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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs3806624

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:27723132 (GRCh38.p7) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.38255 (48036/125568, TOPMED)
A=0.3994 (12240/30648, GnomAD)
A=0.263 (1315/5008, 1000G) (+ 2 more)
G=0.457 (1762/3854, ALSPAC)
G=0.456 (1690/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EOMES : 2KB Upstream Variant
Publications
5 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.p7 chr 3 NC_000003.12:g.27723132A>G
GRCh37.p13 chr 3 NC_000003.11:g.27764623A>G
EOMES RefSeqGene NG_042182.1:g.4584T>C
Gene: EOMES, eomesodermin (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
EOMES transcript variant 1 NM_001278182.1:c. N/A Upstream Transcript Variant
EOMES transcript variant 3 NM_001278183.1:c. N/A Upstream Transcript Variant
EOMES transcript variant 2 NM_005442.3:c. N/A Upstream Transcript Variant
EOMES transcript variant X1 XM_005265510.3:c. N/A Upstream 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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.38255 G=0.61745
The Genome Aggregation Database Global Study-wide 30648 A=0.3994 G=0.6006
The Genome Aggregation Database European Sub 18250 A=0.5321 G=0.4679
The Genome Aggregation Database African Sub 8690 A=0.165 G=0.835
The Genome Aggregation Database East Asian Sub 1612 A=0.168 G=0.832
The Genome Aggregation Database Other Sub 960 A=0.45 G=0.55
The Genome Aggregation Database American Sub 834 A=0.28 G=0.72
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.51 G=0.49
1000Genomes Global Study-wide 5008 A=0.263 G=0.737
1000Genomes African Sub 1322 A=0.125 G=0.875
1000Genomes East Asian Sub 1008 A=0.151 G=0.849
1000Genomes Europe Sub 1006 A=0.533 G=0.467
1000Genomes South Asian Sub 978 A=0.22 G=0.78
1000Genomes American Sub 694 A=0.35 G=0.65
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.543 G=0.457
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.544 G=0.456
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= G Note
GRCh38.p7 chr 3 NC_000003.12:g.27723132A= NC_000003.12:g.27723132A>G
GRCh37.p13 chr 3 NC_000003.11:g.27764623A= NC_000003.11:g.27764623A>G
EOMES RefSeqGene NG_042182.1:g.4584T= NG_042182.1:g.4584T>C
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#.

5 Frequency, 101 SubSNP submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4993017 Aug 28, 2002 (107)
2 BCM_SSAHASNP ss14238235 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss19549480 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss20182539 Feb 27, 2004 (120)
5 SSAHASNP ss22003273 Apr 05, 2004 (123)
6 ABI ss44377650 Mar 14, 2006 (126)
7 ILLUMINA ss65760038 Oct 16, 2006 (127)
8 ILLUMINA ss67305089 Dec 01, 2006 (127)
9 ILLUMINA ss67710205 Dec 01, 2006 (127)
10 ILLUMINA ss68222248 Dec 12, 2006 (127)
11 PERLEGEN ss68856974 May 18, 2007 (127)
12 ILLUMINA ss70783742 May 24, 2008 (130)
13 ILLUMINA ss71360395 May 18, 2007 (127)
14 ILLUMINA ss74950639 Dec 06, 2007 (129)
15 HGSV ss81201176 Dec 15, 2007 (130)
16 KRIBB_YJKIM ss84192186 Dec 15, 2007 (130)
17 HGSV ss84312313 Dec 15, 2007 (130)
18 HUMANGENOME_JCVI ss95996091 Feb 05, 2009 (130)
19 BGI ss103921846 Dec 01, 2009 (131)
20 SNP500CANCER ss105435440 Feb 05, 2009 (130)
21 1000GENOMES ss109938535 Jan 24, 2009 (130)
22 1000GENOMES ss111456888 Jan 25, 2009 (130)
23 ILLUMINA-UK ss117023742 Feb 14, 2009 (130)
24 ENSEMBL ss135355782 Dec 01, 2009 (131)
25 ILLUMINA ss154271384 Dec 01, 2009 (131)
26 ILLUMINA ss159448117 Dec 01, 2009 (131)
27 ILLUMINA ss160644962 Dec 01, 2009 (131)
28 COMPLETE_GENOMICS ss161985543 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss163253973 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss166335592 Jul 04, 2010 (132)
31 ILLUMINA ss173647403 Jul 04, 2010 (132)
32 BUSHMAN ss202328712 Jul 04, 2010 (132)
33 BCM-HGSC-SUB ss206201809 Jul 04, 2010 (132)
34 1000GENOMES ss220049132 Jul 14, 2010 (132)
35 1000GENOMES ss231757875 Jul 14, 2010 (132)
36 1000GENOMES ss239182959 Jul 15, 2010 (132)
37 BL ss253003712 May 09, 2011 (134)
38 GMI ss277062351 May 04, 2012 (137)
39 GMI ss284617603 Apr 25, 2013 (138)
40 PJP ss293030001 May 09, 2011 (134)
41 ILLUMINA ss480843416 May 04, 2012 (137)
42 ILLUMINA ss480860476 May 04, 2012 (137)
43 ILLUMINA ss481794509 Sep 08, 2015 (146)
44 ILLUMINA ss485216593 May 04, 2012 (137)
45 ILLUMINA ss537197736 Sep 08, 2015 (146)
46 TISHKOFF ss556507312 Apr 25, 2013 (138)
47 SSMP ss650178979 Apr 25, 2013 (138)
48 ILLUMINA ss778897430 Sep 08, 2015 (146)
49 ILLUMINA ss783054254 Sep 08, 2015 (146)
50 ILLUMINA ss784012641 Sep 08, 2015 (146)
51 ILLUMINA ss832312143 Sep 08, 2015 (146)
52 ILLUMINA ss834358637 Sep 08, 2015 (146)
53 EVA-GONL ss978408488 Aug 21, 2014 (142)
54 JMKIDD_LAB ss1070275506 Aug 21, 2014 (142)
55 1000GENOMES ss1303303243 Aug 21, 2014 (142)
56 DDI ss1429368663 Apr 01, 2015 (144)
57 EVA_GENOME_DK ss1579896827 Apr 01, 2015 (144)
58 EVA_DECODE ss1587873164 Apr 01, 2015 (144)
59 EVA_UK10K_ALSPAC ss1606688016 Apr 01, 2015 (144)
60 EVA_UK10K_TWINSUK ss1649682049 Apr 01, 2015 (144)
61 EVA_SVP ss1712562977 Apr 01, 2015 (144)
62 ILLUMINA ss1752464171 Sep 08, 2015 (146)
63 HAMMER_LAB ss1799041857 Sep 08, 2015 (146)
64 WEILL_CORNELL_DGM ss1921655159 Feb 12, 2016 (147)
65 ILLUMINA ss1946077429 Feb 12, 2016 (147)
66 ILLUMINA ss1958547272 Feb 12, 2016 (147)
67 GENOMED ss1969354055 Jul 19, 2016 (147)
68 JJLAB ss2021386334 Sep 14, 2016 (149)
69 ILLUMINA ss2094925165 Dec 20, 2016 (150)
70 ILLUMINA ss2095126958 Dec 20, 2016 (150)
71 ILLUMINA ss2095126959 Dec 20, 2016 (150)
72 USC_VALOUEV ss2149452128 Dec 20, 2016 (150)
73 HUMAN_LONGEVITY ss2250100064 Dec 20, 2016 (150)
74 TOPMED ss2417167944 Dec 20, 2016 (150)
75 SYSTEMSBIOZJU ss2625191401 Nov 08, 2017 (151)
76 ILLUMINA ss2633927922 Nov 08, 2017 (151)
77 ILLUMINA ss2635117648 Nov 08, 2017 (151)
78 GRF ss2704818917 Nov 08, 2017 (151)
79 ILLUMINA ss2710968509 Nov 08, 2017 (151)
80 GNOMAD ss2790937192 Nov 08, 2017 (151)
81 SWEGEN ss2992030740 Nov 08, 2017 (151)
82 ILLUMINA ss3022222783 Nov 08, 2017 (151)
83 BIOINF_KMB_FNS_UNIBA ss3024455543 Nov 08, 2017 (151)
84 CSHL ss3344943439 Nov 08, 2017 (151)
85 TOPMED ss3385894177 Nov 08, 2017 (151)
86 ILLUMINA ss3625810246 Jul 19, 2018 (151)
87 ILLUMINA ss3628618524 Jul 19, 2018 (151)
88 ILLUMINA ss3631875306 Jul 19, 2018 (151)
89 ILLUMINA ss3633286460 Jul 19, 2018 (151)
90 ILLUMINA ss3634003154 Jul 19, 2018 (151)
91 ILLUMINA ss3634885844 Jul 19, 2018 (151)
92 ILLUMINA ss3635687254 Jul 19, 2018 (151)
93 ILLUMINA ss3636582499 Jul 19, 2018 (151)
94 ILLUMINA ss3637439574 Jul 19, 2018 (151)
95 ILLUMINA ss3638404052 Jul 19, 2018 (151)
96 ILLUMINA ss3639205946 Jul 19, 2018 (151)
97 ILLUMINA ss3639904061 Jul 19, 2018 (151)
98 ILLUMINA ss3640593147 Jul 19, 2018 (151)
99 ILLUMINA ss3643361822 Jul 19, 2018 (151)
100 ILLUMINA ss3643951085 Jul 19, 2018 (151)
101 ILLUMINA ss3644809996 Jul 19, 2018 (151)
102 1000Genomes NC_000003.11 - 27764623 Jul 19, 2018 (151)
103 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 27764623 Jul 19, 2018 (151)
104 The Genome Aggregation Database NC_000003.11 - 27764623 Jul 19, 2018 (151)
105 Trans-Omics for Precision Medicine NC_000003.12 - 27723132 Jul 19, 2018 (151)
106 UK 10K study - Twins NC_000003.11 - 27764623 Jul 19, 2018 (151)
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)
rs13092970 Sep 24, 2004 (123)
rs58409036 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss81201176, ss84312313, ss3639205946, ss3639904061, ss3643951085 NC_000003.9:27739626:A= NC_000003.12:27723131:A= (self)
ss109938535, ss111456888, ss117023742, ss161985543, ss163253973, ss166335592, ss202328712, ss206201809, ss253003712, ss277062351, ss284617603, ss293030001, ss480843416, ss1587873164, ss1712562977, ss2094925165, ss2635117648, ss3643361822 NC_000003.10:27739626:A= NC_000003.12:27723131:A= (self)
14465823, 8030294, 131564946, 8030294, ss220049132, ss231757875, ss239182959, ss480860476, ss481794509, ss485216593, ss537197736, ss556507312, ss650178979, ss778897430, ss783054254, ss784012641, ss832312143, ss834358637, ss978408488, ss1070275506, ss1303303243, ss1429368663, ss1579896827, ss1606688016, ss1649682049, ss1752464171, ss1799041857, ss1921655159, ss1946077429, ss1958547272, ss1969354055, ss2021386334, ss2095126958, ss2095126959, ss2149452128, ss2417167944, ss2625191401, ss2633927922, ss2704818917, ss2710968509, ss2790937192, ss2992030740, ss3022222783, ss3344943439, ss3625810246, ss3628618524, ss3631875306, ss3633286460, ss3634003154, ss3634885844, ss3635687254, ss3636582499, ss3637439574, ss3638404052, ss3640593147, ss3644809996 NC_000003.11:27764622:A= NC_000003.12:27723131:A= (self)
247354308, ss2250100064, ss3024455543, ss3385894177 NC_000003.12:27723131:A= NC_000003.12:27723131:A= (self)
ss14238235, ss19549480, ss20182539, ss22003273 NT_022517.16:27704587:A= NC_000003.12:27723131:A= (self)
ss4993017, ss44377650, ss65760038, ss67305089, ss67710205, ss68222248, ss68856974, ss70783742, ss71360395, ss74950639, ss84192186, ss95996091, ss103921846, ss105435440, ss135355782, ss154271384, ss159448117, ss160644962, ss173647403 NT_022517.18:27704622:A= NC_000003.12:27723131:A= (self)
ss81201176, ss84312313, ss3639205946, ss3639904061, ss3643951085 NC_000003.9:27739626:A>G NC_000003.12:27723131:A>G (self)
ss109938535, ss111456888, ss117023742, ss161985543, ss163253973, ss166335592, ss202328712, ss206201809, ss253003712, ss277062351, ss284617603, ss293030001, ss480843416, ss1587873164, ss1712562977, ss2094925165, ss2635117648, ss3643361822 NC_000003.10:27739626:A>G NC_000003.12:27723131:A>G (self)
14465823, 8030294, 131564946, 8030294, ss220049132, ss231757875, ss239182959, ss480860476, ss481794509, ss485216593, ss537197736, ss556507312, ss650178979, ss778897430, ss783054254, ss784012641, ss832312143, ss834358637, ss978408488, ss1070275506, ss1303303243, ss1429368663, ss1579896827, ss1606688016, ss1649682049, ss1752464171, ss1799041857, ss1921655159, ss1946077429, ss1958547272, ss1969354055, ss2021386334, ss2095126958, ss2095126959, ss2149452128, ss2417167944, ss2625191401, ss2633927922, ss2704818917, ss2710968509, ss2790937192, ss2992030740, ss3022222783, ss3344943439, ss3625810246, ss3628618524, ss3631875306, ss3633286460, ss3634003154, ss3634885844, ss3635687254, ss3636582499, ss3637439574, ss3638404052, ss3640593147, ss3644809996 NC_000003.11:27764622:A>G NC_000003.12:27723131:A>G (self)
247354308, ss2250100064, ss3024455543, ss3385894177 NC_000003.12:27723131:A>G NC_000003.12:27723131:A>G (self)
ss14238235, ss19549480, ss20182539, ss22003273 NT_022517.16:27704587:A>G NC_000003.12:27723131:A>G (self)
ss4993017, ss44377650, ss65760038, ss67305089, ss67710205, ss68222248, ss68856974, ss70783742, ss71360395, ss74950639, ss84192186, ss95996091, ss103921846, ss105435440, ss135355782, ss154271384, ss159448117, ss160644962, ss173647403 NT_022517.18:27704622:A>G NC_000003.12:27723131:A>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

5 citations for rs3806624
PMID Title Author Year Journal
19602281 Regression based predictor for p53 transactivation. Gowrisankar S et al. 2009 BMC bioinformatics
20817676 Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements. Bandele OJ et al. 2011 Nucleic acids research
24149102 Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma. Frampton M et al. 2013 Nature communications
26405224 Familial predisposition and genetic risk factors for lymphoma. Cerhan JR et al. 2015 Blood
26956414 Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia. Berndt SI et al. 2016 Nature communications

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: 0.1.4.post833+d3ba21e