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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.

rs10900602

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:783006 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.030496 (8072/264690, TOPMED)
A=0.022254 (3064/137682, GnomAD)
A=0.17153 (4847/28258, 14KJPN) (+ 9 more)
A=0.17196 (2882/16760, 8.3KJPN)
A=0.0050 (33/6666, ALFA)
A=0.0595 (381/6404, 1000G_30x)
A=0.0639 (320/5008, 1000G)
A=0.1808 (528/2920, KOREAN)
A=0.1763 (323/1832, Korea1K)
A=0.086 (46/532, SGDP_PRJ)
A=0.028 (6/216, Qatari)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Non Coding Transcript 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 6666 A=0.0050 C=0.0000, G=0.9950, T=0.0000
European Sub 6534 A=0.0035 C=0.0000, G=0.9965, T=0.0000
African Sub 86 A=0.06 C=0.00, G=0.94, T=0.00
African Others Sub 6 A=0.0 C=0.0, G=1.0, T=0.0
African American Sub 80 A=0.06 C=0.00, G=0.94, T=0.00
Asian Sub 6 A=0.5 C=0.0, G=0.5, T=0.0
East Asian Sub 4 A=0.8 C=0.0, G=0.2, T=0.0
Other Asian Sub 2 A=0.0 C=0.0, G=1.0, T=0.0
Latin American 1 Sub 0 A=0 C=0, G=0, T=0
Latin American 2 Sub 2 A=1.0 C=0.0, G=0.0, T=0.0
South Asian Sub 4 A=0.0 C=0.0, G=1.0, T=0.0
Other Sub 34 A=0.00 C=0.00, G=1.00, T=0.00


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 A=0.030496 G=0.969504
gnomAD - Genomes Global Study-wide 137682 A=0.022254 G=0.977746
gnomAD - Genomes European Sub 75488 A=0.00117 G=0.99883
gnomAD - Genomes African Sub 40388 A=0.03892 G=0.96108
gnomAD - Genomes American Sub 13364 A=0.05941 G=0.94059
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.0097 G=0.9903
gnomAD - Genomes East Asian Sub 3036 A=0.1673 G=0.8327
gnomAD - Genomes Other Sub 2090 A=0.0335 G=0.9665
14KJPN JAPANESE Study-wide 28258 A=0.17153 G=0.82847
8.3KJPN JAPANESE Study-wide 16760 A=0.17196 G=0.82804
Allele Frequency Aggregator Total Global 6666 A=0.0050 C=0.0000, G=0.9950, T=0.0000
Allele Frequency Aggregator European Sub 6534 A=0.0035 C=0.0000, G=0.9965, T=0.0000
Allele Frequency Aggregator African Sub 86 A=0.06 C=0.00, G=0.94, T=0.00
Allele Frequency Aggregator Other Sub 34 A=0.00 C=0.00, G=1.00, T=0.00
Allele Frequency Aggregator Asian Sub 6 A=0.5 C=0.0, G=0.5, T=0.0
Allele Frequency Aggregator South Asian Sub 4 A=0.0 C=0.0, G=1.0, T=0.0
Allele Frequency Aggregator Latin American 2 Sub 2 A=1.0 C=0.0, G=0.0, T=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 A=0 C=0, G=0, T=0
1000Genomes_30x Global Study-wide 6404 A=0.0595 G=0.9405
1000Genomes_30x African Sub 1786 A=0.0403 G=0.9597
1000Genomes_30x Europe Sub 1266 A=0.0016 G=0.9984
1000Genomes_30x South Asian Sub 1202 A=0.0266 G=0.9734
1000Genomes_30x East Asian Sub 1170 A=0.1735 G=0.8265
1000Genomes_30x American Sub 980 A=0.073 G=0.927
1000Genomes Global Study-wide 5008 A=0.0639 G=0.9361
1000Genomes African Sub 1322 A=0.0446 G=0.9554
1000Genomes East Asian Sub 1008 A=0.1726 G=0.8274
1000Genomes Europe Sub 1006 A=0.0070 G=0.9930
1000Genomes South Asian Sub 978 A=0.030 G=0.970
1000Genomes American Sub 694 A=0.073 G=0.927
KOREAN population from KRGDB KOREAN Study-wide 2920 A=0.1808 G=0.8192, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.1763 G=0.8237
SGDP_PRJ Global Study-wide 532 A=0.086 G=0.912, T=0.002
Qatari Global Study-wide 216 A=0.028 G=0.972
The Danish reference pan genome Danish Study-wide 40 A=0.00 G=1.00
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.783006A>C
GRCh38.p14 chr 1 NC_000001.11:g.783006A>G
GRCh38.p14 chr 1 NC_000001.11:g.783006A>T
GRCh37.p13 chr 1 NC_000001.10:g.718386A>C
GRCh37.p13 chr 1 NC_000001.10:g.718386A>G
GRCh37.p13 chr 1 NC_000001.10:g.718386A>T
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_007065319.1:n.1405A>C N/A Non Coding Transcript Variant
LINC01409 transcript variant X1 XR_007065319.1:n.1405A>G N/A Non Coding Transcript Variant
LINC01409 transcript variant X1 XR_007065319.1:n.1405A>T N/A Non Coding Transcript Variant
LINC01409 transcript variant X2 XR_007065320.1: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 A= C G T
GRCh38.p14 chr 1 NC_000001.11:g.783006= NC_000001.11:g.783006A>C NC_000001.11:g.783006A>G NC_000001.11:g.783006A>T
GRCh37.p13 chr 1 NC_000001.10:g.718386= NC_000001.10:g.718386A>C NC_000001.10:g.718386A>G NC_000001.10:g.718386A>T
LINC01409 transcript variant X1 XR_007065319.1:n.1405= XR_007065319.1:n.1405A>C XR_007065319.1:n.1405A>G XR_007065319.1:n.1405A>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#.

42 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15452114 Feb 28, 2004 (123)
2 CSHL-HAPMAP ss16425635 Feb 27, 2004 (120)
3 SC_SNP ss18098246 Feb 27, 2004 (120)
4 SC_SNP ss18177049 Feb 27, 2004 (120)
5 BCMHGSC_JDW ss87155358 Mar 23, 2008 (129)
6 HUMANGENOME_JCVI ss97913173 Feb 06, 2009 (130)
7 ENSEMBL ss138907281 Dec 01, 2009 (147)
8 BCM-HGSC-SUB ss205506307 Jul 04, 2010 (132)
9 GMI ss275680539 May 04, 2012 (137)
10 GMI ss283987300 Apr 25, 2013 (138)
11 SSMP ss647515855 Apr 25, 2013 (138)
12 1000GENOMES ss1289337975 Aug 21, 2014 (142)
13 DDI ss1425684726 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1573851060 Apr 01, 2015 (144)
15 HAMMER_LAB ss1793705474 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1917959736 Feb 12, 2016 (147)
17 SYSTEMSBIOZJU ss2624264726 Nov 08, 2017 (151)
18 GRF ss2697374024 Nov 08, 2017 (151)
19 GNOMAD ss2750633105 Nov 08, 2017 (151)
20 SWEGEN ss2986147737 Nov 08, 2017 (151)
21 CSHL ss3343272184 Nov 08, 2017 (151)
22 URBANLAB ss3646581100 Oct 11, 2018 (152)
23 PACBIO ss3783302027 Jul 12, 2019 (153)
24 PACBIO ss3788979909 Jul 12, 2019 (153)
25 PACBIO ss3793852446 Jul 12, 2019 (153)
26 KHV_HUMAN_GENOMES ss3798743099 Jul 12, 2019 (153)
27 EVA ss3825981370 Apr 25, 2020 (154)
28 EVA ss3836378315 Apr 25, 2020 (154)
29 EVA ss3841782313 Apr 25, 2020 (154)
30 SGDP_PRJ ss3847993841 Apr 25, 2020 (154)
31 KRGDB ss3892833283 Apr 25, 2020 (154)
32 KOGIC ss3943628383 Apr 25, 2020 (154)
33 TOPMED ss4436422601 Apr 25, 2021 (155)
34 TOMMO_GENOMICS ss5142049460 Apr 25, 2021 (155)
35 1000G_HIGH_COVERAGE ss5240861422 Oct 12, 2022 (156)
36 EVA ss5316180747 Oct 12, 2022 (156)
37 1000G_HIGH_COVERAGE ss5512485699 Oct 12, 2022 (156)
38 SANFORD_IMAGENETICS ss5624747899 Oct 12, 2022 (156)
39 TOMMO_GENOMICS ss5666187759 Oct 12, 2022 (156)
40 YY_MCH ss5800243128 Oct 12, 2022 (156)
41 EVA ss5831417620 Oct 12, 2022 (156)
42 EVA ss5979925971 Oct 12, 2022 (156)
43 1000Genomes NC_000001.10 - 718386 Oct 11, 2018 (152)
44 1000Genomes_30x NC_000001.11 - 783006 Oct 12, 2022 (156)
45 The Danish reference pan genome NC_000001.10 - 718386 Apr 25, 2020 (154)
46 gnomAD - Genomes NC_000001.11 - 783006 Apr 25, 2021 (155)
47 KOREAN population from KRGDB NC_000001.10 - 718386 Apr 25, 2020 (154)
48 Korean Genome Project NC_000001.11 - 783006 Apr 25, 2020 (154)
49 Qatari NC_000001.10 - 718386 Apr 25, 2020 (154)
50 SGDP_PRJ NC_000001.10 - 718386 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 718386 Apr 25, 2021 (155)
52 14KJPN NC_000001.11 - 783006 Oct 12, 2022 (156)
53 TopMed NC_000001.11 - 783006 Apr 25, 2021 (155)
54 ALFA NC_000001.11 - 783006 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)
rs11490921 Sep 24, 2004 (123)
rs77614743 Jul 19, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
4612032041 NC_000001.11:783005:A:C NC_000001.11:783005:A:C (self)
ss87155358, ss205506307, ss275680539, ss283987300 NC_000001.9:708248:A:G NC_000001.11:783005:A:G (self)
2641, 1358294, 10677, 1666, 10821, 18767, ss647515855, ss1289337975, ss1425684726, ss1573851060, ss1793705474, ss1917959736, ss2624264726, ss2697374024, ss2750633105, ss2986147737, ss3343272184, ss3783302027, ss3788979909, ss3793852446, ss3825981370, ss3836378315, ss3847993841, ss3892833283, ss5142049460, ss5316180747, ss5624747899, ss5831417620, ss5979925971 NC_000001.10:718385:A:G NC_000001.11:783005:A:G (self)
11634, 53950, 6384, 24863, 28936, 4612032041, ss3646581100, ss3798743099, ss3841782313, ss3943628383, ss4436422601, ss5240861422, ss5512485699, ss5666187759, ss5800243128 NC_000001.11:783005:A:G NC_000001.11:783005:A:G (self)
ss15452114, ss97913173, ss138907281 NT_004350.19:197017:A:G NC_000001.11:783005:A:G (self)
ss16425635, ss18098246, ss18177049 NT_034471.3:197017:A:G NC_000001.11:783005:A:G (self)
10677, 10821, ss3847993841, ss3892833283 NC_000001.10:718385:A:T NC_000001.11:783005:A:T (self)
4612032041 NC_000001.11:783005:A:T NC_000001.11:783005: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 rs10900602

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