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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 HGVS 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.

rs10906117

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:6263590 (GRCh38.p13) 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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.398258 (105415/264690, TOPMED)
A=0.388145 (54348/140020, GnomAD)
A=0.37671 (8167/21680, ALFA) (+ 17 more)
G=0.37399 (6268/16760, 8.3KJPN)
A=0.4633 (2320/5008, 1000G)
A=0.3234 (1449/4480, Estonian)
A=0.3077 (1186/3854, ALSPAC)
A=0.3223 (1195/3708, TWINSUK)
G=0.3604 (1056/2930, KOREAN)
G=0.3870 (709/1832, Korea1K)
A=0.3644 (414/1136, Daghestan)
A=0.293 (292/998, GoNL)
A=0.302 (181/600, NorthernSweden)
A=0.296 (132/446, SGDP_PRJ)
A=0.456 (145/318, HapMap)
A=0.338 (73/216, Qatari)
G=0.374 (80/214, Vietnamese)
A=0.13 (12/94, Ancient Sardinia)
A=0.26 (12/46, Siberian)
A=0.33 (13/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 10 NC_000010.11:g.6263590A>C
GRCh38.p13 chr 10 NC_000010.11:g.6263590A>G
GRCh38.p13 chr 10 NC_000010.11:g.6263590A>T
GRCh37.p13 chr 10 NC_000010.10:g.6305553A>C
GRCh37.p13 chr 10 NC_000010.10:g.6305553A>G
GRCh37.p13 chr 10 NC_000010.10:g.6305553A>T
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

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 21680 A=0.37671 C=0.00000, G=0.62329
European Sub 18492 A=0.34772 C=0.00000, G=0.65228
African Sub 1356 A=0.6342 C=0.0000, G=0.3658
African Others Sub 58 A=0.64 C=0.00, G=0.36
African American Sub 1298 A=0.6341 C=0.0000, G=0.3659
Asian Sub 78 A=0.92 C=0.00, G=0.08
East Asian Sub 62 A=0.92 C=0.00, G=0.08
Other Asian Sub 16 A=0.94 C=0.00, G=0.06
Latin American 1 Sub 50 A=0.68 C=0.00, G=0.32
Latin American 2 Sub 210 A=0.757 C=0.000, G=0.243
South Asian Sub 42 A=0.69 C=0.00, G=0.31
Other Sub 1452 A=0.4015 C=0.0000, G=0.5985


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 264690 A=0.398258 G=0.601742
gnomAD - Genomes Global Study-wide 140020 A=0.388145 G=0.611855
gnomAD - Genomes European Sub 75870 A=0.32749 G=0.67251
gnomAD - Genomes African Sub 41910 A=0.47297 G=0.52703
gnomAD - Genomes American Sub 13646 A=0.40349 G=0.59651
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.4196 G=0.5804
gnomAD - Genomes East Asian Sub 3122 A=0.6006 G=0.3994
gnomAD - Genomes Other Sub 2152 A=0.4205 G=0.5795
8.3KJPN JAPANESE Study-wide 16760 A=0.62601 G=0.37399
1000Genomes Global Study-wide 5008 A=0.4633 G=0.5367
1000Genomes African Sub 1322 A=0.5159 G=0.4841
1000Genomes East Asian Sub 1008 A=0.6101 G=0.3899
1000Genomes Europe Sub 1006 A=0.3439 G=0.6561
1000Genomes South Asian Sub 978 A=0.390 G=0.610
1000Genomes American Sub 694 A=0.427 G=0.573
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.3234 G=0.6766
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3077 G=0.6923
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3223 G=0.6777
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6396 G=0.3604, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.6130 G=0.3870
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.3644 G=0.6356
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.374 G=0.626
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.326 G=0.674
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.426 G=0.574
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.287 G=0.713
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.38 G=0.62
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.33 G=0.67
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.293 G=0.707
Northern Sweden ACPOP Study-wide 600 A=0.302 G=0.698
SGDP_PRJ Global Study-wide 446 A=0.296 G=0.704
HapMap Global Study-wide 318 A=0.456 G=0.544
HapMap American Sub 116 A=0.276 G=0.724
HapMap African Sub 114 A=0.570 G=0.430
HapMap Asian Sub 88 A=0.55 G=0.45
Qatari Global Study-wide 216 A=0.338 G=0.662
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.626 G=0.374
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 94 A=0.13 G=0.87
Siberian Global Study-wide 46 A=0.26 G=0.74
The Danish reference pan genome Danish Study-wide 40 A=0.33 G=0.68
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= C G T
GRCh38.p13 chr 10 NC_000010.11:g.6263590= NC_000010.11:g.6263590A>C NC_000010.11:g.6263590A>G NC_000010.11:g.6263590A>T
GRCh37.p13 chr 10 NC_000010.10:g.6305553= NC_000010.10:g.6305553A>C NC_000010.10:g.6305553A>G NC_000010.10:g.6305553A>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#.

72 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16090760 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17408714 Feb 27, 2004 (120)
3 SC_SNP ss18448482 Feb 27, 2004 (120)
4 ABI ss39719613 Mar 14, 2006 (126)
5 BCMHGSC_JDW ss88080902 Mar 23, 2008 (129)
6 BGI ss102850373 Dec 01, 2009 (131)
7 1000GENOMES ss109197375 Jan 23, 2009 (130)
8 ENSEMBL ss131661793 Dec 01, 2009 (131)
9 GMI ss154522695 Dec 01, 2009 (131)
10 ENSEMBL ss161352528 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss167742999 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss170369202 Jul 04, 2010 (132)
13 BUSHMAN ss201097436 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss207081052 Jul 04, 2010 (132)
15 1000GENOMES ss224544520 Jul 14, 2010 (132)
16 1000GENOMES ss235038051 Jul 15, 2010 (132)
17 1000GENOMES ss241773867 Jul 15, 2010 (132)
18 BL ss254025755 May 09, 2011 (134)
19 GMI ss280464736 May 04, 2012 (137)
20 GMI ss286122471 Apr 25, 2013 (138)
21 ILLUMINA ss482626742 May 04, 2012 (137)
22 ILLUMINA ss484174520 May 04, 2012 (137)
23 ILLUMINA ss536363381 Sep 08, 2015 (146)
24 TISHKOFF ss561745373 Apr 25, 2013 (138)
25 SSMP ss656251600 Apr 25, 2013 (138)
26 ILLUMINA ss780554756 Sep 08, 2015 (146)
27 ILLUMINA ss782533180 Sep 08, 2015 (146)
28 ILLUMINA ss836046901 Sep 08, 2015 (146)
29 EVA-GONL ss987157262 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1076731665 Aug 21, 2014 (142)
31 1000GENOMES ss1336129943 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397571510 Sep 08, 2015 (146)
33 DDI ss1426208819 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1574889223 Apr 01, 2015 (144)
35 EVA_DECODE ss1596805215 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1623911668 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1666905701 Apr 01, 2015 (144)
38 HAMMER_LAB ss1806238271 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1930478187 Feb 12, 2016 (147)
40 GENOMED ss1967049528 Jul 19, 2016 (147)
41 JJLAB ss2025962217 Sep 14, 2016 (149)
42 USC_VALOUEV ss2154204258 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2172358103 Dec 20, 2016 (150)
44 TOPMED ss2335067244 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2627450009 Nov 08, 2017 (151)
46 ILLUMINA ss2632669796 Nov 08, 2017 (151)
47 GRF ss2698428164 Nov 08, 2017 (151)
48 GNOMAD ss2885104713 Nov 08, 2017 (151)
49 SWEGEN ss3005875554 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3026764626 Nov 08, 2017 (151)
51 TOPMED ss3110662956 Nov 08, 2017 (151)
52 CSHL ss3348941924 Nov 08, 2017 (151)
53 ILLUMINA ss3626378160 Oct 12, 2018 (152)
54 ILLUMINA ss3630697704 Oct 12, 2018 (152)
55 ILLUMINA ss3641659096 Oct 12, 2018 (152)
56 EGCUT_WGS ss3673402661 Jul 13, 2019 (153)
57 EVA_DECODE ss3689206461 Jul 13, 2019 (153)
58 ACPOP ss3737026873 Jul 13, 2019 (153)
59 EVA ss3747699589 Jul 13, 2019 (153)
60 PACBIO ss3786570177 Jul 13, 2019 (153)
61 PACBIO ss3791764070 Jul 13, 2019 (153)
62 PACBIO ss3796645850 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3813062573 Jul 13, 2019 (153)
64 EVA ss3831946997 Apr 26, 2020 (154)
65 EVA ss3839504328 Apr 26, 2020 (154)
66 EVA ss3844970310 Apr 26, 2020 (154)
67 SGDP_PRJ ss3873453403 Apr 26, 2020 (154)
68 KRGDB ss3921388838 Apr 26, 2020 (154)
69 KOGIC ss3967131262 Apr 26, 2020 (154)
70 EVA ss3985455307 Apr 26, 2021 (155)
71 TOPMED ss4841241613 Apr 26, 2021 (155)
72 TOMMO_GENOMICS ss5196096632 Apr 26, 2021 (155)
73 1000Genomes NC_000010.10 - 6305553 Oct 12, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 6305553 Oct 12, 2018 (152)
75 Genome-wide autozygosity in Daghestan NC_000010.9 - 6345559 Apr 26, 2020 (154)
76 Genetic variation in the Estonian population NC_000010.10 - 6305553 Oct 12, 2018 (152)
77 The Danish reference pan genome NC_000010.10 - 6305553 Apr 26, 2020 (154)
78 gnomAD - Genomes NC_000010.11 - 6263590 Apr 26, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000010.10 - 6305553 Apr 26, 2020 (154)
80 HapMap NC_000010.11 - 6263590 Apr 26, 2020 (154)
81 KOREAN population from KRGDB NC_000010.10 - 6305553 Apr 26, 2020 (154)
82 Korean Genome Project NC_000010.11 - 6263590 Apr 26, 2020 (154)
83 Northern Sweden NC_000010.10 - 6305553 Jul 13, 2019 (153)
84 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000010.10 - 6305553 Apr 26, 2021 (155)
85 Qatari NC_000010.10 - 6305553 Apr 26, 2020 (154)
86 SGDP_PRJ NC_000010.10 - 6305553 Apr 26, 2020 (154)
87 Siberian NC_000010.10 - 6305553 Apr 26, 2020 (154)
88 8.3KJPN NC_000010.10 - 6305553 Apr 26, 2021 (155)
89 TopMed NC_000010.11 - 6263590 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000010.10 - 6305553 Oct 12, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000010.10 - 6305553 Jul 13, 2019 (153)
92 ALFA NC_000010.11 - 6263590 Apr 26, 2021 (155)
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
10421436529 NC_000010.11:6263589:A:C NC_000010.11:6263589:A:C
43119, ss88080902, ss109197375, ss167742999, ss170369202, ss201097436, ss207081052, ss254025755, ss280464736, ss286122471, ss482626742, ss1397571510, ss1596805215 NC_000010.9:6345558:A:G NC_000010.11:6263589:A:G (self)
48471245, 26932056, 19140909, 2014427, 12012151, 28566232, 10311738, 681234, 12520117, 25470383, 6720612, 54065939, 26932056, 5978549, ss224544520, ss235038051, ss241773867, ss484174520, ss536363381, ss561745373, ss656251600, ss780554756, ss782533180, ss836046901, ss987157262, ss1076731665, ss1336129943, ss1426208819, ss1574889223, ss1623911668, ss1666905701, ss1806238271, ss1930478187, ss1967049528, ss2025962217, ss2154204258, ss2335067244, ss2627450009, ss2632669796, ss2698428164, ss2885104713, ss3005875554, ss3348941924, ss3626378160, ss3630697704, ss3641659096, ss3673402661, ss3737026873, ss3747699589, ss3786570177, ss3791764070, ss3796645850, ss3831946997, ss3839504328, ss3873453403, ss3921388838, ss3985455307, ss5196096632 NC_000010.10:6305552:A:G NC_000010.11:6263589:A:G (self)
342414657, 330047, 23509263, 35682891, 56787268, 10421436529, ss2172358103, ss3026764626, ss3110662956, ss3689206461, ss3813062573, ss3844970310, ss3967131262, ss4841241613 NC_000010.11:6263589:A:G NC_000010.11:6263589:A:G (self)
ss39719613, ss102850373, ss131661793, ss154522695, ss161352528 NT_008705.16:6245552:A:G NC_000010.11:6263589:A:G (self)
ss16090760, ss17408714, ss18448482 NT_077569.2:668448:A:G NC_000010.11:6263589:A:G (self)
28566232, ss3921388838 NC_000010.10:6305552:A:T NC_000010.11:6263589:A:T (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 rs10906117

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad