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dbSNP Short Genetic Variations

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.

rs6905288

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:43791136 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.44133 (55417/125568, TOPMED)
G=0.4408 (13609/30872, GnomAD)
G=0.355 (1777/5008, 1000G) (+ 3 more)
G=0.416 (1864/4480, Estonian)
G=0.431 (1663/3854, ALSPAC)
G=0.427 (1583/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
16 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 6 NC_000006.12:g.43791136G>A
GRCh37.p13 chr 6 NC_000006.11:g.43758873G>A
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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
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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 125568 G=0.44133 A=0.55867
gnomAD - Genomes Global Study-wide 30872 G=0.4408 A=0.5592
gnomAD - Genomes European Sub 18442 G=0.4315 A=0.5685
gnomAD - Genomes African Sub 8698 G=0.502 A=0.498
gnomAD - Genomes East Asian Sub 1616 G=0.287 A=0.713
gnomAD - Genomes Other Sub 978 G=0.39 A=0.61
gnomAD - Genomes American Sub 838 G=0.38 A=0.62
gnomAD - Genomes Ashkenazi Jewish Sub 300 G=0.40 A=0.60
1000Genomes Global Study-wide 5008 G=0.355 A=0.645
1000Genomes African Sub 1322 G=0.499 A=0.501
1000Genomes East Asian Sub 1008 G=0.259 A=0.741
1000Genomes Europe Sub 1006 G=0.404 A=0.596
1000Genomes South Asian Sub 978 G=0.18 A=0.82
1000Genomes American Sub 694 G=0.40 A=0.60
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.416 A=0.584
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.431 A=0.569
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.427 A=0.573
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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 Note
GRCh38.p12 chr 6 NC_000006.12:g.43791136G= NC_000006.12:g.43791136G>A
GRCh37.p13 chr 6 NC_000006.11:g.43758873G= NC_000006.11:g.43758873G>A
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#.

90 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10280381 Jul 11, 2003 (116)
2 SC_SNP ss12796212 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss17127325 Feb 27, 2004 (120)
4 SSAHASNP ss22388157 Apr 05, 2004 (123)
5 ABI ss42676750 Mar 15, 2006 (126)
6 AFFY ss66111986 Nov 30, 2006 (127)
7 PERLEGEN ss68975412 May 17, 2007 (127)
8 AFFY ss76093202 Dec 08, 2007 (130)
9 HGSV ss77725249 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss82345327 Dec 16, 2007 (130)
11 HGSV ss83969949 Dec 15, 2007 (130)
12 HGSV ss84830464 Dec 15, 2007 (130)
13 HGSV ss85787662 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss93450765 Mar 24, 2008 (129)
15 HUMANGENOME_JCVI ss98494466 Feb 06, 2009 (130)
16 SNP500CANCER ss105438074 Feb 06, 2009 (130)
17 BGI ss105996674 Feb 06, 2009 (130)
18 1000GENOMES ss110031446 Jan 24, 2009 (130)
19 ILLUMINA-UK ss116442687 Feb 14, 2009 (130)
20 ENSEMBL ss143872200 Dec 01, 2009 (131)
21 ENSEMBL ss144051006 Dec 01, 2009 (131)
22 GMI ss156865833 Dec 01, 2009 (131)
23 ILLUMINA ss160823552 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss162298752 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss163455082 Jul 04, 2010 (132)
26 AFFY ss172480159 Jul 04, 2010 (132)
27 ILLUMINA ss174162156 Jul 04, 2010 (132)
28 BUSHMAN ss201755447 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss207563191 Jul 04, 2010 (132)
30 1000GENOMES ss211831925 Jul 14, 2010 (132)
31 1000GENOMES ss222363757 Jul 14, 2010 (132)
32 1000GENOMES ss233450762 Jul 14, 2010 (132)
33 1000GENOMES ss240512387 Jul 15, 2010 (132)
34 GMI ss278775063 May 04, 2012 (137)
35 GMI ss285394975 Apr 25, 2013 (138)
36 PJP ss293847908 May 09, 2011 (134)
37 ILLUMINA ss410944776 Sep 17, 2011 (135)
38 ILLUMINA ss482400413 Sep 08, 2015 (146)
39 EXOME_CHIP ss491386450 May 04, 2012 (137)
40 ILLUMINA ss537408359 Sep 08, 2015 (146)
41 TISHKOFF ss559173850 Apr 25, 2013 (138)
42 SSMP ss653112783 Apr 25, 2013 (138)
43 ILLUMINA ss780686130 Sep 08, 2015 (146)
44 ILLUMINA ss783359637 Sep 08, 2015 (146)
45 EVA-GONL ss982876074 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1073574652 Aug 21, 2014 (142)
47 1000GENOMES ss1319918364 Aug 21, 2014 (142)
48 DDI ss1430705450 Apr 01, 2015 (144)
49 EVA_GENOME_DK ss1581651209 Apr 01, 2015 (144)
50 EVA_DECODE ss1592412288 Apr 01, 2015 (144)
51 EVA_UK10K_ALSPAC ss1615469122 Apr 01, 2015 (144)
52 EVA_UK10K_TWINSUK ss1658463155 Apr 01, 2015 (144)
53 EVA_SVP ss1712859747 Apr 01, 2015 (144)
54 ILLUMINA ss1752638155 Sep 08, 2015 (146)
55 HAMMER_LAB ss1804405839 Sep 08, 2015 (146)
56 ILLUMINA ss1917805980 Feb 12, 2016 (147)
57 WEILL_CORNELL_DGM ss1926132321 Feb 12, 2016 (147)
58 ILLUMINA ss1946178669 Feb 12, 2016 (147)
59 ILLUMINA ss1958906383 Feb 12, 2016 (147)
60 GENOMED ss1970384469 Jul 19, 2016 (147)
61 JJLAB ss2023705668 Sep 14, 2016 (149)
62 ILLUMINA ss2094827761 Dec 20, 2016 (150)
63 ILLUMINA ss2095183450 Dec 20, 2016 (150)
64 USC_VALOUEV ss2151884192 Dec 20, 2016 (150)
65 HUMAN_LONGEVITY ss2283646713 Dec 20, 2016 (150)
66 TOPMED ss2452022723 Dec 20, 2016 (150)
67 SYSTEMSBIOZJU ss2626340234 Nov 08, 2017 (151)
68 ILLUMINA ss2634447168 Nov 08, 2017 (151)
69 GRF ss2707483094 Nov 08, 2017 (151)
70 ILLUMINA ss2711078057 Nov 08, 2017 (151)
71 GNOMAD ss2838404010 Nov 08, 2017 (151)
72 AFFY ss2985368728 Nov 08, 2017 (151)
73 AFFY ss2986000091 Nov 08, 2017 (151)
74 SWEGEN ss2998980264 Nov 08, 2017 (151)
75 ILLUMINA ss3022617728 Nov 08, 2017 (151)
76 BIOINF_KMB_FNS_UNIBA ss3025644020 Nov 08, 2017 (151)
77 CSHL ss3346938387 Nov 08, 2017 (151)
78 TOPMED ss3496058554 Nov 08, 2017 (151)
79 ILLUMINA ss3625902187 Oct 12, 2018 (152)
80 ILLUMINA ss3629537737 Oct 12, 2018 (152)
81 ILLUMINA ss3629537738 Oct 12, 2018 (152)
82 ILLUMINA ss3635066063 Oct 12, 2018 (152)
83 ILLUMINA ss3636788778 Oct 12, 2018 (152)
84 ILLUMINA ss3638628140 Oct 12, 2018 (152)
85 ILLUMINA ss3640773362 Oct 12, 2018 (152)
86 ILLUMINA ss3644911727 Oct 12, 2018 (152)
87 URBANLAB ss3648339794 Oct 12, 2018 (152)
88 ILLUMINA ss3653134401 Oct 12, 2018 (152)
89 ILLUMINA ss3653134402 Oct 12, 2018 (152)
90 ILLUMINA ss3654134087 Oct 12, 2018 (152)
91 1000Genomes NC_000006.11 - 43758873 Oct 12, 2018 (152)
92 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 43758873 Oct 12, 2018 (152)
93 Genetic variation in the Estonian population NC_000006.11 - 43758873 Oct 12, 2018 (152)
94 gnomAD - Genomes NC_000006.11 - 43758873 Oct 12, 2018 (152)
95 TopMed NC_000006.12 - 43791136 Oct 12, 2018 (152)
96 UK 10K study - Twins NC_000006.11 - 43758873 Oct 12, 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)
rs13194806 Sep 24, 2004 (123)
rs56555242 May 25, 2008 (130)
rs60057782 May 25, 2008 (130)
rs61109254 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77725249, ss83969949, ss84830464, ss85787662 NC_000006.9:43866850:G:A NC_000006.12:43791135:G:A (self)
ss93450765, ss110031446, ss116442687, ss162298752, ss163455082, ss201755447, ss207563191, ss211831925, ss278775063, ss285394975, ss293847908, ss1592412288, ss1712859747 NC_000006.10:43866850:G:A NC_000006.12:43791135:G:A (self)
31699545, 17679216, 12609706, 179031767, 17679216, ss222363757, ss233450762, ss240512387, ss482400413, ss491386450, ss537408359, ss559173850, ss653112783, ss780686130, ss783359637, ss982876074, ss1073574652, ss1319918364, ss1430705450, ss1581651209, ss1615469122, ss1658463155, ss1752638155, ss1804405839, ss1917805980, ss1926132321, ss1946178669, ss1958906383, ss1970384469, ss2023705668, ss2094827761, ss2095183450, ss2151884192, ss2452022723, ss2626340234, ss2634447168, ss2707483094, ss2711078057, ss2838404010, ss2985368728, ss2986000091, ss2998980264, ss3022617728, ss3346938387, ss3625902187, ss3629537737, ss3629537738, ss3635066063, ss3636788778, ss3638628140, ss3640773362, ss3644911727, ss3653134401, ss3653134402, ss3654134087 NC_000006.11:43758872:G:A NC_000006.12:43791135:G:A (self)
336781815, ss2283646713, ss3025644020, ss3496058554, ss3648339794 NC_000006.12:43791135:G:A NC_000006.12:43791135:G:A (self)
ss10280381, ss12796212, ss17127325, ss22388157 NT_007592.13:34555999:G:A NC_000006.12:43791135:G:A (self)
ss42676750, ss66111986, ss68975412, ss76093202, ss82345327, ss98494466, ss105438074, ss105996674, ss143872200, ss144051006, ss156865833, ss160823552, ss172480159, ss174162156, ss410944776 NT_007592.15:43698872:G:A NC_000006.12:43791135:G:A (self)
Help

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

16 citations for rs6905288
PMID Title Author Year Journal
20935629 Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Heid IM et al. 2010 Nature genetics
21466928 Genetics and epigenetics of obesity. Herrera BM et al. 2011 Maturitas
21953277 Association studies of novel obesity-related gene variants with quantitative metabolic phenotypes in a population-based sample of 6,039 Danish individuals. Burgdorf KS et al. 2012 Diabetologia
22651247 Sex differences in human adipose tissues - the biology of pear shape. Karastergiou K et al. 2012 Biology of sex differences
23057767 Inflammatory gene variants and the risk of biliary tract cancers and stones: a population-based study in China. Castro FA et al. 2012 BMC cancer
23221025 Replication study of 15 recently published Loci for body fat distribution in the Japanese population. Hotta K et al. 2013 Journal of atherosclerosis and thrombosis
23998998 Abdominal obesity and lower gray matter volume: a Mendelian randomization study. Debette S et al. 2014 Neurobiology of aging
26667837 Polymorphisms in Host Immunity-Modulating Genes and Risk of Invasive Aspergillosis: Results from the AspBIOmics Consortium. Lupiañez CB et al. 2015 Infection and immunity
26848030 Effects of Obesity Related Genetic Variations on Visceral and Subcutaneous Fat Distribution in a Chinese Population. Wang T et al. 2016 Scientific reports
27104953 Effects of Genetic Loci Associated with Central Obesity on Adipocyte Lipolysis. Strawbridge RJ et al. 2016 PloS one
27195708 Investigation of Genetic Variation Underlying Central Obesity amongst South Asians. Scott WR et al. 2016 PloS one
27427429 Commentary: Two-sample Mendelian randomization: opportunities and challenges. Lawlor DA et al. 2016 International journal of epidemiology
28333968 A genome-wide association study of thyroid stimulating hormone and free thyroxine in Danish children and adolescents. Nielsen TR et al. 2017 PloS one
28401323 Exploring single nucleotide polymorphisms previously related to obesity and metabolic traits in pediatric-onset type 2 diabetes. Miranda-Lora AL et al. 2017 Acta diabetologica
28860667 A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors. Brænne I et al. 2017 Scientific reports
29660117 Polymorphisms of genes involved in inflammation and blood vessel development influence the risk of varicose veins. Shadrina A et al. 2018 Clinical genetics

Genomic regions, transcripts, and products
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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.post104+4a6ee9c