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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.

rs3212236

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:24648227 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.240217 (63583/264690, TOPMED)
C=0.210731 (29528/140122, GnomAD)
C=0.18427 (8814/47832, ALFA) (+ 16 more)
T=0.37918 (6355/16760, 8.3KJPN)
C=0.3578 (1792/5008, 1000G)
C=0.1152 (516/4480, Estonian)
C=0.1821 (702/3854, ALSPAC)
C=0.1750 (649/3708, TWINSUK)
T=0.4157 (1218/2930, KOREAN)
T=0.4203 (770/1832, Korea1K)
C=0.166 (166/998, GoNL)
T=0.434 (343/790, PRJEB37584)
C=0.153 (92/600, NorthernSweden)
T=0.345 (131/380, SGDP_PRJ)
C=0.324 (70/216, Qatari)
T=0.319 (67/210, Vietnamese)
C=0.17 (7/40, GENOME_DK)
T=0.50 (10/20, Siberian)
C=0.50 (10/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
9 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 6 NC_000006.12:g.24648227T>C
GRCh37.p13 chr 6 NC_000006.11:g.24648455T>C
KIAA0319 RefSeqGene NG_016206.1:g.2929A>G
TDP2 RefSeqGene NG_052787.1:g.23661A>G
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 47832 T=0.81573 C=0.18427
European Sub 36252 T=0.83093 C=0.16907
African Sub 6066 T=0.8007 C=0.1993
African Others Sub 210 T=0.795 C=0.205
African American Sub 5856 T=0.8009 C=0.1991
Asian Sub 442 T=0.367 C=0.633
East Asian Sub 374 T=0.396 C=0.604
Other Asian Sub 68 T=0.21 C=0.79
Latin American 1 Sub 522 T=0.776 C=0.224
Latin American 2 Sub 842 T=0.601 C=0.399
South Asian Sub 162 T=0.549 C=0.451
Other Sub 3546 T=0.8111 C=0.1889


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
TopMed Global Study-wide 264690 T=0.759783 C=0.240217
gnomAD - Genomes Global Study-wide 140122 T=0.789269 C=0.210731
gnomAD - Genomes European Sub 75904 T=0.83234 C=0.16766
gnomAD - Genomes African Sub 41978 T=0.79592 C=0.20408
gnomAD - Genomes American Sub 13642 T=0.63107 C=0.36893
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.7903 C=0.2097
gnomAD - Genomes East Asian Sub 3122 T=0.3619 C=0.6381
gnomAD - Genomes Other Sub 2152 T=0.7616 C=0.2384
Allele Frequency Aggregator Total Global 47832 T=0.81573 C=0.18427
Allele Frequency Aggregator European Sub 36252 T=0.83093 C=0.16907
Allele Frequency Aggregator African Sub 6066 T=0.8007 C=0.1993
Allele Frequency Aggregator Other Sub 3546 T=0.8111 C=0.1889
Allele Frequency Aggregator Latin American 2 Sub 842 T=0.601 C=0.399
Allele Frequency Aggregator Latin American 1 Sub 522 T=0.776 C=0.224
Allele Frequency Aggregator Asian Sub 442 T=0.367 C=0.633
Allele Frequency Aggregator South Asian Sub 162 T=0.549 C=0.451
8.3KJPN JAPANESE Study-wide 16760 T=0.37918 C=0.62082
1000Genomes Global Study-wide 5008 T=0.6422 C=0.3578
1000Genomes African Sub 1322 T=0.7980 C=0.2020
1000Genomes East Asian Sub 1008 T=0.3720 C=0.6280
1000Genomes Europe Sub 1006 T=0.8091 C=0.1909
1000Genomes South Asian Sub 978 T=0.559 C=0.441
1000Genomes American Sub 694 T=0.612 C=0.388
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8848 C=0.1152
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8179 C=0.1821
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8250 C=0.1750
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.4157 C=0.5843
Korean Genome Project KOREAN Study-wide 1832 T=0.4203 C=0.5797
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.834 C=0.166
CNV burdens in cranial meningiomas Global Study-wide 790 T=0.434 C=0.566
CNV burdens in cranial meningiomas CRM Sub 790 T=0.434 C=0.566
Northern Sweden ACPOP Study-wide 600 T=0.847 C=0.153
SGDP_PRJ Global Study-wide 380 T=0.345 C=0.655
Qatari Global Study-wide 216 T=0.676 C=0.324
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.319 C=0.681
The Danish reference pan genome Danish Study-wide 40 T=0.82 C=0.17
Siberian Global Study-wide 20 T=0.50 C=0.50
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
GRCh38.p13 chr 6 NC_000006.12:g.24648227= NC_000006.12:g.24648227T>C
GRCh37.p13 chr 6 NC_000006.11:g.24648455= NC_000006.11:g.24648455T>C
KIAA0319 RefSeqGene NG_016206.1:g.2929= NG_016206.1:g.2929A>G
TDP2 RefSeqGene NG_052787.1:g.23661= NG_052787.1:g.23661A>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#.

59 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 FHCRC ss4472620 May 29, 2002 (105)
2 YUSUKE ss4963733 Aug 28, 2002 (108)
3 WI_SSAHASNP ss6494170 Feb 20, 2003 (111)
4 CSHL-HAPMAP ss19671951 Feb 27, 2004 (120)
5 PGA-UW-FHCRC ss23144600 Sep 20, 2004 (126)
6 ABI ss42855212 Mar 10, 2006 (126)
7 HGSV ss85994688 Dec 14, 2007 (130)
8 BGI ss104286911 Dec 01, 2009 (131)
9 ILLUMINA-UK ss116357695 Feb 14, 2009 (130)
10 GMI ss156652390 Dec 01, 2009 (131)
11 ILLUMINA ss160616213 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss162127636 Jul 04, 2010 (132)
13 ILLUMINA ss173574899 Jul 04, 2010 (132)
14 1000GENOMES ss222266235 Jul 14, 2010 (132)
15 1000GENOMES ss233365583 Jul 14, 2010 (132)
16 1000GENOMES ss240440531 Jul 15, 2010 (132)
17 GMI ss278692271 May 04, 2012 (137)
18 PJP ss293810502 May 09, 2011 (134)
19 ILLUMINA ss481679377 Sep 08, 2015 (146)
20 ILLUMINA ss537168115 Sep 08, 2015 (146)
21 TISHKOFF ss559074377 Apr 25, 2013 (138)
22 SSMP ss652983631 Apr 25, 2013 (138)
23 EVA-GONL ss982693321 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1073461230 Aug 21, 2014 (142)
25 1000GENOMES ss1319364702 Aug 21, 2014 (142)
26 DDI ss1430671790 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1581575500 Apr 01, 2015 (144)
28 EVA_DECODE ss1592244541 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1615165849 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1658159882 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1925947591 Feb 12, 2016 (147)
32 GENOMED ss1970337316 Jul 19, 2016 (147)
33 JJLAB ss2023595129 Sep 14, 2016 (149)
34 USC_VALOUEV ss2151759950 Nov 08, 2017 (151)
35 HUMAN_LONGEVITY ss2282592460 Dec 20, 2016 (150)
36 TOPMED ss2450947844 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2626285641 Nov 08, 2017 (151)
38 GRF ss2707350172 Nov 08, 2017 (151)
39 GNOMAD ss2836891476 Nov 08, 2017 (151)
40 SWEGEN ss2998682401 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3025584050 Nov 08, 2017 (151)
42 CSHL ss3346886393 Nov 08, 2017 (151)
43 TOPMED ss3492659241 Nov 08, 2017 (151)
44 ILLUMINA ss3629467662 Oct 12, 2018 (152)
45 ILLUMINA ss3636765146 Oct 12, 2018 (152)
46 ILLUMINA ss3638612952 Oct 12, 2018 (152)
47 EGCUT_WGS ss3666614307 Jul 13, 2019 (153)
48 EVA_DECODE ss3716789086 Jul 13, 2019 (153)
49 ACPOP ss3733296730 Jul 13, 2019 (153)
50 EVA ss3764739260 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3807901829 Jul 13, 2019 (153)
52 EVA ss3829789033 Apr 26, 2020 (154)
53 SGDP_PRJ ss3864126582 Apr 26, 2020 (154)
54 KRGDB ss3910892170 Apr 26, 2020 (154)
55 KOGIC ss3958699099 Apr 26, 2020 (154)
56 EVA ss3984563274 Apr 26, 2021 (155)
57 EVA ss4017260723 Apr 26, 2021 (155)
58 TOPMED ss4696912226 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5176603811 Apr 26, 2021 (155)
60 1000Genomes NC_000006.11 - 24648455 Oct 12, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 24648455 Oct 12, 2018 (152)
62 Genetic variation in the Estonian population NC_000006.11 - 24648455 Oct 12, 2018 (152)
63 The Danish reference pan genome NC_000006.11 - 24648455 Apr 26, 2020 (154)
64 gnomAD - Genomes NC_000006.12 - 24648227 Apr 26, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000006.11 - 24648455 Apr 26, 2020 (154)
66 KOREAN population from KRGDB NC_000006.11 - 24648455 Apr 26, 2020 (154)
67 Korean Genome Project NC_000006.12 - 24648227 Apr 26, 2020 (154)
68 Northern Sweden NC_000006.11 - 24648455 Jul 13, 2019 (153)
69 CNV burdens in cranial meningiomas NC_000006.11 - 24648455 Apr 26, 2021 (155)
70 Qatari NC_000006.11 - 24648455 Apr 26, 2020 (154)
71 SGDP_PRJ NC_000006.11 - 24648455 Apr 26, 2020 (154)
72 Siberian NC_000006.11 - 24648455 Apr 26, 2020 (154)
73 8.3KJPN NC_000006.11 - 24648455 Apr 26, 2021 (155)
74 TopMed NC_000006.12 - 24648227 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000006.11 - 24648455 Oct 12, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000006.11 - 24648455 Jul 13, 2019 (153)
77 ALFA NC_000006.12 - 24648227 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).

Associated ID History Updated (Build)
rs3777666 Oct 09, 2002 (108)
rs17249827 Mar 10, 2006 (126)
rs57545361 May 23, 2008 (130)
rs386580890 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85994688 NC_000006.9:24756433:T:C NC_000006.12:24648226:T:C (self)
ss116357695, ss160616213, ss162127636, ss278692271, ss293810502, ss1592244541 NC_000006.10:24756433:T:C NC_000006.12:24648226:T:C (self)
31123938, 17342573, 12352555, 7740439, 7695435, 18069564, 6581595, 112652, 7989521, 16143562, 4276304, 34573118, 17342573, 3839282, ss222266235, ss233365583, ss240440531, ss481679377, ss537168115, ss559074377, ss652983631, ss982693321, ss1073461230, ss1319364702, ss1430671790, ss1581575500, ss1615165849, ss1658159882, ss1925947591, ss1970337316, ss2023595129, ss2151759950, ss2450947844, ss2626285641, ss2707350172, ss2836891476, ss2998682401, ss3346886393, ss3629467662, ss3636765146, ss3638612952, ss3666614307, ss3733296730, ss3764739260, ss3829789033, ss3864126582, ss3910892170, ss3984563274, ss4017260723, ss5176603811 NC_000006.11:24648454:T:C NC_000006.12:24648226:T:C (self)
219904042, 15077100, 334122778, 534289784, 1176006307, ss2282592460, ss3025584050, ss3492659241, ss3716789086, ss3807901829, ss3958699099, ss4696912226 NC_000006.12:24648226:T:C NC_000006.12:24648226:T:C (self)
ss19671951 NT_007592.13:15506705:T:C NC_000006.12:24648226:T:C (self)
ss4472620, ss4963733, ss6494170, ss23144600, ss42855212, ss104286911, ss156652390, ss173574899 NT_007592.15:24588454:T:C NC_000006.12:24648226: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.

9 citations for rs3212236
PMID Title Author Year Journal
15717286 Strong evidence that KIAA0319 on chromosome 6p is a susceptibility gene for developmental dyslexia. Cope N et al. 2005 American journal of human genetics
17033633 Further evidence that the KIAA0319 gene confers susceptibility to developmental dyslexia. Harold D et al. 2006 Molecular psychiatry
19325871 A common variant associated with dyslexia reduces expression of the KIAA0319 gene. Dennis MY et al. 2009 PLoS genetics
21165691 Investigation of dyslexia and SLI risk variants in reading- and language-impaired subjects. Newbury DF et al. 2011 Behavior genetics
21507613 Genetic influences of cortical gray matter in language-related regions in healthy controls and schizophrenia. Jamadar S et al. 2011 Schizophrenia research
22262880 Genetic variants of FOXP2 and KIAA0319/TTRAP/THEM2 locus are associated with altered brain activation in distinct language-related regions. Pinel P et al. 2012 The Journal of neuroscience
27098879 KIAA0319 gene polymorphisms are associated with developmental dyslexia in Chinese Uyghur children. Zhao H et al. 2016 Journal of human genetics
27464509 Opposite Associations between Individual KIAA0319 Polymorphisms and Developmental Dyslexia Risk across Populations: A Stratified Meta-Analysis by the Study Population. Shao S et al. 2016 Scientific reports
31204720 Association between <i>KIAA0319</i> SNPs and risk of dyslexia: a meta-analysis. Deng KG et al. 2019 Journal of genetics
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