Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1383139

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:98174448 (GRCh38.p14) 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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.460055 (121772/264690, TOPMED)
G=0.473407 (66222/139884, GnomAD)
A=0.48705 (29293/60144, ALFA) (+ 20 more)
G=0.30207 (8536/28258, 14KJPN)
G=0.30018 (5031/16760, 8.3KJPN)
G=0.4260 (2728/6404, 1000G_30x)
G=0.4211 (2109/5008, 1000G)
G=0.4690 (2101/4480, Estonian)
A=0.4909 (1892/3854, ALSPAC)
G=0.4889 (1813/3708, TWINSUK)
G=0.3137 (919/2930, KOREAN)
G=0.4803 (1001/2084, HGDP_Stanford)
G=0.4234 (801/1892, HapMap)
G=0.2986 (547/1832, Korea1K)
G=0.487 (486/998, GoNL)
G=0.332 (262/788, PRJEB37584)
G=0.497 (298/600, NorthernSweden)
G=0.318 (129/406, SGDP_PRJ)
A=0.403 (87/216, Qatari)
G=0.336 (72/214, Vietnamese)
A=0.471 (48/102, Ancient Sardinia)
G=0.38 (16/42, Siberian)
A=0.47 (19/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 60144 G=0.51295 A=0.48705, C=0.00000
European Sub 50954 G=0.51117 A=0.48883, C=0.00000
African Sub 2312 G=0.6021 A=0.3979, C=0.0000
African Others Sub 86 G=0.58 A=0.42, C=0.00
African American Sub 2226 G=0.6029 A=0.3971, C=0.0000
Asian Sub 88 G=0.41 A=0.59, C=0.00
East Asian Sub 70 G=0.41 A=0.59, C=0.00
Other Asian Sub 18 G=0.39 A=0.61, C=0.00
Latin American 1 Sub 132 G=0.583 A=0.417, C=0.000
Latin American 2 Sub 710 G=0.458 A=0.542, C=0.000
South Asian Sub 4872 G=0.4959 A=0.5041, C=0.0000
Other Sub 1076 G=0.5195 A=0.4805, C=0.0000


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=0.460055 A=0.539945
gnomAD - Genomes Global Study-wide 139884 G=0.473407 A=0.526593
gnomAD - Genomes European Sub 75774 G=0.49620 A=0.50380
gnomAD - Genomes African Sub 41894 G=0.46030 A=0.53970
gnomAD - Genomes American Sub 13630 G=0.40888 A=0.59112
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.5332 A=0.4668
gnomAD - Genomes East Asian Sub 3120 G=0.3272 A=0.6728
gnomAD - Genomes Other Sub 2150 G=0.4544 A=0.5456
Allele Frequency Aggregator Total Global 60144 G=0.51295 A=0.48705, C=0.00000
Allele Frequency Aggregator European Sub 50954 G=0.51117 A=0.48883, C=0.00000
Allele Frequency Aggregator South Asian Sub 4872 G=0.4959 A=0.5041, C=0.0000
Allele Frequency Aggregator African Sub 2312 G=0.6021 A=0.3979, C=0.0000
Allele Frequency Aggregator Other Sub 1076 G=0.5195 A=0.4805, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 710 G=0.458 A=0.542, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 132 G=0.583 A=0.417, C=0.000
Allele Frequency Aggregator Asian Sub 88 G=0.41 A=0.59, C=0.00
14KJPN JAPANESE Study-wide 28258 G=0.30207 A=0.69793
8.3KJPN JAPANESE Study-wide 16760 G=0.30018 A=0.69982
1000Genomes_30x Global Study-wide 6404 G=0.4260 A=0.5740
1000Genomes_30x African Sub 1786 G=0.4569 A=0.5431
1000Genomes_30x Europe Sub 1266 G=0.4897 A=0.5103
1000Genomes_30x South Asian Sub 1202 G=0.4642 A=0.5358
1000Genomes_30x East Asian Sub 1170 G=0.2983 A=0.7017
1000Genomes_30x American Sub 980 G=0.393 A=0.607
1000Genomes Global Study-wide 5008 G=0.4211 A=0.5789
1000Genomes African Sub 1322 G=0.4493 A=0.5507
1000Genomes East Asian Sub 1008 G=0.2956 A=0.7044
1000Genomes Europe Sub 1006 G=0.4871 A=0.5129
1000Genomes South Asian Sub 978 G=0.466 A=0.534
1000Genomes American Sub 694 G=0.390 A=0.610
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4690 A=0.5310
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5091 A=0.4909
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4889 A=0.5111
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.3137 A=0.6863, C=0.0000, T=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.4803 A=0.5197
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.347 A=0.653
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.531 A=0.469
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.537 A=0.463
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.466 A=0.534
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.636 A=0.364
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.380 A=0.620
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.62 A=0.38
HapMap Global Study-wide 1892 G=0.4234 A=0.5766
HapMap American Sub 770 G=0.452 A=0.548
HapMap African Sub 692 G=0.428 A=0.572
HapMap Asian Sub 254 G=0.299 A=0.701
HapMap Europe Sub 176 G=0.460 A=0.540
Korean Genome Project KOREAN Study-wide 1832 G=0.2986 A=0.7014
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.487 A=0.513
CNV burdens in cranial meningiomas Global Study-wide 788 G=0.332 A=0.668
CNV burdens in cranial meningiomas CRM Sub 788 G=0.332 A=0.668
Northern Sweden ACPOP Study-wide 600 G=0.497 A=0.503
SGDP_PRJ Global Study-wide 406 G=0.318 A=0.682
Qatari Global Study-wide 216 G=0.597 A=0.403
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.336 A=0.664
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 102 G=0.529 A=0.471
Siberian Global Study-wide 42 G=0.38 A=0.62
The Danish reference pan genome Danish Study-wide 40 G=0.53 A=0.47
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.p14 chr 15 NC_000015.10:g.98174448G>A
GRCh38.p14 chr 15 NC_000015.10:g.98174448G>C
GRCh38.p14 chr 15 NC_000015.10:g.98174448G>T
GRCh37.p13 chr 15 NC_000015.9:g.98717677G>A
GRCh37.p13 chr 15 NC_000015.9:g.98717677G>C
GRCh37.p13 chr 15 NC_000015.9:g.98717677G>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
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 C T
GRCh38.p14 chr 15 NC_000015.10:g.98174448= NC_000015.10:g.98174448G>A NC_000015.10:g.98174448G>C NC_000015.10:g.98174448G>T
GRCh37.p13 chr 15 NC_000015.9:g.98717677= NC_000015.9:g.98717677G>A NC_000015.9:g.98717677G>C NC_000015.9:g.98717677G>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#.

90 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2174178 Oct 23, 2000 (88)
2 BCM_SSAHASNP ss10789776 Jul 11, 2003 (116)
3 WI_SSAHASNP ss12332825 Jul 11, 2003 (116)
4 ABI ss43721713 Mar 14, 2006 (126)
5 ILLUMINA ss67091491 Nov 30, 2006 (127)
6 ILLUMINA ss67425496 Nov 30, 2006 (127)
7 ILLUMINA ss68153111 Dec 12, 2006 (127)
8 ILLUMINA ss70611508 May 24, 2008 (130)
9 ILLUMINA ss71158972 May 17, 2007 (127)
10 ILLUMINA ss75798020 Dec 07, 2007 (129)
11 HGSV ss80945135 Dec 15, 2007 (130)
12 KRIBB_YJKIM ss83748004 Dec 15, 2007 (130)
13 BGI ss106451189 Feb 04, 2009 (130)
14 1000GENOMES ss109082859 Jan 23, 2009 (130)
15 1000GENOMES ss114630506 Jan 25, 2009 (130)
16 ILLUMINA-UK ss118351765 Feb 14, 2009 (130)
17 ILLUMINA ss153404047 Dec 01, 2009 (131)
18 GMI ss156925838 Dec 01, 2009 (131)
19 ILLUMINA ss159263146 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss168563488 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss170383405 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss171588502 Jul 04, 2010 (132)
23 ILLUMINA ss172459631 Jul 04, 2010 (132)
24 1000GENOMES ss227067443 Jul 14, 2010 (132)
25 1000GENOMES ss236900815 Jul 15, 2010 (132)
26 1000GENOMES ss243264935 Jul 15, 2010 (132)
27 BL ss255239539 May 09, 2011 (134)
28 GMI ss282384889 May 04, 2012 (137)
29 GMI ss287011730 Apr 25, 2013 (138)
30 PJP ss291786333 May 09, 2011 (134)
31 ILLUMINA ss536861959 Sep 08, 2015 (146)
32 TISHKOFF ss564687327 Apr 25, 2013 (138)
33 SSMP ss660430832 Apr 25, 2013 (138)
34 ILLUMINA ss832775356 Aug 21, 2014 (142)
35 ILLUMINA ss833366186 Aug 21, 2014 (142)
36 EVA-GONL ss992138647 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1080382685 Aug 21, 2014 (142)
38 1000GENOMES ss1354822317 Aug 21, 2014 (142)
39 DDI ss1427733652 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1577775849 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1633724509 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1676718542 Apr 01, 2015 (144)
43 EVA_SVP ss1713515974 Apr 01, 2015 (144)
44 HAMMER_LAB ss1808355097 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1935541509 Feb 12, 2016 (147)
46 GENOMED ss1968188008 Jul 19, 2016 (147)
47 JJLAB ss2028556799 Sep 14, 2016 (149)
48 USC_VALOUEV ss2156965004 Nov 08, 2017 (151)
49 HUMAN_LONGEVITY ss2209529726 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2628773413 Nov 08, 2017 (151)
51 GRF ss2701455163 Nov 08, 2017 (151)
52 GNOMAD ss2938769732 Nov 08, 2017 (151)
53 SWEGEN ss3013837555 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3028103069 Nov 08, 2017 (151)
55 CSHL ss3351268361 Nov 08, 2017 (151)
56 ILLUMINA ss3627444389 Oct 12, 2018 (152)
57 ILLUMINA ss3638105787 Oct 12, 2018 (152)
58 ILLUMINA ss3639065487 Oct 12, 2018 (152)
59 ILLUMINA ss3639841719 Oct 12, 2018 (152)
60 ILLUMINA ss3643088460 Oct 12, 2018 (152)
61 ILLUMINA ss3643891689 Oct 12, 2018 (152)
62 URBANLAB ss3650430842 Oct 12, 2018 (152)
63 EGCUT_WGS ss3680970888 Jul 13, 2019 (153)
64 EVA_DECODE ss3698565973 Jul 13, 2019 (153)
65 ACPOP ss3741216363 Jul 13, 2019 (153)
66 EVA ss3753510775 Jul 13, 2019 (153)
67 PACBIO ss3787942121 Jul 13, 2019 (153)
68 PACBIO ss3792939262 Jul 13, 2019 (153)
69 PACBIO ss3797823942 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3818812859 Jul 13, 2019 (153)
71 EVA ss3834404475 Apr 27, 2020 (154)
72 HGDP ss3847535109 Apr 27, 2020 (154)
73 SGDP_PRJ ss3883634436 Apr 27, 2020 (154)
74 KRGDB ss3932895353 Apr 27, 2020 (154)
75 KOGIC ss3976840216 Apr 27, 2020 (154)
76 EVA ss3984707182 Apr 26, 2021 (155)
77 EVA ss3985738087 Apr 26, 2021 (155)
78 TOPMED ss5003216526 Apr 26, 2021 (155)
79 TOMMO_GENOMICS ss5217776159 Apr 26, 2021 (155)
80 1000G_HIGH_COVERAGE ss5299639049 Oct 16, 2022 (156)
81 EVA ss5421421670 Oct 16, 2022 (156)
82 HUGCELL_USP ss5493232347 Oct 16, 2022 (156)
83 1000G_HIGH_COVERAGE ss5601637703 Oct 16, 2022 (156)
84 SANFORD_IMAGENETICS ss5658185047 Oct 16, 2022 (156)
85 TOMMO_GENOMICS ss5772056957 Oct 16, 2022 (156)
86 YY_MCH ss5815634076 Oct 16, 2022 (156)
87 EVA ss5828664470 Oct 16, 2022 (156)
88 EVA ss5851433086 Oct 16, 2022 (156)
89 EVA ss5877244676 Oct 16, 2022 (156)
90 EVA ss5949613289 Oct 16, 2022 (156)
91 1000Genomes NC_000015.9 - 98717677 Oct 12, 2018 (152)
92 1000Genomes_30x NC_000015.10 - 98174448 Oct 16, 2022 (156)
93 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 98717677 Oct 12, 2018 (152)
94 Genetic variation in the Estonian population NC_000015.9 - 98717677 Oct 12, 2018 (152)
95 The Danish reference pan genome NC_000015.9 - 98717677 Apr 27, 2020 (154)
96 gnomAD - Genomes NC_000015.10 - 98174448 Apr 26, 2021 (155)
97 Genome of the Netherlands Release 5 NC_000015.9 - 98717677 Apr 27, 2020 (154)
98 HGDP-CEPH-db Supplement 1 NC_000015.8 - 96535200 Apr 27, 2020 (154)
99 HapMap NC_000015.10 - 98174448 Apr 27, 2020 (154)
100 KOREAN population from KRGDB NC_000015.9 - 98717677 Apr 27, 2020 (154)
101 Korean Genome Project NC_000015.10 - 98174448 Apr 27, 2020 (154)
102 Northern Sweden NC_000015.9 - 98717677 Jul 13, 2019 (153)
103 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000015.9 - 98717677 Apr 26, 2021 (155)
104 CNV burdens in cranial meningiomas NC_000015.9 - 98717677 Apr 26, 2021 (155)
105 Qatari NC_000015.9 - 98717677 Apr 27, 2020 (154)
106 SGDP_PRJ NC_000015.9 - 98717677 Apr 27, 2020 (154)
107 Siberian NC_000015.9 - 98717677 Apr 27, 2020 (154)
108 8.3KJPN NC_000015.9 - 98717677 Apr 26, 2021 (155)
109 14KJPN NC_000015.10 - 98174448 Oct 16, 2022 (156)
110 TopMed NC_000015.10 - 98174448 Apr 26, 2021 (155)
111 UK 10K study - Twins NC_000015.9 - 98717677 Oct 12, 2018 (152)
112 A Vietnamese Genetic Variation Database NC_000015.9 - 98717677 Jul 13, 2019 (153)
113 ALFA NC_000015.10 - 98174448 Apr 26, 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)
rs58362595 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
213001, ss80945135, ss109082859, ss114630506, ss118351765, ss168563488, ss170383405, ss171588502, ss255239539, ss282384889, ss287011730, ss291786333, ss1713515974, ss3639065487, ss3639841719, ss3643088460, ss3643891689, ss3847535109 NC_000015.8:96535199:G:A NC_000015.10:98174447:G:A (self)
67942539, 37735446, 26709136, 3993923, 16836451, 40072747, 14501228, 964014, 256711, 17583431, 35651416, 9481358, 75745466, 37735446, 8388080, ss227067443, ss236900815, ss243264935, ss536861959, ss564687327, ss660430832, ss832775356, ss833366186, ss992138647, ss1080382685, ss1354822317, ss1427733652, ss1577775849, ss1633724509, ss1676718542, ss1808355097, ss1935541509, ss1968188008, ss2028556799, ss2156965004, ss2628773413, ss2701455163, ss2938769732, ss3013837555, ss3351268361, ss3627444389, ss3638105787, ss3680970888, ss3741216363, ss3753510775, ss3787942121, ss3792939262, ss3797823942, ss3834404475, ss3883634436, ss3932895353, ss3984707182, ss3985738087, ss5217776159, ss5421421670, ss5658185047, ss5828664470, ss5949613289 NC_000015.9:98717676:G:A NC_000015.10:98174447:G:A (self)
89163638, 478940467, 1326539, 33218217, 105894061, 218762186, 11119985260, ss2209529726, ss3028103069, ss3650430842, ss3698565973, ss3818812859, ss3976840216, ss5003216526, ss5299639049, ss5493232347, ss5601637703, ss5772056957, ss5815634076, ss5851433086, ss5877244676 NC_000015.10:98174447:G:A NC_000015.10:98174447:G:A (self)
ss2174178, ss43721713, ss67091491, ss67425496, ss68153111, ss70611508, ss71158972, ss75798020, ss83748004, ss106451189, ss153404047, ss156925838, ss159263146, ss172459631 NT_010274.17:13683203:G:A NC_000015.10:98174447:G:A (self)
ss10789776, ss12332825 NT_035325.4:159413:G:A NC_000015.10:98174447:G:A (self)
40072747, ss3932895353 NC_000015.9:98717676:G:C NC_000015.10:98174447:G:C (self)
11119985260 NC_000015.10:98174447:G:C NC_000015.10:98174447:G:C (self)
40072747, ss3932895353 NC_000015.9:98717676:G:T NC_000015.10:98174447: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.

1 citation for rs1383139
PMID Title Author Year Journal
19118814 Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. Beecham GW et al. 2009 American journal of human genetics
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.post774+babeb33