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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs11902171

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:186678500 (GRCh38.p13) 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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.219744 (58164/264690, TOPMED)
C=0.08866 (1486/16760, 8.3KJPN)
C=0.14284 (2240/15682, ALFA) (+ 15 more)
C=0.1761 (882/5008, 1000G)
C=0.2174 (974/4480, Estonian)
C=0.2740 (1056/3854, ALSPAC)
C=0.2902 (1076/3708, TWINSUK)
C=0.0702 (205/2922, KOREAN)
C=0.0584 (107/1832, Korea1K)
C=0.273 (272/998, GoNL)
C=0.052 (41/788, PRJEB37584)
C=0.272 (163/600, NorthernSweden)
C=0.172 (55/320, HapMap)
C=0.208 (45/216, Qatari)
C=0.114 (24/210, Vietnamese)
G=0.444 (80/180, SGDP_PRJ)
C=0.23 (9/40, GENOME_DK)
G=0.42 (5/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ITGAV : 3 Prime UTR 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.p13 chr 2 NC_000002.12:g.186678500G>A
GRCh38.p13 chr 2 NC_000002.12:g.186678500G>C
GRCh37.p13 chr 2 NC_000002.11:g.187543227G>A
GRCh37.p13 chr 2 NC_000002.11:g.187543227G>C
Gene: ITGAV, integrin subunit alpha V (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ITGAV transcript variant 1 NM_002210.5:c.*1208= N/A 3 Prime UTR Variant
ITGAV transcript variant 3 NM_001145000.3:c.*1208= N/A 3 Prime UTR Variant
ITGAV transcript variant 2 NM_001144999.3:c.*1208= N/A 3 Prime UTR 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

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 15682 G=0.85716 A=0.00000, C=0.14284
European Sub 12226 G=0.83003 A=0.00000, C=0.16997
African Sub 2248 G=0.9511 A=0.0000, C=0.0489
African Others Sub 92 G=0.97 A=0.00, C=0.03
African American Sub 2156 G=0.9504 A=0.0000, C=0.0496
Asian Sub 84 G=1.00 A=0.00, C=0.00
East Asian Sub 68 G=1.00 A=0.00, C=0.00
Other Asian Sub 16 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 104 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 412 G=1.000 A=0.000, C=0.000
South Asian Sub 68 G=0.99 A=0.00, C=0.01
Other Sub 540 G=0.906 A=0.000, C=0.094


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
TopMed Global Study-wide 264690 G=0.780256 C=0.219744
8.3KJPN JAPANESE Study-wide 16760 G=0.91134 C=0.08866
1000Genomes Global Study-wide 5008 G=0.8239 C=0.1761
1000Genomes African Sub 1322 G=0.8389 C=0.1611
1000Genomes East Asian Sub 1008 G=0.9226 C=0.0774
1000Genomes Europe Sub 1006 G=0.7515 C=0.2485
1000Genomes South Asian Sub 978 G=0.785 C=0.215
1000Genomes American Sub 694 G=0.811 C=0.189
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7826 C=0.2174
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7260 C=0.2740
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7098 C=0.2902
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9298 C=0.0702
Korean Genome Project KOREAN Study-wide 1832 G=0.9416 C=0.0584
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.727 C=0.273
CNV burdens in cranial meningiomas Global Study-wide 788 G=0.948 C=0.052
CNV burdens in cranial meningiomas CRM Sub 788 G=0.948 C=0.052
Northern Sweden ACPOP Study-wide 600 G=0.728 C=0.272
HapMap Global Study-wide 320 G=0.828 C=0.172
HapMap American Sub 118 G=0.729 C=0.271
HapMap African Sub 112 G=0.848 C=0.152
HapMap Asian Sub 90 G=0.93 C=0.07
Qatari Global Study-wide 216 G=0.792 C=0.208
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.886 C=0.114
SGDP_PRJ Global Study-wide 180 G=0.444 C=0.556
The Danish reference pan genome Danish Study-wide 40 G=0.78 C=0.23
Siberian Global Study-wide 12 G=0.42 C=0.58
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 C
GRCh38.p13 chr 2 NC_000002.12:g.186678500= NC_000002.12:g.186678500G>A NC_000002.12:g.186678500G>C
GRCh37.p13 chr 2 NC_000002.11:g.187543227= NC_000002.11:g.187543227G>A NC_000002.11:g.187543227G>C
ITGAV transcript variant 1 NM_002210.5:c.*1208= NM_002210.5:c.*1208G>A NM_002210.5:c.*1208G>C
ITGAV transcript variant 1 NM_002210.4:c.*1208= NM_002210.4:c.*1208G>A NM_002210.4:c.*1208G>C
ITGAV transcript variant 3 NM_001145000.3:c.*1208= NM_001145000.3:c.*1208G>A NM_001145000.3:c.*1208G>C
ITGAV transcript variant 3 NM_001145000.2:c.*1208= NM_001145000.2:c.*1208G>A NM_001145000.2:c.*1208G>C
ITGAV transcript variant 2 NM_001144999.3:c.*1208= NM_001144999.3:c.*1208G>A NM_001144999.3:c.*1208G>C
ITGAV transcript variant 2 NM_001144999.2:c.*1208= NM_001144999.2:c.*1208G>A NM_001144999.2:c.*1208G>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#.

61 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17679649 Feb 28, 2004 (120)
2 PERLEGEN ss23699473 Sep 20, 2004 (123)
3 ILLUMINA ss65737048 Oct 16, 2006 (127)
4 PERLEGEN ss68838220 May 18, 2007 (127)
5 CGM_KYOTO ss76874612 Dec 06, 2007 (129)
6 PGA-UW-FHCRC ss86213386 Mar 23, 2008 (129)
7 1000GENOMES ss110435477 Jan 24, 2009 (130)
8 ILLUMINA ss160015684 Dec 01, 2009 (131)
9 ENSEMBL ss161216873 Dec 01, 2009 (131)
10 BUSHMAN ss201499433 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss205651758 Jul 04, 2010 (132)
12 1000GENOMES ss219707946 Jul 14, 2010 (132)
13 1000GENOMES ss231511959 Jul 14, 2010 (132)
14 1000GENOMES ss238990611 Jul 15, 2010 (132)
15 GMI ss276827753 May 04, 2012 (137)
16 ILLUMINA ss480128430 Sep 08, 2015 (146)
17 GSK-GENETICS ss491261357 May 04, 2012 (137)
18 ILLUMINA ss533183133 Sep 08, 2015 (146)
19 RSG_UW ss538956577 Apr 25, 2013 (138)
20 TISHKOFF ss556099173 Apr 25, 2013 (138)
21 SSMP ss649761717 Apr 25, 2013 (138)
22 EVA-GONL ss977755044 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1069787198 Aug 21, 2014 (142)
24 1000GENOMES ss1300840545 Aug 21, 2014 (142)
25 DDI ss1428853040 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1579243509 Apr 01, 2015 (144)
27 EVA_DECODE ss1587198932 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1605369575 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1648363608 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1921002529 Feb 12, 2016 (147)
31 GENOMED ss1968977252 Jul 19, 2016 (147)
32 JJLAB ss2021042106 Sep 14, 2016 (149)
33 USC_VALOUEV ss2149107290 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2237445892 Dec 20, 2016 (150)
35 TOPMED ss2403878949 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2625024027 Nov 08, 2017 (151)
37 GRF ss2703748929 Nov 08, 2017 (151)
38 GNOMAD ss2784005417 Nov 08, 2017 (151)
39 SWEGEN ss2991035666 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3024282189 Nov 08, 2017 (151)
41 TOPMED ss3333010198 Nov 08, 2017 (151)
42 CSHL ss3344654798 Nov 08, 2017 (151)
43 ILLUMINA ss3628244487 Oct 11, 2018 (152)
44 ILLUMINA ss3636492957 Oct 11, 2018 (152)
45 OMUKHERJEE_ADBS ss3646276121 Oct 11, 2018 (152)
46 EGCUT_WGS ss3658915657 Jul 13, 2019 (153)
47 EVA_DECODE ss3705628317 Jul 13, 2019 (153)
48 ACPOP ss3729200691 Jul 13, 2019 (153)
49 EVA ss3757847208 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3802205244 Jul 13, 2019 (153)
51 EVA ss3825615042 Apr 25, 2020 (154)
52 EVA ss3827406543 Apr 25, 2020 (154)
53 EVA ss3837122792 Apr 25, 2020 (154)
54 EVA ss3842543335 Apr 25, 2020 (154)
55 SGDP_PRJ ss3854187274 Apr 25, 2020 (154)
56 KRGDB ss3899849496 Apr 25, 2020 (154)
57 KOGIC ss3949696416 Apr 25, 2020 (154)
58 EVA ss3984495186 Apr 26, 2021 (155)
59 EVA ss3986020492 Apr 26, 2021 (155)
60 TOPMED ss4537423818 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5155585598 Apr 26, 2021 (155)
62 1000Genomes NC_000002.11 - 187543227 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 187543227 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000002.11 - 187543227 Oct 11, 2018 (152)
65 The Danish reference pan genome NC_000002.11 - 187543227 Apr 25, 2020 (154)
66 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 84922643 (NC_000002.12:186678499:G:A 1/139996)
Row 84922644 (NC_000002.12:186678499:G:C 31383/139960)

- Apr 26, 2021 (155)
67 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 84922643 (NC_000002.12:186678499:G:A 1/139996)
Row 84922644 (NC_000002.12:186678499:G:C 31383/139960)

- Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000002.11 - 187543227 Apr 25, 2020 (154)
69 HapMap NC_000002.12 - 186678500 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000002.11 - 187543227 Apr 25, 2020 (154)
71 Korean Genome Project NC_000002.12 - 186678500 Apr 25, 2020 (154)
72 Northern Sweden NC_000002.11 - 187543227 Jul 13, 2019 (153)
73 CNV burdens in cranial meningiomas NC_000002.11 - 187543227 Apr 26, 2021 (155)
74 Qatari NC_000002.11 - 187543227 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000002.11 - 187543227 Apr 25, 2020 (154)
76 Siberian NC_000002.11 - 187543227 Apr 25, 2020 (154)
77 8.3KJPN NC_000002.11 - 187543227 Apr 26, 2021 (155)
78 TopMed NC_000002.12 - 186678500 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000002.11 - 187543227 Oct 11, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000002.11 - 187543227 Jul 13, 2019 (153)
81 ALFA NC_000002.12 - 186678500 Apr 26, 2021 (155)
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
4914570658 NC_000002.12:186678499:G:A NC_000002.12:186678499:G:A
ss110435477, ss160015684, ss201499433, ss205651758, ss276827753, ss491261357, ss1587198932 NC_000002.10:187251471:G:C NC_000002.12:186678499:G:C (self)
11914230, 6583208, 4653905, 5408448, 2892653, 7026890, 2485556, 44521, 3044459, 6204254, 1623644, 13554905, 6583208, 1435080, ss219707946, ss231511959, ss238990611, ss480128430, ss533183133, ss556099173, ss649761717, ss977755044, ss1069787198, ss1300840545, ss1428853040, ss1579243509, ss1605369575, ss1648363608, ss1921002529, ss1968977252, ss2021042106, ss2149107290, ss2403878949, ss2625024027, ss2703748929, ss2784005417, ss2991035666, ss3344654798, ss3628244487, ss3636492957, ss3646276121, ss3658915657, ss3729200691, ss3757847208, ss3825615042, ss3827406543, ss3837122792, ss3854187274, ss3899849496, ss3984495186, ss3986020492, ss5155585598 NC_000002.11:187543226:G:C NC_000002.12:186678499:G:C (self)
1970982, 6074417, 212972768, 341246697, 4914570658, ss2237445892, ss3024282189, ss3333010198, ss3705628317, ss3802205244, ss3842543335, ss3949696416, ss4537423818 NC_000002.12:186678499:G:C NC_000002.12:186678499:G:C (self)
ss17679649 NT_005403.14:37752642:G:C NC_000002.12:186678499:G:C (self)
ss23699473, ss65737048, ss68838220, ss76874612, ss86213386, ss161216873, ss538956577 NT_005403.17:37752644:G:C NC_000002.12:186678499:G:C (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 rs11902171
PMID Title Author Year Journal
20926544 Allele polymorphisms of tumor integrins correlate with peritoneal carcinosis capability of gastric cancer cells in radically resected patients. Scartozzi M et al. 2011 Annals of oncology
22271436 Single-nucleotide polymorphisms of integrins are associated with the risk and lymph node metastasis of oral squamous cell carcinoma. Ma XR et al. 2012 Medical oncology (Northwood, London, England)
22808003 Role of vascular endothelial growth factor (VEGF) and VEGF-R genotyping in guiding the metastatic process in pT4a resected gastric cancer patients. Scartozzi M et al. 2012 PloS one
23065910 Genetic variants in the integrin gene predicted microRNA-binding sites were associated with the risk of prostate cancer. Liu J et al. 2014 Molecular carcinogenesis
25114582 MicroRNA binding site polymorphisms as biomarkers in cancer management and research. Cipollini M et al. 2014 Pharmacogenomics and personalized medicine
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad