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dbSNP Short Genetic Variations

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.

rs2541386

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:216801959 (GRCh38.p12) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.02131 (2676/125568, TOPMED)
T=0.0203 (628/30980, GnomAD)
T=0.026 (131/5008, 1000G) (+ 2 more)
T=0.001 (3/3854, ALSPAC)
T=0.000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101928278 : 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.p12 chr 2 NC_000002.12:g.216801959T>C
GRCh37.p13 chr 2 NC_000002.11:g.217666682T>C
Gene: LOC101928278, uncharacterized LOC101928278 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928278 transcript variant X1 XR_001739169.1:n.3014T>C N/A Non Coding Transcript Variant
LOC101928278 transcript variant X2 XR_001739170.2:n. N/A Genic Upstream Transcript Variant
LOC101928278 transcript variant X3 XR_001739171.2:n. N/A Genic 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
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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
TopMed Global Study-wide 125568 T=0.02131 C=0.97869
gnomAD - Genomes Global Study-wide 30980 T=0.0203 C=0.9797
gnomAD - Genomes European Sub 18506 T=0.0003 C=0.9997
gnomAD - Genomes African Sub 8732 T=0.070 C=0.930
gnomAD - Genomes East Asian Sub 1620 T=0.000 C=1.000
gnomAD - Genomes Other Sub 982 T=0.01 C=0.99
gnomAD - Genomes American Sub 838 T=0.00 C=1.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.00 C=1.00
1000Genomes Global Study-wide 5008 T=0.026 C=0.974
1000Genomes African Sub 1322 T=0.095 C=0.905
1000Genomes East Asian Sub 1008 T=0.000 C=1.000
1000Genomes Europe Sub 1006 T=0.000 C=1.000
1000Genomes South Asian Sub 978 T=0.00 C=1.00
1000Genomes American Sub 694 T=0.01 C=0.99
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.001 C=0.999
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.000 C=1.000
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 T= C Note
GRCh38.p12 chr 2 NC_000002.12:g.216801959T= NC_000002.12:g.21680195...

NC_000002.12:g.216801959T>C

GRCh37.p13 chr 2 NC_000002.11:g.217666682T= NC_000002.11:g.21766668...

NC_000002.11:g.217666682T>C

LOC101928278 transcript variant X1 XR_001739169.1:n.3014T= XR_001739169.1:n.3014T>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#.

54 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3562674 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss9973647 Jul 11, 2003 (116)
3 SSAHASNP ss21561630 Apr 05, 2004 (121)
4 AFFY ss66110471 Dec 02, 2006 (127)
5 AFFY ss76089932 Dec 07, 2007 (129)
6 HGSV ss78313649 Dec 07, 2007 (129)
7 KRIBB_YJKIM ss81815036 Dec 16, 2007 (130)
8 HGSV ss83417416 Dec 16, 2007 (130)
9 BCMHGSC_JDW ss91546583 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss96472231 Feb 06, 2009 (130)
11 BGI ss106160880 Feb 06, 2009 (130)
12 1000GENOMES ss110762530 Jan 25, 2009 (130)
13 1000GENOMES ss111653316 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118078023 Feb 14, 2009 (130)
15 ENSEMBL ss135969338 Dec 01, 2009 (131)
16 ENSEMBL ss138630421 Dec 01, 2009 (131)
17 GMI ss154709014 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss165483446 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss165904592 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss167572845 Jul 04, 2010 (132)
21 AFFY ss172468509 Jul 04, 2010 (132)
22 BUSHMAN ss201739454 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss205609463 Jul 04, 2010 (132)
24 1000GENOMES ss219812838 Jul 14, 2010 (132)
25 1000GENOMES ss231586785 Jul 14, 2010 (132)
26 1000GENOMES ss239045331 Jul 15, 2010 (132)
27 BL ss253877099 May 09, 2011 (134)
28 GMI ss276898146 May 04, 2012 (137)
29 GMI ss284541653 Apr 25, 2013 (138)
30 PJP ss292487570 May 09, 2011 (134)
31 TISHKOFF ss556219782 Apr 25, 2013 (138)
32 SSMP ss649885762 Apr 25, 2013 (138)
33 JMKIDD_LAB ss1069941690 Aug 21, 2014 (142)
34 1000GENOMES ss1301647793 Aug 21, 2014 (142)
35 DDI ss1428911333 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1579323435 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1605794329 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1648788362 Apr 01, 2015 (144)
39 EVA_SVP ss1712530769 Apr 01, 2015 (144)
40 HAMMER_LAB ss1798356884 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1921206122 Feb 12, 2016 (147)
42 GENOMED ss1969025214 Jul 19, 2016 (147)
43 JJLAB ss2021151347 Sep 14, 2016 (149)
44 USC_VALOUEV ss2149212877 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2239155473 Dec 20, 2016 (150)
46 TOPMED ss2405613168 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2625075005 Nov 08, 2017 (151)
48 GRF ss2703861823 Nov 08, 2017 (151)
49 GNOMAD ss2786338255 Nov 08, 2017 (151)
50 SWEGEN ss2991359314 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3024333632 Nov 08, 2017 (151)
52 TOPMED ss3338421097 Nov 08, 2017 (151)
53 CSHL ss3344741677 Nov 08, 2017 (151)
54 URBANLAB ss3647274306 Oct 11, 2018 (152)
55 1000Genomes NC_000002.11 - 217666682 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 217666682 Oct 11, 2018 (152)
57 gnomAD - Genomes NC_000002.11 - 217666682 Oct 11, 2018 (152)
58 TopMed NC_000002.12 - 216801959 Oct 11, 2018 (152)
59 UK 10K study - Twins NC_000002.11 - 217666682 Oct 11, 2018 (152)
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)
rs61049410 Feb 27, 2009 (130)
rs61477441 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78313649, ss83417416 NC_000002.9:217492187:T:C NC_000002.12:216801958:T:C (self)
ss91546583, ss110762530, ss111653316, ss118078023, ss165483446, ss165904592, ss167572845, ss201739454, ss205609463, ss253877099, ss276898146, ss284541653, ss292487570, ss1712530769 NC_000002.10:217374926:T:C NC_000002.12:216801958:T:C (self)
12753084, 7052606, 115828116, 7052606, ss219812838, ss231586785, ss239045331, ss556219782, ss649885762, ss1069941690, ss1301647793, ss1428911333, ss1579323435, ss1605794329, ss1648788362, ss1798356884, ss1921206122, ss1969025214, ss2021151347, ss2149212877, ss2405613168, ss2625075005, ss2703861823, ss2786338255, ss2991359314, ss3344741677 NC_000002.11:217666681:T:C NC_000002.12:216801958:T:C (self)
217534344, ss2239155473, ss3024333632, ss3338421097, ss3647274306 NC_000002.12:216801958:T:C NC_000002.12:216801958:T:C (self)
ss9973647 NT_005403.13:67826017:T:C NC_000002.12:216801958:T:C (self)
ss21561630 NT_005403.14:67876096:T:C NC_000002.12:216801958:T:C (self)
ss3562674, ss66110471, ss76089932, ss81815036, ss96472231, ss106160880, ss135969338, ss138630421, ss154709014, ss172468509 NT_005403.17:67876099:T:C NC_000002.12:216801958:T:C (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 rs2541386

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.post104+4a6ee9c