Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

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.

rs10120688

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr9:22056500 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.49826 (62565/125568, TOPMED)
A=0.4853 (14929/30764, GnomAD)
G=0.423 (2120/5008, 1000G) (+ 2 more)
A=0.482 (1859/3854, ALSPAC)
G=0.499 (1852/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDKN2B-AS1 : Intron Variant
Publications
12 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 9 NC_000009.12:g.22056500G>A
GRCh37.p13 chr 9 NC_000009.11:g.22056499G>A
Gene: CDKN2B-AS1, CDKN2B antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDKN2B-AS1 transcript variant 1 NR_003529.3:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 2 NR_047532.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 13 NR_047533.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 4 NR_047534.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 5 NR_047535.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 6 NR_047536.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 7 NR_047537.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 8 NR_047538.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 9 NR_047539.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 10 NR_047540.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 11 NR_047541.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 12 NR_047542.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 3 NR_047543.1:n. N/A Intron Variant
CDKN2B-AS1 transcript variant 14 NR_120536.1:n. N/A Intron 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.49826 A=0.50174
The Genome Aggregation Database Global Study-wide 30764 G=0.5147 A=0.4853
The Genome Aggregation Database European Sub 18400 G=0.5191 A=0.4809
The Genome Aggregation Database African Sub 8640 G=0.574 A=0.426
The Genome Aggregation Database East Asian Sub 1614 G=0.327 A=0.673
The Genome Aggregation Database Other Sub 972 G=0.47 A=0.53
The Genome Aggregation Database American Sub 838 G=0.29 A=0.71
The Genome Aggregation Database Ashkenazi Jewish Sub 300 G=0.33 A=0.67
1000Genomes Global Study-wide 5008 G=0.423 A=0.577
1000Genomes African Sub 1322 G=0.576 A=0.424
1000Genomes East Asian Sub 1008 G=0.277 A=0.723
1000Genomes Europe Sub 1006 G=0.501 A=0.499
1000Genomes South Asian Sub 978 G=0.39 A=0.61
1000Genomes American Sub 694 G=0.28 A=0.72
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.518 A=0.482
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.499 A=0.501
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= A Note
GRCh38.p7 chr 9 NC_000009.12:g.22056500G= NC_000009.12:g.22056500G>A
GRCh37.p13 chr 9 NC_000009.11:g.22056499G= NC_000009.11:g.22056499G>A
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, 100 SubSNP submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13978559 Dec 05, 2003 (119)
2 SC_SNP ss15697525 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss18012621 Feb 27, 2004 (120)
4 SSAHASNP ss22806370 Apr 05, 2004 (121)
5 ABI ss43347301 Mar 13, 2006 (126)
6 ILLUMINA ss66696991 Nov 29, 2006 (127)
7 ILLUMINA ss66870969 Nov 29, 2006 (127)
8 ILLUMINA ss66948554 Nov 29, 2006 (127)
9 ILLUMINA ss70359508 May 16, 2007 (127)
10 ILLUMINA ss70466448 May 25, 2008 (130)
11 ILLUMINA ss70987743 May 16, 2007 (127)
12 ILLUMINA ss75643104 Dec 07, 2007 (129)
13 AFFY ss76731195 Dec 07, 2007 (129)
14 HGSV ss83029240 Dec 15, 2007 (130)
15 KRIBB_YJKIM ss84908428 Dec 15, 2007 (130)
16 BCMHGSC_JDW ss94028489 Mar 25, 2008 (129)
17 HUMANGENOME_JCVI ss97786402 Feb 06, 2009 (130)
18 BGI ss105669591 Feb 06, 2009 (130)
19 1000GENOMES ss108673492 Jan 23, 2009 (130)
20 WTCCC ss120257495 Dec 01, 2009 (131)
21 ILLUMINA ss121268916 Dec 01, 2009 (131)
22 ENSEMBL ss134182115 Dec 01, 2009 (131)
23 ENSEMBL ss144012808 Dec 01, 2009 (131)
24 ILLUMINA ss152576308 Dec 01, 2009 (131)
25 GMI ss157303042 Dec 01, 2009 (131)
26 ILLUMINA ss159110468 Dec 01, 2009 (131)
27 ILLUMINA ss159866225 Dec 01, 2009 (131)
28 COMPLETE_GENOMICS ss163937417 Jul 04, 2010 (132)
29 ILLUMINA ss169272217 Jul 04, 2010 (132)
30 ILLUMINA ss169703493 Jul 04, 2010 (132)
31 BUSHMAN ss200219797 Jul 04, 2010 (132)
32 BCM-HGSC-SUB ss206756222 Jul 04, 2010 (132)
33 1000GENOMES ss210738306 Jul 14, 2010 (132)
34 1000GENOMES ss224175651 Jul 14, 2010 (132)
35 WTCCC ss230393033 Jul 04, 2010 (132)
36 1000GENOMES ss234764728 Jul 15, 2010 (132)
37 1000GENOMES ss241550240 Jul 15, 2010 (132)
38 ILLUMINA ss244267931 Jul 04, 2010 (132)
39 GMI ss280149910 May 04, 2012 (137)
40 PJP ss294416740 May 09, 2011 (134)
41 ILLUMINA ss410882248 Sep 17, 2011 (135)
42 ILLUMINA ss479194145 May 04, 2012 (137)
43 ILLUMINA ss479196553 May 04, 2012 (137)
44 ILLUMINA ss479531209 Sep 08, 2015 (146)
45 ILLUMINA ss484398094 May 04, 2012 (137)
46 ILLUMINA ss536578761 Sep 08, 2015 (146)
47 TISHKOFF ss561303412 Apr 25, 2013 (138)
48 SSMP ss655735283 Apr 25, 2013 (138)
49 ILLUMINA ss778723665 Sep 08, 2015 (146)
50 ILLUMINA ss782645411 Sep 08, 2015 (146)
51 ILLUMINA ss783614760 Sep 08, 2015 (146)
52 ILLUMINA ss825329239 Apr 01, 2015 (144)
53 ILLUMINA ss831895680 Sep 08, 2015 (146)
54 ILLUMINA ss834183083 Sep 08, 2015 (146)
55 EVA-GONL ss986413973 Aug 21, 2014 (142)
56 JMKIDD_LAB ss1076193170 Aug 21, 2014 (142)
57 1000GENOMES ss1333297704 Aug 21, 2014 (142)
58 DDI ss1431782373 Apr 01, 2015 (144)
59 EVA_GENOME_DK ss1583029033 Apr 01, 2015 (144)
60 EVA_DECODE ss1596048181 Apr 01, 2015 (144)
61 EVA_UK10K_ALSPAC ss1622456924 Apr 01, 2015 (144)
62 EVA_UK10K_TWINSUK ss1665450957 Apr 01, 2015 (144)
63 EVA_SVP ss1713099049 Apr 01, 2015 (144)
64 ILLUMINA ss1752771486 Sep 08, 2015 (146)
65 HAMMER_LAB ss1805924192 Sep 08, 2015 (146)
66 WEILL_CORNELL_DGM ss1929697310 Feb 12, 2016 (147)
67 ILLUMINA ss1946255384 Feb 12, 2016 (147)
68 ILLUMINA ss1959173003 Feb 12, 2016 (147)
69 GENOMED ss1971178581 Jul 19, 2016 (147)
70 JJLAB ss2025560715 Sep 14, 2016 (149)
71 USC_VALOUEV ss2153786945 Dec 20, 2016 (150)
72 HUMAN_LONGEVITY ss2310208849 Dec 20, 2016 (150)
73 TOPMED ss2480285752 Dec 20, 2016 (150)
74 SYSTEMSBIOZJU ss2627254988 Nov 08, 2017 (151)
75 ILLUMINA ss2634849979 Nov 08, 2017 (151)
76 ILLUMINA ss2634849980 Nov 08, 2017 (151)
77 ILLUMINA ss2635194004 Nov 08, 2017 (151)
78 GRF ss2709591486 Nov 08, 2017 (151)
79 ILLUMINA ss2711159823 Nov 08, 2017 (151)
80 GNOMAD ss2876535395 Nov 08, 2017 (151)
81 SWEGEN ss3004537293 Nov 08, 2017 (151)
82 ILLUMINA ss3022917035 Nov 08, 2017 (151)
83 BIOINF_KMB_FNS_UNIBA ss3026570101 Nov 08, 2017 (151)
84 CSHL ss3348570014 Nov 08, 2017 (151)
85 TOPMED ss3584594212 Nov 08, 2017 (151)
86 ILLUMINA ss3625980836 Jul 20, 2018 (151)
87 ILLUMINA ss3630235850 Jul 20, 2018 (151)
88 ILLUMINA ss3632743335 Jul 20, 2018 (151)
89 ILLUMINA ss3633529129 Jul 20, 2018 (151)
90 ILLUMINA ss3634257188 Jul 20, 2018 (151)
91 ILLUMINA ss3635207631 Jul 20, 2018 (151)
92 ILLUMINA ss3635935309 Jul 20, 2018 (151)
93 ILLUMINA ss3636952203 Jul 20, 2018 (151)
94 ILLUMINA ss3637688600 Jul 20, 2018 (151)
95 ILLUMINA ss3638805957 Jul 20, 2018 (151)
96 ILLUMINA ss3639407678 Jul 20, 2018 (151)
97 ILLUMINA ss3639736044 Jul 20, 2018 (151)
98 ILLUMINA ss3640914921 Jul 20, 2018 (151)
99 ILLUMINA ss3643733344 Jul 20, 2018 (151)
100 ILLUMINA ss3644988696 Jul 20, 2018 (151)
101 1000Genomes NC_000009.11 - 22056499 Jul 20, 2018 (151)
102 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 22056499 Jul 20, 2018 (151)
103 The Genome Aggregation Database NC_000009.11 - 22056499 Jul 20, 2018 (151)
104 Trans-Omics for Precision Medicine NC_000009.12 - 22056500 Jul 20, 2018 (151)
105 UK 10K study - Twins NC_000009.11 - 22056499 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)
rs60168433 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss83029240, ss3639407678, ss3639736044 NC_000009.9:22046498:G= NC_000009.12:22056499:G= (self)
ss76731195, ss94028489, ss108673492, ss163937417, ss200219797, ss206756222, ss210738306, ss280149910, ss294416740, ss479194145, ss825329239, ss1596048181, ss1713099049, ss2635194004, ss3643733344 NC_000009.10:22046498:G= NC_000009.12:22056499:G= (self)
45536960, 25330752, 217163150, 25330752, ss224175651, ss234764728, ss241550240, ss479196553, ss479531209, ss484398094, ss536578761, ss561303412, ss655735283, ss778723665, ss782645411, ss783614760, ss831895680, ss834183083, ss986413973, ss1076193170, ss1333297704, ss1431782373, ss1583029033, ss1622456924, ss1665450957, ss1752771486, ss1805924192, ss1929697310, ss1946255384, ss1959173003, ss1971178581, ss2025560715, ss2153786945, ss2480285752, ss2627254988, ss2634849979, ss2634849980, ss2709591486, ss2711159823, ss2876535395, ss3004537293, ss3022917035, ss3348570014, ss3625980836, ss3630235850, ss3632743335, ss3633529129, ss3634257188, ss3635207631, ss3635935309, ss3636952203, ss3637688600, ss3638805957, ss3640914921, ss3644988696 NC_000009.11:22056498:G= NC_000009.12:22056499:G= (self)
408176956, ss2310208849, ss3026570101, ss3584594212 NC_000009.12:22056499:G= NC_000009.12:22056499:G= (self)
ss13978559, ss15697525, ss18012621, ss22806370 NT_008413.16:22046498:G= NC_000009.12:22056499:G= (self)
ss230393033 NT_008413.17:22046498:G= NC_000009.12:22056499:G= (self)
ss43347301, ss66696991, ss66870969, ss66948554, ss70359508, ss70466448, ss70987743, ss75643104, ss84908428, ss97786402, ss105669591, ss120257495, ss121268916, ss134182115, ss144012808, ss152576308, ss157303042, ss159110468, ss159866225, ss169272217, ss169703493, ss244267931, ss410882248 NT_008413.18:22046498:G= NC_000009.12:22056499:G= (self)
ss83029240, ss3639407678, ss3639736044 NC_000009.9:22046498:G>A NC_000009.12:22056499:G>A (self)
ss76731195, ss94028489, ss108673492, ss163937417, ss200219797, ss206756222, ss210738306, ss280149910, ss294416740, ss479194145, ss825329239, ss1596048181, ss1713099049, ss2635194004, ss3643733344 NC_000009.10:22046498:G>A NC_000009.12:22056499:G>A (self)
45536960, 25330752, 217163150, 25330752, ss224175651, ss234764728, ss241550240, ss479196553, ss479531209, ss484398094, ss536578761, ss561303412, ss655735283, ss778723665, ss782645411, ss783614760, ss831895680, ss834183083, ss986413973, ss1076193170, ss1333297704, ss1431782373, ss1583029033, ss1622456924, ss1665450957, ss1752771486, ss1805924192, ss1929697310, ss1946255384, ss1959173003, ss1971178581, ss2025560715, ss2153786945, ss2480285752, ss2627254988, ss2634849979, ss2634849980, ss2709591486, ss2711159823, ss2876535395, ss3004537293, ss3022917035, ss3348570014, ss3625980836, ss3630235850, ss3632743335, ss3633529129, ss3634257188, ss3635207631, ss3635935309, ss3636952203, ss3637688600, ss3638805957, ss3640914921, ss3644988696 NC_000009.11:22056498:G>A NC_000009.12:22056499:G>A (self)
408176956, ss2310208849, ss3026570101, ss3584594212 NC_000009.12:22056499:G>A NC_000009.12:22056499:G>A (self)
ss13978559, ss15697525, ss18012621, ss22806370 NT_008413.16:22046498:G>A NC_000009.12:22056499:G>A (self)
ss230393033 NT_008413.17:22046498:G>A NC_000009.12:22056499:G>A (self)
ss43347301, ss66696991, ss66870969, ss66948554, ss70359508, ss70466448, ss70987743, ss75643104, ss84908428, ss97786402, ss105669591, ss120257495, ss121268916, ss134182115, ss144012808, ss152576308, ss157303042, ss159110468, ss159866225, ss169272217, ss169703493, ss244267931, ss410882248 NT_008413.18:22046498:G>A NC_000009.12:22056499:G>A (self)
Help

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

12 citations for rs10120688
PMID Title Author Year Journal
20395613 Confirmation of an association of single-nucleotide polymorphism rs1333040 on 9p21 with familial and sporadic intracranial aneurysms in Japanese patients. Hashikata H et al. 2010 Stroke
21854539 Genetic determinants of platelet reactivity during acetylsalicylic acid therapy in diabetic patients: evaluation of 27 polymorphisms within candidate genes. Postula M et al. 2011 Journal of thrombosis and haemostasis
22521085 Glaucoma risk alleles at CDKN2B-AS1 are associated with lower intraocular pressure, normal-tension glaucoma, and advanced glaucoma. Burdon KP et al. 2012 Ophthalmology
22570617 Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. Wiggs JL et al. 2012 PLoS genetics
22605921 Genome-wide association study of primary open angle glaucoma risk and quantitative traits. Gibson J et al. 2012 Molecular vision
22792221 Common variants on chromosome 9p21 are associated with normal tension glaucoma. Takamoto M et al. 2012 PloS one
23963167 Investigation of known genetic risk factors for primary open angle glaucoma in two populations of African ancestry. Liu Y et al. 2013 Investigative ophthalmology & visual science
24002674 Genome-wide association study and meta-analysis of intraocular pressure. Ozel AB et al. 2014 Human genetics
24875940 Evaluation of genetic association of the INK4 locus with primary open angle glaucoma in East Indian population. Vishal M et al. 2014 Scientific reports
26690118 An Updated Review on the Genetics of Primary Open Angle Glaucoma. Abu-Amero K et al. 2015 International journal of molecular sciences
26729200 Association of well-characterized lung cancer lncRNA polymorphisms with lung cancer susceptibility and platinum-based chemotherapy response. Gong WJ et al. 2016 Tumour biology
27249003 Clinical Significance of Long Non-Coding RNA CASC8 rs10505477 Polymorphism in Lung Cancer Susceptibility, Platinum-Based Chemotherapy Response, and Toxicity. Hu L et al. 2016 International journal of environmental research and public health

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