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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.

rs1339866

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99553713 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.312229 (88031/281944, ALFA)
A=0.412180 (109100/264690, TOPMED)
A=0.417636 (58439/139928, GnomAD) (+ 18 more)
A=0.46830 (36846/78680, PAGE_STUDY)
A=0.38550 (6461/16760, 8.3KJPN)
A=0.4301 (2154/5008, 1000G)
A=0.3795 (1700/4480, Estonian)
A=0.2950 (1137/3854, ALSPAC)
A=0.2775 (1029/3708, TWINSUK)
A=0.4273 (1252/2930, KOREAN)
A=0.3709 (773/2084, HGDP_Stanford)
A=0.4952 (933/1884, HapMap)
A=0.308 (307/998, GoNL)
A=0.406 (311/766, PRJEB37584)
A=0.422 (253/600, NorthernSweden)
C=0.362 (121/334, SGDP_PRJ)
A=0.356 (77/216, Qatari)
A=0.341 (73/214, Vietnamese)
A=0.26 (12/46, Ancient Sardinia)
A=0.35 (14/40, GENOME_DK)
C=0.36 (13/36, 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.99553713C>A
GRCh38.p13 chr 1 NC_000001.11:g.99553713C>T
GRCh37.p13 chr 1 NC_000001.10:g.100019269C>A
GRCh37.p13 chr 1 NC_000001.10:g.100019269C>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
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 281944 C=0.687771 A=0.312229
European Sub 247048 C=0.701681 A=0.298319
African Sub 8384 C=0.3533 A=0.6467
African Others Sub 318 C=0.286 A=0.714
African American Sub 8066 C=0.3559 A=0.6441
Asian Sub 3942 C=0.6334 A=0.3666
East Asian Sub 3196 C=0.5864 A=0.4136
Other Asian Sub 746 C=0.835 A=0.165
Latin American 1 Sub 1132 C=0.6466 A=0.3534
Latin American 2 Sub 7222 C=0.6644 A=0.3356
South Asian Sub 5224 C=0.6799 A=0.3201
Other Sub 8992 C=0.6698 A=0.3302


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 C=0.587820 A=0.412180
gnomAD - Genomes Global Study-wide 139928 C=0.582364 A=0.417636
gnomAD - Genomes European Sub 75782 C=0.68493 A=0.31507
gnomAD - Genomes African Sub 41942 C=0.34755 A=0.65245
gnomAD - Genomes American Sub 13604 C=0.67973 A=0.32027
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.7389 A=0.2611
gnomAD - Genomes East Asian Sub 3128 C=0.6109 A=0.3891
gnomAD - Genomes Other Sub 2152 C=0.6487 A=0.3513
The PAGE Study Global Study-wide 78680 C=0.53170 A=0.46830
The PAGE Study AfricanAmerican Sub 32506 C=0.35950 A=0.64050
The PAGE Study Mexican Sub 10808 C=0.66451 A=0.33549
The PAGE Study Asian Sub 8314 C=0.6286 A=0.3714
The PAGE Study PuertoRican Sub 7914 C=0.6442 A=0.3558
The PAGE Study NativeHawaiian Sub 4534 C=0.7653 A=0.2347
The PAGE Study Cuban Sub 4230 C=0.6901 A=0.3099
The PAGE Study Dominican Sub 3828 C=0.5266 A=0.4734
The PAGE Study CentralAmerican Sub 2448 C=0.6373 A=0.3627
The PAGE Study SouthAmerican Sub 1982 C=0.6524 A=0.3476
The PAGE Study NativeAmerican Sub 1260 C=0.6373 A=0.3627
The PAGE Study SouthAsian Sub 856 C=0.679 A=0.321
8.3KJPN JAPANESE Study-wide 16760 C=0.61450 A=0.38550
1000Genomes Global Study-wide 5008 C=0.5699 A=0.4301
1000Genomes African Sub 1322 C=0.3071 A=0.6929
1000Genomes East Asian Sub 1008 C=0.6280 A=0.3720
1000Genomes Europe Sub 1006 C=0.6948 A=0.3052
1000Genomes South Asian Sub 978 C=0.666 A=0.334
1000Genomes American Sub 694 C=0.670 A=0.330
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6205 A=0.3795
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7050 A=0.2950
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7225 A=0.2775
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5727 A=0.4273, T=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.6291 A=0.3709
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.602 A=0.398
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.647 A=0.353
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.700 A=0.300
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.725 A=0.275
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.211 A=0.789
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.759 A=0.241
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.94 A=0.06
HapMap Global Study-wide 1884 C=0.5048 A=0.4952
HapMap American Sub 764 C=0.618 A=0.382
HapMap African Sub 690 C=0.287 A=0.713
HapMap Asian Sub 254 C=0.622 A=0.378
HapMap Europe Sub 176 C=0.699 A=0.301
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.692 A=0.308
CNV burdens in cranial meningiomas Global Study-wide 766 C=0.594 A=0.406
CNV burdens in cranial meningiomas CRM Sub 766 C=0.594 A=0.406
Northern Sweden ACPOP Study-wide 600 C=0.578 A=0.422
SGDP_PRJ Global Study-wide 334 C=0.362 A=0.638
Qatari Global Study-wide 216 C=0.644 A=0.356
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.659 A=0.341
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 46 C=0.74 A=0.26
The Danish reference pan genome Danish Study-wide 40 C=0.65 A=0.35
Siberian Global Study-wide 36 C=0.36 A=0.64
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.99553713= NC_000001.11:g.99553713C>A NC_000001.11:g.99553713C>T
GRCh37.p13 chr 1 NC_000001.10:g.100019269= NC_000001.10:g.100019269C>A NC_000001.10:g.100019269C>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#.

110 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2115174 Oct 23, 2000 (88)
2 SC_JCM ss5867440 Feb 20, 2003 (111)
3 PERLEGEN ss23842325 Sep 20, 2004 (123)
4 AFFY ss65980842 Dec 01, 2006 (127)
5 ILLUMINA ss66829161 Dec 01, 2006 (127)
6 ILLUMINA ss67078035 Dec 01, 2006 (127)
7 ILLUMINA ss67409483 Dec 01, 2006 (127)
8 ILLUMINA ss70423807 May 18, 2007 (127)
9 ILLUMINA ss70604680 May 26, 2008 (130)
10 ILLUMINA ss71150919 May 18, 2007 (127)
11 ILLUMINA ss75879061 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss83727041 Dec 16, 2007 (130)
13 HGSV ss85621961 Dec 16, 2007 (130)
14 BGI ss102767778 Dec 01, 2009 (131)
15 1000GENOMES ss110890570 Jan 25, 2009 (130)
16 ILLUMINA-UK ss118918994 Feb 15, 2009 (130)
17 ILLUMINA ss121645939 Dec 01, 2009 (131)
18 ILLUMINA ss153368954 Dec 01, 2009 (131)
19 ILLUMINA ss159256105 Dec 01, 2009 (131)
20 ILLUMINA ss160335489 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss163738537 Jul 04, 2010 (132)
22 ILLUMINA ss170372458 Jul 04, 2010 (132)
23 ILLUMINA ss172411123 Jul 04, 2010 (132)
24 BUSHMAN ss198832393 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss205274047 Jul 04, 2010 (132)
26 1000GENOMES ss210458555 Jul 14, 2010 (132)
27 1000GENOMES ss218548515 Jul 14, 2010 (132)
28 1000GENOMES ss230656632 Jul 14, 2010 (132)
29 1000GENOMES ss238323638 Jul 15, 2010 (132)
30 GMI ss275945249 May 04, 2012 (137)
31 GMI ss284105630 Apr 25, 2013 (138)
32 PJP ss290580455 May 09, 2011 (134)
33 ILLUMINA ss479922528 May 04, 2012 (137)
34 ILLUMINA ss479930422 May 04, 2012 (137)
35 ILLUMINA ss480560477 Sep 08, 2015 (146)
36 ILLUMINA ss484759460 May 04, 2012 (137)
37 ILLUMINA ss536851771 Sep 08, 2015 (146)
38 TISHKOFF ss554480307 Apr 25, 2013 (138)
39 SSMP ss648253763 Apr 25, 2013 (138)
40 ILLUMINA ss778426541 Sep 08, 2015 (146)
41 ILLUMINA ss782826458 Aug 21, 2014 (142)
42 ILLUMINA ss783791332 Sep 08, 2015 (146)
43 ILLUMINA ss825393081 Jul 19, 2016 (147)
44 ILLUMINA ss832079871 Apr 01, 2015 (144)
45 ILLUMINA ss832768348 Aug 21, 2014 (142)
46 ILLUMINA ss833359178 Aug 21, 2014 (142)
47 ILLUMINA ss833881978 Sep 08, 2015 (146)
48 EVA-GONL ss975482768 Aug 21, 2014 (142)
49 JMKIDD_LAB ss1068127510 Aug 21, 2014 (142)
50 1000GENOMES ss1292106830 Aug 21, 2014 (142)
51 DDI ss1425910935 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1574271325 Apr 01, 2015 (144)
53 EVA_DECODE ss1584861062 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1600816444 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1643810477 Apr 01, 2015 (144)
56 EVA_SVP ss1712357121 Apr 01, 2015 (144)
57 ILLUMINA ss1751859102 Sep 08, 2015 (146)
58 HAMMER_LAB ss1794807400 Sep 08, 2015 (146)
59 WEILL_CORNELL_DGM ss1918682385 Feb 12, 2016 (147)
60 ILLUMINA ss1946002820 Feb 12, 2016 (147)
61 ILLUMINA ss1958296782 Feb 12, 2016 (147)
62 GENOMED ss1966820730 Jul 19, 2016 (147)
63 JJLAB ss2019862653 Sep 14, 2016 (149)
64 USC_VALOUEV ss2147881368 Dec 20, 2016 (150)
65 HUMAN_LONGEVITY ss2165029419 Dec 20, 2016 (150)
66 TOPMED ss2327380204 Dec 20, 2016 (150)
67 SYSTEMSBIOZJU ss2624442820 Nov 08, 2017 (151)
68 ILLUMINA ss2632553603 Nov 08, 2017 (151)
69 GRF ss2697808721 Nov 08, 2017 (151)
70 ILLUMINA ss2710678271 Nov 08, 2017 (151)
71 GNOMAD ss2758635512 Nov 08, 2017 (151)
72 SWEGEN ss2987305402 Nov 08, 2017 (151)
73 ILLUMINA ss3021113785 Nov 08, 2017 (151)
74 BIOINF_KMB_FNS_UNIBA ss3023694931 Nov 08, 2017 (151)
75 TOPMED ss3084644770 Nov 08, 2017 (151)
76 CSHL ss3343595817 Nov 08, 2017 (151)
77 ILLUMINA ss3625546132 Oct 11, 2018 (152)
78 ILLUMINA ss3626165248 Oct 11, 2018 (152)
79 ILLUMINA ss3630587777 Oct 11, 2018 (152)
80 ILLUMINA ss3632903274 Oct 11, 2018 (152)
81 ILLUMINA ss3633598272 Oct 11, 2018 (152)
82 ILLUMINA ss3634339246 Oct 11, 2018 (152)
83 ILLUMINA ss3636016801 Oct 11, 2018 (152)
84 ILLUMINA ss3637042339 Oct 11, 2018 (152)
85 ILLUMINA ss3637775442 Oct 11, 2018 (152)
86 ILLUMINA ss3638905825 Oct 11, 2018 (152)
87 ILLUMINA ss3639450869 Oct 11, 2018 (152)
88 ILLUMINA ss3640046606 Oct 11, 2018 (152)
89 ILLUMINA ss3642785627 Oct 11, 2018 (152)
90 ILLUMINA ss3644498782 Oct 11, 2018 (152)
91 ILLUMINA ss3651444565 Oct 11, 2018 (152)
92 EGCUT_WGS ss3655390432 Jul 12, 2019 (153)
93 EVA_DECODE ss3687366734 Jul 12, 2019 (153)
94 ILLUMINA ss3725048126 Jul 12, 2019 (153)
95 ACPOP ss3727313879 Jul 12, 2019 (153)
96 ILLUMINA ss3744050993 Jul 12, 2019 (153)
97 ILLUMINA ss3744640215 Jul 12, 2019 (153)
98 EVA ss3746573873 Jul 12, 2019 (153)
99 PAGE_CC ss3770827992 Jul 12, 2019 (153)
100 ILLUMINA ss3772141452 Jul 12, 2019 (153)
101 KHV_HUMAN_GENOMES ss3799574627 Jul 12, 2019 (153)
102 EVA ss3826326450 Apr 25, 2020 (154)
103 HGDP ss3847343733 Apr 25, 2020 (154)
104 SGDP_PRJ ss3849477148 Apr 25, 2020 (154)
105 KRGDB ss3894555153 Apr 25, 2020 (154)
106 EVA ss3984461728 Apr 25, 2021 (155)
107 EVA ss3984814953 Apr 25, 2021 (155)
108 EVA ss4016927681 Apr 25, 2021 (155)
109 TOPMED ss4460690641 Apr 25, 2021 (155)
110 TOMMO_GENOMICS ss5145312446 Apr 25, 2021 (155)
111 1000Genomes NC_000001.10 - 100019269 Oct 11, 2018 (152)
112 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100019269 Oct 11, 2018 (152)
113 Genetic variation in the Estonian population NC_000001.10 - 100019269 Oct 11, 2018 (152)
114 The Danish reference pan genome NC_000001.10 - 100019269 Apr 25, 2020 (154)
115 gnomAD - Genomes NC_000001.11 - 99553713 Apr 25, 2021 (155)
116 Genome of the Netherlands Release 5 NC_000001.10 - 100019269 Apr 25, 2020 (154)
117 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99791857 Apr 25, 2020 (154)
118 HapMap NC_000001.11 - 99553713 Apr 25, 2020 (154)
119 KOREAN population from KRGDB NC_000001.10 - 100019269 Apr 25, 2020 (154)
120 Northern Sweden NC_000001.10 - 100019269 Jul 12, 2019 (153)
121 The PAGE Study NC_000001.11 - 99553713 Jul 12, 2019 (153)
122 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100019269 Apr 25, 2021 (155)
123 CNV burdens in cranial meningiomas NC_000001.10 - 100019269 Apr 25, 2021 (155)
124 Qatari NC_000001.10 - 100019269 Apr 25, 2020 (154)
125 SGDP_PRJ NC_000001.10 - 100019269 Apr 25, 2020 (154)
126 Siberian NC_000001.10 - 100019269 Apr 25, 2020 (154)
127 8.3KJPN NC_000001.10 - 100019269 Apr 25, 2021 (155)
128 TopMed NC_000001.11 - 99553713 Apr 25, 2021 (155)
129 UK 10K study - Twins NC_000001.10 - 100019269 Oct 11, 2018 (152)
130 A Vietnamese Genetic Variation Database NC_000001.10 - 100019269 Jul 12, 2019 (153)
131 ALFA NC_000001.11 - 99553713 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)
rs61168078 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85621961, ss3638905825, ss3639450869 NC_000001.8:99731289:C:A NC_000001.11:99553712:C:A (self)
21625, ss110890570, ss118918994, ss163738537, ss198832393, ss205274047, ss210458555, ss275945249, ss284105630, ss290580455, ss479922528, ss825393081, ss1584861062, ss1712357121, ss3642785627, ss3847343733 NC_000001.9:99791856:C:A NC_000001.11:99553712:C:A (self)
2870370, 1583337, 1128680, 1628863, 686866, 1732547, 598744, 40880, 11040, 724315, 1494128, 397722, 3281753, 1583337, 341079, ss218548515, ss230656632, ss238323638, ss479930422, ss480560477, ss484759460, ss536851771, ss554480307, ss648253763, ss778426541, ss782826458, ss783791332, ss832079871, ss832768348, ss833359178, ss833881978, ss975482768, ss1068127510, ss1292106830, ss1425910935, ss1574271325, ss1600816444, ss1643810477, ss1751859102, ss1794807400, ss1918682385, ss1946002820, ss1958296782, ss1966820730, ss2019862653, ss2147881368, ss2327380204, ss2624442820, ss2632553603, ss2697808721, ss2710678271, ss2758635512, ss2987305402, ss3021113785, ss3343595817, ss3625546132, ss3626165248, ss3630587777, ss3632903274, ss3633598272, ss3634339246, ss3636016801, ss3637042339, ss3637775442, ss3640046606, ss3644498782, ss3651444565, ss3655390432, ss3727313879, ss3744050993, ss3744640215, ss3746573873, ss3772141452, ss3826326450, ss3849477148, ss3894555153, ss3984461728, ss3984814953, ss4016927681, ss5145312446 NC_000001.10:100019268:C:A NC_000001.11:99553712:C:A (self)
20291262, 136494, 49461, 15302815, 24296976, 9143902666, ss2165029419, ss3023694931, ss3084644770, ss3687366734, ss3725048126, ss3770827992, ss3799574627, ss4460690641 NC_000001.11:99553712:C:A NC_000001.11:99553712:C:A (self)
ss2115174, ss5867440, ss23842325, ss65980842, ss66829161, ss67078035, ss67409483, ss70423807, ss70604680, ss71150919, ss75879061, ss83727041, ss102767778, ss121645939, ss153368954, ss159256105, ss160335489, ss170372458, ss172411123 NT_032977.9:69991186:C:A NC_000001.11:99553712:C:A (self)
1732547, ss3894555153 NC_000001.10:100019268:C:T NC_000001.11:99553712:C: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 rs1339866

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