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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.

rs10947089

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:30742358 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.07900 (9920/125568, TOPMED)
G=0.0588 (4950/84202, GnomAD)
G=0.0715 (2201/30800, GnomAD) (+ 4 more)
G=0.0830 (1240/14948, ExAC)
G=0.098 (489/5008, 1000G)
G=0.033 (126/3854, ALSPAC)
G=0.032 (119/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FLOT1 : Intron Variant
LOC105379695 : 2KB Upstream 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 6 NC_000006.12:g.30742358A>G
GRCh37.p13 chr 6 NC_000006.11:g.30710135A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2222098A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2222204A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1997468A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2003064A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1998209A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2003794A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2043154A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2042452A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2052609A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2058229A>G
Gene: FLOT1, flotillin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FLOT1 transcript variant 2 NM_001318875.1:c. N/A Intron Variant
FLOT1 transcript variant 1 NM_005803.3:c. N/A Intron Variant
FLOT1 transcript variant X1 XM_005248780.3:c. N/A Intron Variant
FLOT1 transcript variant X4 XM_006714947.3:c. N/A Intron Variant
FLOT1 transcript variant X2 XM_017010157.1:c. N/A Intron Variant
FLOT1 transcript variant X3 XM_017010158.1:c. N/A Intron Variant
Gene: LOC105379695, uncharacterized LOC105379695 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105379695 transcript variant X1 XR_001744079.1:n. N/A Upstream Transcript 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
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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
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.92100 G=0.07900
The Genome Aggregation Database Global Study-wide 84202 A=0.9412 G=0.0588
The Genome Aggregation Database European Sub 44986 A=0.9685 G=0.0315
The Genome Aggregation Database Asian Sub 16902 A=0.8909 G=0.1091
The Genome Aggregation Database American Sub 11868 A=0.9626 G=0.0374
The Genome Aggregation Database African Sub 6584 A=0.844 G=0.156
The Genome Aggregation Database Other Sub 2066 A=0.941 G=0.059
The Genome Aggregation Database Ashkenazi Jewish Sub 1796 A=0.947 G=0.053
The Genome Aggregation Database Global Study-wide 30800 A=0.9285 G=0.0715
The Genome Aggregation Database European Sub 18386 A=0.9711 G=0.0289
The Genome Aggregation Database African Sub 8690 A=0.841 G=0.159
The Genome Aggregation Database East Asian Sub 1608 A=0.895 G=0.105
The Genome Aggregation Database Other Sub 976 A=0.95 G=0.05
The Genome Aggregation Database American Sub 838 A=0.95 G=0.05
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.94 G=0.06
The Exome Aggregation Consortium Global Study-wide 14948 A=0.9170 G=0.0830
The Exome Aggregation Consortium Europe Sub 9768 A=0.948 G=0.052
The Exome Aggregation Consortium Asian Sub 2614 A=0.855 G=0.145
The Exome Aggregation Consortium African Sub 1710 A=0.822 G=0.178
The Exome Aggregation Consortium American Sub 720 A=0.95 G=0.05
The Exome Aggregation Consortium Other Sub 136 A=0.93 G=0.07
1000Genomes Global Study-wide 5008 A=0.902 G=0.098
1000Genomes African Sub 1322 A=0.828 G=0.172
1000Genomes East Asian Sub 1008 A=0.921 G=0.079
1000Genomes Europe Sub 1006 A=0.961 G=0.039
1000Genomes South Asian Sub 978 A=0.89 G=0.11
1000Genomes American Sub 694 A=0.95 G=0.05
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.967 G=0.033
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.968 G=0.032
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 A= G Note
GRCh38.p7 chr 6 NC_000006.12:g.30742358A= NC_000006.12:g.30742358A>G
GRCh37.p13 chr 6 NC_000006.11:g.30710135A= NC_000006.11:g.30710135A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2222098A= NT_113891.3:g.2222098A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2222204A= NT_113891.2:g.2222204A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1997468A= NT_167248.2:g.1997468A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2003064A= NT_167248.1:g.2003064A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1998209A= NT_167245.2:g.1998209A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2003794A= NT_167245.1:g.2003794A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2043154A= NT_167249.2:g.2043154A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2042452A= NT_167249.1:g.2042452A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2052609A= NT_167246.2:g.2052609A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2058229A= NT_167246.1:g.2058229A>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#.

7 Frequency, 62 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15409322 Feb 27, 2004 (120)
2 SC_SNP ss18234670 Feb 27, 2004 (120)
3 BGI ss104294103 Dec 01, 2009 (131)
4 ILLUMINA ss152885058 Dec 01, 2009 (131)
5 ILLUMINA ss159154890 Dec 01, 2009 (131)
6 ILLUMINA ss159941879 Dec 01, 2009 (131)
7 ILLUMINA ss169726850 Jul 04, 2010 (132)
8 ILLUMINA ss170791419 Jul 04, 2010 (132)
9 1000GENOMES ss222294478 Jul 14, 2010 (137)
10 1000GENOMES ss233389207 Jul 14, 2010 (137)
11 1000GENOMES ss240460945 Jul 15, 2010 (137)
12 GMI ss278716978 May 04, 2012 (137)
13 ILLUMINA ss410890428 Sep 17, 2011 (137)
14 ILLUMINA ss479413991 May 04, 2012 (137)
15 ILLUMINA ss479417446 May 04, 2012 (137)
16 ILLUMINA ss479833522 Sep 08, 2015 (146)
17 ILLUMINA ss484506936 May 04, 2012 (137)
18 CLINSEQ_SNP ss491884246 May 04, 2012 (137)
19 ILLUMINA ss536656813 Sep 08, 2015 (146)
20 TISHKOFF ss559104971 Apr 25, 2013 (138)
21 SSMP ss653022952 Apr 25, 2013 (138)
22 ILLUMINA ss778747183 Sep 08, 2015 (146)
23 ILLUMINA ss782700023 Sep 08, 2015 (146)
24 ILLUMINA ss783668077 Sep 08, 2015 (146)
25 ILLUMINA ss831951155 Sep 08, 2015 (146)
26 ILLUMINA ss834206824 Sep 08, 2015 (146)
27 EVA-GONL ss982750317 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1073496484 Aug 21, 2014 (142)
29 1000GENOMES ss1319528178 Aug 21, 2014 (142)
30 EVA_DECODE ss1592297570 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1615260626 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1658254659 Apr 01, 2015 (144)
33 EVA_EXAC ss1688221912 Apr 01, 2015 (144)
34 EVA_MGP ss1711119580 Apr 01, 2015 (144)
35 ILLUMINA ss1752626473 Sep 08, 2015 (146)
36 HAMMER_LAB ss1804350076 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1926001935 Feb 12, 2016 (147)
38 GENOMED ss1970351605 Jul 19, 2016 (147)
39 JJLAB ss2023630058 Sep 14, 2016 (149)
40 USC_VALOUEV ss2151795317 Nov 08, 2017 (151)
41 HUMAN_LONGEVITY ss2282902481 Dec 20, 2016 (150)
42 TOPMED ss2451273818 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2626301180 Nov 08, 2017 (151)
44 ILLUMINA ss2634425990 Nov 08, 2017 (151)
45 GRF ss2707387799 Nov 08, 2017 (151)
46 GNOMAD ss2735634499 Nov 08, 2017 (151)
47 GNOMAD ss2747576646 Nov 08, 2017 (151)
48 GNOMAD ss2837357200 Nov 08, 2017 (151)
49 AFFY ss2985991436 Nov 08, 2017 (151)
50 SWEGEN ss2998774143 Nov 08, 2017 (151)
51 TOPMED ss3493696428 Nov 08, 2017 (151)
52 ILLUMINA ss3629495877 Jul 20, 2018 (151)
53 ILLUMINA ss3632344989 Jul 20, 2018 (151)
54 ILLUMINA ss3633414023 Jul 20, 2018 (151)
55 ILLUMINA ss3634136390 Jul 20, 2018 (151)
56 ILLUMINA ss3635054836 Jul 20, 2018 (151)
57 ILLUMINA ss3635817491 Jul 20, 2018 (151)
58 ILLUMINA ss3636774858 Jul 20, 2018 (151)
59 ILLUMINA ss3637570253 Jul 20, 2018 (151)
60 ILLUMINA ss3638618054 Jul 20, 2018 (151)
61 ILLUMINA ss3640762134 Jul 20, 2018 (151)
62 BIOINF_KMB_FNS_UNIBA ss3645942684 Jul 20, 2018 (151)
63 1000Genomes NC_000006.11 - 30710135 Jul 20, 2018 (151)
64 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 30710135 Jul 20, 2018 (151)
65 The Exome Aggregation Consortium NC_000006.11 - 30710135 Jul 20, 2018 (151)
66 The Genome Aggregation Database NC_000006.11 - 30710135 Jul 20, 2018 (151)
67 The Genome Aggregation Database NC_000006.11 - 30710135 Jul 20, 2018 (151)
68 Trans-Omics for Precision Medicine NC_000006.12 - 30742358 Jul 20, 2018 (151)
69 UK 10K study - Twins NC_000006.11 - 30710135 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)
rs116355317 May 04, 2012 (137)
rs116864750 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss278716978, ss479413991, ss491884246, ss1592297570 NC_000006.10:30818113:A= NC_000006.12:30742357:A= (self)
31294267, 17448078, 8246222, 177984957, 4649234, 17448078, ss222294478, ss233389207, ss240460945, ss479417446, ss479833522, ss484506936, ss536656813, ss559104971, ss653022952, ss778747183, ss782700023, ss783668077, ss831951155, ss834206824, ss982750317, ss1073496484, ss1319528178, ss1615260626, ss1658254659, ss1688221912, ss1711119580, ss1752626473, ss1804350076, ss1926001935, ss1970351605, ss2023630058, ss2151795317, ss2451273818, ss2626301180, ss2634425990, ss2707387799, ss2735634499, ss2747576646, ss2837357200, ss2985991436, ss2998774143, ss3629495877, ss3632344989, ss3633414023, ss3634136390, ss3635054836, ss3635817491, ss3636774858, ss3637570253, ss3638618054, ss3640762134 NC_000006.11:30710134:A= NC_000006.12:30742357:A= (self)
334940247, ss2282902481, ss3493696428, ss3645942684 NC_000006.12:30742357:A= NC_000006.12:30742357:A= (self)
ss15409322, ss18234670 NT_007592.13:21566568:A= NC_000006.12:30742357:A= (self)
ss104294103, ss152885058, ss159154890, ss159941879, ss169726850, ss170791419, ss410890428 NT_007592.15:30650134:A= NC_000006.12:30742357:A= (self)
ss278716978, ss479413991, ss491884246, ss1592297570 NC_000006.10:30818113:A>G NC_000006.12:30742357:A>G (self)
31294267, 17448078, 8246222, 177984957, 4649234, 17448078, ss222294478, ss233389207, ss240460945, ss479417446, ss479833522, ss484506936, ss536656813, ss559104971, ss653022952, ss778747183, ss782700023, ss783668077, ss831951155, ss834206824, ss982750317, ss1073496484, ss1319528178, ss1615260626, ss1658254659, ss1688221912, ss1711119580, ss1752626473, ss1804350076, ss1926001935, ss1970351605, ss2023630058, ss2151795317, ss2451273818, ss2626301180, ss2634425990, ss2707387799, ss2735634499, ss2747576646, ss2837357200, ss2985991436, ss2998774143, ss3629495877, ss3632344989, ss3633414023, ss3634136390, ss3635054836, ss3635817491, ss3636774858, ss3637570253, ss3638618054, ss3640762134 NC_000006.11:30710134:A>G NC_000006.12:30742357:A>G (self)
334940247, ss2282902481, ss3493696428, ss3645942684 NC_000006.12:30742357:A>G NC_000006.12:30742357:A>G (self)
ss15409322, ss18234670 NT_007592.13:21566568:A>G NC_000006.12:30742357:A>G (self)
ss104294103, ss152885058, ss159154890, ss159941879, ss169726850, ss170791419, ss410890428 NT_007592.15:30650134:A>G NC_000006.12:30742357:A>G (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 rs10947089

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: 0.1.4.post833+d3ba21e