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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs2394415

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:31102909 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.312656 (82757/264690, TOPMED)
A=0.317182 (44382/139926, GnomAD)
A=0.03461 (978/28258, 14KJPN) (+ 15 more)
A=0.03556 (596/16760, 8.3KJPN)
A=0.11413 (1320/11566, ALFA)
A=0.2658 (1702/6404, 1000G_30x)
A=0.2562 (1283/5008, 1000G)
A=0.2625 (1176/4480, Estonian)
A=0.2867 (1105/3854, ALSPAC)
A=0.2942 (1091/3708, TWINSUK)
A=0.0664 (194/2922, KOREAN)
A=0.308 (307/998, GoNL)
A=0.205 (123/600, NorthernSweden)
A=0.213 (46/216, Qatari)
A=0.084 (18/214, Vietnamese)
G=0.435 (81/186, SGDP_PRJ)
A=0.38 (15/40, GENOME_DK)
G=0.38 (10/26, Siberian)
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 11566 G=0.88587 A=0.11413
European Sub 9556 G=0.8713 A=0.1287
African Sub 1054 G=0.9801 A=0.0199
African Others Sub 30 G=1.00 A=0.00
African American Sub 1024 G=0.9795 A=0.0205
Asian Sub 98 G=1.00 A=0.00
East Asian Sub 78 G=1.00 A=0.00
Other Asian Sub 20 G=1.00 A=0.00
Latin American 1 Sub 48 G=1.00 A=0.00
Latin American 2 Sub 310 G=1.000 A=0.000
South Asian Sub 60 G=1.00 A=0.00
Other Sub 440 G=0.843 A=0.157


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 G=0.687344 A=0.312656
gnomAD - Genomes Global Study-wide 139926 G=0.682818 A=0.317182
gnomAD - Genomes European Sub 75830 G=0.71344 A=0.28656
gnomAD - Genomes African Sub 41890 G=0.59656 A=0.40344
gnomAD - Genomes American Sub 13608 G=0.71781 A=0.28219
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.6723 A=0.3277
gnomAD - Genomes East Asian Sub 3130 G=0.9466 A=0.0534
gnomAD - Genomes Other Sub 2148 G=0.6941 A=0.3059
14KJPN JAPANESE Study-wide 28258 G=0.96539 A=0.03461
8.3KJPN JAPANESE Study-wide 16760 G=0.96444 A=0.03556
Allele Frequency Aggregator Total Global 11566 G=0.88587 A=0.11413
Allele Frequency Aggregator European Sub 9556 G=0.8713 A=0.1287
Allele Frequency Aggregator African Sub 1054 G=0.9801 A=0.0199
Allele Frequency Aggregator Other Sub 440 G=0.843 A=0.157
Allele Frequency Aggregator Latin American 2 Sub 310 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 98 G=1.00 A=0.00
Allele Frequency Aggregator South Asian Sub 60 G=1.00 A=0.00
Allele Frequency Aggregator Latin American 1 Sub 48 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.7342 A=0.2658
1000Genomes_30x African Sub 1786 G=0.5649 A=0.4351
1000Genomes_30x Europe Sub 1266 G=0.7212 A=0.2788
1000Genomes_30x South Asian Sub 1202 G=0.8136 A=0.1864
1000Genomes_30x East Asian Sub 1170 G=0.9496 A=0.0504
1000Genomes_30x American Sub 980 G=0.705 A=0.295
1000Genomes Global Study-wide 5008 G=0.7438 A=0.2562
1000Genomes African Sub 1322 G=0.5734 A=0.4266
1000Genomes East Asian Sub 1008 G=0.9504 A=0.0496
1000Genomes Europe Sub 1006 G=0.7217 A=0.2783
1000Genomes South Asian Sub 978 G=0.814 A=0.186
1000Genomes American Sub 694 G=0.702 A=0.298
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7375 A=0.2625
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7133 A=0.2867
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7058 A=0.2942
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9336 A=0.0664
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.692 A=0.308
Northern Sweden ACPOP Study-wide 600 G=0.795 A=0.205
Qatari Global Study-wide 216 G=0.787 A=0.213
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.916 A=0.084
SGDP_PRJ Global Study-wide 186 G=0.435 A=0.565
The Danish reference pan genome Danish Study-wide 40 G=0.62 A=0.38
Siberian Global Study-wide 26 G=0.38 A=0.62
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 6 NC_000006.12:g.31102909G>A
GRCh38.p14 chr 6 NC_000006.12:g.31102909G>C
GRCh37.p13 chr 6 NC_000006.11:g.31070686G>A
GRCh37.p13 chr 6 NC_000006.11:g.31070686G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2585289A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2585289A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2585395A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2585395A>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2360927G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2360927G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2366523G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2366523G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2362273G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2362273G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2367858G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2367858G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2406405G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2406405G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2405703G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2405703G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2413409G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2413409G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2419029G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2419029G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2447023G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2447023G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2452608G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2452608G>C
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 G= A C
GRCh38.p14 chr 6 NC_000006.12:g.31102909= NC_000006.12:g.31102909G>A NC_000006.12:g.31102909G>C
GRCh37.p13 chr 6 NC_000006.11:g.31070686= NC_000006.11:g.31070686G>A NC_000006.11:g.31070686G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2585289A>G NT_113891.3:g.2585289= NT_113891.3:g.2585289A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2585395A>G NT_113891.2:g.2585395= NT_113891.2:g.2585395A>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2360927= NT_167248.2:g.2360927G>A NT_167248.2:g.2360927G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2366523= NT_167248.1:g.2366523G>A NT_167248.1:g.2366523G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2362273= NT_167245.2:g.2362273G>A NT_167245.2:g.2362273G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2367858= NT_167245.1:g.2367858G>A NT_167245.1:g.2367858G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2406405= NT_167249.2:g.2406405G>A NT_167249.2:g.2406405G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2405703= NT_167249.1:g.2405703G>A NT_167249.1:g.2405703G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2413409= NT_167246.2:g.2413409G>A NT_167246.2:g.2413409G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2419029= NT_167246.1:g.2419029G>A NT_167246.1:g.2419029G>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2447023= NT_167247.2:g.2447023G>A NT_167247.2:g.2447023G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2452608= NT_167247.1:g.2452608G>A NT_167247.1:g.2452608G>C
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#.

61 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3356945 Sep 28, 2001 (100)
2 SC_JCM ss3528343 Sep 28, 2001 (126)
3 SC_JCM ss11255979 Jul 11, 2003 (126)
4 SI_MHC_SNP ss12686492 Oct 31, 2003 (126)
5 ABI ss42658622 Mar 11, 2006 (126)
6 HGSV ss78789777 Dec 07, 2007 (129)
7 COMPLETE_GENOMICS ss162186671 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss163329321 Jul 04, 2010 (132)
9 BUSHMAN ss201609190 Jul 04, 2010 (132)
10 BL ss254171948 May 09, 2011 (137)
11 1000GENOMES ss333180652 May 09, 2011 (137)
12 TISHKOFF ss559107708 Apr 25, 2013 (138)
13 SSMP ss653026139 Apr 25, 2013 (138)
14 EVA-GONL ss982754876 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1073499412 Aug 21, 2014 (142)
16 1000GENOMES ss1319538812 Aug 21, 2014 (142)
17 EVA_GENOME_DK ss1581600583 Apr 01, 2015 (144)
18 EVA_DECODE ss1592301769 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1615267251 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1658261284 Apr 01, 2015 (144)
21 HAMMER_LAB ss1804351651 Sep 08, 2015 (146)
22 WEILL_CORNELL_DGM ss1926006188 Feb 12, 2016 (147)
23 GENOMED ss1970352840 Jul 19, 2016 (147)
24 JJLAB ss2023633046 Sep 14, 2016 (149)
25 USC_VALOUEV ss2151798558 Nov 08, 2017 (151)
26 HUMAN_LONGEVITY ss2282922452 Dec 20, 2016 (150)
27 GRF ss2707391358 Nov 08, 2017 (151)
28 SWEGEN ss2998780672 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3025601917 Nov 08, 2017 (151)
30 EGCUT_WGS ss3666702617 Jul 13, 2019 (153)
31 EVA_DECODE ss3716893047 Jul 13, 2019 (153)
32 ACPOP ss3733349713 Jul 13, 2019 (153)
33 EVA ss3764810621 Jul 13, 2019 (153)
34 PACBIO ss3785419861 Jul 13, 2019 (153)
35 PACBIO ss3790779425 Jul 13, 2019 (153)
36 PACBIO ss3795656798 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3807964877 Jul 13, 2019 (153)
38 EVA ss3829823369 Apr 26, 2020 (154)
39 EVA ss3838389076 Apr 26, 2020 (154)
40 EVA ss3843830474 Apr 26, 2020 (154)
41 SGDP_PRJ ss3864236901 Apr 26, 2020 (154)
42 KRGDB ss3911012600 Apr 26, 2020 (154)
43 VINODS ss4025206165 Apr 26, 2021 (155)
44 VINODS ss4025225172 Apr 26, 2021 (155)
45 VINODS ss4025244349 Apr 26, 2021 (155)
46 VINODS ss4025262459 Apr 26, 2021 (155)
47 TOPMED ss4698301868 Apr 26, 2021 (155)
48 TOMMO_GENOMICS ss5176813043 Apr 26, 2021 (155)
49 1000G_HIGH_COVERAGE ss5267918144 Oct 17, 2022 (156)
50 EVA ss5364700028 Oct 17, 2022 (156)
51 HUGCELL_USP ss5465656369 Oct 17, 2022 (156)
52 EVA ss5508419761 Oct 17, 2022 (156)
53 1000G_HIGH_COVERAGE ss5553570176 Oct 17, 2022 (156)
54 SANFORD_IMAGENETICS ss5640073655 Oct 17, 2022 (156)
55 TOMMO_GENOMICS ss5714662263 Oct 17, 2022 (156)
56 YY_MCH ss5807295019 Oct 17, 2022 (156)
57 EVA ss5842013522 Oct 17, 2022 (156)
58 EVA ss5842013523 Oct 17, 2022 (156)
59 EVA ss5855276588 Oct 17, 2022 (156)
60 EVA ss5883226267 Oct 17, 2022 (156)
61 EVA ss5968577281 Oct 17, 2022 (156)
62 1000Genomes NC_000006.11 - 31070686 Oct 12, 2018 (152)
63 1000Genomes_30x NC_000006.12 - 31102909 Oct 17, 2022 (156)
64 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 31070686 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000006.11 - 31070686 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000006.11 - 31070686 Apr 26, 2020 (154)
67 gnomAD - Genomes NC_000006.12 - 31102909 Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000006.11 - 31070686 Apr 26, 2020 (154)
69 KOREAN population from KRGDB NC_000006.11 - 31070686 Apr 26, 2020 (154)
70 Northern Sweden NC_000006.11 - 31070686 Jul 13, 2019 (153)
71 Qatari NC_000006.11 - 31070686 Apr 26, 2020 (154)
72 SGDP_PRJ NC_000006.11 - 31070686 Apr 26, 2020 (154)
73 Siberian NC_000006.11 - 31070686 Apr 26, 2020 (154)
74 8.3KJPN NC_000006.11 - 31070686 Apr 26, 2021 (155)
75 14KJPN NC_000006.12 - 31102909 Oct 17, 2022 (156)
76 TopMed NC_000006.12 - 31102909 Apr 26, 2021 (155)
77 UK 10K study - Twins NC_000006.11 - 31070686 Oct 12, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000006.11 - 31070686 Jul 13, 2019 (153)
79 ALFA NC_000006.12 - 31102909 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)
rs2517547 Mar 11, 2006 (126)
rs7452737 Mar 11, 2006 (126)
rs9263583 Mar 11, 2006 (126)
rs144999676 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78789777 NC_000006.9:31178664:G:A NC_000006.12:31102908:G:A (self)
ss162186671, ss163329321, ss201609190, ss254171948, ss1592301769 NC_000006.10:31178664:G:A NC_000006.12:31102908:G:A (self)
31305399, 17455522, 12440865, 7765522, 7754464, 18189994, 6634578, 8048118, 16253881, 4314912, 34782350, 17455522, 3868199, ss333180652, ss559107708, ss653026139, ss982754876, ss1073499412, ss1319538812, ss1581600583, ss1615267251, ss1658261284, ss1804351651, ss1926006188, ss1970352840, ss2023633046, ss2151798558, ss2707391358, ss2998780672, ss3666702617, ss3733349713, ss3764810621, ss3785419861, ss3790779425, ss3795656798, ss3829823369, ss3838389076, ss3864236901, ss3911012600, ss5176813043, ss5364700028, ss5508419761, ss5640073655, ss5842013522, ss5968577281 NC_000006.11:31070685:G:A NC_000006.12:31102908:G:A (self)
41096111, 221127786, 48499367, 535679426, 8442366684, ss2282922452, ss3025601917, ss3716893047, ss3807964877, ss3843830474, ss4698301868, ss5267918144, ss5465656369, ss5553570176, ss5714662263, ss5807295019, ss5855276588, ss5883226267 NC_000006.12:31102908:G:A NC_000006.12:31102908:G:A (self)
ss11255979, ss12686492 NT_007592.13:21927199:G:A NC_000006.12:31102908:G:A (self)
ss3356945, ss3528343, ss42658622 NT_007592.15:31010685:G:A NC_000006.12:31102908:G:A (self)
ss4025206165 NT_167245.2:2362272:G:A NC_000006.12:31102908:G:A (self)
ss4025225172 NT_167246.2:2413408:G:A NC_000006.12:31102908:G:A (self)
ss4025244349 NT_167247.2:2447022:G:A NC_000006.12:31102908:G:A (self)
ss4025262459 NT_167248.2:2360926:G:A NC_000006.12:31102908:G:A (self)
ss5842013523 NC_000006.11:31070685:G:C NC_000006.12:31102908:G:C
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 rs2394415

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