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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.

rs9682412

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:20759 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.217522 (57576/264690, TOPMED)
A=0.218998 (30661/140006, GnomAD)
A=0.00039 (11/28258, 14KJPN) (+ 4 more)
A=0.21244 (4013/18890, ALFA)
A=0.1930 (1236/6404, 1000G_30x)
C=0.0000 (0/2930, KOREAN)
G=0.0000 (0/2930, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01986 : Intron Variant
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 18890 T=0.78756 A=0.21244
European Sub 14286 T=0.78363 A=0.21637
African Sub 2946 T=0.7855 A=0.2145
African Others Sub 114 T=0.781 A=0.219
African American Sub 2832 T=0.7857 A=0.2143
Asian Sub 112 T=1.000 A=0.000
East Asian Sub 86 T=1.00 A=0.00
Other Asian Sub 26 T=1.00 A=0.00
Latin American 1 Sub 146 T=0.788 A=0.212
Latin American 2 Sub 610 T=0.826 A=0.174
South Asian Sub 98 T=0.84 A=0.16
Other Sub 692 T=0.802 A=0.198


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 T=0.782478 A=0.217522
gnomAD - Genomes Global Study-wide 140006 T=0.781002 A=0.218998
gnomAD - Genomes European Sub 75874 T=0.78218 A=0.21782
gnomAD - Genomes African Sub 41880 T=0.77333 A=0.22667
gnomAD - Genomes American Sub 13652 T=0.77403 A=0.22597
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.6799 A=0.3201
gnomAD - Genomes East Asian Sub 3130 T=0.9994 A=0.0006
gnomAD - Genomes Other Sub 2146 T=0.7717 A=0.2283
14KJPN JAPANESE Study-wide 28258 T=0.99961 A=0.00039
Allele Frequency Aggregator Total Global 18890 T=0.78756 A=0.21244
Allele Frequency Aggregator European Sub 14286 T=0.78363 A=0.21637
Allele Frequency Aggregator African Sub 2946 T=0.7855 A=0.2145
Allele Frequency Aggregator Other Sub 692 T=0.802 A=0.198
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.826 A=0.174
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.788 A=0.212
Allele Frequency Aggregator Asian Sub 112 T=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 T=0.84 A=0.16
1000Genomes_30x Global Study-wide 6404 T=0.8070 A=0.1930
1000Genomes_30x African Sub 1786 T=0.7413 A=0.2587
1000Genomes_30x Europe Sub 1266 T=0.7457 A=0.2543
1000Genomes_30x South Asian Sub 1202 T=0.8220 A=0.1780
1000Genomes_30x East Asian Sub 1170 T=0.9983 A=0.0017
1000Genomes_30x American Sub 980 T=0.759 A=0.241
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0010 C=0.0000, G=0.0000
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 3 NC_000003.12:g.20759T>A
GRCh38.p14 chr 3 NC_000003.12:g.20759T>C
GRCh38.p14 chr 3 NC_000003.12:g.20759T>G
GRCh37.p13 chr 3 NC_000003.11:g.62437A>T
GRCh37.p13 chr 3 NC_000003.11:g.62437A>C
GRCh37.p13 chr 3 NC_000003.11:g.62437A>G
Gene: LINC01986, long intergenic non-protein coding RNA 1986 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01986 transcript NR_110824.1: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
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 T= A C G
GRCh38.p14 chr 3 NC_000003.12:g.20759= NC_000003.12:g.20759T>A NC_000003.12:g.20759T>C NC_000003.12:g.20759T>G
GRCh37.p13 chr 3 NC_000003.11:g.62437A>T NC_000003.11:g.62437= NC_000003.11:g.62437A>C NC_000003.11:g.62437A>G
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#.

67 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13481676 Dec 05, 2003 (119)
2 SSAHASNP ss21897753 Apr 05, 2004 (121)
3 BCMHGSC_JDW ss91957940 Mar 24, 2008 (129)
4 HUMANGENOME_JCVI ss99067899 Feb 04, 2009 (130)
5 BGI ss106234437 Feb 04, 2009 (130)
6 1000GENOMES ss111926631 Jan 25, 2009 (130)
7 ILLUMINA-UK ss116933709 Feb 14, 2009 (130)
8 ENSEMBL ss133204243 Dec 01, 2009 (131)
9 ENSEMBL ss138663877 Dec 01, 2009 (131)
10 GMI ss154962269 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss165981544 Jul 04, 2010 (132)
12 BUSHMAN ss201990197 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss206138610 Jul 04, 2010 (132)
14 1000GENOMES ss219921851 Jul 14, 2010 (132)
15 1000GENOMES ss231664436 Jul 14, 2010 (132)
16 BL ss252864263 May 09, 2011 (134)
17 GMI ss276971098 May 04, 2012 (137)
18 GMI ss284573496 Apr 25, 2013 (138)
19 PJP ss292775299 May 09, 2011 (134)
20 TISHKOFF ss556354882 Apr 25, 2013 (138)
21 SSMP ss650018248 Apr 25, 2013 (138)
22 EVA-GONL ss978164073 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1070090324 Aug 21, 2014 (142)
24 1000GENOMES ss1302408297 Aug 21, 2014 (142)
25 DDI ss1429295745 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1579800278 Apr 01, 2015 (144)
27 EVA_DECODE ss1587622404 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1606204920 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1649198953 Apr 01, 2015 (144)
30 HAMMER_LAB ss1798694644 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1921415486 Feb 12, 2016 (147)
32 ILLUMINA ss1958526846 Feb 12, 2016 (147)
33 GENOMED ss1969295927 Jul 19, 2016 (147)
34 JJLAB ss2021256232 Sep 14, 2016 (149)
35 USC_VALOUEV ss2149325415 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2625128195 Nov 08, 2017 (151)
37 GRF ss2704678958 Nov 08, 2017 (151)
38 GNOMAD ss2788465970 Nov 08, 2017 (151)
39 SWEGEN ss2991671627 Nov 08, 2017 (151)
40 ILLUMINA ss3022200962 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3024389154 Nov 08, 2017 (151)
42 CSHL ss3344833637 Nov 08, 2017 (151)
43 ILLUMINA ss3652666250 Oct 11, 2018 (152)
44 EVA_DECODE ss3708445556 Jul 13, 2019 (153)
45 ILLUMINA ss3725980600 Jul 13, 2019 (153)
46 ACPOP ss3729543926 Jul 13, 2019 (153)
47 EVA ss3759536313 Jul 13, 2019 (153)
48 PACBIO ss3784206045 Jul 13, 2019 (153)
49 PACBIO ss3789737845 Jul 13, 2019 (153)
50 PACBIO ss3794611541 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3802685217 Jul 13, 2019 (153)
52 EVA ss3827607213 Apr 25, 2020 (154)
53 EVA ss3837224212 Apr 25, 2020 (154)
54 EVA ss3842647351 Apr 25, 2020 (154)
55 SGDP_PRJ ss3855010962 Apr 25, 2020 (154)
56 KRGDB ss3900775875 Apr 25, 2020 (154)
57 TOPMED ss4551018891 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5157372728 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5252706816 Oct 13, 2022 (156)
60 HUGCELL_USP ss5452246631 Oct 13, 2022 (156)
61 1000G_HIGH_COVERAGE ss5530371003 Oct 13, 2022 (156)
62 SANFORD_IMAGENETICS ss5631338417 Oct 13, 2022 (156)
63 TOMMO_GENOMICS ss5688524724 Oct 13, 2022 (156)
64 YY_MCH ss5803392718 Oct 13, 2022 (156)
65 EVA ss5825209662 Oct 13, 2022 (156)
66 EVA ss5867239146 Oct 13, 2022 (156)
67 EVA ss5959593936 Oct 13, 2022 (156)
68 1000Genomes_30x NC_000003.12 - 20759 Oct 13, 2022 (156)
69 gnomAD - Genomes NC_000003.12 - 20759 Apr 26, 2021 (155)
70 KOREAN population from KRGDB NC_000003.11 - 62437 Apr 25, 2020 (154)
71 14KJPN NC_000003.12 - 20759 Oct 13, 2022 (156)
72 TopMed NC_000003.12 - 20759 Apr 26, 2021 (155)
73 ALFA NC_000003.12 - 20759 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91957940, ss111926631, ss116933709, ss165981544, ss201990197, ss206138610, ss252864263, ss276971098, ss284573496, ss292775299, ss1587622404 NC_000003.10:37436:A:A NC_000003.12:20758:T:A (self)
7953269, ss219921851, ss231664436, ss556354882, ss650018248, ss978164073, ss1070090324, ss1302408297, ss1429295745, ss1579800278, ss1606204920, ss1649198953, ss1798694644, ss1921415486, ss1958526846, ss1969295927, ss2021256232, ss2149325415, ss2625128195, ss2704678958, ss2788465970, ss2991671627, ss3022200962, ss3344833637, ss3652666250, ss3729543926, ss3759536313, ss3784206045, ss3789737845, ss3794611541, ss3827607213, ss3837224212, ss3855010962, ss3900775875, ss5157372728, ss5631338417, ss5825209662, ss5959593936 NC_000003.11:62436:A:A NC_000003.12:20758:T:A (self)
17896938, 96340889, 22361828, 388396446, 8008573389, ss3024389154, ss3708445556, ss3725980600, ss3802685217, ss3842647351, ss4551018891, ss5252706816, ss5452246631, ss5530371003, ss5688524724, ss5803392718, ss5867239146 NC_000003.12:20758:T:A NC_000003.12:20758:T:A (self)
ss13481676, ss21897753 NT_022517.16:2436:A:A NC_000003.12:20758:T:A (self)
ss99067899, ss106234437, ss133204243, ss138663877, ss154962269 NT_022517.18:2436:A:A NC_000003.12:20758:T:A (self)
7953269, ss3900775875 NC_000003.11:62436:A:C NC_000003.12:20758:T:C (self)
7953269, ss3900775875 NC_000003.11:62436:A:G NC_000003.12:20758:T:G (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 rs9682412

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