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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.

rs6040708

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:11465784 (GRCh38.p14) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.356300 (94309/264690, TOPMED)
C=0.364456 (50975/139866, GnomAD)
C=0.34577 (9770/28256, 14KJPN) (+ 15 more)
C=0.33287 (6288/18890, ALFA)
C=0.34445 (5773/16760, 8.3KJPN)
C=0.3612 (2313/6404, 1000G_30x)
C=0.3560 (1783/5008, 1000G)
C=0.3355 (1503/4480, Estonian)
C=0.2807 (1082/3854, ALSPAC)
C=0.2807 (1041/3708, TWINSUK)
C=0.2751 (806/2930, KOREAN)
C=0.2898 (531/1832, Korea1K)
C=0.301 (300/998, GoNL)
C=0.263 (158/600, NorthernSweden)
C=0.238 (109/458, SGDP_PRJ)
C=0.375 (81/216, Qatari)
C=0.25 (13/52, Siberian)
C=0.33 (13/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.33287 T=0.66713
European Sub 14286 C=0.30351 T=0.69649
African Sub 2946 C=0.4956 T=0.5044
African Others Sub 114 C=0.439 T=0.561
African American Sub 2832 C=0.4979 T=0.5021
Asian Sub 112 C=0.286 T=0.714
East Asian Sub 86 C=0.28 T=0.72
Other Asian Sub 26 C=0.31 T=0.69
Latin American 1 Sub 146 C=0.308 T=0.692
Latin American 2 Sub 610 C=0.234 T=0.766
South Asian Sub 98 C=0.31 T=0.69
Other Sub 692 C=0.350 T=0.650


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=0.356300 T=0.643700
gnomAD - Genomes Global Study-wide 139866 C=0.364456 T=0.635544
gnomAD - Genomes European Sub 75742 C=0.30209 T=0.69791
gnomAD - Genomes African Sub 41914 C=0.50647 T=0.49353
gnomAD - Genomes American Sub 13622 C=0.30700 T=0.69300
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.2649 T=0.7351
gnomAD - Genomes East Asian Sub 3120 C=0.3349 T=0.6651
gnomAD - Genomes Other Sub 2146 C=0.3537 T=0.6463
14KJPN JAPANESE Study-wide 28256 C=0.34577 T=0.65423
Allele Frequency Aggregator Total Global 18890 C=0.33287 T=0.66713
Allele Frequency Aggregator European Sub 14286 C=0.30351 T=0.69649
Allele Frequency Aggregator African Sub 2946 C=0.4956 T=0.5044
Allele Frequency Aggregator Other Sub 692 C=0.350 T=0.650
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.234 T=0.766
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.308 T=0.692
Allele Frequency Aggregator Asian Sub 112 C=0.286 T=0.714
Allele Frequency Aggregator South Asian Sub 98 C=0.31 T=0.69
8.3KJPN JAPANESE Study-wide 16760 C=0.34445 T=0.65555
1000Genomes_30x Global Study-wide 6404 C=0.3612 T=0.6388
1000Genomes_30x African Sub 1786 C=0.5756 T=0.4244
1000Genomes_30x Europe Sub 1266 C=0.2938 T=0.7062
1000Genomes_30x South Asian Sub 1202 C=0.2105 T=0.7895
1000Genomes_30x East Asian Sub 1170 C=0.3504 T=0.6496
1000Genomes_30x American Sub 980 C=0.255 T=0.745
1000Genomes Global Study-wide 5008 C=0.3560 T=0.6440
1000Genomes African Sub 1322 C=0.5703 T=0.4297
1000Genomes East Asian Sub 1008 C=0.3522 T=0.6478
1000Genomes Europe Sub 1006 C=0.2962 T=0.7038
1000Genomes South Asian Sub 978 C=0.202 T=0.798
1000Genomes American Sub 694 C=0.256 T=0.744
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.3355 T=0.6645
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.2807 T=0.7193
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.2807 T=0.7193
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2751 T=0.7249
Korean Genome Project KOREAN Study-wide 1832 C=0.2898 T=0.7102
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.301 T=0.699
Northern Sweden ACPOP Study-wide 600 C=0.263 T=0.737
SGDP_PRJ Global Study-wide 458 C=0.238 T=0.762
Qatari Global Study-wide 216 C=0.375 T=0.625
Siberian Global Study-wide 52 C=0.25 T=0.75
The Danish reference pan genome Danish Study-wide 40 C=0.33 T=0.68
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.p14 chr 20 NC_000020.11:g.11465784C>T
GRCh37.p13 chr 20 NC_000020.10:g.11446432C>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
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= T
GRCh38.p14 chr 20 NC_000020.11:g.11465784= NC_000020.11:g.11465784C>T
GRCh37.p13 chr 20 NC_000020.10:g.11446432= NC_000020.10:g.11446432C>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#.

79 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8349642 Apr 21, 2003 (114)
2 SC_SNP ss11108010 Jul 11, 2003 (126)
3 SC_JCM ss11336875 Jul 11, 2003 (126)
4 CSHL-HAPMAP ss16893606 Feb 27, 2004 (126)
5 SSAHASNP ss21803000 Apr 05, 2004 (126)
6 HGSV ss77484241 Dec 07, 2007 (129)
7 HGSV ss78348706 Dec 07, 2007 (129)
8 HGSV ss79878543 Dec 14, 2007 (130)
9 HGSV ss82932467 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss91640507 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96215641 Feb 04, 2009 (130)
12 BGI ss103728548 Dec 01, 2009 (131)
13 1000GENOMES ss111734980 Jan 25, 2009 (130)
14 IGMI-SNU ss115462213 Feb 04, 2009 (130)
15 ILLUMINA-UK ss117487326 Dec 01, 2009 (131)
16 ENSEMBL ss133014889 Dec 01, 2009 (131)
17 ENSEMBL ss138211279 Dec 01, 2009 (131)
18 GMI ss156173874 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167823511 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss171909303 Jul 04, 2010 (132)
21 BUSHMAN ss203833338 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208680143 Jul 04, 2010 (132)
23 1000GENOMES ss228261132 Jul 14, 2010 (132)
24 1000GENOMES ss237766108 Jul 15, 2010 (132)
25 1000GENOMES ss243951989 Jul 15, 2010 (132)
26 BL ss255486483 May 09, 2011 (134)
27 GMI ss283303271 May 04, 2012 (137)
28 GMI ss287423935 Apr 25, 2013 (138)
29 PJP ss292612382 May 09, 2011 (134)
30 TISHKOFF ss566140867 Apr 25, 2013 (138)
31 SSMP ss662012552 Apr 25, 2013 (138)
32 EVA-GONL ss994547689 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1082079869 Aug 21, 2014 (142)
34 1000GENOMES ss1364096421 Aug 21, 2014 (142)
35 DDI ss1428998429 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1579440570 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1638430210 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1681424243 Apr 01, 2015 (144)
39 EVA_DECODE ss1698603884 Apr 01, 2015 (144)
40 HAMMER_LAB ss1809426176 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1938057656 Feb 12, 2016 (147)
42 GENOMED ss1969093058 Jul 19, 2016 (147)
43 JJLAB ss2029808652 Sep 14, 2016 (149)
44 USC_VALOUEV ss2158362182 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2241393350 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2629401212 Nov 08, 2017 (151)
47 GRF ss2704035847 Nov 08, 2017 (151)
48 GNOMAD ss2965519318 Nov 08, 2017 (151)
49 SWEGEN ss3017880216 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3028737418 Nov 08, 2017 (151)
51 CSHL ss3352423056 Nov 08, 2017 (151)
52 URBANLAB ss3650972839 Oct 12, 2018 (152)
53 EGCUT_WGS ss3684598040 Jul 13, 2019 (153)
54 EVA_DECODE ss3706575246 Jul 13, 2019 (153)
55 ACPOP ss3743255907 Jul 13, 2019 (153)
56 EVA ss3758431898 Jul 13, 2019 (153)
57 PACBIO ss3788601686 Jul 13, 2019 (153)
58 PACBIO ss3793501665 Jul 13, 2019 (153)
59 PACBIO ss3798388809 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3821605288 Jul 13, 2019 (153)
61 EVA ss3835592054 Apr 27, 2020 (154)
62 EVA ss3841421140 Apr 27, 2020 (154)
63 EVA ss3846928881 Apr 27, 2020 (154)
64 SGDP_PRJ ss3888748295 Apr 27, 2020 (154)
65 KRGDB ss3938938688 Apr 27, 2020 (154)
66 KOGIC ss3981837112 Apr 27, 2020 (154)
67 TOPMED ss5082542844 Apr 27, 2021 (155)
68 TOMMO_GENOMICS ss5228874894 Apr 27, 2021 (155)
69 1000G_HIGH_COVERAGE ss5308112387 Oct 13, 2022 (156)
70 HUGCELL_USP ss5500510756 Oct 13, 2022 (156)
71 EVA ss5512157148 Oct 13, 2022 (156)
72 1000G_HIGH_COVERAGE ss5614208357 Oct 13, 2022 (156)
73 SANFORD_IMAGENETICS ss5662880739 Oct 13, 2022 (156)
74 TOMMO_GENOMICS ss5787872136 Oct 13, 2022 (156)
75 YY_MCH ss5817823138 Oct 13, 2022 (156)
76 EVA ss5845455418 Oct 13, 2022 (156)
77 EVA ss5853072522 Oct 13, 2022 (156)
78 EVA ss5922707152 Oct 13, 2022 (156)
79 EVA ss5957783473 Oct 13, 2022 (156)
80 1000Genomes NC_000020.10 - 11446432 Oct 12, 2018 (152)
81 1000Genomes_30x NC_000020.11 - 11465784 Oct 13, 2022 (156)
82 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 11446432 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000020.10 - 11446432 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000020.10 - 11446432 Apr 27, 2020 (154)
85 gnomAD - Genomes NC_000020.11 - 11465784 Apr 27, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000020.10 - 11446432 Apr 27, 2020 (154)
87 KOREAN population from KRGDB NC_000020.10 - 11446432 Apr 27, 2020 (154)
88 Korean Genome Project NC_000020.11 - 11465784 Apr 27, 2020 (154)
89 Northern Sweden NC_000020.10 - 11446432 Jul 13, 2019 (153)
90 Qatari NC_000020.10 - 11446432 Apr 27, 2020 (154)
91 SGDP_PRJ NC_000020.10 - 11446432 Apr 27, 2020 (154)
92 Siberian NC_000020.10 - 11446432 Apr 27, 2020 (154)
93 8.3KJPN NC_000020.10 - 11446432 Apr 27, 2021 (155)
94 14KJPN NC_000020.11 - 11465784 Oct 13, 2022 (156)
95 TopMed NC_000020.11 - 11465784 Apr 27, 2021 (155)
96 UK 10K study - Twins NC_000020.10 - 11446432 Oct 12, 2018 (152)
97 ALFA NC_000020.11 - 11465784 Apr 27, 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)
rs6514195 May 23, 2006 (127)
rs57351617 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77484241, ss78348706, ss79878543, ss82932467, ss91640507, ss111734980, ss117487326, ss167823511, ss171909303, ss203833338, ss208680143, ss255486483, ss283303271, ss287423935, ss292612382, ss1698603884 NC_000020.9:11394431:C:T NC_000020.11:11465783:C:T (self)
77537021, 42924417, 30336288, 5605509, 19125665, 46116082, 16540772, 20099578, 40765275, 10878536, 86844201, 42924417, ss228261132, ss237766108, ss243951989, ss566140867, ss662012552, ss994547689, ss1082079869, ss1364096421, ss1428998429, ss1579440570, ss1638430210, ss1681424243, ss1809426176, ss1938057656, ss1969093058, ss2029808652, ss2158362182, ss2629401212, ss2704035847, ss2965519318, ss3017880216, ss3352423056, ss3684598040, ss3743255907, ss3758431898, ss3788601686, ss3793501665, ss3798388809, ss3835592054, ss3841421140, ss3888748295, ss3938938688, ss5228874894, ss5512157148, ss5662880739, ss5845455418, ss5957783473 NC_000020.10:11446431:C:T NC_000020.11:11465783:C:T (self)
101734292, 546708743, 38215113, 121709240, 357651789, 10911799816, ss2241393350, ss3028737418, ss3650972839, ss3706575246, ss3821605288, ss3846928881, ss3981837112, ss5082542844, ss5308112387, ss5500510756, ss5614208357, ss5787872136, ss5817823138, ss5853072522, ss5922707152 NC_000020.11:11465783:C:T NC_000020.11:11465783:C:T (self)
ss8349642, ss11108010, ss11336875, ss16893606, ss21803000, ss96215641, ss103728548, ss115462213, ss133014889, ss138211279, ss156173874 NT_011387.8:11386431:C:T NC_000020.11:11465783: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 rs6040708

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.post761+d5e8e07