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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.

rs1171614

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr10:59709780 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.21271 (26710/125568, TOPMED)
T=0.1971 (6072/30804, GnomAD)
T=0.159 (795/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC16A9 : Intron Variant
Publications
6 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 10 NC_000010.11:g.59709780T>C
GRCh37.p13 chr 10 NC_000010.10:g.61469538T>C
Gene: SLC16A9, solute carrier family 16 member 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC16A9 transcript variant 3 NM_001323977.1:c. N/A Intron Variant
SLC16A9 transcript variant 1 NM_194298.2:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant 2 NM_001323981.1:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant 4 NM_001323978.1:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant 5 NM_001323979.1:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant 6 NM_001323980.1:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant X1 XM_017015883.1:c. N/A 5 Prime UTR Variant
SLC16A9 transcript variant X2 XM_017015884.1:c. N/A 5 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
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=0.21271 C=0.78729
The Genome Aggregation Database Global Study-wide 30804 T=0.1971 C=0.8029
The Genome Aggregation Database European Sub 18400 T=0.1987 C=0.8013
The Genome Aggregation Database African Sub 8672 T=0.240 C=0.760
The Genome Aggregation Database East Asian Sub 1616 T=0.001 C=0.999
The Genome Aggregation Database Other Sub 978 T=0.18 C=0.82
The Genome Aggregation Database American Sub 838 T=0.12 C=0.88
The Genome Aggregation Database Ashkenazi Jewish Sub 300 T=0.20 C=0.80
1000Genomes Global Study-wide 5008 T=0.159 C=0.841
1000Genomes African Sub 1322 T=0.238 C=0.762
1000Genomes East Asian Sub 1008 T=0.001 C=0.999
1000Genomes Europe Sub 1006 T=0.242 C=0.758
1000Genomes South Asian Sub 978 T=0.14 C=0.86
1000Genomes American Sub 694 T=0.15 C=0.85
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 Note
GRCh38.p7 chr 10 NC_000010.11:g.59709780T= NC_000010.11:g.59709780T>C
GRCh37.p13 chr 10 NC_000010.10:g.61469538T= NC_000010.10:g.61469538T>C
SLC16A9 transcript variant 1 NM_194298.2:c.-338A= NM_194298.2:c.-338A>G
SLC16A9 transcript variant X2 XM_017015884.1:c.-483A= XM_017015884.1:c.-483A>G
SLC16A9 transcript variant X1 XM_017015883.1:c.-338A= XM_017015883.1:c.-338A>G
SLC16A9 transcript variant 2 NM_001323981.1:c.-421A= NM_001323981.1:c.-421A>G
SLC16A9 transcript variant 4 NM_001323978.1:c.-552A= NM_001323978.1:c.-552A>G
SLC16A9 transcript variant 6 NM_001323980.1:c.-469A= NM_001323980.1:c.-469A>G
SLC16A9 transcript variant 5 NM_001323979.1:c.-239A= NM_001323979.1:c.-239A>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#.

60 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1603876 Oct 18, 2000 (87)
2 SC_JCM ss2544853 Nov 08, 2000 (89)
3 BGI ss5592192 Dec 12, 2002 (110)
4 SC_SNP ss16048044 Feb 27, 2004 (120)
5 SSAHASNP ss20633762 Apr 05, 2004 (121)
6 ILLUMINA ss74872190 Dec 06, 2007 (129)
7 HGSV ss85945681 Dec 15, 2007 (130)
8 CORNELL ss86272140 Mar 23, 2008 (129)
9 BCMHGSC_JDW ss88232720 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97559425 Feb 05, 2009 (130)
11 BGI ss106680396 Feb 05, 2009 (130)
12 1000GENOMES ss113336830 Jan 25, 2009 (130)
13 KRIBB_YJKIM ss119384533 Dec 01, 2009 (131)
14 ENSEMBL ss131898146 Dec 01, 2009 (131)
15 ENSEMBL ss137967160 Dec 01, 2009 (131)
16 ILLUMINA ss153039773 Dec 01, 2009 (131)
17 GMI ss155099285 Dec 01, 2009 (131)
18 ILLUMINA ss159185379 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss168438689 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss170148926 Jul 04, 2010 (132)
21 ILLUMINA ss171482556 Jul 04, 2010 (132)
22 BUSHMAN ss201583693 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss207160236 Jul 04, 2010 (132)
24 1000GENOMES ss224754142 Jul 14, 2010 (132)
25 1000GENOMES ss235195937 Jul 15, 2010 (132)
26 1000GENOMES ss241897993 Jul 15, 2010 (132)
27 BL ss254354439 May 09, 2011 (134)
28 GMI ss280637455 May 04, 2012 (137)
29 PJP ss290848942 May 09, 2011 (134)
30 ILLUMINA ss479768346 May 04, 2012 (137)
31 ILLUMINA ss482621722 May 04, 2012 (137)
32 TISHKOFF ss561987432 Apr 25, 2013 (138)
33 SSMP ss656805772 Apr 25, 2013 (138)
34 ILLUMINA ss781063772 Aug 21, 2014 (142)
35 EVA-GONL ss987541582 Aug 21, 2014 (142)
36 1000GENOMES ss1337637619 Aug 21, 2014 (142)
37 DDI ss1426336880 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1575148387 Apr 01, 2015 (144)
39 EVA_DECODE ss1597207523 Apr 01, 2015 (144)
40 EVA_SVP ss1713183200 Apr 01, 2015 (144)
41 HAMMER_LAB ss1806412246 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1930905376 Feb 12, 2016 (147)
43 ILLUMINA ss1959266196 Feb 12, 2016 (147)
44 JJLAB ss2026175662 Sep 14, 2016 (149)
45 USC_VALOUEV ss2154448605 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2175155925 Dec 20, 2016 (150)
47 TOPMED ss2338187290 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2627558274 Nov 08, 2017 (151)
49 ILLUMINA ss2632716881 Nov 08, 2017 (151)
50 GRF ss2698692937 Nov 08, 2017 (151)
51 GNOMAD ss2889347785 Nov 08, 2017 (151)
52 AFFY ss2985558161 Nov 08, 2017 (151)
53 SWEGEN ss3006560450 Nov 08, 2017 (151)
54 ILLUMINA ss3021243902 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3026878658 Nov 08, 2017 (151)
56 TOPMED ss3121146376 Nov 08, 2017 (151)
57 CSHL ss3349146322 Nov 08, 2017 (151)
58 ILLUMINA ss3637852488 Jul 20, 2018 (151)
59 ILLUMINA ss3641680414 Jul 20, 2018 (151)
60 ILLUMINA ss3642855828 Jul 20, 2018 (151)
61 1000Genomes NC_000010.10 - 61469538 Jul 20, 2018 (151)
62 The Genome Aggregation Database NC_000010.10 - 61469538 Jul 20, 2018 (151)
63 Trans-Omics for Precision Medicine NC_000010.11 - 59709780 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)
rs59129181 May 25, 2008 (130)
rs117224594 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss85945681 NC_000010.8:61139543:T= NC_000010.11:59709779:T= (self)
ss88232720, ss113336830, ss168438689, ss170148926, ss201583693, ss207160236, ss254354439, ss280637455, ss290848942, ss482621722, ss1597207523, ss1713183200, ss3642855828 NC_000010.9:61139543:T= NC_000010.11:59709779:T= (self)
50032713, 23049306, ss224754142, ss235195937, ss241897993, ss479768346, ss561987432, ss656805772, ss781063772, ss987541582, ss1337637619, ss1426336880, ss1575148387, ss1806412246, ss1930905376, ss1959266196, ss2026175662, ss2154448605, ss2338187290, ss2627558274, ss2632716881, ss2698692937, ss2889347785, ss2985558161, ss3006560450, ss3021243902, ss3349146322, ss3637852488, ss3641680414 NC_000010.10:61469537:T= NC_000010.11:59709779:T= (self)
43789026, ss2175155925, ss3026878658, ss3121146376 NC_000010.11:59709779:T= NC_000010.11:59709779:T= (self)
ss16048044, ss20633762 NT_008583.16:10020692:T= NC_000010.11:59709779:T= (self)
ss1603876, ss2544853, ss5592192, ss74872190, ss86272140, ss97559425, ss106680396, ss119384533, ss131898146, ss137967160, ss153039773, ss155099285, ss159185379, ss171482556 NT_030059.13:12274001:T= NC_000010.11:59709779:T= (self)
ss85945681 NC_000010.8:61139543:T>C NC_000010.11:59709779:T>C (self)
ss88232720, ss113336830, ss168438689, ss170148926, ss201583693, ss207160236, ss254354439, ss280637455, ss290848942, ss482621722, ss1597207523, ss1713183200, ss3642855828 NC_000010.9:61139543:T>C NC_000010.11:59709779:T>C (self)
50032713, 23049306, ss224754142, ss235195937, ss241897993, ss479768346, ss561987432, ss656805772, ss781063772, ss987541582, ss1337637619, ss1426336880, ss1575148387, ss1806412246, ss1930905376, ss1959266196, ss2026175662, ss2154448605, ss2338187290, ss2627558274, ss2632716881, ss2698692937, ss2889347785, ss2985558161, ss3006560450, ss3021243902, ss3349146322, ss3637852488, ss3641680414 NC_000010.10:61469537:T>C NC_000010.11:59709779:T>C (self)
43789026, ss2175155925, ss3026878658, ss3121146376 NC_000010.11:59709779:T>C NC_000010.11:59709779:T>C (self)
ss16048044, ss20633762 NT_008583.16:10020692:T>C NC_000010.11:59709779:T>C (self)
ss1603876, ss2544853, ss5592192, ss74872190, ss86272140, ss97559425, ss106680396, ss119384533, ss131898146, ss137967160, ss153039773, ss155099285, ss159185379, ss171482556 NT_030059.13:12274001:T>C NC_000010.11:59709779: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.

6 citations for rs1171614
PMID Title Author Year Journal
16385451 A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Grupe A et al. 2006 American journal of human genetics
24376456 Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9. Simino J et al. 2013 Frontiers in genetics
25569235 Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. Demirkan A et al. 2015 PLoS genetics
25788527 Uric Acid and Cardiovascular Events: A Mendelian Randomization Study. Kleber ME et al. 2015 Journal of the American Society of Nephrology
27073872 Genetic Influences on Metabolite Levels: A Comparison across Metabolomic Platforms. Yet I et al. 2016 PloS one
28793914 Performance of gout definitions for genetic epidemiological studies: analysis of UK Biobank. Cadzow M et al. 2017 Arthritis research & therapy

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