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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.

rs2654849

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:99475533 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.43129 (54156/125568, TOPMED)
G=0.4048 (12477/30822, GnomAD)
T=0.479 (2401/5008, 1000G) (+ 2 more)
G=0.379 (1460/3854, ALSPAC)
G=0.365 (1352/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 4 NC_000004.12:g.99475533G>T
GRCh37.p13 chr 4 NC_000004.11:g.100396690G>T
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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 G=0.43129 T=0.56871
The Genome Aggregation Database Global Study-wide 30822 G=0.4048 T=0.5952
The Genome Aggregation Database European Sub 18436 G=0.3471 T=0.6529
The Genome Aggregation Database African Sub 8666 G=0.493 T=0.507
The Genome Aggregation Database East Asian Sub 1608 G=0.609 T=0.391
The Genome Aggregation Database Other Sub 978 G=0.39 T=0.61
The Genome Aggregation Database American Sub 834 G=0.39 T=0.61
The Genome Aggregation Database Ashkenazi Jewish Sub 300 G=0.38 T=0.62
1000Genomes Global Study-wide 5008 G=0.521 T=0.479
1000Genomes African Sub 1322 G=0.514 T=0.486
1000Genomes East Asian Sub 1008 G=0.638 T=0.362
1000Genomes Europe Sub 1006 G=0.379 T=0.621
1000Genomes South Asian Sub 978 G=0.61 T=0.39
1000Genomes American Sub 694 G=0.44 T=0.56
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.379 T=0.621
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.365 T=0.635
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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= T Note
GRCh38.p7 chr 4 NC_000004.12:g.99475533G= NC_000004.12:g.99475533G>T
GRCh37.p13 chr 4 NC_000004.11:g.100396690G= NC_000004.11:g.10039669...

NC_000004.11:g.100396690G>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#.

5 Frequency, 72 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3743653 Sep 28, 2001 (100)
2 TSC-CSHL ss4055450 Nov 05, 2001 (101)
3 CSHL-HAPMAP ss17043877 Feb 27, 2004 (120)
4 PERLEGEN ss23330399 Sep 20, 2004 (123)
5 ABI ss42189809 Mar 13, 2006 (126)
6 ILLUMINA ss67265812 Dec 01, 2006 (127)
7 ILLUMINA ss67665695 Dec 01, 2006 (127)
8 ILLUMINA ss68209274 Dec 12, 2006 (127)
9 ILLUMINA ss70744214 May 26, 2008 (130)
10 ILLUMINA ss71315658 May 17, 2007 (127)
11 ILLUMINA ss75796150 Dec 07, 2007 (129)
12 HGSV ss77295577 Dec 07, 2007 (129)
13 KRIBB_YJKIM ss84065463 Dec 16, 2007 (130)
14 BCMHGSC_JDW ss92704061 Mar 24, 2008 (129)
15 BGI ss104099027 Dec 01, 2009 (131)
16 1000GENOMES ss108172375 Jan 23, 2009 (130)
17 1000GENOMES ss110293579 Jan 24, 2009 (130)
18 ILLUMINA-UK ss117114217 Feb 14, 2009 (130)
19 ENSEMBL ss139783186 Dec 01, 2009 (131)
20 ILLUMINA ss154226087 Dec 01, 2009 (131)
21 GMI ss157652883 Dec 01, 2009 (131)
22 ILLUMINA ss159402599 Dec 01, 2009 (131)
23 ENSEMBL ss161477383 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss162381420 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss163919788 Jul 04, 2010 (132)
26 COMPLETE_GENOMICS ss166946127 Jul 04, 2010 (132)
27 ILLUMINA ss173420090 Jul 04, 2010 (132)
28 BUSHMAN ss198923081 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss206565474 Jul 04, 2010 (132)
30 1000GENOMES ss221099623 Jul 14, 2010 (132)
31 1000GENOMES ss232515890 Jul 14, 2010 (132)
32 1000GENOMES ss239780660 Jul 15, 2010 (132)
33 BL ss253373646 May 09, 2011 (134)
34 GMI ss277845171 May 04, 2012 (137)
35 GMI ss284968187 Apr 25, 2013 (138)
36 PJP ss293147897 May 09, 2011 (134)
37 ILLUMINA ss537113008 Sep 08, 2015 (146)
38 TISHKOFF ss557722357 Apr 25, 2013 (138)
39 SSMP ss651526787 Apr 25, 2013 (138)
40 ILLUMINA ss832914308 Aug 21, 2014 (142)
41 ILLUMINA ss833505138 Aug 21, 2014 (142)
42 EVA-GONL ss980452125 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1071788554 Aug 21, 2014 (142)
44 1000GENOMES ss1310986026 Aug 21, 2014 (142)
45 DDI ss1429983405 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1580688341 Apr 01, 2015 (144)
47 EVA_DECODE ss1589956246 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1610740102 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1653734135 Apr 01, 2015 (144)
50 EVA_SVP ss1712693273 Apr 01, 2015 (144)
51 HAMMER_LAB ss1801912040 Sep 08, 2015 (146)
52 WEILL_CORNELL_DGM ss1923691958 Feb 12, 2016 (147)
53 GENOMED ss1969817339 Jul 19, 2016 (147)
54 JJLAB ss2022432138 Sep 14, 2016 (149)
55 USC_VALOUEV ss2150561326 Dec 20, 2016 (150)
56 HUMAN_LONGEVITY ss2265438898 Dec 20, 2016 (150)
57 TOPMED ss2433257636 Dec 20, 2016 (150)
58 SYSTEMSBIOZJU ss2625715003 Nov 08, 2017 (151)
59 ILLUMINA ss2635135006 Nov 08, 2017 (151)
60 GRF ss2706038023 Nov 08, 2017 (151)
61 GNOMAD ss2812872846 Nov 08, 2017 (151)
62 AFFY ss2985298940 Nov 08, 2017 (151)
63 SWEGEN ss2995213229 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3024991432 Nov 08, 2017 (151)
65 CSHL ss3345862763 Nov 08, 2017 (151)
66 TOPMED ss3437282337 Nov 08, 2017 (151)
67 ILLUMINA ss3629025907 Jul 20, 2018 (151)
68 ILLUMINA ss3638501899 Jul 20, 2018 (151)
69 ILLUMINA ss3639253315 Jul 20, 2018 (151)
70 ILLUMINA ss3639925309 Jul 20, 2018 (151)
71 ILLUMINA ss3643452047 Jul 20, 2018 (151)
72 ILLUMINA ss3643971406 Jul 20, 2018 (151)
73 1000Genomes NC_000004.11 - 100396690 Jul 20, 2018 (151)
74 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 100396690 Jul 20, 2018 (151)
75 The Genome Aggregation Database NC_000004.11 - 100396690 Jul 20, 2018 (151)
76 Trans-Omics for Precision Medicine NC_000004.12 - 99475533 Jul 20, 2018 (151)
77 UK 10K study - Twins NC_000004.11 - 100396690 Jul 20, 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)
rs61249087 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77295577, ss3639253315, ss3639925309, ss3643971406 NC_000004.9:100753867:G= NC_000004.12:99475532:G= (self)
ss92704061, ss108172375, ss110293579, ss117114217, ss162381420, ss163919788, ss166946127, ss198923081, ss206565474, ss253373646, ss277845171, ss284968187, ss293147897, ss1589956246, ss1712693273, ss2635135006, ss3643452047 NC_000004.10:100615712:G= NC_000004.12:99475532:G= (self)
22428420, 12476644, 153500601, 12476644, ss221099623, ss232515890, ss239780660, ss537113008, ss557722357, ss651526787, ss832914308, ss833505138, ss980452125, ss1071788554, ss1310986026, ss1429983405, ss1580688341, ss1610740102, ss1653734135, ss1801912040, ss1923691958, ss1969817339, ss2022432138, ss2150561326, ss2433257636, ss2625715003, ss2706038023, ss2812872846, ss2985298940, ss2995213229, ss3345862763, ss3629025907, ss3638501899 NC_000004.11:100396689:G= NC_000004.12:99475532:G= (self)
288843431, ss2265438898, ss3024991432, ss3437282337 NC_000004.12:99475532:G= NC_000004.12:99475532:G= (self)
ss17043877 NT_016354.16:24891393:G= NC_000004.12:99475532:G= (self)
ss3743653, ss4055450, ss23330399, ss42189809, ss67265812, ss67665695, ss68209274, ss70744214, ss71315658, ss75796150, ss84065463, ss104099027, ss139783186, ss154226087, ss157652883, ss159402599, ss161477383, ss173420090 NT_016354.19:24944410:G= NC_000004.12:99475532:G= (self)
ss77295577, ss3639253315, ss3639925309, ss3643971406 NC_000004.9:100753867:G>T NC_000004.12:99475532:G>T (self)
ss92704061, ss108172375, ss110293579, ss117114217, ss162381420, ss163919788, ss166946127, ss198923081, ss206565474, ss253373646, ss277845171, ss284968187, ss293147897, ss1589956246, ss1712693273, ss2635135006, ss3643452047 NC_000004.10:100615712:G>T NC_000004.12:99475532:G>T (self)
22428420, 12476644, 153500601, 12476644, ss221099623, ss232515890, ss239780660, ss537113008, ss557722357, ss651526787, ss832914308, ss833505138, ss980452125, ss1071788554, ss1310986026, ss1429983405, ss1580688341, ss1610740102, ss1653734135, ss1801912040, ss1923691958, ss1969817339, ss2022432138, ss2150561326, ss2433257636, ss2625715003, ss2706038023, ss2812872846, ss2985298940, ss2995213229, ss3345862763, ss3629025907, ss3638501899 NC_000004.11:100396689:G>T NC_000004.12:99475532:G>T (self)
288843431, ss2265438898, ss3024991432, ss3437282337 NC_000004.12:99475532:G>T NC_000004.12:99475532:G>T (self)
ss17043877 NT_016354.16:24891393:G>T NC_000004.12:99475532:G>T (self)
ss3743653, ss4055450, ss23330399, ss42189809, ss67265812, ss67665695, ss68209274, ss70744214, ss71315658, ss75796150, ss84065463, ss104099027, ss139783186, ss154226087, ss157652883, ss159402599, ss161477383, ss173420090 NT_016354.19:24944410:G>T NC_000004.12:99475532: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.

1 citation for rs2654849
PMID Title Author Year Journal
20158305 Associations between ADH gene variants and alcohol phenotypes in Dutch adults. van Beek JH et al. 2010 Twin research and human genetics

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