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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs6836706

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:9962627 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.48347 (60708/125568, TOPMED)
A=0.4774 (14751/30900, GnomAD)
A=0.417 (2086/5008, 1000G) (+ 2 more)
A=0.425 (1637/3854, ALSPAC)
A=0.419 (1552/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC2A9 : Intron Variant
Publications
0 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 4 NC_000004.12:g.9962627T>A
GRCh37.p13 chr 4 NC_000004.11:g.9964251T>A
SLC2A9 RefSeqGene NG_011540.1:g.82622A>T
Gene: SLC2A9, solute carrier family 2 member 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC2A9 transcript variant 2 NM_001001290.1:c. N/A Intron Variant
SLC2A9 transcript variant 1 NM_020041.2:c. N/A Intron Variant
SLC2A9 transcript variant X5 XM_006713968.3:c. N/A Intron Variant
SLC2A9 transcript variant X22 XM_006713969.2:c. N/A Intron Variant
SLC2A9 transcript variant X1 XM_011513856.2:c. N/A Intron Variant
SLC2A9 transcript variant X3 XM_011513857.1:c. N/A Intron Variant
SLC2A9 transcript variant X4 XM_011513858.1:c. N/A Intron Variant
SLC2A9 transcript variant X7 XM_011513859.2:c. N/A Intron Variant
SLC2A9 transcript variant X8 XM_011513860.2:c. N/A Intron Variant
SLC2A9 transcript variant X10 XM_011513861.2:c. N/A Intron Variant
SLC2A9 transcript variant X11 XM_011513862.2:c. N/A Intron Variant
SLC2A9 transcript variant X12 XM_011513863.2:c. N/A Intron Variant
SLC2A9 transcript variant X14 XM_011513864.2:c. N/A Intron Variant
SLC2A9 transcript variant X17 XM_011513865.2:c. N/A Intron Variant
SLC2A9 transcript variant X18 XM_011513866.2:c. N/A Intron Variant
SLC2A9 transcript variant X17 XM_011513867.2:c. N/A Intron Variant
SLC2A9 transcript variant X21 XM_011513868.2:c. N/A Intron Variant
SLC2A9 transcript variant X2 XM_017008457.1:c. N/A Intron Variant
SLC2A9 transcript variant X9 XM_017008458.1:c. N/A Intron Variant
SLC2A9 transcript variant X16 XM_017008459.1:c. N/A Intron Variant
SLC2A9 transcript variant X20 XM_017008460.1:c. N/A Intron Variant
SLC2A9 transcript variant X24 XR_001741290.1:n. N/A Intron Variant
SLC2A9 transcript variant X25 XR_001741291.1:n. N/A Intron Variant
SLC2A9 transcript variant X6 XR_925341.2: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 T=0.51653 A=0.48347
The Genome Aggregation Database Global Study-wide 30900 T=0.5226 A=0.4774
The Genome Aggregation Database European Sub 18466 T=0.5777 A=0.4223
The Genome Aggregation Database African Sub 8698 T=0.331 A=0.669
The Genome Aggregation Database East Asian Sub 1620 T=0.885 A=0.115
The Genome Aggregation Database Other Sub 978 T=0.59 A=0.41
The Genome Aggregation Database American Sub 836 T=0.49 A=0.51
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.61 A=0.39
1000Genomes Global Study-wide 5008 T=0.583 A=0.417
1000Genomes African Sub 1322 T=0.280 A=0.720
1000Genomes East Asian Sub 1008 T=0.893 A=0.107
1000Genomes Europe Sub 1006 T=0.572 A=0.428
1000Genomes South Asian Sub 978 T=0.75 A=0.25
1000Genomes American Sub 694 T=0.49 A=0.51
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.575 A=0.425
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.581 A=0.419
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= A Note
GRCh38.p7 chr 4 NC_000004.12:g.9962627T= NC_000004.12:g.9962627T>A
GRCh37.p13 chr 4 NC_000004.11:g.9964251T= NC_000004.11:g.9964251T>A
SLC2A9 RefSeqGene NG_011540.1:g.82622A= NG_011540.1:g.82622A>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#.

5 Frequency, 41 SubSNP submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10148778 Jul 11, 2003 (116)
2 CSHL-HAPMAP ss17813565 Feb 27, 2004 (120)
3 BCMHGSC_JDW ss92466395 Mar 24, 2008 (129)
4 1000GENOMES ss111769443 Jan 25, 2009 (130)
5 1000GENOMES ss112907056 Jan 25, 2009 (130)
6 ILLUMINA-UK ss116867152 Dec 01, 2009 (131)
7 ENSEMBL ss139437957 Dec 01, 2009 (131)
8 ENSEMBL ss161585416 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss163079123 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss166132768 Jul 04, 2010 (132)
11 BUSHMAN ss198026936 Jul 04, 2010 (132)
12 1000GENOMES ss220736447 Jul 14, 2010 (132)
13 1000GENOMES ss232255046 Jul 14, 2010 (132)
14 1000GENOMES ss239577641 Jul 15, 2010 (132)
15 BL ss252927706 May 09, 2011 (134)
16 GMI ss284844259 Apr 25, 2013 (138)
17 PJP ss293138445 May 09, 2011 (134)
18 TISHKOFF ss557306104 Apr 25, 2013 (138)
19 SSMP ss651068219 Apr 25, 2013 (138)
20 EVA-GONL ss979756268 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1071268652 Aug 21, 2014 (142)
22 1000GENOMES ss1308404202 Aug 21, 2014 (142)
23 DDI ss1429770685 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1580410661 Apr 01, 2015 (144)
25 EVA_DECODE ss1589244316 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1609387657 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1652381690 Apr 01, 2015 (144)
28 HAMMER_LAB ss1801007446 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1922996861 Feb 12, 2016 (147)
30 GENOMED ss1969655568 Sep 14, 2016 (149)
31 JJLAB ss2022068550 Sep 14, 2016 (149)
32 USC_VALOUEV ss2150179863 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2260339618 Dec 20, 2016 (150)
34 TOPMED ss2427835623 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2625536497 Nov 08, 2017 (151)
36 GRF ss2705622843 Nov 08, 2017 (151)
37 GNOMAD ss2805556144 Nov 08, 2017 (151)
38 SWEGEN ss2994130429 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3024803081 Nov 08, 2017 (151)
40 CSHL ss3345540791 Nov 08, 2017 (151)
41 TOPMED ss3420146005 Nov 08, 2017 (151)
42 1000Genomes NC_000004.11 - 9964251 Jul 20, 2018 (151)
43 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 9964251 Jul 20, 2018 (151)
44 The Genome Aggregation Database NC_000004.11 - 9964251 Jul 20, 2018 (151)
45 Trans-Omics for Precision Medicine NC_000004.12 - 9962627 Jul 20, 2018 (151)
46 UK 10K study - Twins NC_000004.11 - 9964251 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss92466395, ss111769443, ss112907056, ss116867152, ss163079123, ss166132768, ss198026936, ss252927706, ss284844259, ss293138445, ss1589244316 NC_000004.10:9573348:T= NC_000004.12:9962626:T= (self)
19751089, 10993075, 146183899, 10993075, ss220736447, ss232255046, ss239577641, ss557306104, ss651068219, ss979756268, ss1071268652, ss1308404202, ss1429770685, ss1580410661, ss1609387657, ss1652381690, ss1801007446, ss1922996861, ss1969655568, ss2022068550, ss2150179863, ss2427835623, ss2625536497, ss2705622843, ss2805556144, ss2994130429, ss3345540791 NC_000004.11:9964250:T= NC_000004.12:9962626:T= (self)
275007634, ss2260339618, ss3024803081, ss3420146005 NC_000004.12:9962626:T= NC_000004.12:9962626:T= (self)
ss10148778, ss17813565 NT_006316.15:639608:T= NC_000004.12:9962626:T= (self)
ss139437957, ss161585416 NT_006316.16:1146047:T= NC_000004.12:9962626:T= (self)
ss92466395, ss111769443, ss112907056, ss116867152, ss163079123, ss166132768, ss198026936, ss252927706, ss284844259, ss293138445, ss1589244316 NC_000004.10:9573348:T>A NC_000004.12:9962626:T>A (self)
19751089, 10993075, 146183899, 10993075, ss220736447, ss232255046, ss239577641, ss557306104, ss651068219, ss979756268, ss1071268652, ss1308404202, ss1429770685, ss1580410661, ss1609387657, ss1652381690, ss1801007446, ss1922996861, ss1969655568, ss2022068550, ss2150179863, ss2427835623, ss2625536497, ss2705622843, ss2805556144, ss2994130429, ss3345540791 NC_000004.11:9964250:T>A NC_000004.12:9962626:T>A (self)
275007634, ss2260339618, ss3024803081, ss3420146005 NC_000004.12:9962626:T>A NC_000004.12:9962626:T>A (self)
ss10148778, ss17813565 NT_006316.15:639608:T>A NC_000004.12:9962626:T>A (self)
ss139437957, ss161585416 NT_006316.16:1146047:T>A NC_000004.12:9962626:T>A (self)
Help

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

No publications for rs6836706

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