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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.

rs11259096

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr10:14436619 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.05809 (12321/212118, GnomAD)
C=0.10840 (13612/125568, TOPMED)
C=0.0909 (5739/63144, ExAC) (+ 6 more)
C=0.1029 (3181/30916, GnomAD)
C=0.1103 (1136/10296, GO-ESP)
C=0.104 (519/5008, 1000G)
C=0.037 (165/4480, Estonian)
C=0.044 (169/3854, ALSPAC)
C=0.047 (175/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR1265 : Non Coding Transcript Variant
Publications
2 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 10 NC_000010.11:g.14436619T>C
GRCh38.p12 chr 10 NC_000010.11:g.14436619T>G
GRCh37.p13 chr 10 NC_000010.10:g.14478618T>C
GRCh37.p13 chr 10 NC_000010.10:g.14478618T>G
Gene: MIR1265, microRNA 1265 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MIR1265 transcript NR_031668.1:n.44T>C N/A Non Coding Transcript Variant
MIR1265 transcript NR_031668.1:n.44T>G 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
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
gnomAD - Exomes Global Study-wide 212118 T=0.94191 C=0.05809
gnomAD - Exomes European Sub 111558 T=0.95054 C=0.04946
gnomAD - Exomes Asian Sub 43002 T=0.9605 C=0.0395
gnomAD - Exomes American Sub 30672 T=0.9666 C=0.0334
gnomAD - Exomes African Sub 13066 T=0.7445 C=0.2555
gnomAD - Exomes Ashkenazi Jewish Sub 9014 T=0.946 C=0.054
gnomAD - Exomes Other Sub 4806 T=0.947 C=0.053
TopMed Global Study-wide 125568 T=0.89160 C=0.10840
ExAC Global Study-wide 63144 T=0.9091 C=0.0909
ExAC Europe Sub 34566 T=0.9224 C=0.0776
ExAC Asian Sub 16134 T=0.9507 C=0.0493
ExAC African Sub 6670 T=0.707 C=0.293
ExAC American Sub 5304 T=0.951 C=0.049
ExAC Other Sub 470 T=0.90 C=0.10
gnomAD - Genomes Global Study-wide 30916 T=0.8971 C=0.1029
gnomAD - Genomes European Sub 18476 T=0.9551 C=0.0449
gnomAD - Genomes African Sub 8702 T=0.738 C=0.262
gnomAD - Genomes East Asian Sub 1622 T=1.000 C=0.000
gnomAD - Genomes Other Sub 978 T=0.96 C=0.04
gnomAD - Genomes American Sub 836 T=0.97 C=0.03
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.95 C=0.05
GO Exome Sequencing Project Global Study-wide 10296 T=0.8897 C=0.1103
GO Exome Sequencing Project European American Sub 7160 T=0.947 C=0.053
GO Exome Sequencing Project African American Sub 3136 T=0.758 C=0.242
1000Genomes Global Study-wide 5008 T=0.896 C=0.104
1000Genomes African Sub 1322 T=0.711 C=0.289
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.951 C=0.049
1000Genomes South Asian Sub 978 T=0.93 C=0.07
1000Genomes American Sub 694 T=0.97 C=0.03
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.963 C=0.037
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.956 C=0.044
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.953 C=0.047
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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 T= C G Note
GRCh38.p12 chr 10 NC_000010.11:g.14...

NC_000010.11:g.14436619T=

NC_000010.11:g.14...

NC_000010.11:g.14436619T>C

NC_000010.11:g.14...

NC_000010.11:g.14436619T>G

GRCh37.p13 chr 10 NC_000010.10:g.14...

NC_000010.10:g.14478618T=

NC_000010.10:g.14...

NC_000010.10:g.14478618T>C

NC_000010.10:g.14...

NC_000010.10:g.14478618T>G

MIR1265 transcript NR_031668.1:n.44T= NR_031668.1:n.44T>C NR_031668.1:n.44T>G
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#.

64 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18215086 Feb 27, 2004 (120)
2 SC_SNP ss18664860 Feb 27, 2004 (120)
3 ILLUMINA ss75107628 Dec 06, 2007 (129)
4 AFFY ss76723198 Dec 06, 2007 (129)
5 1000GENOMES ss115397193 Jan 25, 2009 (130)
6 KRIBB_YJKIM ss119682976 Dec 01, 2009 (131)
7 ILLUMINA ss159976018 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss169174057 Jul 04, 2010 (132)
9 ILLUMINA ss171231885 Jul 04, 2010 (132)
10 1000GENOMES ss224582827 Jul 14, 2010 (132)
11 1000GENOMES ss235068682 Jul 15, 2010 (132)
12 ILLUMINA ss479514983 May 04, 2012 (137)
13 ILLUMINA ss479518862 May 04, 2012 (137)
14 ILLUMINA ss479969830 Sep 08, 2015 (146)
15 ILLUMINA ss484556685 May 04, 2012 (137)
16 CLINSEQ_SNP ss491621572 May 04, 2012 (137)
17 ILLUMINA ss536692813 Sep 08, 2015 (146)
18 TISHKOFF ss561790506 Apr 25, 2013 (138)
19 NHLBI-ESP ss712935847 Apr 25, 2013 (138)
20 ILLUMINA ss778689400 Aug 21, 2014 (142)
21 ILLUMINA ss782725003 Aug 21, 2014 (142)
22 ILLUMINA ss783692453 Aug 21, 2014 (142)
23 ILLUMINA ss831976656 Apr 01, 2015 (144)
24 ILLUMINA ss834148109 Aug 21, 2014 (142)
25 JMKIDD_LAB ss974473955 Aug 21, 2014 (142)
26 EVA-GONL ss987226325 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1067511027 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1076785889 Aug 21, 2014 (142)
29 1000GENOMES ss1336390069 Aug 21, 2014 (142)
30 HAMMER_LAB ss1397574354 Sep 08, 2015 (146)
31 DDI ss1426232287 Apr 01, 2015 (144)
32 EVA_FINRISK ss1584066933 Apr 01, 2015 (144)
33 EVA_DECODE ss1596879876 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1624051335 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1667045368 Apr 01, 2015 (144)
36 EVA_EXAC ss1689822230 Apr 01, 2015 (144)
37 EVA_MGP ss1711248321 Apr 01, 2015 (144)
38 EVA_SVP ss1713160412 Apr 01, 2015 (144)
39 ILLUMINA ss1751958374 Sep 08, 2015 (146)
40 HAMMER_LAB ss1806270427 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1930551727 Feb 12, 2016 (147)
42 JJLAB ss2026001811 Sep 14, 2016 (149)
43 USC_VALOUEV ss2154246470 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2172889566 Dec 20, 2016 (150)
45 TOPMED ss2335598859 Dec 20, 2016 (150)
46 ILLUMINA ss2632680271 Nov 08, 2017 (151)
47 GNOMAD ss2738121071 Nov 08, 2017 (151)
48 GNOMAD ss2748349348 Nov 08, 2017 (151)
49 GNOMAD ss2885819201 Nov 08, 2017 (151)
50 SWEGEN ss3005985804 Nov 08, 2017 (151)
51 TOPMED ss3112291477 Nov 08, 2017 (151)
52 CSHL ss3348977221 Nov 08, 2017 (151)
53 ILLUMINA ss3626394651 Oct 12, 2018 (152)
54 ILLUMINA ss3630707714 Oct 12, 2018 (152)
55 ILLUMINA ss3632940253 Oct 12, 2018 (152)
56 ILLUMINA ss3633636970 Oct 12, 2018 (152)
57 ILLUMINA ss3634392061 Oct 12, 2018 (152)
58 ILLUMINA ss3635329733 Oct 12, 2018 (152)
59 ILLUMINA ss3636072626 Oct 12, 2018 (152)
60 ILLUMINA ss3637080331 Oct 12, 2018 (152)
61 ILLUMINA ss3637836138 Oct 12, 2018 (152)
62 ILLUMINA ss3640099409 Oct 12, 2018 (152)
63 ILLUMINA ss3642840614 Oct 12, 2018 (152)
64 OMUKHERJEE_ADBS ss3646403038 Oct 12, 2018 (152)
65 1000Genomes NC_000010.10 - 14478618 Oct 12, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 14478618 Oct 12, 2018 (152)
67 Genetic variation in the Estonian population NC_000010.10 - 14478618 Oct 12, 2018 (152)
68 ExAC NC_000010.10 - 14478618 Oct 12, 2018 (152)
69 gnomAD - Genomes NC_000010.10 - 14478618 Oct 12, 2018 (152)
70 gnomAD - Exomes NC_000010.10 - 14478618 Oct 12, 2018 (152)
71 GO Exome Sequencing Project NC_000010.10 - 14478618 Oct 12, 2018 (152)
72 TopMed NC_000010.11 - 14436619 Oct 12, 2018 (152)
73 UK 10K study - Twins NC_000010.10 - 14478618 Oct 12, 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss115397193, ss159976018, ss169174057, ss479514983, ss491621572, ss1397574354, ss1596879876, ss1713160412, ss3642840614 NC_000010.9:14518623:T= NC_000010.11:14436618:T= (self)
48740593, 27086077, 19252573, 36786, 19520722, 5790479, 959835, 27086077, ss224582827, ss235068682, ss479518862, ss479969830, ss484556685, ss536692813, ss561790506, ss712935847, ss778689400, ss782725003, ss783692453, ss831976656, ss834148109, ss974473955, ss987226325, ss1067511027, ss1076785889, ss1336390069, ss1426232287, ss1584066933, ss1624051335, ss1667045368, ss1689822230, ss1711248321, ss1751958374, ss1806270427, ss1930551727, ss2026001811, ss2154246470, ss2335598859, ss2632680271, ss2738121071, ss2748349348, ss2885819201, ss3005985804, ss3348977221, ss3626394651, ss3630707714, ss3632940253, ss3633636970, ss3634392061, ss3635329733, ss3636072626, ss3637080331, ss3637836138, ss3640099409, ss3646403038 NC_000010.10:14478617:T= NC_000010.11:14436618:T= (self)
37023958, ss2172889566, ss3112291477 NC_000010.11:14436618:T= NC_000010.11:14436618:T= (self)
ss75107628, ss76723198, ss119682976, ss171231885 NT_008705.16:14418617:T= NC_000010.11:14436618:T= (self)
ss18215086, ss18664860 NT_077569.2:8841513:T= NC_000010.11:14436618:T= (self)
ss115397193, ss159976018, ss169174057, ss479514983, ss491621572, ss1397574354, ss1596879876, ss1713160412, ss3642840614 NC_000010.9:14518623:T>C NC_000010.11:14436618:T>C (self)
48740593, 27086077, 19252573, 36786, 19520722, 5790479, 959835, 27086077, ss224582827, ss235068682, ss479518862, ss479969830, ss484556685, ss536692813, ss561790506, ss712935847, ss778689400, ss782725003, ss783692453, ss831976656, ss834148109, ss974473955, ss987226325, ss1067511027, ss1076785889, ss1336390069, ss1426232287, ss1584066933, ss1624051335, ss1667045368, ss1689822230, ss1711248321, ss1751958374, ss1806270427, ss1930551727, ss2026001811, ss2154246470, ss2335598859, ss2632680271, ss2738121071, ss2748349348, ss2885819201, ss3005985804, ss3348977221, ss3626394651, ss3630707714, ss3632940253, ss3633636970, ss3634392061, ss3635329733, ss3636072626, ss3637080331, ss3637836138, ss3640099409, ss3646403038 NC_000010.10:14478617:T>C NC_000010.11:14436618:T>C (self)
37023958, ss2172889566, ss3112291477 NC_000010.11:14436618:T>C NC_000010.11:14436618:T>C (self)
ss75107628, ss76723198, ss119682976, ss171231885 NT_008705.16:14418617:T>C NC_000010.11:14436618:T>C (self)
ss18215086, ss18664860 NT_077569.2:8841513:T>C NC_000010.11:14436618:T>C (self)
ss1806270427 NC_000010.10:14478617:T>G NC_000010.11:14436618:T>G (self)
Help

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

2 citations for rs11259096
PMID Title Author Year Journal
19458495 Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Duan S et al. 2009 RNA biology
22906193 A map of human microRNA variation uncovers unexpectedly high levels of variability. Carbonell J et al. 2012 Genome medicine

Genomic regions, transcripts, and products
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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