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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.

rs6587837

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:58684061 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.184370 (48801/264690, TOPMED)
T=0.197580 (27641/139898, GnomAD)
T=0.17797 (5029/28258, 14KJPN) (+ 15 more)
T=0.17643 (2957/16760, 8.3KJPN)
T=0.11619 (1788/15388, ALFA)
T=0.2272 (1455/6404, 1000G_30x)
T=0.2294 (1149/5008, 1000G)
T=0.2449 (1097/4480, Estonian)
T=0.1622 (625/3854, ALSPAC)
T=0.1632 (605/3708, TWINSUK)
T=0.2140 (627/2930, KOREAN)
T=0.155 (155/998, GoNL)
T=0.232 (139/600, NorthernSweden)
G=0.409 (95/232, SGDP_PRJ)
T=0.139 (30/216, Qatari)
T=0.218 (47/216, Vietnamese)
T=0.12 (5/40, GENOME_DK)
G=0.45 (9/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MYSM1 : 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 15388 G=0.88381 A=0.00000, T=0.11619
European Sub 12130 G=0.86620 A=0.00000, T=0.13380
African Sub 2082 G=0.9400 A=0.0000, T=0.0600
African Others Sub 82 G=0.94 A=0.00, T=0.06
African American Sub 2000 G=0.9400 A=0.0000, T=0.0600
Asian Sub 58 G=1.00 A=0.00, T=0.00
East Asian Sub 46 G=1.00 A=0.00, T=0.00
Other Asian Sub 12 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 88 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 412 G=1.000 A=0.000, T=0.000
South Asian Sub 56 G=0.96 A=0.00, T=0.04
Other Sub 562 G=0.932 A=0.000, T=0.068


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=0.815630 T=0.184370
gnomAD - Genomes Global Study-wide 139898 G=0.802420 T=0.197580
gnomAD - Genomes European Sub 75782 G=0.80634 T=0.19366
gnomAD - Genomes African Sub 41894 G=0.79174 T=0.20826
gnomAD - Genomes American Sub 13630 G=0.81827 T=0.18173
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.8299 T=0.1701
gnomAD - Genomes East Asian Sub 3124 G=0.7452 T=0.2548
gnomAD - Genomes Other Sub 2146 G=0.8127 T=0.1873
14KJPN JAPANESE Study-wide 28258 G=0.82203 T=0.17797
8.3KJPN JAPANESE Study-wide 16760 G=0.82357 T=0.17643
Allele Frequency Aggregator Total Global 15388 G=0.88381 A=0.00000, T=0.11619
Allele Frequency Aggregator European Sub 12130 G=0.86620 A=0.00000, T=0.13380
Allele Frequency Aggregator African Sub 2082 G=0.9400 A=0.0000, T=0.0600
Allele Frequency Aggregator Other Sub 562 G=0.932 A=0.000, T=0.068
Allele Frequency Aggregator Latin American 2 Sub 412 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 88 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 58 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 56 G=0.96 A=0.00, T=0.04
1000Genomes_30x Global Study-wide 6404 G=0.7728 T=0.2272
1000Genomes_30x African Sub 1786 G=0.7660 T=0.2340
1000Genomes_30x Europe Sub 1266 G=0.8136 T=0.1864
1000Genomes_30x South Asian Sub 1202 G=0.6972 T=0.3028
1000Genomes_30x East Asian Sub 1170 G=0.7846 T=0.2154
1000Genomes_30x American Sub 980 G=0.811 T=0.189
1000Genomes Global Study-wide 5008 G=0.7706 T=0.2294
1000Genomes African Sub 1322 G=0.7716 T=0.2284
1000Genomes East Asian Sub 1008 G=0.7857 T=0.2143
1000Genomes Europe Sub 1006 G=0.8042 T=0.1958
1000Genomes South Asian Sub 978 G=0.690 T=0.310
1000Genomes American Sub 694 G=0.811 T=0.189
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7551 T=0.2449
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8378 T=0.1622
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8368 T=0.1632
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7860 T=0.2140
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.845 T=0.155
Northern Sweden ACPOP Study-wide 600 G=0.768 T=0.232
SGDP_PRJ Global Study-wide 232 G=0.409 T=0.591
Qatari Global Study-wide 216 G=0.861 T=0.139
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.782 T=0.218
The Danish reference pan genome Danish Study-wide 40 G=0.88 T=0.12
Siberian Global Study-wide 20 G=0.45 T=0.55
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.58684061G>A
GRCh38.p14 chr 1 NC_000001.11:g.58684061G>T
GRCh37.p13 chr 1 NC_000001.10:g.59149733G>A
GRCh37.p13 chr 1 NC_000001.10:g.59149733G>T
MYSM1 RefSeqGene (LRG_1411) NG_065323.2:g.21017C>T
MYSM1 RefSeqGene (LRG_1411) NG_065323.2:g.21017C>A
Gene: MYSM1, Myb like, SWIRM and MPN domains 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MYSM1 transcript NM_001085487.3:c.498+1092…

NM_001085487.3:c.498+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X1 XM_006710314.4:c.498+1092…

XM_006710314.4:c.498+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X2 XM_011540573.4:c.297+1092…

XM_011540573.4:c.297+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X3 XM_011540574.3:c.231+1092…

XM_011540574.3:c.231+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X5 XM_047443717.1:c.-262+109…

XM_047443717.1:c.-262+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X6 XM_047443718.1:c.-262+109…

XM_047443718.1:c.-262+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X7 XM_047443719.1:c.-262+109…

XM_047443719.1:c.-262+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X8 XM_047443720.1:c.498+1092…

XM_047443720.1:c.498+1092C>T

 		N/A Intron Variant
MYSM1 transcript variant X4 XR_946533.3: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 G= A T
GRCh38.p14 chr 1 NC_000001.11:g.58684061= NC_000001.11:g.58684061G>A NC_000001.11:g.58684061G>T
GRCh37.p13 chr 1 NC_000001.10:g.59149733= NC_000001.10:g.59149733G>A NC_000001.10:g.59149733G>T
MYSM1 RefSeqGene (LRG_1411) NG_065323.2:g.21017= NG_065323.2:g.21017C>T NG_065323.2:g.21017C>A
MYSM1 transcript NM_001085487.2:c.498+1092= NM_001085487.2:c.498+1092C>T NM_001085487.2:c.498+1092C>A
MYSM1 transcript NM_001085487.3:c.498+1092= NM_001085487.3:c.498+1092C>T NM_001085487.3:c.498+1092C>A
MYSM1 transcript variant X1 XM_005270418.1:c.297+1092= XM_005270418.1:c.297+1092C>T XM_005270418.1:c.297+1092C>A
MYSM1 transcript variant X2 XM_005270419.1:c.186+1092= XM_005270419.1:c.186+1092C>T XM_005270419.1:c.186+1092C>A
MYSM1 transcript variant X1 XM_006710314.4:c.498+1092= XM_006710314.4:c.498+1092C>T XM_006710314.4:c.498+1092C>A
MYSM1 transcript variant X2 XM_011540573.4:c.297+1092= XM_011540573.4:c.297+1092C>T XM_011540573.4:c.297+1092C>A
MYSM1 transcript variant X3 XM_011540574.3:c.231+1092= XM_011540574.3:c.231+1092C>T XM_011540574.3:c.231+1092C>A
MYSM1 transcript variant X5 XM_047443717.1:c.-262+1092= XM_047443717.1:c.-262+1092C>T XM_047443717.1:c.-262+1092C>A
MYSM1 transcript variant X6 XM_047443718.1:c.-262+1092= XM_047443718.1:c.-262+1092C>T XM_047443718.1:c.-262+1092C>A
MYSM1 transcript variant X7 XM_047443719.1:c.-262+1092= XM_047443719.1:c.-262+1092C>T XM_047443719.1:c.-262+1092C>A
MYSM1 transcript variant X8 XM_047443720.1:c.498+1092= XM_047443720.1:c.498+1092C>T XM_047443720.1:c.498+1092C>A
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#.

61 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9819585 Jul 11, 2003 (116)
2 SC_SNP ss11111826 Jul 11, 2003 (116)
3 SC_SNP ss15441481 Feb 27, 2004 (120)
4 ABI ss43887189 Mar 14, 2006 (126)
5 HUMANGENOME_JCVI ss99210106 Feb 06, 2009 (130)
6 BGI ss106568741 Feb 06, 2009 (130)
7 1000GENOMES ss110500360 Jan 24, 2009 (130)
8 ENSEMBL ss138931560 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss163422295 Jul 04, 2010 (132)
10 BUSHMAN ss198495751 Jul 04, 2010 (132)
11 1000GENOMES ss218400900 Jul 14, 2010 (132)
12 1000GENOMES ss230546503 Jul 14, 2010 (132)
13 1000GENOMES ss238238997 Jul 15, 2010 (132)
14 GMI ss275837948 May 04, 2012 (137)
15 GMI ss284055540 Apr 25, 2013 (138)
16 PJP ss290517282 May 09, 2011 (134)
17 TISHKOFF ss554142753 Apr 25, 2013 (138)
18 SSMP ss647989525 Apr 25, 2013 (138)
19 EVA-GONL ss975189598 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1067909055 Aug 21, 2014 (142)
21 1000GENOMES ss1290999656 Aug 21, 2014 (142)
22 DDI ss1425817812 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1574079755 Apr 01, 2015 (144)
24 EVA_DECODE ss1584556334 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1600232571 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1643226604 Apr 01, 2015 (144)
27 HAMMER_LAB ss1794410592 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1918397327 Feb 12, 2016 (147)
29 GENOMED ss1966752417 Jul 19, 2016 (147)
30 JJLAB ss2019715365 Sep 14, 2016 (149)
31 USC_VALOUEV ss2147730505 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2162726452 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624371307 Nov 08, 2017 (151)
34 GRF ss2697644302 Nov 08, 2017 (151)
35 GNOMAD ss2755444306 Nov 08, 2017 (151)
36 SWEGEN ss2986860349 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3023618538 Nov 08, 2017 (151)
38 CSHL ss3343467043 Nov 08, 2017 (151)
39 URBANLAB ss3646668602 Oct 11, 2018 (152)
40 EGCUT_WGS ss3654926135 Jul 12, 2019 (153)
41 EVA_DECODE ss3686824910 Jul 12, 2019 (153)
42 ACPOP ss3727071104 Jul 12, 2019 (153)
43 EVA ss3746239396 Jul 12, 2019 (153)
44 KHV_HUMAN_GENOMES ss3799246735 Jul 12, 2019 (153)
45 EVA ss3826186166 Apr 25, 2020 (154)
46 SGDP_PRJ ss3848902689 Apr 25, 2020 (154)
47 KRGDB ss3893917241 Apr 25, 2020 (154)
48 TOPMED ss4450665309 Apr 25, 2021 (155)
49 TOMMO_GENOMICS ss5144067897 Apr 25, 2021 (155)
50 1000G_HIGH_COVERAGE ss5242361539 Oct 12, 2022 (156)
51 EVA ss5318895932 Oct 12, 2022 (156)
52 HUGCELL_USP ss5443413605 Oct 12, 2022 (156)
53 EVA ss5505860736 Oct 12, 2022 (156)
54 1000G_HIGH_COVERAGE ss5514683281 Oct 12, 2022 (156)
55 SANFORD_IMAGENETICS ss5625582227 Oct 12, 2022 (156)
56 TOMMO_GENOMICS ss5668873698 Oct 12, 2022 (156)
57 YY_MCH ss5800620466 Oct 12, 2022 (156)
58 EVA ss5831995449 Oct 12, 2022 (156)
59 EVA ss5848917938 Oct 12, 2022 (156)
60 EVA ss5908367777 Oct 12, 2022 (156)
61 EVA ss5937417375 Oct 12, 2022 (156)
62 1000Genomes NC_000001.10 - 59149733 Oct 11, 2018 (152)
63 1000Genomes_30x NC_000001.11 - 58684061 Oct 12, 2022 (156)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 59149733 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 59149733 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 59149733 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 58684061 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 59149733 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 59149733 Apr 25, 2020 (154)
70 Northern Sweden NC_000001.10 - 59149733 Jul 12, 2019 (153)
71 Qatari NC_000001.10 - 59149733 Apr 25, 2020 (154)
72 SGDP_PRJ NC_000001.10 - 59149733 Apr 25, 2020 (154)
73 Siberian NC_000001.10 - 59149733 Apr 25, 2020 (154)
74 8.3KJPN NC_000001.10 - 59149733 Apr 25, 2021 (155)
75 14KJPN NC_000001.11 - 58684061 Oct 12, 2022 (156)
76 TopMed NC_000001.11 - 58684061 Apr 25, 2021 (155)
77 UK 10K study - Twins NC_000001.10 - 59149733 Oct 11, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000001.10 - 59149733 Jul 12, 2019 (153)
79 ALFA NC_000001.11 - 58684061 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
7424823084 NC_000001.11:58684060:G:A NC_000001.11:58684060:G:A (self)
ss110500360, ss163422295, ss198495751, ss275837948, ss284055540, ss290517282, ss1584556334 NC_000001.9:58922320:G:T NC_000001.11:58684060:G:T (self)
1721548, 940638, 664383, 1513379, 400442, 1094635, 355969, 439257, 919669, 246859, 2037204, 940638, 195332, ss218400900, ss230546503, ss238238997, ss554142753, ss647989525, ss975189598, ss1067909055, ss1290999656, ss1425817812, ss1574079755, ss1600232571, ss1643226604, ss1794410592, ss1918397327, ss1966752417, ss2019715365, ss2147730505, ss2624371307, ss2697644302, ss2755444306, ss2986860349, ss3343467043, ss3654926135, ss3727071104, ss3746239396, ss3826186166, ss3848902689, ss3893917241, ss5144067897, ss5318895932, ss5505860736, ss5625582227, ss5831995449, ss5937417375 NC_000001.10:59149732:G:T NC_000001.11:58684060:G:T (self)
2209216, 12147853, 2710802, 14271644, 7424823084, ss2162726452, ss3023618538, ss3646668602, ss3686824910, ss3799246735, ss4450665309, ss5242361539, ss5443413605, ss5514683281, ss5668873698, ss5800620466, ss5848917938, ss5908367777 NC_000001.11:58684060:G:T NC_000001.11:58684060:G:T (self)
ss9819585, ss11111826 NT_032977.5:11598643:G:T NC_000001.11:58684060:G:T (self)
ss15441481, ss43887189, ss99210106, ss106568741, ss138931560 NT_032977.9:29121650:G:T NC_000001.11:58684060: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 rs6587837

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