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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.

rs1094559

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:155877819 (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=0.187767 (49700/264690, TOPMED)
G=0.186502 (26086/139870, GnomAD)
G=0.12598 (2245/17820, ALFA) (+ 13 more)
G=0.05274 (884/16760, 8.3KJPN)
G=0.2142 (1372/6404, 1000G_30x)
G=0.2037 (1020/5008, 1000G)
G=0.0636 (285/4480, Estonian)
G=0.0620 (239/3854, ALSPAC)
G=0.0636 (236/3708, TWINSUK)
G=0.0567 (166/2930, KOREAN)
G=0.060 (60/998, GoNL)
G=0.062 (37/600, NorthernSweden)
G=0.067 (35/522, SGDP_PRJ)
G=0.181 (39/216, Qatari)
G=0.09 (5/56, Siberian)
G=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SYT11 : 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 17820 G=0.12598 A=0.87402, C=0.00000, T=0.00000
European Sub 13630 G=0.06163 A=0.93837, C=0.00000, T=0.00000
African Sub 2536 G=0.4791 A=0.5209, C=0.0000, T=0.0000
African Others Sub 96 G=0.58 A=0.42, C=0.00, T=0.00
African American Sub 2440 G=0.4750 A=0.5250, C=0.0000, T=0.0000
Asian Sub 112 G=0.062 A=0.938, C=0.000, T=0.000
East Asian Sub 86 G=0.08 A=0.92, C=0.00, T=0.00
Other Asian Sub 26 G=0.00 A=1.00, C=0.00, T=0.00
Latin American 1 Sub 146 G=0.116 A=0.884, C=0.000, T=0.000
Latin American 2 Sub 610 G=0.066 A=0.934, C=0.000, T=0.000
South Asian Sub 98 G=0.13 A=0.87, C=0.00, T=0.00
Other Sub 688 G=0.164 A=0.836, C=0.000, 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
TopMed Global Study-wide 264690 G=0.187767 A=0.812233
gnomAD - Genomes Global Study-wide 139870 G=0.186502 A=0.813498
gnomAD - Genomes European Sub 75832 G=0.06884 A=0.93116
gnomAD - Genomes African Sub 41830 G=0.45513 A=0.54487
gnomAD - Genomes American Sub 13612 G=0.07964 A=0.92036
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.0648 A=0.9352
gnomAD - Genomes East Asian Sub 3124 G=0.0637 A=0.9363
gnomAD - Genomes Other Sub 2152 G=0.1533 A=0.8467
Allele Frequency Aggregator Total Global 17820 G=0.12598 A=0.87402, C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 13630 G=0.06163 A=0.93837, C=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 2536 G=0.4791 A=0.5209, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 688 G=0.164 A=0.836, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.066 A=0.934, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.116 A=0.884, C=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.062 A=0.938, C=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.13 A=0.87, C=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.05274 A=0.94726
1000Genomes_30x Global Study-wide 6404 G=0.2142 A=0.7858
1000Genomes_30x African Sub 1786 G=0.5795 A=0.4205
1000Genomes_30x Europe Sub 1266 G=0.0837 A=0.9163
1000Genomes_30x South Asian Sub 1202 G=0.0765 A=0.9235
1000Genomes_30x East Asian Sub 1170 G=0.0658 A=0.9342
1000Genomes_30x American Sub 980 G=0.063 A=0.937
1000Genomes Global Study-wide 5008 G=0.2037 A=0.7963
1000Genomes African Sub 1322 G=0.5673 A=0.4327
1000Genomes East Asian Sub 1008 G=0.0625 A=0.9375
1000Genomes Europe Sub 1006 G=0.0795 A=0.9205
1000Genomes South Asian Sub 978 G=0.080 A=0.920
1000Genomes American Sub 694 G=0.071 A=0.929
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.0636 A=0.9364
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.0620 A=0.9380
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.0636 A=0.9364
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0567 A=0.9433, C=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.060 A=0.940
Northern Sweden ACPOP Study-wide 600 G=0.062 A=0.938
SGDP_PRJ Global Study-wide 522 G=0.067 A=0.933
Qatari Global Study-wide 216 G=0.181 A=0.819
Siberian Global Study-wide 56 G=0.09 A=0.91
The Danish reference pan genome Danish Study-wide 40 G=0.17 A=0.82
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.155877819G>A
GRCh38.p14 chr 1 NC_000001.11:g.155877819G>C
GRCh38.p14 chr 1 NC_000001.11:g.155877819G>T
GRCh37.p13 chr 1 NC_000001.10:g.155847610G>A
GRCh37.p13 chr 1 NC_000001.10:g.155847610G>C
GRCh37.p13 chr 1 NC_000001.10:g.155847610G>T
Gene: SYT11, synaptotagmin 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SYT11 transcript NM_152280.5:c.862-2681G>A N/A Intron Variant
SYT11 transcript variant X2 XM_005245014.4:c.862-2681…

XM_005245014.4:c.862-2681G>A

 		N/A Intron Variant
SYT11 transcript variant X1 XM_017000759.3:c.862-2681…

XM_017000759.3:c.862-2681G>A

 		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 G= A C T
GRCh38.p14 chr 1 NC_000001.11:g.155877819= NC_000001.11:g.155877819G>A NC_000001.11:g.155877819G>C NC_000001.11:g.155877819G>T
GRCh37.p13 chr 1 NC_000001.10:g.155847610= NC_000001.10:g.155847610G>A NC_000001.10:g.155847610G>C NC_000001.10:g.155847610G>T
SYT11 transcript NM_152280.4:c.862-2681= NM_152280.4:c.862-2681G>A NM_152280.4:c.862-2681G>C NM_152280.4:c.862-2681G>T
SYT11 transcript NM_152280.5:c.862-2681= NM_152280.5:c.862-2681G>A NM_152280.5:c.862-2681G>C NM_152280.5:c.862-2681G>T
SYT11 transcript variant X1 XM_005245014.1:c.862-2681= XM_005245014.1:c.862-2681G>A XM_005245014.1:c.862-2681G>C XM_005245014.1:c.862-2681G>T
SYT11 transcript variant X2 XM_005245014.4:c.862-2681= XM_005245014.4:c.862-2681G>A XM_005245014.4:c.862-2681G>C XM_005245014.4:c.862-2681G>T
SYT11 transcript variant X1 XM_017000759.3:c.862-2681= XM_017000759.3:c.862-2681G>A XM_017000759.3:c.862-2681G>C XM_017000759.3:c.862-2681G>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#.

68 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1102286 Oct 13, 2000 (86)
2 KWOK ss1713536 Oct 18, 2000 (87)
3 SC_JCM ss2597569 Nov 08, 2000 (89)
4 WI_SSAHASNP ss11355415 Jul 11, 2003 (116)
5 ABI ss41333993 Mar 14, 2006 (126)
6 HGSV ss78444623 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss87826599 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss99251646 Feb 06, 2009 (130)
9 ENSEMBL ss138084441 Dec 01, 2009 (131)
10 ENSEMBL ss143188175 Dec 01, 2009 (131)
11 GMI ss155761442 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss165232307 Jul 04, 2010 (132)
13 BL ss253513486 May 09, 2011 (134)
14 GMI ss276053424 May 04, 2012 (137)
15 GMI ss284153665 Apr 25, 2013 (138)
16 PJP ss290638296 May 09, 2011 (134)
17 1000GENOMES ss328955469 May 09, 2011 (134)
18 SSMP ss648418481 Apr 25, 2013 (138)
19 EVA-GONL ss975690122 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1068274020 Aug 21, 2014 (142)
21 1000GENOMES ss1292957821 Aug 21, 2014 (142)
22 DDI ss1425980330 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1574395729 Apr 01, 2015 (144)
24 EVA_DECODE ss1585071868 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1601230264 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1644224297 Apr 01, 2015 (144)
27 HAMMER_LAB ss1795101374 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1918923784 Feb 12, 2016 (147)
29 GENOMED ss1966868690 Jul 19, 2016 (147)
30 JJLAB ss2019976979 Sep 14, 2016 (149)
31 USC_VALOUEV ss2148002276 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2166608540 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624496372 Nov 08, 2017 (151)
34 GRF ss2697975012 Nov 08, 2017 (151)
35 GNOMAD ss2761417676 Nov 08, 2017 (151)
36 SWEGEN ss2987765734 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3023745426 Nov 08, 2017 (151)
38 CSHL ss3343713413 Nov 08, 2017 (151)
39 URBANLAB ss3646792763 Oct 11, 2018 (152)
40 EGCUT_WGS ss3655704832 Jul 12, 2019 (153)
41 EVA_DECODE ss3687798537 Jul 12, 2019 (153)
42 ACPOP ss3727491606 Jul 12, 2019 (153)
43 EVA ss3746817150 Jul 12, 2019 (153)
44 PACBIO ss3783568548 Jul 12, 2019 (153)
45 PACBIO ss3789199503 Jul 12, 2019 (153)
46 PACBIO ss3794071508 Jul 12, 2019 (153)
47 KHV_HUMAN_GENOMES ss3799817494 Jul 12, 2019 (153)
48 EVA ss3826427434 Apr 25, 2020 (154)
49 EVA ss3836608282 Apr 25, 2020 (154)
50 EVA ss3842017558 Apr 25, 2020 (154)
51 SGDP_PRJ ss3850021921 Apr 25, 2020 (154)
52 KRGDB ss3895234941 Apr 25, 2020 (154)
53 TOPMED ss4468612836 Apr 25, 2021 (155)
54 TOMMO_GENOMICS ss5146525672 Apr 25, 2021 (155)
55 1000G_HIGH_COVERAGE ss5244321663 Oct 12, 2022 (156)
56 EVA ss5322102821 Oct 12, 2022 (156)
57 HUGCELL_USP ss5444911285 Oct 12, 2022 (156)
58 EVA ss5506031383 Oct 12, 2022 (156)
59 1000G_HIGH_COVERAGE ss5517664522 Oct 12, 2022 (156)
60 SANFORD_IMAGENETICS ss5626606385 Oct 12, 2022 (156)
61 TOMMO_GENOMICS ss5673736239 Oct 12, 2022 (156)
62 TOMMO_GENOMICS ss5673736240 Oct 12, 2022 (156)
63 YY_MCH ss5801266313 Oct 12, 2022 (156)
64 EVA ss5832675821 Oct 12, 2022 (156)
65 EVA ss5849111061 Oct 12, 2022 (156)
66 EVA ss5910276789 Oct 12, 2022 (156)
67 EVA ss5938400536 Oct 12, 2022 (156)
68 EVA ss5979990503 Oct 12, 2022 (156)
69 1000Genomes NC_000001.10 - 155847610 Oct 11, 2018 (152)
70 1000Genomes_30x NC_000001.11 - 155877819 Oct 12, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 155847610 Oct 11, 2018 (152)
72 Genetic variation in the Estonian population NC_000001.10 - 155847610 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000001.10 - 155847610 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000001.11 - 155877819 Apr 25, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000001.10 - 155847610 Apr 25, 2020 (154)
76 KOREAN population from KRGDB NC_000001.10 - 155847610 Apr 25, 2020 (154)
77 Northern Sweden NC_000001.10 - 155847610 Jul 12, 2019 (153)
78 Qatari NC_000001.10 - 155847610 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000001.10 - 155847610 Apr 25, 2020 (154)
80 Siberian NC_000001.10 - 155847610 Apr 25, 2020 (154)
81 8.3KJPN NC_000001.10 - 155847610 Apr 25, 2021 (155)
82 14KJPN

Submission ignored due to conflicting rows:
Row 7573343 (NC_000001.11:155877818:G:A 26748/28256)
Row 7573344 (NC_000001.11:155877818:G:T 13/28256)

- Oct 12, 2022 (156)
83 14KJPN

Submission ignored due to conflicting rows:
Row 7573343 (NC_000001.11:155877818:G:A 26748/28256)
Row 7573344 (NC_000001.11:155877818:G:T 13/28256)

- Oct 12, 2022 (156)
84 TopMed NC_000001.11 - 155877819 Apr 25, 2021 (155)
85 UK 10K study - Twins NC_000001.10 - 155847610 Oct 11, 2018 (152)
86 ALFA NC_000001.11 - 155877819 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78444623 NC_000001.8:152660682:G:A NC_000001.11:155877818:G:A (self)
ss87826599, ss165232307, ss253513486, ss276053424, ss284153665, ss290638296, ss1585071868 NC_000001.9:154114233:G:A NC_000001.11:155877818:G:A (self)
3750984, 2039286, 1443080, 1710940, 885246, 2412335, 776471, 965714, 2038901, 518630, 4494979, 2039286, ss328955469, ss648418481, ss975690122, ss1068274020, ss1292957821, ss1425980330, ss1574395729, ss1601230264, ss1644224297, ss1795101374, ss1918923784, ss1966868690, ss2019976979, ss2148002276, ss2624496372, ss2697975012, ss2761417676, ss2987765734, ss3343713413, ss3655704832, ss3727491606, ss3746817150, ss3783568548, ss3789199503, ss3794071508, ss3826427434, ss3836608282, ss3850021921, ss3895234941, ss5146525672, ss5322102821, ss5506031383, ss5626606385, ss5832675821, ss5938400536, ss5979990503 NC_000001.10:155847609:G:A NC_000001.11:155877818:G:A (self)
5190457, 27312682, 32219171, 2734374738, ss2166608540, ss3023745426, ss3646792763, ss3687798537, ss3799817494, ss3842017558, ss4468612836, ss5244321663, ss5444911285, ss5517664522, ss5673736239, ss5801266313, ss5849111061, ss5910276789 NC_000001.11:155877818:G:A NC_000001.11:155877818:G:A (self)
ss1102286, ss1713536, ss2597569, ss41333993, ss99251646, ss138084441, ss143188175, ss155761442 NT_004487.19:7336251:G:A NC_000001.11:155877818:G:A (self)
ss11355415 NT_004668.15:2300010:G:A NC_000001.11:155877818:G:A (self)
2412335, ss3895234941 NC_000001.10:155847609:G:C NC_000001.11:155877818:G:C (self)
2734374738 NC_000001.11:155877818:G:C NC_000001.11:155877818:G:C (self)
2734374738, ss5673736240 NC_000001.11:155877818:G:T NC_000001.11:155877818: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.

No publications for rs1094559

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