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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.

rs2000175

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:6273889 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.052042 (13775/264690, TOPMED)
C=0.044312 (6212/140188, GnomAD)
C=0.02504 (473/18890, ALFA) (+ 15 more)
C=0.21366 (3581/16760, 8.3KJPN)
C=0.0695 (348/5008, 1000G)
C=0.0058 (26/4480, Estonian)
C=0.0008 (3/3854, ALSPAC)
C=0.0008 (3/3708, TWINSUK)
C=0.2017 (591/2930, KOREAN)
C=0.2036 (373/1832, Korea1K)
C=0.001 (1/998, GoNL)
C=0.000 (0/600, NorthernSweden)
C=0.049 (27/554, SGDP_PRJ)
C=0.108 (35/324, HapMap)
C=0.000 (0/216, Qatari)
C=0.142 (30/212, Vietnamese)
C=0.02 (1/56, Siberian)
C=0.00 (0/40, 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.6273889C>A
GRCh38.p13 chr 10 NC_000010.11:g.6273889C>G
GRCh38.p13 chr 10 NC_000010.11:g.6273889C>T
GRCh37.p13 chr 10 NC_000010.10:g.6315852C>A
GRCh37.p13 chr 10 NC_000010.10:g.6315852C>G
GRCh37.p13 chr 10 NC_000010.10:g.6315852C>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 18890 C=0.02504 G=0.97496
European Sub 14286 C=0.00308 G=0.99692
African Sub 2946 C=0.1083 G=0.8917
African Others Sub 114 C=0.175 G=0.825
African American Sub 2832 C=0.1056 G=0.8944
Asian Sub 112 C=0.250 G=0.750
East Asian Sub 86 C=0.27 G=0.73
Other Asian Sub 26 C=0.19 G=0.81
Latin American 1 Sub 146 C=0.034 G=0.966
Latin American 2 Sub 610 C=0.075 G=0.925
South Asian Sub 98 C=0.02 G=0.98
Other Sub 692 C=0.042 G=0.958


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 C=0.052042 G=0.947958
gnomAD - Genomes Global Study-wide 140188 C=0.044312 G=0.955688
gnomAD - Genomes European Sub 75962 C=0.00207 G=0.99793
gnomAD - Genomes African Sub 41970 C=0.11091 G=0.88909
gnomAD - Genomes American Sub 13654 C=0.05295 G=0.94705
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.0012 G=0.9988
gnomAD - Genomes East Asian Sub 3126 C=0.1878 G=0.8122
gnomAD - Genomes Other Sub 2154 C=0.0399 G=0.9601
8.3KJPN JAPANESE Study-wide 16760 C=0.21366 G=0.78634
1000Genomes Global Study-wide 5008 C=0.0695 G=0.9305
1000Genomes African Sub 1322 C=0.1180 G=0.8820
1000Genomes East Asian Sub 1008 C=0.1508 G=0.8492
1000Genomes Europe Sub 1006 C=0.0010 G=0.9990
1000Genomes South Asian Sub 978 C=0.004 G=0.996
1000Genomes American Sub 694 C=0.050 G=0.950
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.0058 G=0.9942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.0008 G=0.9992
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.0008 G=0.9992
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2017 A=0.0000, G=0.7983, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 C=0.2036 G=0.7964
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.001 G=0.999
Northern Sweden ACPOP Study-wide 600 C=0.000 G=1.000
SGDP_PRJ Global Study-wide 554 C=0.049 G=0.951
HapMap Global Study-wide 324 C=0.108 G=0.892
HapMap American Sub 120 C=0.000 G=1.000
HapMap African Sub 118 C=0.161 G=0.839
HapMap Asian Sub 86 C=0.19 G=0.81
Qatari Global Study-wide 216 C=0.000 G=1.000
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.142 G=0.858
Siberian Global Study-wide 56 C=0.02 G=0.98
The Danish reference pan genome Danish Study-wide 40 C=0.00 G=1.00
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 C= A G T
GRCh38.p13 chr 10 NC_000010.11:g.6273889= NC_000010.11:g.6273889C>A NC_000010.11:g.6273889C>G NC_000010.11:g.6273889C>T
GRCh37.p13 chr 10 NC_000010.10:g.6315852= NC_000010.10:g.6315852C>A NC_000010.10:g.6315852C>G NC_000010.10:g.6315852C>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#.

68 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2914357 Jan 12, 2001 (92)
2 SC_JCM ss6059561 Feb 20, 2003 (126)
3 BCM_SSAHASNP ss10599835 Jul 11, 2003 (116)
4 SC_SNP ss16093937 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss17383309 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss19159999 Feb 27, 2004 (120)
7 SSAHASNP ss20685015 Apr 05, 2004 (121)
8 HGSV ss78121006 Dec 05, 2007 (129)
9 BCMHGSC_JDW ss88080948 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97532702 Feb 06, 2009 (130)
11 BGI ss102850389 Dec 01, 2009 (131)
12 1000GENOMES ss109197478 Jan 23, 2009 (130)
13 1000GENOMES ss115305433 Jan 25, 2009 (130)
14 ILLUMINA-UK ss119003938 Dec 01, 2009 (131)
15 ENSEMBL ss131661859 Dec 01, 2009 (131)
16 ENSEMBL ss137961484 Dec 01, 2009 (131)
17 GMI ss154522796 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss167743360 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss168978904 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss170369414 Jul 04, 2010 (132)
21 BUSHMAN ss201097523 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss207204569 Jul 04, 2010 (132)
23 1000GENOMES ss224544557 Jul 14, 2010 (132)
24 1000GENOMES ss241773907 Jul 15, 2010 (132)
25 BL ss254025844 May 09, 2011 (134)
26 GMI ss280464773 May 04, 2012 (137)
27 GMI ss286122488 Apr 25, 2013 (138)
28 PJP ss290900169 May 09, 2011 (134)
29 TISHKOFF ss561745429 Apr 25, 2013 (138)
30 SSMP ss656251661 Apr 25, 2013 (138)
31 EVA-GONL ss987157348 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1076731737 Aug 21, 2014 (142)
33 1000GENOMES ss1336130255 Aug 21, 2014 (142)
34 DDI ss1426208854 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1574889265 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1623911837 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1666905870 Apr 01, 2015 (144)
38 HAMMER_LAB ss1806238315 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1930478275 Feb 12, 2016 (147)
40 GENOMED ss1967049563 Jul 19, 2016 (147)
41 JJLAB ss2025962277 Sep 14, 2016 (149)
42 USC_VALOUEV ss2154204312 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2172358760 Dec 20, 2016 (150)
44 TOPMED ss2335067858 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2627450044 Nov 08, 2017 (151)
46 GRF ss2698428222 Nov 08, 2017 (151)
47 GNOMAD ss2885105557 Nov 08, 2017 (151)
48 SWEGEN ss3005875673 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3026764652 Nov 08, 2017 (151)
50 TOPMED ss3110664854 Nov 08, 2017 (151)
51 CSHL ss3348941959 Nov 08, 2017 (151)
52 URBANLAB ss3649280466 Oct 12, 2018 (152)
53 EGCUT_WGS ss3673402795 Jul 13, 2019 (153)
54 EVA_DECODE ss3689206632 Jul 13, 2019 (153)
55 ACPOP ss3737026957 Jul 13, 2019 (153)
56 EVA ss3747699713 Jul 13, 2019 (153)
57 PACBIO ss3786570212 Jul 13, 2019 (153)
58 PACBIO ss3791764100 Jul 13, 2019 (153)
59 PACBIO ss3796645880 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3813062674 Jul 13, 2019 (153)
61 EVA ss3831947045 Apr 26, 2020 (154)
62 EVA ss3839504359 Apr 26, 2020 (154)
63 EVA ss3844970341 Apr 26, 2020 (154)
64 SGDP_PRJ ss3873453556 Apr 26, 2020 (154)
65 KRGDB ss3921389028 Apr 26, 2020 (154)
66 KOGIC ss3967131430 Apr 26, 2020 (154)
67 TOPMED ss4841244024 Apr 26, 2021 (155)
68 TOMMO_GENOMICS ss5196096983 Apr 26, 2021 (155)
69 1000Genomes NC_000010.10 - 6315852 Oct 12, 2018 (152)
70 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 6315852 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000010.10 - 6315852 Oct 12, 2018 (152)
72 The Danish reference pan genome NC_000010.10 - 6315852 Apr 26, 2020 (154)
73 gnomAD - Genomes NC_000010.11 - 6273889 Apr 26, 2021 (155)
74 Genome of the Netherlands Release 5 NC_000010.10 - 6315852 Apr 26, 2020 (154)
75 HapMap NC_000010.11 - 6273889 Apr 26, 2020 (154)
76 KOREAN population from KRGDB NC_000010.10 - 6315852 Apr 26, 2020 (154)
77 Korean Genome Project NC_000010.11 - 6273889 Apr 26, 2020 (154)
78 Northern Sweden NC_000010.10 - 6315852 Jul 13, 2019 (153)
79 Qatari NC_000010.10 - 6315852 Apr 26, 2020 (154)
80 SGDP_PRJ NC_000010.10 - 6315852 Apr 26, 2020 (154)
81 Siberian NC_000010.10 - 6315852 Apr 26, 2020 (154)
82 8.3KJPN NC_000010.10 - 6315852 Apr 26, 2021 (155)
83 TopMed NC_000010.11 - 6273889 Apr 26, 2021 (155)
84 UK 10K study - Twins NC_000010.10 - 6315852 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000010.10 - 6315852 Jul 13, 2019 (153)
86 ALFA NC_000010.11 - 6273889 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).

Associated ID History Updated (Build)
rs4500391 Mar 10, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
28566422, ss3921389028 NC_000010.10:6315851:C:A NC_000010.11:6273888:C:A (self)
ss78121006 NC_000010.8:6355857:C:G NC_000010.11:6273888:C:G (self)
ss88080948, ss109197478, ss115305433, ss119003938, ss167743360, ss168978904, ss170369414, ss201097523, ss207204569, ss254025844, ss280464773, ss286122488, ss290900169 NC_000010.9:6355857:C:G NC_000010.11:6273888:C:G (self)
48471572, 26932246, 19141043, 2014468, 12012232, 28566422, 10311822, 12520205, 25470536, 6720666, 54066290, 26932246, 5978606, ss224544557, ss241773907, ss561745429, ss656251661, ss987157348, ss1076731737, ss1336130255, ss1426208854, ss1574889265, ss1623911837, ss1666905870, ss1806238315, ss1930478275, ss1967049563, ss2025962277, ss2154204312, ss2335067858, ss2627450044, ss2698428222, ss2885105557, ss3005875673, ss3348941959, ss3673402795, ss3737026957, ss3747699713, ss3786570212, ss3791764100, ss3796645880, ss3831947045, ss3839504359, ss3873453556, ss3921389028, ss5196096983 NC_000010.10:6315851:C:G NC_000010.11:6273888:C:G (self)
342416724, 330078, 23509431, 35684463, 56789679, 4220087771, ss2172358760, ss3026764652, ss3110664854, ss3649280466, ss3689206632, ss3813062674, ss3844970341, ss3967131430, ss4841244024 NC_000010.11:6273888:C:G NC_000010.11:6273888:C:G (self)
ss2914357, ss6059561, ss97532702, ss102850389, ss131661859, ss137961484, ss154522796 NT_008705.16:6255851:C:G NC_000010.11:6273888:C:G (self)
ss10599835, ss16093937, ss17383309, ss19159999, ss20685015 NT_077569.2:678747:C:G NC_000010.11:6273888:C:G (self)
28566422, ss3921389028 NC_000010.10:6315851:C:T NC_000010.11:6273888:C: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 rs2000175

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