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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 Aliases 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.

rs11126936

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr2:27260233 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.36851 (46273/125568, TOPMED)
T=0.3466 (10852/31306, GnomAD)
T=0.391 (1958/5008, 1000G) (+ 4 more)
T=0.211 (945/4480, Estonian)
T=0.229 (882/3854, ALSPAC)
T=0.229 (849/3708, TWINSUK)
T=0.27 (159/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC30A3 : Intron Variant
Publications
3 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.27260233G>T
GRCh37.p13 chr 2 NC_000002.11:g.27483101G>T
Gene: SLC30A3, solute carrier family 30 member 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC30A3 transcript variant 2 NM_001318949.2:c. N/A Intron Variant
SLC30A3 transcript variant 3 NM_001318950.1:c. N/A Intron Variant
SLC30A3 transcript variant 4 NM_001318951.2:c. N/A Intron Variant
SLC30A3 transcript variant 1 NM_003459.5:c. N/A Intron Variant
SLC30A3 transcript variant X1 XM_005264547.2:c. N/A Intron Variant
SLC30A3 transcript variant X2 XM_005264548.3:c. N/A Intron Variant
SLC30A3 transcript variant X6 XM_011533102.2:c. N/A Intron Variant
SLC30A3 transcript variant X7 XM_011533103.2:c. N/A Intron Variant
SLC30A3 transcript variant X3 XM_017004873.1:c. N/A Intron Variant
SLC30A3 transcript variant X4 XM_017004874.1:c. N/A Intron Variant
SLC30A3 transcript variant X5 XM_017004875.2:c. 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
TopMed Global Study-wide 125568 G=0.63149 T=0.36851
gnomAD - Genomes Global Study-wide 31306 G=0.6534 T=0.3466
gnomAD - Genomes European Sub 18854 G=0.7753 T=0.2247
gnomAD - Genomes African Sub 8684 G=0.358 T=0.642
gnomAD - Genomes East Asian Sub 1554 G=0.855 T=0.145
gnomAD - Genomes Other Sub 1080 G=0.725 T=0.275
gnomAD - Genomes American Sub 844 G=0.49 T=0.51
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.69 T=0.31
1000Genomes Global Study-wide 5008 G=0.609 T=0.391
1000Genomes African Sub 1322 G=0.298 T=0.702
1000Genomes East Asian Sub 1008 G=0.845 T=0.155
1000Genomes Europe Sub 1006 G=0.769 T=0.231
1000Genomes South Asian Sub 978 G=0.65 T=0.35
1000Genomes American Sub 694 G=0.57 T=0.43
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.789 T=0.211
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.771 T=0.229
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.771 T=0.229
Northern Sweden ACPOP Study-wide 600 G=0.73 T=0.27
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= T Note
GRCh38.p12 chr 2 NC_000002.12:g.27260233= NC_000002.12:g.27260233G>T
GRCh37.p13 chr 2 NC_000002.11:g.27483101= NC_000002.11:g.27483101G>T
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#.

66 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17671568 Feb 27, 2004 (120)
2 SC_SNP ss18227263 Feb 27, 2004 (120)
3 ABI ss44273335 Mar 14, 2006 (126)
4 AFFY ss66419259 Nov 29, 2006 (127)
5 AFFY ss76183510 Dec 06, 2007 (129)
6 HGSV ss78317510 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82856127 Dec 15, 2007 (130)
8 HGSV ss83441401 Dec 14, 2007 (130)
9 HGSV ss85279645 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss91096386 Mar 24, 2008 (129)
11 BGI ss103467527 Dec 01, 2009 (131)
12 1000GENOMES ss109343609 Jan 24, 2009 (130)
13 1000GENOMES ss109987431 Jan 24, 2009 (130)
14 ENSEMBL ss138409750 Dec 01, 2009 (131)
15 ENSEMBL ss161254724 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss163220616 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss166319224 Jul 04, 2010 (132)
18 AFFY ss172737249 Jul 04, 2010 (132)
19 BUSHMAN ss200191229 Jul 04, 2010 (132)
20 1000GENOMES ss219133557 Jul 14, 2010 (132)
21 1000GENOMES ss231085997 Jul 14, 2010 (132)
22 1000GENOMES ss238659901 Jul 15, 2010 (132)
23 BL ss252988934 May 09, 2011 (134)
24 GMI ss276394716 May 04, 2012 (137)
25 PJP ss292532005 May 09, 2011 (134)
26 ILLUMINA ss410833292 Sep 17, 2011 (135)
27 ILLUMINA ss479530056 May 04, 2012 (137)
28 ILLUMINA ss484057854 May 04, 2012 (137)
29 ILLUMINA ss533065183 Sep 08, 2015 (146)
30 TISHKOFF ss555432487 Apr 25, 2013 (138)
31 SSMP ss649012717 Apr 25, 2013 (138)
32 ILLUMINA ss779603887 Sep 08, 2015 (146)
33 ILLUMINA ss781004414 Sep 08, 2015 (146)
34 ILLUMINA ss835075949 Sep 08, 2015 (146)
35 EVA-GONL ss976613925 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1068952228 Aug 21, 2014 (142)
37 1000GENOMES ss1296392166 Aug 21, 2014 (142)
38 DDI ss1428514362 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1578790362 Apr 01, 2015 (144)
40 EVA_DECODE ss1586018353 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1603066473 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1646060506 Apr 01, 2015 (144)
43 EVA_SVP ss1712440120 Apr 01, 2015 (144)
44 HAMMER_LAB ss1796453850 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1919846089 Feb 12, 2016 (147)
46 GENOMED ss1968721824 Jul 19, 2016 (147)
47 JJLAB ss2020451663 Sep 14, 2016 (149)
48 USC_VALOUEV ss2148496026 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2228518663 Dec 20, 2016 (150)
50 TOPMED ss2394434340 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624741294 Nov 08, 2017 (151)
52 ILLUMINA ss2633587427 Nov 08, 2017 (151)
53 GRF ss2703057069 Nov 08, 2017 (151)
54 GNOMAD ss2771087081 Nov 08, 2017 (151)
55 SWEGEN ss2989171212 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3023992200 Nov 08, 2017 (151)
57 TOPMED ss3302418795 Nov 08, 2017 (151)
58 CSHL ss3344130023 Nov 08, 2017 (151)
59 ILLUMINA ss3628018445 Oct 11, 2018 (152)
60 ILLUMINA ss3631555941 Oct 11, 2018 (152)
61 ILLUMINA ss3642083551 Oct 11, 2018 (152)
62 EGCUT_WGS ss3657125904 Jul 13, 2019 (153)
63 EVA_DECODE ss3703487571 Jul 13, 2019 (153)
64 ACPOP ss3728256318 Jul 13, 2019 (153)
65 EVA ss3756502845 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3800883617 Jul 13, 2019 (153)
67 1000Genomes NC_000002.11 - 27483101 Oct 11, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 27483101 Oct 11, 2018 (152)
69 Genetic variation in the Estonian population NC_000002.11 - 27483101 Oct 11, 2018 (152)
70 gnomAD - Genomes NC_000002.11 - 27483101 Jul 13, 2019 (153)
71 Northern Sweden NC_000002.11 - 27483101 Jul 13, 2019 (153)
72 TopMed NC_000002.12 - 27260233 Oct 11, 2018 (152)
73 UK 10K study - Twins NC_000002.11 - 27483101 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)
rs57783499 May 24, 2008 (130)
rs59862131 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78317510, ss83441401, ss85279645 NC_000002.9:27394751:G:T NC_000002.12:27260232:G:T (self)
ss91096386, ss109343609, ss109987431, ss163220616, ss166319224, ss200191229, ss252988934, ss276394716, ss292532005, ss484057854, ss1586018353, ss1712440120 NC_000002.10:27336604:G:T NC_000002.12:27260232:G:T (self)
7310378, 4058215, 2864152, 19904414, 1541183, 4058215, ss219133557, ss231085997, ss238659901, ss479530056, ss533065183, ss555432487, ss649012717, ss779603887, ss781004414, ss835075949, ss976613925, ss1068952228, ss1296392166, ss1428514362, ss1578790362, ss1603066473, ss1646060506, ss1796453850, ss1919846089, ss1968721824, ss2020451663, ss2148496026, ss2394434340, ss2624741294, ss2633587427, ss2703057069, ss2771087081, ss2989171212, ss3344130023, ss3628018445, ss3631555941, ss3642083551, ss3657125904, ss3728256318, ss3756502845 NC_000002.11:27483100:G:T NC_000002.12:27260232:G:T (self)
188510190, ss2228518663, ss3023992200, ss3302418795, ss3703487571, ss3800883617 NC_000002.12:27260232:G:T NC_000002.12:27260232:G:T (self)
ss17671568, ss18227263 NT_022184.13:6299033:G:T NC_000002.12:27260232:G:T (self)
ss44273335, ss66419259, ss76183510, ss82856127, ss103467527, ss138409750, ss161254724, ss172737249, ss410833292 NT_022184.15:6304987:G:T NC_000002.12:27260232:G:T (self)
Help

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

3 citations for rs11126936
PMID Title Author Year Journal
24338343 The effects of interactions between selenium and zinc serum concentration and SEP15 and SLC30A3 gene polymorphisms on memory scores in a population of mature and elderly adults. da Rocha TJ et al. 2014 Genes & nutrition
27750116 Common variants in the chromosome 2p23 region containing the SLC30A3 (ZnT3) gene are associated with schizophrenia in female but not male individuals in a large collection of European samples. Perez-Becerril C et al. 2016 Psychiatry research
29149619 Association of SNPs in genes encoding zinc transporters on blood zinc levels in humans. Fujihara J et al. 2018 Legal medicine (Tokyo, Japan)

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.post308+0fe9b3b