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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.

rs12409740

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:167168635 (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=0.327122 (86586/264690, TOPMED)
A=0.356896 (72430/202944, ALFA)
A=0.320809 (44896/139946, GnomAD) (+ 18 more)
A=0.30949 (24351/78682, PAGE_STUDY)
A=0.06116 (1025/16760, 8.3KJPN)
A=0.3007 (1506/5008, 1000G)
A=0.3710 (1662/4480, Estonian)
A=0.3371 (1299/3854, ALSPAC)
A=0.3533 (1310/3708, TWINSUK)
A=0.0809 (237/2930, KOREAN)
A=0.3090 (644/2084, HGDP_Stanford)
A=0.2595 (491/1892, HapMap)
A=0.0770 (141/1832, Korea1K)
A=0.339 (338/998, GoNL)
A=0.328 (197/600, NorthernSweden)
G=0.356 (94/264, SGDP_PRJ)
A=0.333 (72/216, Qatari)
A=0.047 (10/212, Vietnamese)
A=0.48 (44/92, Ancient Sardinia)
A=0.33 (13/40, GENOME_DK)
G=0.35 (12/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105371601 : Intron Variant
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.167168635G>A
GRCh37.p13 chr 1 NC_000001.10:g.167137872G>A
Gene: LOC105371601, uncharacterized LOC105371601 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371601 transcript XR_922250.2:n. N/A Intron Variant
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 202944 G=0.643104 A=0.356896
European Sub 175604 G=0.646984 A=0.353016
African Sub 7100 G=0.7673 A=0.2327
African Others Sub 264 G=0.822 A=0.178
African American Sub 6836 G=0.7652 A=0.2348
Asian Sub 736 G=0.931 A=0.069
East Asian Sub 590 G=0.942 A=0.058
Other Asian Sub 146 G=0.884 A=0.116
Latin American 1 Sub 842 G=0.665 A=0.335
Latin American 2 Sub 6902 G=0.4313 A=0.5687
South Asian Sub 5048 G=0.5658 A=0.4342
Other Sub 6712 G=0.6518 A=0.3482


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=0.672878 A=0.327122
gnomAD - Genomes Global Study-wide 139946 G=0.679191 A=0.320809
gnomAD - Genomes European Sub 75826 G=0.65125 A=0.34875
gnomAD - Genomes African Sub 41888 G=0.74947 A=0.25053
gnomAD - Genomes American Sub 13638 G=0.55081 A=0.44919
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.7172 A=0.2828
gnomAD - Genomes East Asian Sub 3124 G=0.9446 A=0.0554
gnomAD - Genomes Other Sub 2150 G=0.6651 A=0.3349
The PAGE Study Global Study-wide 78682 G=0.69051 A=0.30949
The PAGE Study AfricanAmerican Sub 32510 G=0.74903 A=0.25097
The PAGE Study Mexican Sub 10806 G=0.43504 A=0.56496
The PAGE Study Asian Sub 8316 G=0.9400 A=0.0600
The PAGE Study PuertoRican Sub 7918 G=0.6377 A=0.3623
The PAGE Study NativeHawaiian Sub 4532 G=0.8151 A=0.1849
The PAGE Study Cuban Sub 4226 G=0.6290 A=0.3710
The PAGE Study Dominican Sub 3828 G=0.6899 A=0.3101
The PAGE Study CentralAmerican Sub 2450 G=0.4718 A=0.5282
The PAGE Study SouthAmerican Sub 1980 G=0.5328 A=0.4672
The PAGE Study NativeAmerican Sub 1260 G=0.5841 A=0.4159
The PAGE Study SouthAsian Sub 856 G=0.553 A=0.447
8.3KJPN JAPANESE Study-wide 16760 G=0.93884 A=0.06116
1000Genomes Global Study-wide 5008 G=0.6993 A=0.3007
1000Genomes African Sub 1322 G=0.7451 A=0.2549
1000Genomes East Asian Sub 1008 G=0.9464 A=0.0536
1000Genomes Europe Sub 1006 G=0.6630 A=0.3370
1000Genomes South Asian Sub 978 G=0.546 A=0.454
1000Genomes American Sub 694 G=0.522 A=0.478
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6290 A=0.3710
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6629 A=0.3371
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6467 A=0.3533
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.9191 A=0.0809
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.6910 A=0.3090
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.889 A=0.111
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.626 A=0.374
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.723 A=0.277
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.628 A=0.372
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.843 A=0.157
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.278 A=0.722
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.62 A=0.38
HapMap Global Study-wide 1892 G=0.7405 A=0.2595
HapMap American Sub 770 G=0.652 A=0.348
HapMap African Sub 692 G=0.789 A=0.211
HapMap Asian Sub 254 G=0.933 A=0.067
HapMap Europe Sub 176 G=0.659 A=0.341
Korean Genome Project KOREAN Study-wide 1832 G=0.9230 A=0.0770
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.661 A=0.339
Northern Sweden ACPOP Study-wide 600 G=0.672 A=0.328
SGDP_PRJ Global Study-wide 264 G=0.356 A=0.644
Qatari Global Study-wide 216 G=0.667 A=0.333
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.953 A=0.047
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 92 G=0.52 A=0.48
The Danish reference pan genome Danish Study-wide 40 G=0.68 A=0.33
Siberian Global Study-wide 34 G=0.35 A=0.65
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.167168635= NC_000001.11:g.167168635G>A
GRCh37.p13 chr 1 NC_000001.10:g.167137872= NC_000001.10:g.167137872G>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#.

110 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19145574 Feb 28, 2004 (120)
2 SSAHASNP ss20501198 Apr 05, 2004 (121)
3 PERLEGEN ss23145062 Sep 20, 2004 (123)
4 ABI ss41162219 Mar 13, 2006 (126)
5 ILLUMINA ss67003507 Dec 02, 2006 (127)
6 ILLUMINA ss67322244 Dec 02, 2006 (127)
7 ILLUMINA ss68128077 Dec 12, 2006 (127)
8 PERLEGEN ss68783608 May 18, 2007 (127)
9 ILLUMINA ss70566465 May 26, 2008 (130)
10 ILLUMINA ss71106499 May 18, 2007 (127)
11 ILLUMINA ss75433578 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss85215922 Dec 15, 2007 (130)
13 HUMANGENOME_JCVI ss99258322 Feb 06, 2009 (130)
14 BGI ss102793597 Dec 01, 2009 (131)
15 1000GENOMES ss108672606 Jan 23, 2009 (130)
16 ENSEMBL ss139180989 Dec 01, 2009 (131)
17 ILLUMINA ss153187703 Dec 01, 2009 (131)
18 GMI ss155884221 Dec 01, 2009 (131)
19 ILLUMINA ss159215253 Dec 01, 2009 (131)
20 ILLUMINA ss160055747 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss167240012 Jul 04, 2010 (132)
22 ILLUMINA ss172054196 Jul 04, 2010 (132)
23 BUSHMAN ss199198604 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss205255065 Jul 04, 2010 (132)
25 1000GENOMES ss218698160 Jul 14, 2010 (132)
26 1000GENOMES ss230767054 Jul 14, 2010 (132)
27 1000GENOMES ss238408294 Jul 15, 2010 (132)
28 BL ss253580788 May 09, 2011 (134)
29 GMI ss276088388 May 04, 2012 (137)
30 PJP ss290656246 May 09, 2011 (134)
31 ILLUMINA ss479730266 May 04, 2012 (137)
32 ILLUMINA ss479736034 May 04, 2012 (137)
33 ILLUMINA ss480288396 Sep 08, 2015 (146)
34 ILLUMINA ss484663446 May 04, 2012 (137)
35 ILLUMINA ss536778229 Sep 08, 2015 (146)
36 TISHKOFF ss554807964 Apr 25, 2013 (138)
37 SSMP ss648475450 Apr 25, 2013 (138)
38 ILLUMINA ss778780519 Sep 08, 2015 (146)
39 ILLUMINA ss782778586 Sep 08, 2015 (146)
40 ILLUMINA ss783744579 Sep 08, 2015 (146)
41 ILLUMINA ss832031137 Sep 08, 2015 (146)
42 ILLUMINA ss832727654 Jul 12, 2019 (153)
43 ILLUMINA ss834240456 Sep 08, 2015 (146)
44 EVA-GONL ss975776335 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1068337137 Aug 21, 2014 (142)
46 1000GENOMES ss1293281297 Aug 21, 2014 (142)
47 DDI ss1426006450 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1574452533 Apr 01, 2015 (144)
49 EVA_DECODE ss1585161264 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1601403158 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1644397191 Apr 01, 2015 (144)
52 EVA_SVP ss1712378611 Apr 01, 2015 (144)
53 ILLUMINA ss1751879364 Sep 08, 2015 (146)
54 HAMMER_LAB ss1795217906 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1919012577 Feb 12, 2016 (147)
56 ILLUMINA ss1958328844 Feb 12, 2016 (147)
57 GENOMED ss1966889755 Jul 19, 2016 (147)
58 JJLAB ss2020021867 Sep 14, 2016 (149)
59 USC_VALOUEV ss2148049104 Dec 20, 2016 (150)
60 HUMAN_LONGEVITY ss2167250768 Dec 20, 2016 (150)
61 TOPMED ss2329786892 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2624520572 Nov 08, 2017 (151)
63 ILLUMINA ss2632588206 Nov 08, 2017 (151)
64 ILLUMINA ss2635004179 Nov 08, 2017 (151)
65 GRF ss2698026534 Nov 08, 2017 (151)
66 GNOMAD ss2762317387 Nov 08, 2017 (151)
67 SWEGEN ss2987896335 Nov 08, 2017 (151)
68 ILLUMINA ss3021147914 Nov 08, 2017 (151)
69 BIOINF_KMB_FNS_UNIBA ss3023768872 Nov 08, 2017 (151)
70 TOPMED ss3094436218 Nov 08, 2017 (151)
71 CSHL ss3343752767 Nov 08, 2017 (151)
72 ILLUMINA ss3626231749 Oct 11, 2018 (152)
73 ILLUMINA ss3630620314 Oct 11, 2018 (152)
74 ILLUMINA ss3632913739 Oct 11, 2018 (152)
75 ILLUMINA ss3633609253 Oct 11, 2018 (152)
76 ILLUMINA ss3634356359 Oct 11, 2018 (152)
77 ILLUMINA ss3635302623 Oct 11, 2018 (152)
78 ILLUMINA ss3636035303 Oct 11, 2018 (152)
79 ILLUMINA ss3637053122 Oct 11, 2018 (152)
80 ILLUMINA ss3637793439 Oct 11, 2018 (152)
81 ILLUMINA ss3638913321 Oct 11, 2018 (152)
82 ILLUMINA ss3639768710 Oct 11, 2018 (152)
83 ILLUMINA ss3640063713 Oct 11, 2018 (152)
84 ILLUMINA ss3640988286 Oct 11, 2018 (152)
85 ILLUMINA ss3641282338 Oct 11, 2018 (152)
86 ILLUMINA ss3642802119 Oct 11, 2018 (152)
87 ILLUMINA ss3643822047 Oct 11, 2018 (152)
88 URBANLAB ss3646811426 Oct 11, 2018 (152)
89 ILLUMINA ss3651484494 Oct 11, 2018 (152)
90 EGCUT_WGS ss3655839303 Jul 12, 2019 (153)
91 EVA_DECODE ss3687956479 Jul 12, 2019 (153)
92 ILLUMINA ss3725076282 Jul 12, 2019 (153)
93 ACPOP ss3727564116 Jul 12, 2019 (153)
94 ILLUMINA ss3744657242 Jul 12, 2019 (153)
95 EVA ss3746917620 Jul 12, 2019 (153)
96 PAGE_CC ss3770849464 Jul 12, 2019 (153)
97 ILLUMINA ss3772158302 Jul 12, 2019 (153)
98 KHV_HUMAN_GENOMES ss3799918325 Jul 12, 2019 (153)
99 EVA ss3826471386 Apr 25, 2020 (154)
100 EVA ss3836631833 Apr 25, 2020 (154)
101 EVA ss3842041676 Apr 25, 2020 (154)
102 HGDP ss3847352736 Apr 25, 2020 (154)
103 SGDP_PRJ ss3850189674 Apr 25, 2020 (154)
104 KRGDB ss3895422172 Apr 25, 2020 (154)
105 KOGIC ss3945830740 Apr 25, 2020 (154)
106 EVA ss3984831614 Apr 25, 2021 (155)
107 EVA ss4016943464 Apr 25, 2021 (155)
108 TOPMED ss4471401387 Apr 25, 2021 (155)
109 TOMMO_GENOMICS ss5146886001 Apr 25, 2021 (155)
110 EVA ss5237275793 Apr 25, 2021 (155)
111 1000Genomes NC_000001.10 - 167137872 Oct 11, 2018 (152)
112 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 167137872 Oct 11, 2018 (152)
113 Genetic variation in the Estonian population NC_000001.10 - 167137872 Oct 11, 2018 (152)
114 The Danish reference pan genome NC_000001.10 - 167137872 Apr 25, 2020 (154)
115 gnomAD - Genomes NC_000001.11 - 167168635 Apr 25, 2021 (155)
116 Genome of the Netherlands Release 5 NC_000001.10 - 167137872 Apr 25, 2020 (154)
117 HGDP-CEPH-db Supplement 1 NC_000001.9 - 165404496 Apr 25, 2020 (154)
118 HapMap NC_000001.11 - 167168635 Apr 25, 2020 (154)
119 KOREAN population from KRGDB NC_000001.10 - 167137872 Apr 25, 2020 (154)
120 Korean Genome Project NC_000001.11 - 167168635 Apr 25, 2020 (154)
121 Northern Sweden NC_000001.10 - 167137872 Jul 12, 2019 (153)
122 The PAGE Study NC_000001.11 - 167168635 Jul 12, 2019 (153)
123 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 167137872 Apr 25, 2021 (155)
124 Qatari NC_000001.10 - 167137872 Apr 25, 2020 (154)
125 SGDP_PRJ NC_000001.10 - 167137872 Apr 25, 2020 (154)
126 Siberian NC_000001.10 - 167137872 Apr 25, 2020 (154)
127 8.3KJPN NC_000001.10 - 167137872 Apr 25, 2021 (155)
128 TopMed NC_000001.11 - 167168635 Apr 25, 2021 (155)
129 UK 10K study - Twins NC_000001.10 - 167137872 Oct 11, 2018 (152)
130 A Vietnamese Genetic Variation Database NC_000001.10 - 167137872 Jul 12, 2019 (153)
131 ALFA NC_000001.11 - 167168635 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)
rs60837369 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638913321, ss3639768710, ss3643822047 NC_000001.8:163869529:G:A NC_000001.11:167168634:G:A (self)
30628, ss108672606, ss167240012, ss199198604, ss205255065, ss253580788, ss276088388, ss290656246, ss479730266, ss1585161264, ss1712378611, ss2635004179, ss3642802119, ss3847352736 NC_000001.9:165404495:G:A NC_000001.11:167168634:G:A (self)
4085212, 2228401, 1577551, 1745224, 969100, 2599566, 848981, 57541, 1054507, 2206654, 565458, 4855308, 2228401, 479236, ss218698160, ss230767054, ss238408294, ss479736034, ss480288396, ss484663446, ss536778229, ss554807964, ss648475450, ss778780519, ss782778586, ss783744579, ss832031137, ss832727654, ss834240456, ss975776335, ss1068337137, ss1293281297, ss1426006450, ss1574452533, ss1601403158, ss1644397191, ss1751879364, ss1795217906, ss1919012577, ss1958328844, ss1966889755, ss2020021867, ss2148049104, ss2329786892, ss2624520572, ss2632588206, ss2698026534, ss2762317387, ss2987896335, ss3021147914, ss3343752767, ss3626231749, ss3630620314, ss3632913739, ss3633609253, ss3634356359, ss3635302623, ss3636035303, ss3637053122, ss3637793439, ss3640063713, ss3640988286, ss3641282338, ss3651484494, ss3655839303, ss3727564116, ss3744657242, ss3746917620, ss3772158302, ss3826471386, ss3836631833, ss3850189674, ss3895422172, ss3984831614, ss4016943464, ss5146886001, ss5237275793 NC_000001.10:167137871:G:A NC_000001.11:167168634:G:A (self)
29596911, 196148, 2208741, 70933, 21973312, 35007722, 4458821744, ss2167250768, ss3023768872, ss3094436218, ss3646811426, ss3687956479, ss3725076282, ss3770849464, ss3799918325, ss3842041676, ss3945830740, ss4471401387 NC_000001.11:167168634:G:A NC_000001.11:167168634:G:A (self)
ss23145062, ss41162219, ss67003507, ss67322244, ss68128077, ss68783608, ss70566465, ss71106499, ss75433578, ss85215922, ss99258322, ss102793597, ss139180989, ss153187703, ss155884221, ss159215253, ss160055747, ss172054196 NT_004487.19:18626513:G:A NC_000001.11:167168634:G:A (self)
ss19145574, ss20501198 NT_004668.16:5643343:G:A NC_000001.11:167168634: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 rs12409740

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