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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.

rs3856039

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:80400478 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.362330 (50745/140052, GnomAD)
G=0.14460 (4086/28258, 14KJPN)
G=0.14338 (2403/16760, 8.3KJPN) (+ 14 more)
G=0.30301 (4727/15600, ALFA)
G=0.3242 (2076/6404, 1000G_30x)
G=0.3223 (1614/5008, 1000G)
G=0.3395 (1521/4480, Estonian)
G=0.3786 (1459/3854, ALSPAC)
G=0.3910 (1450/3708, TWINSUK)
G=0.1338 (392/2930, KOREAN)
G=0.1283 (235/1832, Korea1K)
G=0.310 (309/998, GoNL)
G=0.317 (190/600, NorthernSweden)
A=0.386 (95/246, SGDP_PRJ)
A=0.444 (96/216, Qatari)
G=0.35 (14/40, GENOME_DK)
A=0.47 (14/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
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 15600 A=0.69699 G=0.30301, T=0.00000
European Sub 11704 A=0.68908 G=0.31092, T=0.00000
African Sub 2462 A=0.6966 G=0.3034, T=0.0000
African Others Sub 90 A=0.68 G=0.32, T=0.00
African American Sub 2372 A=0.6973 G=0.3027, T=0.0000
Asian Sub 108 A=0.870 G=0.130, T=0.000
East Asian Sub 84 A=0.85 G=0.15, T=0.00
Other Asian Sub 24 A=0.96 G=0.04, T=0.00
Latin American 1 Sub 146 A=0.719 G=0.281, T=0.000
Latin American 2 Sub 610 A=0.792 G=0.208, T=0.000
South Asian Sub 94 A=0.65 G=0.35, T=0.00
Other Sub 476 A=0.735 G=0.265, T=0.000


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
gnomAD - Genomes Global Study-wide 140052 A=0.637670 G=0.362330
gnomAD - Genomes European Sub 75864 A=0.63163 G=0.36837
gnomAD - Genomes African Sub 41936 A=0.60123 G=0.39877
gnomAD - Genomes American Sub 13656 A=0.70958 G=0.29042
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.6952 G=0.3048
gnomAD - Genomes East Asian Sub 3124 A=0.8912 G=0.1088
gnomAD - Genomes Other Sub 2148 A=0.6476 G=0.3524
14KJPN JAPANESE Study-wide 28258 A=0.85540 G=0.14460
8.3KJPN JAPANESE Study-wide 16760 A=0.85662 G=0.14338
Allele Frequency Aggregator Total Global 15600 A=0.69699 G=0.30301, T=0.00000
Allele Frequency Aggregator European Sub 11704 A=0.68908 G=0.31092, T=0.00000
Allele Frequency Aggregator African Sub 2462 A=0.6966 G=0.3034, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.792 G=0.208, T=0.000
Allele Frequency Aggregator Other Sub 476 A=0.735 G=0.265, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.719 G=0.281, T=0.000
Allele Frequency Aggregator Asian Sub 108 A=0.870 G=0.130, T=0.000
Allele Frequency Aggregator South Asian Sub 94 A=0.65 G=0.35, T=0.00
1000Genomes_30x Global Study-wide 6404 A=0.6758 G=0.3242
1000Genomes_30x African Sub 1786 A=0.5773 G=0.4227
1000Genomes_30x Europe Sub 1266 A=0.6114 G=0.3886
1000Genomes_30x South Asian Sub 1202 A=0.6273 G=0.3727
1000Genomes_30x East Asian Sub 1170 A=0.8889 G=0.1111
1000Genomes_30x American Sub 980 A=0.744 G=0.256
1000Genomes Global Study-wide 5008 A=0.6777 G=0.3223
1000Genomes African Sub 1322 A=0.5802 G=0.4198
1000Genomes East Asian Sub 1008 A=0.8889 G=0.1111
1000Genomes Europe Sub 1006 A=0.6083 G=0.3917
1000Genomes South Asian Sub 978 A=0.620 G=0.380
1000Genomes American Sub 694 A=0.739 G=0.261
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.6605 G=0.3395
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6214 G=0.3786
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6090 G=0.3910
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.8662 G=0.1338
Korean Genome Project KOREAN Study-wide 1832 A=0.8717 G=0.1283
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.690 G=0.310
Northern Sweden ACPOP Study-wide 600 A=0.683 G=0.317
SGDP_PRJ Global Study-wide 246 A=0.386 G=0.614
Qatari Global Study-wide 216 A=0.444 G=0.556
The Danish reference pan genome Danish Study-wide 40 A=0.65 G=0.35
Siberian Global Study-wide 30 A=0.47 G=0.53
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 1 NC_000001.11:g.80400478A>G
GRCh38.p14 chr 1 NC_000001.11:g.80400478A>T
GRCh37.p13 chr 1 NC_000001.10:g.80866163A>G
GRCh37.p13 chr 1 NC_000001.10:g.80866163A>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 A= G T
GRCh38.p14 chr 1 NC_000001.11:g.80400478= NC_000001.11:g.80400478A>G NC_000001.11:g.80400478A>T
GRCh37.p13 chr 1 NC_000001.10:g.80866163= NC_000001.10:g.80866163A>G NC_000001.10:g.80866163A>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#.

53 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5161348 Oct 08, 2002 (108)
2 TSC-CSHL ss5246980 Oct 08, 2002 (108)
3 SC_JCM ss6021456 Feb 20, 2003 (111)
4 SC_SNP ss13438502 Dec 05, 2003 (119)
5 ABI ss41084663 Mar 15, 2006 (126)
6 COMPLETE_GENOMICS ss166747009 Jul 04, 2010 (132)
7 BUSHMAN ss198677980 Jul 04, 2010 (132)
8 GMI ss275894879 May 04, 2012 (137)
9 1000GENOMES ss328724164 May 09, 2011 (134)
10 TISHKOFF ss554304373 Apr 25, 2013 (138)
11 SSMP ss648161530 Apr 25, 2013 (138)
12 EVA-GONL ss975343469 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1068026852 Aug 21, 2014 (142)
14 1000GENOMES ss1291590553 Aug 21, 2014 (142)
15 DDI ss1425869636 Apr 01, 2015 (144)
16 EVA_GENOME_DK ss1574179501 Apr 01, 2015 (144)
17 EVA_DECODE ss1584717174 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1600541450 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1643535483 Apr 01, 2015 (144)
20 HAMMER_LAB ss1794621901 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1918547504 Feb 12, 2016 (147)
22 JJLAB ss2019794242 Sep 14, 2016 (149)
23 USC_VALOUEV ss2147810832 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2163967876 Dec 20, 2016 (150)
25 SYSTEMSBIOZJU ss2624408179 Nov 08, 2017 (151)
26 GRF ss2697731602 Nov 08, 2017 (151)
27 GNOMAD ss2757144783 Nov 08, 2017 (151)
28 SWEGEN ss2987093342 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3023659338 Nov 08, 2017 (151)
30 CSHL ss3343534207 Nov 08, 2017 (151)
31 EGCUT_WGS ss3655172733 Jul 12, 2019 (153)
32 ACPOP ss3727199328 Jul 12, 2019 (153)
33 EVA ss3746415786 Jul 12, 2019 (153)
34 KHV_HUMAN_GENOMES ss3799421608 Jul 12, 2019 (153)
35 EVA ss3826261042 Apr 25, 2020 (154)
36 EVA ss3836519074 Apr 25, 2020 (154)
37 EVA ss3841926161 Apr 25, 2020 (154)
38 SGDP_PRJ ss3849208750 Apr 25, 2020 (154)
39 KRGDB ss3894257304 Apr 25, 2020 (154)
40 KOGIC ss3944845002 Apr 25, 2020 (154)
41 TOMMO_GENOMICS ss5144725868 Apr 25, 2021 (155)
42 1000G_HIGH_COVERAGE ss5242871940 Oct 12, 2022 (156)
43 EVA ss5319847087 Oct 12, 2022 (156)
44 HUGCELL_USP ss5443875487 Oct 12, 2022 (156)
45 EVA ss5505916763 Oct 12, 2022 (156)
46 1000G_HIGH_COVERAGE ss5515474127 Oct 12, 2022 (156)
47 SANFORD_IMAGENETICS ss5625875984 Oct 12, 2022 (156)
48 TOMMO_GENOMICS ss5669719052 Oct 12, 2022 (156)
49 YY_MCH ss5800746875 Oct 12, 2022 (156)
50 EVA ss5832191963 Oct 12, 2022 (156)
51 EVA ss5908958777 Oct 12, 2022 (156)
52 EVA ss5937722891 Oct 12, 2022 (156)
53 EVA ss5979967286 Oct 12, 2022 (156)
54 1000Genomes NC_000001.10 - 80866163 Oct 11, 2018 (152)
55 1000Genomes_30x NC_000001.11 - 80400478 Oct 12, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 80866163 Oct 11, 2018 (152)
57 Genetic variation in the Estonian population NC_000001.10 - 80866163 Oct 11, 2018 (152)
58 The Danish reference pan genome NC_000001.10 - 80866163 Apr 25, 2020 (154)
59 gnomAD - Genomes NC_000001.11 - 80400478 Apr 25, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000001.10 - 80866163 Apr 25, 2020 (154)
61 KOREAN population from KRGDB NC_000001.10 - 80866163 Apr 25, 2020 (154)
62 Korean Genome Project NC_000001.11 - 80400478 Apr 25, 2020 (154)
63 Northern Sweden NC_000001.10 - 80866163 Jul 12, 2019 (153)
64 Qatari NC_000001.10 - 80866163 Apr 25, 2020 (154)
65 SGDP_PRJ NC_000001.10 - 80866163 Apr 25, 2020 (154)
66 Siberian NC_000001.10 - 80866163 Apr 25, 2020 (154)
67 8.3KJPN NC_000001.10 - 80866163 Apr 25, 2021 (155)
68 14KJPN NC_000001.11 - 80400478 Oct 12, 2022 (156)
69 UK 10K study - Twins NC_000001.10 - 80866163 Oct 11, 2018 (152)
70 ALFA NC_000001.11 - 80400478 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)
rs35614434 May 23, 2006 (127)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss166747009, ss198677980, ss275894879, ss1584717174 NC_000001.9:80638750:A:G NC_000001.11:80400477:A:G (self)
2334538, 1280478, 910981, 1574494, 550809, 1434698, 484193, 589434, 1225730, 327186, 2695175, 1280478, ss328724164, ss554304373, ss648161530, ss975343469, ss1068026852, ss1291590553, ss1425869636, ss1574179501, ss1600541450, ss1643535483, ss1794621901, ss1918547504, ss2019794242, ss2147810832, ss2624408179, ss2697731602, ss2757144783, ss2987093342, ss3343534207, ss3655172733, ss3727199328, ss3746415786, ss3826261042, ss3836519074, ss3849208750, ss3894257304, ss5144725868, ss5319847087, ss5505916763, ss5625875984, ss5832191963, ss5937722891, ss5979967286 NC_000001.10:80866162:A:G NC_000001.11:80400477:A:G (self)
3000062, 16494076, 1223003, 3556156, 10430395263, ss2163967876, ss3023659338, ss3799421608, ss3841926161, ss3944845002, ss5242871940, ss5443875487, ss5515474127, ss5669719052, ss5800746875, ss5908958777 NC_000001.11:80400477:A:G NC_000001.11:80400477:A:G (self)
ss13438502 NT_004483.15:2535233:A:G NC_000001.11:80400477:A:G (self)
ss5161348, ss5246980, ss6021456, ss41084663 NT_032977.9:50838080:A:G NC_000001.11:80400477:A:G (self)
10430395263 NC_000001.11:80400477:A:T NC_000001.11:80400477:A: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 rs3856039

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.post761+d5e8e07