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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.

rs3115859

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:819123 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.30805 (5163/16760, 8.3KJPN)
G=0.3965 (2425/6116, ALFA)
G=0.3361 (1683/5008, 1000G) (+ 10 more)
G=0.1536 (592/3854, ALSPAC)
G=0.1572 (583/3708, TWINSUK)
G=0.3147 (922/2930, KOREAN)
G=0.173 (173/998, GoNL)
G=0.148 (89/600, NorthernSweden)
G=0.235 (114/486, SGDP_PRJ)
G=0.264 (57/216, Qatari)
G=0.264 (56/212, Vietnamese)
G=0.19 (10/52, Siberian)
G=0.05 (2/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FAM87B : Non Coding Transcript 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.819123G>A
GRCh38.p13 chr 1 NC_000001.11:g.819123G>C
GRCh38.p13 chr 1 NC_000001.11:g.819123G>T
GRCh37.p13 chr 1 NC_000001.10:g.754503G>A
GRCh37.p13 chr 1 NC_000001.10:g.754503G>C
GRCh37.p13 chr 1 NC_000001.10:g.754503G>T
Gene: FAM87B, family with sequence similarity 87 member B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
FAM87B transcript NR_103536.1:n.1233G>A N/A Non Coding Transcript Variant
FAM87B transcript NR_103536.1:n.1233G>C N/A Non Coding Transcript Variant
FAM87B transcript NR_103536.1:n.1233G>T N/A Non Coding Transcript 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 6116 G=0.3965 A=0.6035, C=0.0000, T=0.0000
European Sub 4734 G=0.2537 A=0.7463, C=0.0000, T=0.0000
African Sub 1060 G=0.9849 A=0.0151, C=0.0000, T=0.0000
African Others Sub 52 G=1.00 A=0.00, C=0.00, T=0.00
African American Sub 1008 G=0.9841 A=0.0159, C=0.0000, T=0.0000
Asian Sub 4 G=1.0 A=0.0, C=0.0, T=0.0
East Asian Sub 4 G=1.0 A=0.0, C=0.0, T=0.0
Other Asian Sub 0 G=0 A=0, C=0, T=0
Latin American 1 Sub 18 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 50 G=1.00 A=0.00, C=0.00, T=0.00
South Asian Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
Other Sub 248 G=0.427 A=0.573, 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
8.3KJPN JAPANESE Study-wide 16760 G=0.30805 A=0.69195
1000Genomes Global Study-wide 5008 G=0.3361 A=0.6639
1000Genomes African Sub 1322 G=0.6626 A=0.3374
1000Genomes East Asian Sub 1008 G=0.2371 A=0.7629
1000Genomes Europe Sub 1006 G=0.1610 A=0.8390
1000Genomes South Asian Sub 978 G=0.229 A=0.771
1000Genomes American Sub 694 G=0.262 A=0.738
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.1536 A=0.8464
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1572 A=0.8428
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.3147 A=0.6853
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.173 A=0.827
Northern Sweden ACPOP Study-wide 600 G=0.148 A=0.852
SGDP_PRJ Global Study-wide 486 G=0.235 A=0.765
Qatari Global Study-wide 216 G=0.264 A=0.736
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.264 A=0.736
Siberian Global Study-wide 52 G=0.19 A=0.81
The Danish reference pan genome Danish Study-wide 40 G=0.05 A=0.95
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.p13 chr 1 NC_000001.11:g.819123= NC_000001.11:g.819123G>A NC_000001.11:g.819123G>C NC_000001.11:g.819123G>T
GRCh37.p13 chr 1 NC_000001.10:g.754503= NC_000001.10:g.754503G>A NC_000001.10:g.754503G>C NC_000001.10:g.754503G>T
FAM87B transcript NR_103536.1:n.1233= NR_103536.1:n.1233G>A NR_103536.1:n.1233G>C NR_103536.1:n.1233G>T
FLJ40008 transcript NM_207464.1:c.*614A>G NM_207464.1:c.*614= NM_207464.1:c.*614A>C NM_207464.1:c.*614A>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#.

63 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4358509 Mar 26, 2002 (103)
2 CSHL-HAPMAP ss16441556 Feb 27, 2004 (120)
3 HGSV ss79007220 Dec 07, 2007 (129)
4 HGSV ss83141195 Dec 15, 2007 (130)
5 HGSV ss83444268 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss87155685 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss97913189 Feb 05, 2009 (130)
8 BGI ss105111654 Dec 01, 2009 (131)
9 1000GENOMES ss107938266 Jan 22, 2009 (130)
10 1000GENOMES ss109937206 Jan 24, 2009 (130)
11 ILLUMINA-UK ss118438224 Feb 14, 2009 (130)
12 ENSEMBL ss137752195 Dec 01, 2009 (131)
13 ENSEMBL ss138898847 Dec 01, 2009 (131)
14 GMI ss154522307 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162980837 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss165981009 Jul 04, 2010 (132)
17 BUSHMAN ss197885397 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205215402 Jul 04, 2010 (132)
19 1000GENOMES ss218190369 Jul 14, 2010 (132)
20 1000GENOMES ss230395432 Jul 14, 2010 (132)
21 1000GENOMES ss238114958 Jul 15, 2010 (132)
22 BL ss252864071 May 09, 2011 (134)
23 GMI ss275680755 May 04, 2012 (137)
24 GMI ss283987360 Apr 25, 2013 (138)
25 PJP ss290493769 May 09, 2011 (134)
26 TISHKOFF ss553710359 Apr 25, 2013 (138)
27 SSMP ss647516088 Apr 25, 2013 (138)
28 EVA-GONL ss974769238 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1067612329 Aug 21, 2014 (142)
30 1000GENOMES ss1289338860 Aug 21, 2014 (142)
31 DDI ss1425684797 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1573851134 Apr 01, 2015 (144)
33 EVA_DECODE ss1584129436 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1599378278 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1642372311 Apr 01, 2015 (144)
36 HAMMER_LAB ss1793705695 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1917960146 Feb 12, 2016 (147)
38 GENOMED ss1966667319 Jul 19, 2016 (147)
39 JJLAB ss2019498345 Sep 14, 2016 (149)
40 USC_VALOUEV ss2147484256 Dec 20, 2016 (150)
41 TOPMED ss2321502737 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624264751 Nov 08, 2017 (151)
43 GRF ss2697374449 Nov 08, 2017 (151)
44 GNOMAD ss2750636625 Nov 08, 2017 (151)
45 SWEGEN ss2986148560 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023513708 Nov 08, 2017 (151)
47 TOPMED ss3066396022 Nov 08, 2017 (151)
48 TOPMED ss3066396023 Nov 08, 2017 (151)
49 CSHL ss3343272398 Nov 08, 2017 (151)
50 URBANLAB ss3646581183 Oct 11, 2018 (152)
51 EVA_DECODE ss3685991947 Jul 12, 2019 (153)
52 ACPOP ss3726716187 Jul 12, 2019 (153)
53 EVA ss3745720850 Jul 12, 2019 (153)
54 PACBIO ss3783302103 Jul 12, 2019 (153)
55 PACBIO ss3788979973 Jul 12, 2019 (153)
56 PACBIO ss3793852510 Jul 12, 2019 (153)
57 KHV_HUMAN_GENOMES ss3798743444 Jul 12, 2019 (153)
58 EVA ss3825981423 Apr 25, 2020 (154)
59 EVA ss3836378368 Apr 25, 2020 (154)
60 EVA ss3841782370 Apr 25, 2020 (154)
61 SGDP_PRJ ss3847994768 Apr 25, 2020 (154)
62 KRGDB ss3892835123 Apr 25, 2020 (154)
63 TOMMO_GENOMICS ss5142051001 Apr 25, 2021 (155)
64 1000Genomes NC_000001.10 - 754503 Oct 11, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 754503 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 754503 Apr 25, 2020 (154)
67 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 61059 (NC_000001.11:819122:G:A 94870/139896)
Row 61060 (NC_000001.11:819122:G:T 1/140048)

- Apr 25, 2021 (155)
68 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 61059 (NC_000001.11:819122:G:A 94870/139896)
Row 61060 (NC_000001.11:819122:G:T 1/140048)

- Apr 25, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000001.10 - 754503 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000001.10 - 754503 Apr 25, 2020 (154)
71 Northern Sweden NC_000001.10 - 754503 Jul 12, 2019 (153)
72 Qatari NC_000001.10 - 754503 Apr 25, 2020 (154)
73 SGDP_PRJ NC_000001.10 - 754503 Apr 25, 2020 (154)
74 Siberian NC_000001.10 - 754503 Apr 25, 2020 (154)
75 8.3KJPN NC_000001.10 - 754503 Apr 25, 2021 (155)
76 UK 10K study - Twins NC_000001.10 - 754503 Oct 11, 2018 (152)
77 A Vietnamese Genetic Variation Database NC_000001.10 - 754503 Jul 12, 2019 (153)
78 ALFA NC_000001.11 - 819123 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)
rs59107215 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss79007220, ss83141195, ss83444268 NC_000001.8:794365:G:A NC_000001.11:819122:G:A (self)
ss87155685, ss107938266, ss109937206, ss118438224, ss162980837, ss165981009, ss197885397, ss205215402, ss252864071, ss275680755, ss283987360, ss290493769, ss1584129436 NC_000001.9:744365:G:A NC_000001.11:819122:G:A (self)
3573, 167, 1358368, 311, 12517, 1052, 2076, 11748, 610, 20308, 167, 38, ss218190369, ss230395432, ss238114958, ss553710359, ss647516088, ss974769238, ss1067612329, ss1289338860, ss1425684797, ss1573851134, ss1599378278, ss1642372311, ss1793705695, ss1917960146, ss1966667319, ss2019498345, ss2147484256, ss2321502737, ss2624264751, ss2697374449, ss2750636625, ss2986148560, ss3343272398, ss3726716187, ss3745720850, ss3783302103, ss3788979973, ss3793852510, ss3825981423, ss3836378368, ss3847994768, ss3892835123, ss5142051001 NC_000001.10:754502:G:A NC_000001.11:819122:G:A (self)
10659091674, ss3023513708, ss3066396022, ss3646581183, ss3685991947, ss3798743444, ss3841782370 NC_000001.11:819122:G:A NC_000001.11:819122:G:A (self)
ss4358509, ss97913189, ss105111654, ss137752195, ss138898847, ss154522307 NT_004350.19:233134:G:A NC_000001.11:819122:G:A (self)
ss16441556 NT_034471.3:233134:G:A NC_000001.11:819122:G:A (self)
10659091674, ss3066396023 NC_000001.11:819122:G:C NC_000001.11:819122:G:C (self)
10659091674 NC_000001.11:819122:G:T NC_000001.11:819122:G:T
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 rs3115859

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