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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.

rs3107

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:20279975 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.242064 (64072/264690, TOPMED)
G=0.16356 (12871/78694, PAGE_STUDY)
G=0.34413 (7489/21762, ALFA) (+ 15 more)
G=0.02291 (384/16760, 8.3KJPN)
G=0.1847 (925/5008, 1000G)
G=0.2957 (1324/4478, Estonian)
G=0.3324 (1281/3854, ALSPAC)
G=0.3126 (1159/3708, TWINSUK)
G=0.0341 (100/2930, KOREAN)
G=0.0404 (74/1832, Korea1K)
G=0.347 (346/998, GoNL)
G=0.288 (173/600, NorthernSweden)
G=0.124 (66/532, SGDP_PRJ)
G=0.329 (71/216, Qatari)
G=0.093 (20/216, Vietnamese)
G=0.13 (7/54, Siberian)
G=0.50 (20/40, GENOME_DK)
T=0.50 (20/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.20279975G>C
GRCh38.p13 chr 1 NC_000001.11:g.20279975G>T
GRCh37.p13 chr 1 NC_000001.10:g.20606468G>C
GRCh37.p13 chr 1 NC_000001.10:g.20606468G>T
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 21762 G=0.34413 C=0.00000, T=0.65587
European Sub 18638 G=0.36179 C=0.00000, T=0.63821
African Sub 1350 G=0.1526 C=0.0000, T=0.8474
African Others Sub 40 G=0.12 C=0.00, T=0.88
African American Sub 1310 G=0.1534 C=0.0000, T=0.8466
Asian Sub 54 G=0.02 C=0.00, T=0.98
East Asian Sub 50 G=0.02 C=0.00, T=0.98
Other Asian Sub 4 G=0.0 C=0.0, T=1.0
Latin American 1 Sub 42 G=0.62 C=0.00, T=0.38
Latin American 2 Sub 122 G=0.385 C=0.000, T=0.615
South Asian Sub 30 G=0.40 C=0.00, T=0.60
Other Sub 1526 G=0.2975 C=0.0000, T=0.7025


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=0.242064 T=0.757936
The PAGE Study Global Study-wide 78694 G=0.16356 T=0.83644
The PAGE Study AfricanAmerican Sub 32514 G=0.13653 T=0.86347
The PAGE Study Mexican Sub 10808 G=0.19994 T=0.80006
The PAGE Study Asian Sub 8318 G=0.0373 T=0.9627
The PAGE Study PuertoRican Sub 7916 G=0.2695 T=0.7305
The PAGE Study NativeHawaiian Sub 4534 G=0.1045 T=0.8955
The PAGE Study Cuban Sub 4228 G=0.3098 T=0.6902
The PAGE Study Dominican Sub 3828 G=0.1962 T=0.8038
The PAGE Study CentralAmerican Sub 2450 G=0.1637 T=0.8363
The PAGE Study SouthAmerican Sub 1982 G=0.1988 T=0.8012
The PAGE Study NativeAmerican Sub 1260 G=0.2500 T=0.7500
The PAGE Study SouthAsian Sub 856 G=0.214 T=0.786
8.3KJPN JAPANESE Study-wide 16760 G=0.02291 T=0.97709
1000Genomes Global Study-wide 5008 G=0.1847 T=0.8153
1000Genomes African Sub 1322 G=0.0998 T=0.9002
1000Genomes East Asian Sub 1008 G=0.0883 T=0.9117
1000Genomes Europe Sub 1006 G=0.3479 T=0.6521
1000Genomes South Asian Sub 978 G=0.212 T=0.788
1000Genomes American Sub 694 G=0.212 T=0.788
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.2957 T=0.7043
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3324 T=0.6676
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3126 T=0.6874
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0341 C=0.0000, T=0.9659
Korean Genome Project KOREAN Study-wide 1832 G=0.0404 T=0.9596
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.347 T=0.653
Northern Sweden ACPOP Study-wide 600 G=0.288 T=0.712
SGDP_PRJ Global Study-wide 532 G=0.124 T=0.876
Qatari Global Study-wide 216 G=0.329 T=0.671
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.093 T=0.907
Siberian Global Study-wide 54 G=0.13 T=0.87
The Danish reference pan genome Danish Study-wide 40 G=0.50 T=0.50
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= C T
GRCh38.p13 chr 1 NC_000001.11:g.20279975= NC_000001.11:g.20279975G>C NC_000001.11:g.20279975G>T
GRCh37.p13 chr 1 NC_000001.10:g.20606468= NC_000001.10:g.20606468G>C NC_000001.10:g.20606468G>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#.

81 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss3138 Sep 19, 2000 (36)
2 WI_SSAHASNP ss6407020 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9864856 Jul 11, 2003 (116)
4 SSAHASNP ss20560715 Apr 05, 2004 (121)
5 HGSV ss82396750 Dec 15, 2007 (130)
6 HGSV ss84708053 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss87281736 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97923608 Feb 05, 2009 (130)
9 BGI ss102725548 Dec 01, 2009 (131)
10 1000GENOMES ss110153185 Jan 24, 2009 (130)
11 ENSEMBL ss137833225 Dec 01, 2009 (131)
12 ENSEMBL ss139090428 Dec 01, 2009 (131)
13 GMI ss154734436 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss163154714 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss163936318 Jul 04, 2010 (132)
16 BUSHMAN ss198131983 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss205121892 Jul 04, 2010 (132)
18 1000GENOMES ss218272299 Jul 14, 2010 (132)
19 1000GENOMES ss230453717 Jul 14, 2010 (132)
20 1000GENOMES ss238163613 Jul 15, 2010 (132)
21 BL ss252966693 May 09, 2011 (134)
22 GMI ss275744557 May 04, 2012 (137)
23 GMI ss284014358 Apr 25, 2013 (138)
24 PJP ss290781586 May 09, 2011 (134)
25 ILLUMINA ss482207076 May 04, 2012 (137)
26 ILLUMINA ss483242768 May 04, 2012 (137)
27 ILLUMINA ss535461332 Sep 08, 2015 (146)
28 TISHKOFF ss553866821 Apr 25, 2013 (138)
29 SSMP ss647625442 Apr 25, 2013 (138)
30 ILLUMINA ss780204412 Sep 08, 2015 (146)
31 ILLUMINA ss782064896 Sep 08, 2015 (146)
32 ILLUMINA ss835689086 Sep 08, 2015 (146)
33 EVA-GONL ss974923826 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067719245 Aug 21, 2014 (142)
35 1000GENOMES ss1289949175 Aug 21, 2014 (142)
36 DDI ss1425737980 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1573927387 Apr 01, 2015 (144)
38 EVA_DECODE ss1584281965 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1599681939 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1642675972 Apr 01, 2015 (144)
41 HAMMER_LAB ss1794027156 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1918135577 Feb 12, 2016 (147)
43 ILLUMINA ss1958250130 Feb 12, 2016 (147)
44 GENOMED ss1966700320 Jul 19, 2016 (147)
45 JJLAB ss2019579478 Sep 14, 2016 (149)
46 USC_VALOUEV ss2147582971 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2160547772 Dec 20, 2016 (150)
48 TOPMED ss2322730061 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624306042 Nov 08, 2017 (151)
50 ILLUMINA ss2632486918 Nov 08, 2017 (151)
51 GRF ss2697487476 Nov 08, 2017 (151)
52 SWEGEN ss2986429323 Nov 08, 2017 (151)
53 ILLUMINA ss3021063527 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3023554844 Nov 08, 2017 (151)
55 TOPMED ss3070350357 Nov 08, 2017 (151)
56 CSHL ss3343356649 Nov 08, 2017 (151)
57 ILLUMINA ss3626042979 Oct 11, 2018 (152)
58 ILLUMINA ss3630524724 Oct 11, 2018 (152)
59 ILLUMINA ss3641576656 Oct 11, 2018 (152)
60 URBANLAB ss3646616926 Oct 11, 2018 (152)
61 ILLUMINA ss3651388450 Oct 11, 2018 (152)
62 EGCUT_WGS ss3654499587 Jul 12, 2019 (153)
63 EVA_DECODE ss3686300623 Jul 12, 2019 (153)
64 ILLUMINA ss3725003449 Jul 12, 2019 (153)
65 ACPOP ss3726850231 Jul 12, 2019 (153)
66 EVA ss3745913880 Jul 12, 2019 (153)
67 PAGE_CC ss3770791222 Jul 12, 2019 (153)
68 PACBIO ss3783346332 Jul 12, 2019 (153)
69 PACBIO ss3789016993 Jul 12, 2019 (153)
70 PACBIO ss3793889463 Jul 12, 2019 (153)
71 KHV_HUMAN_GENOMES ss3798934105 Jul 12, 2019 (153)
72 EVA ss3826059335 Apr 25, 2020 (154)
73 EVA ss3836417724 Apr 25, 2020 (154)
74 EVA ss3841822149 Apr 25, 2020 (154)
75 SGDP_PRJ ss3848359610 Apr 25, 2020 (154)
76 KRGDB ss3893267997 Apr 25, 2020 (154)
77 KOGIC ss3943984384 Apr 25, 2020 (154)
78 GNOMAD ss3989452188 Apr 27, 2021 (155)
79 GNOMAD ss3989452190 Apr 27, 2021 (155)
80 TOPMED ss4441382653 Apr 27, 2021 (155)
81 TOMMO_GENOMICS ss5142823816 Apr 27, 2021 (155)
82 1000Genomes NC_000001.10 - 20606468 Oct 11, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 20606468 Oct 11, 2018 (152)
84 Genetic variation in the Estonian population NC_000001.10 - 20606468 Oct 11, 2018 (152)
85 The Danish reference pan genome NC_000001.10 - 20606468 Apr 25, 2020 (154)
86 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4402288 (NC_000001.11:20279974:G:C 1/139966)
Row 4402290 (NC_000001.11:20279974:G:T 104641/139898)

- Apr 27, 2021 (155)
87 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4402288 (NC_000001.11:20279974:G:C 1/139966)
Row 4402290 (NC_000001.11:20279974:G:T 104641/139898)

- Apr 27, 2021 (155)
88 Genome of the Netherlands Release 5 NC_000001.10 - 20606468 Apr 25, 2020 (154)
89 KOREAN population from KRGDB NC_000001.10 - 20606468 Apr 25, 2020 (154)
90 Korean Genome Project NC_000001.11 - 20279975 Apr 25, 2020 (154)
91 Northern Sweden NC_000001.10 - 20606468 Jul 12, 2019 (153)
92 The PAGE Study NC_000001.11 - 20279975 Jul 12, 2019 (153)
93 Qatari NC_000001.10 - 20606468 Apr 25, 2020 (154)
94 SGDP_PRJ NC_000001.10 - 20606468 Apr 25, 2020 (154)
95 Siberian NC_000001.10 - 20606468 Apr 25, 2020 (154)
96 8.3KJPN NC_000001.10 - 20606468 Apr 27, 2021 (155)
97 TopMed NC_000001.11 - 20279975 Apr 27, 2021 (155)
98 UK 10K study - Twins NC_000001.10 - 20606468 Oct 11, 2018 (152)
99 A Vietnamese Genetic Variation Database NC_000001.10 - 20606468 Jul 12, 2019 (153)
100 ALFA NC_000001.11 - 20279975 Apr 27, 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)
rs59408842 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
445391, ss3893267997 NC_000001.10:20606467:G:C NC_000001.11:20279974:G:C (self)
11280279111, ss3989452188 NC_000001.11:20279974:G:C NC_000001.11:20279974:G:C
ss82396750, ss84708053 NC_000001.8:20351773:G:T NC_000001.11:20279974:G:T (self)
ss87281736, ss110153185, ss163154714, ss163936318, ss198131983, ss205121892, ss252966693, ss275744557, ss284014358, ss290781586, ss482207076, ss1584281965 NC_000001.9:20479054:G:T NC_000001.11:20279974:G:T (self)
634096, 333810, 237835, 1417143, 145098, 445391, 135096, 177507, 376590, 99325, 793123, 333810, 71672, ss218272299, ss230453717, ss238163613, ss483242768, ss535461332, ss553866821, ss647625442, ss780204412, ss782064896, ss835689086, ss974923826, ss1067719245, ss1289949175, ss1425737980, ss1573927387, ss1599681939, ss1642675972, ss1794027156, ss1918135577, ss1958250130, ss1966700320, ss2019579478, ss2147582971, ss2322730061, ss2624306042, ss2632486918, ss2697487476, ss2986429323, ss3021063527, ss3343356649, ss3626042979, ss3630524724, ss3641576656, ss3651388450, ss3654499587, ss3726850231, ss3745913880, ss3783346332, ss3789016993, ss3793889463, ss3826059335, ss3836417724, ss3848359610, ss3893267997, ss5142823816 NC_000001.10:20606467:G:T NC_000001.11:20279974:G:T (self)
362385, 12691, 3134956, 4988988, 11280279111, ss2160547772, ss3023554844, ss3070350357, ss3646616926, ss3686300623, ss3725003449, ss3770791222, ss3798934105, ss3841822149, ss3943984384, ss3989452190, ss4441382653 NC_000001.11:20279974:G:T NC_000001.11:20279974:G:T (self)
ss9864856 NT_004610.15:1409717:G:T NC_000001.11:20279974:G:T (self)
ss20560715 NT_004610.16:1409717:G:T NC_000001.11:20279974:G:T (self)
ss3138, ss6407020, ss97923608, ss102725548, ss137833225, ss139090428, ss154734436 NT_004610.19:7286555:G:T NC_000001.11:20279974: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 rs3107

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