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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.

rs2786468

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83271872 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.313544 (82992/264690, TOPMED)
G=0.313674 (43878/139884, GnomAD)
G=0.33067 (5761/17422, ALFA) (+ 6 more)
G=0.24916 (4176/16760, 8.3KJPN)
G=0.2762 (1383/5008, 1000G)
G=0.2276 (667/2930, KOREAN)
G=0.275 (274/998, GoNL)
G=0.199 (103/518, SGDP_PRJ)
G=0.236 (51/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107985037 : 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.83271872G>A
GRCh38.p13 chr 1 NC_000001.11:g.83271872G>C
GRCh37.p13 chr 1 NC_000001.10:g.83737555G>A
GRCh37.p13 chr 1 NC_000001.10:g.83737555G>C
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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

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 17422 G=0.33067 A=0.00000, C=0.66933
European Sub 13554 G=0.34005 A=0.00000, C=0.65995
African Sub 2402 G=0.2648 A=0.0000, C=0.7352
African Others Sub 92 G=0.26 A=0.00, C=0.74
African American Sub 2310 G=0.2649 A=0.0000, C=0.7351
Asian Sub 112 G=0.161 A=0.000, C=0.839
East Asian Sub 86 G=0.16 A=0.00, C=0.84
Other Asian Sub 26 G=0.15 A=0.00, C=0.85
Latin American 1 Sub 146 G=0.390 A=0.000, C=0.610
Latin American 2 Sub 610 G=0.418 A=0.000, C=0.582
South Asian Sub 98 G=0.23 A=0.00, C=0.77
Other Sub 500 G=0.326 A=0.000, C=0.674


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.313544 C=0.686456
gnomAD - Genomes Global Study-wide 139884 G=0.313674 C=0.686326
gnomAD - Genomes European Sub 75808 G=0.33643 C=0.66357
gnomAD - Genomes African Sub 41908 G=0.26048 C=0.73952
gnomAD - Genomes American Sub 13594 G=0.36832 C=0.63168
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.3412 C=0.6588
gnomAD - Genomes East Asian Sub 3110 G=0.1785 C=0.8215
gnomAD - Genomes Other Sub 2146 G=0.3560 C=0.6440
8.3KJPN JAPANESE Study-wide 16760 G=0.24916 C=0.75084
1000Genomes Global Study-wide 5008 G=0.2762 C=0.7238
1000Genomes African Sub 1322 G=0.2405 C=0.7595
1000Genomes East Asian Sub 1008 G=0.1687 C=0.8313
1000Genomes Europe Sub 1006 G=0.3410 C=0.6590
1000Genomes South Asian Sub 978 G=0.265 C=0.735
1000Genomes American Sub 694 G=0.422 C=0.578
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2276 A=0.0000, C=0.7724
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.275 C=0.725
SGDP_PRJ Global Study-wide 518 G=0.199 C=0.801
Qatari Global Study-wide 216 G=0.236 C=0.764
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
GRCh38.p13 chr 1 NC_000001.11:g.83271872= NC_000001.11:g.83271872G>A NC_000001.11:g.83271872G>C
GRCh37.p13 chr 1 NC_000001.10:g.83737555= NC_000001.10:g.83737555G>A NC_000001.10:g.83737555G>C
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#.

44 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3943769 Sep 28, 2001 (100)
2 TSC-CSHL ss5327931 Oct 08, 2002 (108)
3 WI_SSAHASNP ss11342989 Jul 11, 2003 (117)
4 WI_SSAHASNP ss13453568 Dec 05, 2003 (120)
5 CSHL-HAPMAP ss16385892 Feb 27, 2004 (123)
6 CSHL-HAPMAP ss17325472 Feb 27, 2004 (123)
7 PERLEGEN ss23145060 Sep 20, 2004 (126)
8 HGSV ss86006568 Dec 14, 2007 (144)
9 HGSV ss86009054 Dec 14, 2007 (144)
10 BCMHGSC_JDW ss87584962 Mar 23, 2008 (144)
11 BGI ss106581640 Feb 13, 2009 (144)
12 ENSEMBL ss138878422 Dec 01, 2009 (144)
13 GMI ss155266221 Dec 01, 2009 (144)
14 GMI ss275903612 May 04, 2012 (144)
15 GMI ss284085338 Apr 25, 2013 (144)
16 1000GENOMES ss328737866 May 09, 2011 (144)
17 TISHKOFF ss554362925 Apr 25, 2013 (144)
18 SSMP ss648177189 Apr 25, 2013 (144)
19 EVA-GONL ss975366918 Aug 21, 2014 (144)
20 1000GENOMES ss1291674134 Aug 21, 2014 (144)
21 DDI ss1425876676 Apr 01, 2015 (144)
22 HAMMER_LAB ss1794653531 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1918570040 Feb 12, 2016 (147)
24 TOPMED ss2326434224 Dec 20, 2016 (150)
25 SYSTEMSBIOZJU ss2624414026 Nov 08, 2017 (151)
26 GRF ss2697745105 Nov 08, 2017 (151)
27 GNOMAD ss2757378731 Nov 08, 2017 (151)
28 SWEGEN ss2987127935 Nov 08, 2017 (151)
29 TOPMED ss3081769042 Nov 08, 2017 (151)
30 TOPMED ss3081769043 Nov 08, 2017 (151)
31 CSHL ss3343544510 Nov 08, 2017 (151)
32 URBANLAB ss3646706206 Oct 11, 2018 (152)
33 EVA ss3746441739 Jul 12, 2019 (153)
34 PACBIO ss3783464374 Jul 12, 2019 (153)
35 PACBIO ss3789114483 Jul 12, 2019 (153)
36 PACBIO ss3793987272 Jul 12, 2019 (153)
37 KHV_HUMAN_GENOMES ss3799448012 Jul 12, 2019 (153)
38 EVA ss3826272008 Apr 25, 2020 (154)
39 EVA ss3836525133 Apr 25, 2020 (154)
40 EVA ss3841932379 Apr 25, 2020 (154)
41 SGDP_PRJ ss3849253587 Apr 25, 2020 (154)
42 KRGDB ss3894305102 Apr 25, 2020 (154)
43 TOPMED ss4456739627 Apr 25, 2021 (155)
44 TOMMO_GENOMICS ss5144818222 Apr 25, 2021 (155)
45 1000Genomes NC_000001.10 - 83737555 Oct 11, 2018 (152)
46 gnomAD - Genomes NC_000001.11 - 83271872 Apr 25, 2021 (155)
47 Genome of the Netherlands Release 5 NC_000001.10 - 83737555 Apr 25, 2020 (154)
48 KOREAN population from KRGDB NC_000001.10 - 83737555 Apr 25, 2020 (154)
49 Qatari NC_000001.10 - 83737555 Apr 25, 2020 (154)
50 SGDP_PRJ NC_000001.10 - 83737555 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 83737555 Apr 25, 2021 (155)
52 TopMed NC_000001.11 - 83271872 Apr 25, 2021 (155)
53 ALFA NC_000001.11 - 83271872 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)
rs7512873 Aug 27, 2003 (117)
rs9659015 Feb 27, 2004 (120)
rs11163702 Sep 24, 2004 (123)
rs17101581 Mar 11, 2006 (126)
rs58117351 Apr 01, 2015 (144)
rs61791677 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1482496, ss3894305102 NC_000001.10:83737554:G:A NC_000001.11:83271871:G:A (self)
12346007200, ss3081769042 NC_000001.11:83271871:G:A NC_000001.11:83271871:G:A (self)
ss86006568, ss86009054 NC_000001.8:83449575:G:C NC_000001.11:83271871:G:C (self)
ss87584962, ss275903612, ss284085338 NC_000001.9:83510142:G:C NC_000001.11:83271871:G:C (self)
2421527, 573804, 1482496, 611970, 1270567, 2787529, ss328737866, ss554362925, ss648177189, ss975366918, ss1291674134, ss1425876676, ss1794653531, ss1918570040, ss2326434224, ss2624414026, ss2697745105, ss2757378731, ss2987127935, ss3343544510, ss3746441739, ss3783464374, ss3789114483, ss3793987272, ss3826272008, ss3836525133, ss3849253587, ss3894305102, ss5144818222 NC_000001.10:83737554:G:C NC_000001.11:83271871:G:C (self)
17092226, 12815226, 20345962, 12346007200, ss3081769043, ss3646706206, ss3799448012, ss3841932379, ss4456739627 NC_000001.11:83271871:G:C NC_000001.11:83271871:G:C (self)
ss11342989 NT_026943.12:74195:G:C NC_000001.11:83271871:G:C (self)
ss13453568, ss16385892, ss17325472 NT_026943.13:8557728:G:C NC_000001.11:83271871:G:C (self)
ss3943769, ss5327931, ss23145060, ss106581640, ss138878422, ss155266221 NT_032977.9:53709472:G:C NC_000001.11:83271871:G:C (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 rs2786468

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