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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.

rs11575229

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:56356953 (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
T=0.042144 (11155/264690, TOPMED)
T=0.046344 (6424/138616, GnomAD)
T=0.04360 (1232/28258, 14KJPN) (+ 18 more)
T=0.05730 (1395/24346, ALFA)
T=0.04415 (740/16760, 8.3KJPN)
T=0.0311 (199/6404, 1000G_30x)
T=0.0313 (157/5008, 1000G)
T=0.0931 (417/4480, Estonian)
T=0.0625 (241/3854, ALSPAC)
T=0.0669 (248/3708, TWINSUK)
T=0.0462 (135/2922, KOREAN)
T=0.0404 (74/1832, Korea1K)
T=0.0467 (56/1198, HapMap)
T=0.062 (62/998, GoNL)
T=0.055 (33/600, NorthernSweden)
T=0.005 (1/216, Qatari)
T=0.019 (4/214, Vietnamese)
C=0.44 (30/68, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STAT2 : Intron Variant
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 24346 C=0.94270 T=0.05730
European Sub 18124 C=0.92932 T=0.07068
African Sub 4112 C=0.9922 T=0.0078
African Others Sub 148 C=1.000 T=0.000
African American Sub 3964 C=0.9919 T=0.0081
Asian Sub 124 C=0.968 T=0.032
East Asian Sub 96 C=0.99 T=0.01
Other Asian Sub 28 C=0.89 T=0.11
Latin American 1 Sub 168 C=0.964 T=0.036
Latin American 2 Sub 670 C=0.946 T=0.054
South Asian Sub 98 C=1.00 T=0.00
Other Sub 1050 C=0.9657 T=0.0343


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=0.957856 T=0.042144
gnomAD - Genomes Global Study-wide 138616 C=0.953656 T=0.046344
gnomAD - Genomes European Sub 75080 C=0.93356 T=0.06644
gnomAD - Genomes African Sub 41500 C=0.98860 T=0.01140
gnomAD - Genomes American Sub 13478 C=0.94562 T=0.05438
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.9801 T=0.0199
gnomAD - Genomes East Asian Sub 3116 C=0.9705 T=0.0295
gnomAD - Genomes Other Sub 2124 C=0.9661 T=0.0339
14KJPN JAPANESE Study-wide 28258 C=0.95640 T=0.04360
Allele Frequency Aggregator Total Global 24346 C=0.94270 T=0.05730
Allele Frequency Aggregator European Sub 18124 C=0.92932 T=0.07068
Allele Frequency Aggregator African Sub 4112 C=0.9922 T=0.0078
Allele Frequency Aggregator Other Sub 1050 C=0.9657 T=0.0343
Allele Frequency Aggregator Latin American 2 Sub 670 C=0.946 T=0.054
Allele Frequency Aggregator Latin American 1 Sub 168 C=0.964 T=0.036
Allele Frequency Aggregator Asian Sub 124 C=0.968 T=0.032
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.95585 T=0.04415
1000Genomes_30x Global Study-wide 6404 C=0.9689 T=0.0311
1000Genomes_30x African Sub 1786 C=0.9989 T=0.0011
1000Genomes_30x Europe Sub 1266 C=0.9352 T=0.0648
1000Genomes_30x South Asian Sub 1202 C=0.9800 T=0.0200
1000Genomes_30x East Asian Sub 1170 C=0.9675 T=0.0325
1000Genomes_30x American Sub 980 C=0.946 T=0.054
1000Genomes Global Study-wide 5008 C=0.9687 T=0.0313
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=0.9653 T=0.0347
1000Genomes Europe Sub 1006 C=0.9354 T=0.0646
1000Genomes South Asian Sub 978 C=0.981 T=0.019
1000Genomes American Sub 694 C=0.948 T=0.052
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9069 T=0.0931
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9375 T=0.0625
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9331 T=0.0669
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9538 T=0.0462
Korean Genome Project KOREAN Study-wide 1832 C=0.9596 T=0.0404
HapMap Global Study-wide 1198 C=0.9533 T=0.0467
HapMap American Sub 770 C=0.960 T=0.040
HapMap Asian Sub 252 C=0.960 T=0.040
HapMap Europe Sub 176 C=0.915 T=0.085
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.938 T=0.062
Northern Sweden ACPOP Study-wide 600 C=0.945 T=0.055
Qatari Global Study-wide 216 C=0.995 T=0.005
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.981 T=0.019
SGDP_PRJ Global Study-wide 68 C=0.44 T=0.56
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
Siberian Global Study-wide 10 C=0.5 T=0.5
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 12 NC_000012.12:g.56356953C>T
GRCh37.p13 chr 12 NC_000012.11:g.56750737C>T
STAT2 RefSeqGene (LRG_1329) NG_046314.1:g.8301G>A
Gene: STAT2, signal transducer and activator of transcription 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
STAT2 transcript variant 3 NM_001385110.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 4 NM_001385111.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 5 NM_001385113.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 6 NM_001385114.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 7 NM_001385115.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 1 NM_005419.4:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant 2 NM_198332.2:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X1 XM_011538697.3:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X2 XM_011538698.4:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X3 XM_011538699.4:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X4 XM_047429468.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X6 XM_047429470.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X8 XM_047429471.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X9 XM_047429472.1:c.-7-375G>A N/A Intron Variant
STAT2 transcript variant X5 XM_047429469.1:c. N/A Genic Upstream Transcript Variant
STAT2 transcript variant X10 XR_007063122.1:n. N/A Intron Variant
STAT2 transcript variant X7 XR_245953.4:n. N/A Intron 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
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 12 NC_000012.12:g.56356953= NC_000012.12:g.56356953C>T
GRCh37.p13 chr 12 NC_000012.11:g.56750737= NC_000012.11:g.56750737C>T
STAT2 RefSeqGene (LRG_1329) NG_046314.1:g.8301= NG_046314.1:g.8301G>A
STAT2 transcript variant 3 NM_001385110.1:c.-7-375= NM_001385110.1:c.-7-375G>A
STAT2 transcript variant 4 NM_001385111.1:c.-7-375= NM_001385111.1:c.-7-375G>A
STAT2 transcript variant 5 NM_001385113.1:c.-7-375= NM_001385113.1:c.-7-375G>A
STAT2 transcript variant 6 NM_001385114.1:c.-7-375= NM_001385114.1:c.-7-375G>A
STAT2 transcript variant 7 NM_001385115.1:c.-7-375= NM_001385115.1:c.-7-375G>A
STAT2 transcript variant 1 NM_005419.3:c.-7-375= NM_005419.3:c.-7-375G>A
STAT2 transcript variant 1 NM_005419.4:c.-7-375= NM_005419.4:c.-7-375G>A
STAT2 transcript variant 2 NM_198332.1:c.-7-375= NM_198332.1:c.-7-375G>A
STAT2 transcript variant 2 NM_198332.2:c.-7-375= NM_198332.2:c.-7-375G>A
STAT2 transcript variant X1 XM_005269108.1:c.198-375= XM_005269108.1:c.198-375G>A
STAT2 transcript variant X2 XM_005269109.1:c.198-375= XM_005269109.1:c.198-375G>A
STAT2 transcript variant X3 XM_005269110.1:c.198-375= XM_005269110.1:c.198-375G>A
STAT2 transcript variant X4 XM_005269111.1:c.198-375= XM_005269111.1:c.198-375G>A
STAT2 transcript variant X1 XM_011538697.3:c.-7-375= XM_011538697.3:c.-7-375G>A
STAT2 transcript variant X2 XM_011538698.4:c.-7-375= XM_011538698.4:c.-7-375G>A
STAT2 transcript variant X3 XM_011538699.4:c.-7-375= XM_011538699.4:c.-7-375G>A
STAT2 transcript variant X4 XM_047429468.1:c.-7-375= XM_047429468.1:c.-7-375G>A
STAT2 transcript variant X6 XM_047429470.1:c.-7-375= XM_047429470.1:c.-7-375G>A
STAT2 transcript variant X8 XM_047429471.1:c.-7-375= XM_047429471.1:c.-7-375G>A
STAT2 transcript variant X9 XM_047429472.1:c.-7-375= XM_047429472.1:c.-7-375G>A
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#.

53 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss16361212 Feb 28, 2004 (120)
2 ILLUMINA ss75051735 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119691178 Dec 01, 2009 (131)
4 ILLUMINA ss171303238 Jul 04, 2010 (132)
5 1000GENOMES ss235946387 Jul 15, 2010 (132)
6 1000GENOMES ss242503781 Jul 15, 2010 (132)
7 GMI ss281409012 May 04, 2012 (137)
8 ILLUMINA ss536699408 Sep 08, 2015 (146)
9 SSMP ss658743977 Apr 25, 2013 (138)
10 EVA-GONL ss989565895 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1078483900 Aug 21, 2014 (142)
12 1000GENOMES ss1345148146 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1576302338 Apr 01, 2015 (144)
14 EVA_DECODE ss1599239389 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1628656888 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1671650921 Apr 01, 2015 (144)
17 EVA_SVP ss1713330173 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1932931741 Feb 12, 2016 (147)
19 GENOMED ss1967596725 Jul 19, 2016 (147)
20 JJLAB ss2027215841 Sep 14, 2016 (149)
21 USC_VALOUEV ss2155556609 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2190056089 Dec 20, 2016 (150)
23 SYSTEMSBIOZJU ss2628089248 Nov 08, 2017 (151)
24 GRF ss2699901351 Nov 08, 2017 (151)
25 GNOMAD ss2910888255 Nov 08, 2017 (151)
26 AFFY ss2984980420 Nov 08, 2017 (151)
27 SWEGEN ss3009744590 Nov 08, 2017 (151)
28 CSHL ss3350079369 Nov 08, 2017 (151)
29 ILLUMINA ss3626886291 Oct 12, 2018 (152)
30 ILLUMINA ss3637965482 Oct 12, 2018 (152)
31 ILLUMINA ss3642958893 Oct 12, 2018 (152)
32 EGCUT_WGS ss3677013475 Jul 13, 2019 (153)
33 EVA_DECODE ss3693735664 Jul 13, 2019 (153)
34 ACPOP ss3739050724 Jul 13, 2019 (153)
35 EVA ss3750519175 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3815849800 Jul 13, 2019 (153)
37 SGDP_PRJ ss3878343090 Apr 27, 2020 (154)
38 KRGDB ss3926987565 Apr 27, 2020 (154)
39 KOGIC ss3972008030 Apr 27, 2020 (154)
40 EVA ss4017590795 Apr 26, 2021 (155)
41 TOPMED ss4919457453 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5206478844 Apr 26, 2021 (155)
43 1000G_HIGH_COVERAGE ss5290927887 Oct 16, 2022 (156)
44 EVA ss5405845235 Oct 16, 2022 (156)
45 HUGCELL_USP ss5485665485 Oct 16, 2022 (156)
46 1000G_HIGH_COVERAGE ss5588470206 Oct 16, 2022 (156)
47 SANFORD_IMAGENETICS ss5653220278 Oct 16, 2022 (156)
48 TOMMO_GENOMICS ss5756318736 Oct 16, 2022 (156)
49 YY_MCH ss5813327048 Oct 16, 2022 (156)
50 EVA ss5838010565 Oct 16, 2022 (156)
51 EVA ss5850395598 Oct 16, 2022 (156)
52 EVA ss5904524186 Oct 16, 2022 (156)
53 EVA ss5944582750 Oct 16, 2022 (156)
54 1000Genomes NC_000012.11 - 56750737 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000012.12 - 56356953 Oct 16, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 56750737 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000012.11 - 56750737 Oct 12, 2018 (152)
58 The Danish reference pan genome NC_000012.11 - 56750737 Apr 27, 2020 (154)
59 gnomAD - Genomes NC_000012.12 - 56356953 Apr 26, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000012.11 - 56750737 Apr 27, 2020 (154)
61 HapMap NC_000012.12 - 56356953 Apr 27, 2020 (154)
62 KOREAN population from KRGDB NC_000012.11 - 56750737 Apr 27, 2020 (154)
63 Korean Genome Project NC_000012.12 - 56356953 Apr 27, 2020 (154)
64 Northern Sweden NC_000012.11 - 56750737 Jul 13, 2019 (153)
65 Qatari NC_000012.11 - 56750737 Apr 27, 2020 (154)
66 SGDP_PRJ NC_000012.11 - 56750737 Apr 27, 2020 (154)
67 Siberian NC_000012.11 - 56750737 Apr 27, 2020 (154)
68 8.3KJPN NC_000012.11 - 56750737 Apr 26, 2021 (155)
69 14KJPN NC_000012.12 - 56356953 Oct 16, 2022 (156)
70 TopMed NC_000012.12 - 56356953 Apr 26, 2021 (155)
71 UK 10K study - Twins NC_000012.11 - 56750737 Oct 12, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000012.11 - 56750737 Jul 13, 2019 (153)
73 ALFA NC_000012.12 - 56356953 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)
rs386519999 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss281409012, ss1599239389, ss1713330173, ss3642958893 NC_000012.10:55037003:C:T NC_000012.12:56356952:C:T (self)
57901667, 32148049, 22751723, 2975890, 14344389, 34164959, 12335589, 14973671, 30360070, 8072963, 64448151, 32148049, 7136259, ss235946387, ss242503781, ss536699408, ss658743977, ss989565895, ss1078483900, ss1345148146, ss1576302338, ss1628656888, ss1671650921, ss1932931741, ss1967596725, ss2027215841, ss2155556609, ss2628089248, ss2699901351, ss2910888255, ss2984980420, ss3009744590, ss3350079369, ss3626886291, ss3637965482, ss3677013475, ss3739050724, ss3750519175, ss3878343090, ss3926987565, ss4017590795, ss5206478844, ss5405845235, ss5653220278, ss5838010565, ss5944582750 NC_000012.11:56750736:C:T NC_000012.12:56356952:C:T (self)
75996141, 408320079, 822637, 28386031, 90155840, 135003110, 7843463430, ss2190056089, ss3693735664, ss3815849800, ss3972008030, ss4919457453, ss5290927887, ss5485665485, ss5588470206, ss5756318736, ss5813327048, ss5850395598, ss5904524186 NC_000012.12:56356952:C:T NC_000012.12:56356952:C:T (self)
ss16361212, ss75051735, ss119691178, ss171303238 NT_029419.12:18894042:C:T NC_000012.12:56356952: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 rs11575229

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