK)
A=0.0007 (2/2920, KOREAN)
A=0.0417 (87/2084, HGDP_Stanford)
A=0.091 (91/998, GoNL)
A=0.052 (51/984, HapMap)
A=0.087 (52/600, NorthernSweden)
A=0.079 (17/216, Qatari)
A=0.17 (12/72, Ancient Sardinia)
A=0.12 (5/40, GENOME_DK)
G=0.50 (14/28, SGDP_PRJ)
A=0.50 (14/28, SGDP_PRJ)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, 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.1130649G>A
GRCh37.p13 chr 1 NC_000001.10:g.1066029G>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 72054 G=0.93293 A=0.06707
European Sub 58846 G=0.92399 A=0.07601
African Sub 4960 G=0.9897 A=0.0103
African Others Sub 170 G=1.000 A=0.000
African American Sub 4790 G=0.9894 A=0.0106
Asian Sub 224 G=1.000 A=0.000
East Asian Sub 182 G=1.000 A=0.000
Other Asian Sub 42 G=1.00 A=0.00
Latin American 1 Sub 254 G=0.933 A=0.067
Latin American 2 Sub 1232 G=0.9627 A=0.0373
South Asian Sub 4960 G=0.9635 A=0.0365
Other Sub 1578 G=0.9588 A=0.0412


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=0.952363 A=0.047637
gnomAD - Genomes Global Study-wide 140232 G=0.949869 A=0.050131
gnomAD - Genomes European Sub 75932 G=0.92865 A=0.07135
gnomAD - Genomes African Sub 42032 G=0.98672 A=0.01328
gnomAD - Genomes American Sub 13660 G=0.95110 A=0.04890
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9190 A=0.0810
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2154 G=0.9461 A=0.0539
The PAGE Study Global Study-wide 78694 G=0.97439 A=0.02561
The PAGE Study AfricanAmerican Sub 32512 G=0.98579 A=0.01421
The PAGE Study Mexican Sub 10810 G=0.96078 A=0.03922
The PAGE Study Asian Sub 8318 G=0.9987 A=0.0013
The PAGE Study PuertoRican Sub 7918 G=0.9536 A=0.0464
The PAGE Study NativeHawaiian Sub 4534 G=0.9795 A=0.0205
The PAGE Study Cuban Sub 4228 G=0.9272 A=0.0728
The PAGE Study Dominican Sub 3826 G=0.9702 A=0.0298
The PAGE Study CentralAmerican Sub 2450 G=0.9661 A=0.0339
The PAGE Study SouthAmerican Sub 1982 G=0.9667 A=0.0333
The PAGE Study NativeAmerican Sub 1260 G=0.9492 A=0.0508
The PAGE Study SouthAsian Sub 856 G=0.973 A=0.027
1000Genomes Global Study-wide 5008 G=0.9742 A=0.0258
1000Genomes African Sub 1322 G=0.9955 A=0.0045
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9185 A=0.0815
1000Genomes South Asian Sub 978 G=0.979 A=0.021
1000Genomes American Sub 694 G=0.971 A=0.029
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9326 A=0.0674
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9224 A=0.0776
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9310 A=0.0690
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9993 A=0.0007
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.9583 A=0.0417
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.954 A=0.046
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.897 A=0.103
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.912 A=0.087
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.981 A=0.019
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.909 A=0.091
HapMap Global Study-wide 984 G=0.948 A=0.052
HapMap American Sub 600 G=0.945 A=0.055
HapMap Europe Sub 176 G=0.898 A=0.102
HapMap African Sub 118 G=1.000 A=0.000
HapMap Asian Sub 90 G=1.00 A=0.00
Northern Sweden ACPOP Study-wide 600 G=0.913 A=0.087
Qatari Global Study-wide 216 G=0.921 A=0.079
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 72 G=0.83 A=0.17
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
SGDP_PRJ Global Study-wide 28 G=0.50 A=0.50
Siberian Global Study-wide 10 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.1130649= NC_000001.11:g.1130649G>A
GRCh37.p13 chr 1 NC_000001.10:g.1066029= NC_000001.10:g.1066029G>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#.

60 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18297974 Feb 28, 2004 (120)
2 ILLUMINA ss66985791 Nov 29, 2006 (127)
3 ILLUMINA ss67159849 Nov 29, 2006 (127)
4 ILLUMINA ss68122504 Dec 12, 2006 (127)
5 PERLEGEN ss68756320 May 16, 2007 (127)
6 ILLUMINA ss70557431 May 25, 2008 (130)
7 ILLUMINA ss71094930 May 16, 2007 (127)
8 ILLUMINA ss75670784 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss85189554 Dec 15, 2007 (130)
10 ILLUMINA ss153141800 Dec 01, 2009 (131)
11 ILLUMINA ss159205723 Dec 01, 2009 (131)
12 ILLUMINA ss171894161 Jul 04, 2010 (132)
13 1000GENOMES ss230396482 Jul 14, 2010 (132)
14 ILLUMINA ss536758860 Sep 08, 2015 (146)
15 ILLUMINA ss832718158 Jul 12, 2019 (153)
16 EVA-GONL ss974772132 Aug 21, 2014 (142)
17 1000GENOMES ss1289350836 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1573852076 Apr 01, 2015 (144)
19 EVA_DECODE ss1584132056 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1599382838 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1642376871 Apr 01, 2015 (144)
22 EVA_SVP ss1712305556 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1917964045 Feb 12, 2016 (147)
24 ILLUMINA ss1958230810 Feb 12, 2016 (147)
25 JJLAB ss2019499906 Sep 14, 2016 (149)
26 ILLUMINA ss2094948845 Dec 20, 2016 (150)
27 USC_VALOUEV ss2147486693 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2159387295 Dec 20, 2016 (150)
29 TOPMED ss2321526578 Dec 20, 2016 (150)
30 GNOMAD ss2750673336 Nov 08, 2017 (151)
31 SWEGEN ss2986154572 Nov 08, 2017 (151)
32 ILLUMINA ss3021043762 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023514333 Nov 08, 2017 (151)
34 TOPMED ss3066475564 Nov 08, 2017 (151)
35 CSHL ss3343274361 Nov 08, 2017 (151)
36 ILLUMINA ss3626007121 Oct 11, 2018 (152)
37 ILLUMINA ss3637732508 Oct 11, 2018 (152)
38 ILLUMINA ss3638887873 Oct 11, 2018 (152)
39 ILLUMINA ss3639756842 Oct 11, 2018 (152)
40 ILLUMINA ss3642746784 Oct 11, 2018 (152)
41 ILLUMINA ss3643810773 Oct 11, 2018 (152)
42 ILLUMINA ss3651365814 Oct 11, 2018 (152)
43 ILLUMINA ss3651365815 Oct 11, 2018 (152)
44 EGCUT_WGS ss3654265685 Jul 12, 2019 (153)
45 EVA_DECODE ss3685998269 Jul 12, 2019 (153)
46 ILLUMINA ss3724988479 Jul 12, 2019 (153)
47 ACPOP ss3726718818 Jul 12, 2019 (153)
48 EVA ss3745724464 Jul 12, 2019 (153)
49 PAGE_CC ss3770778843 Jul 12, 2019 (153)
50 PACBIO ss3783303057 Jul 12, 2019 (153)
51 PACBIO ss3788980832 Jul 12, 2019 (153)
52 PACBIO ss3793853383 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3798747073 Jul 12, 2019 (153)
54 EVA ss3825982679 Apr 25, 2020 (154)
55 HGDP ss3847322124 Apr 25, 2020 (154)
56 SGDP_PRJ ss3848004282 Apr 25, 2020 (154)
57 KRGDB ss3892847123 Apr 25, 2020 (154)
58 EVA ss3984774101 Apr 25, 2021 (155)
59 EVA ss4016889125 Apr 25, 2021 (155)
60 TOPMED ss4436524238 Apr 25, 2021 (155)
61 1000Genomes NC_000001.10 - 1066029 Oct 11, 2018 (152)
62 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1066029 Oct 11, 2018 (152)
63 Genetic variation in the Estonian population NC_000001.10 - 1066029 Oct 11, 2018 (152)
64 The Danish reference pan genome NC_000001.10 - 1066029 Apr 25, 2020 (154)
65 gnomAD - Genomes NC_000001.11 - 1130649 Apr 25, 2021 (155)
66 Genome of the Netherlands Release 5 NC_000001.10 - 1066029 Apr 25, 2020 (154)
67 HGDP-CEPH-db Supplement 1 NC_000001.9 - 1055892 Apr 25, 2020 (154)
68 HapMap NC_000001.11 - 1130649 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 1066029 Apr 25, 2020 (154)
70 Northern Sweden NC_000001.10 - 1066029 Jul 12, 2019 (153)
71 The PAGE Study NC_000001.11 - 1130649 Jul 12, 2019 (153)
72 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 1066029 Apr 25, 2021 (155)
73 Qatari NC_000001.10 - 1066029 Apr 25, 2020 (154)
74 SGDP_PRJ NC_000001.10 - 1066029 Apr 25, 2020 (154)
75 Siberian NC_000001.10 - 1066029 Apr 25, 2020 (154)
76 TopMed NC_000001.11 - 1130649 Apr 25, 2021 (155)
77 UK 10K study - Twins NC_000001.10 - 1066029 Oct 11, 2018 (152)
78 ALFA NC_000001.11 - 1130649 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)
rs59258561 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638887873, ss3639756842, ss3643810773 NC_000001.8:1105951:G:A NC_000001.11:1130648:G:A (self)
16, ss1584132056, ss1712305556, ss3642746784, ss3847322124 NC_000001.9:1055891:G:A NC_000001.11:1130648:G:A (self)
15975, 5238, 3933, 1359310, 2408, 24517, 3683, 28, 5975, 21262, 3047, 5238, ss230396482, ss536758860, ss832718158, ss974772132, ss1289350836, ss1573852076, ss1599382838, ss1642376871, ss1917964045, ss1958230810, ss2019499906, ss2094948845, ss2147486693, ss2321526578, ss2750673336, ss2986154572, ss3021043762, ss3343274361, ss3626007121, ss3637732508, ss3651365814, ss3651365815, ss3654265685, ss3726718818, ss3745724464, ss3783303057, ss3788980832, ss3793853383, ss3825982679, ss3848004282, ss3892847123, ss3984774101, ss4016889125 NC_000001.10:1066028:G:A NC_000001.11:1130648:G:A (self)
145544, 236, 312, 74061, 130573, 5755279775, ss2159387295, ss3023514333, ss3066475564, ss3685998269, ss3724988479, ss3770778843, ss3798747073, ss4436524238 NC_000001.11:1130648:G:A NC_000001.11:1130648:G:A (self)
ss66985791, ss67159849, ss68122504, ss68756320, ss70557431, ss71094930, ss75670784, ss85189554, ss153141800, ss159205723, ss171894161 NT_004350.19:544660:G:A NC_000001.11:1130648:G:A (self)
ss18297974 NT_077913.2:69739:G:A NC_000001.11:1130648: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 rs12145826

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