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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.

rs11575217

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:56361516 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.042246 (11182/264690, TOPMED)
C=0.009247 (2305/249258, GnomAD_exome)
C=0.008606 (1340/155712, ALFA) (+ 11 more)
C=0.039794 (5577/140148, GnomAD)
C=0.011338 (1369/120744, ExAC)
C=0.03685 (449/12184, GO-ESP)
C=0.0453 (290/6404, 1000G_30x)
C=0.0423 (212/5008, 1000G)
C=0.0005 (2/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
C=0.104 (93/890, HapMap)
C=0.002 (1/534, MGP)
C=0.028 (6/216, Qatari)
A=0.39 (7/18, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
APOF : Synonymous Variant
STAT2 : 2KB Upstream 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 172070 A=0.988237 C=0.011763
European Sub 142586 A=0.999656 C=0.000344
African Sub 14400 A=0.87313 C=0.12687
African Others Sub 494 A=0.854 C=0.146
African American Sub 13906 A=0.87380 C=0.12620
Asian Sub 514 A=1.000 C=0.000
East Asian Sub 416 A=1.000 C=0.000
Other Asian Sub 98 A=1.00 C=0.00
Latin American 1 Sub 896 A=0.965 C=0.035
Latin American 2 Sub 966 A=0.991 C=0.009
South Asian Sub 178 A=1.000 C=0.000
Other Sub 12530 A=0.99138 C=0.00862


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=0.957754 C=0.042246
gnomAD - Exomes Global Study-wide 249258 A=0.990753 C=0.009247
gnomAD - Exomes European Sub 134560 A=0.999740 C=0.000260
gnomAD - Exomes Asian Sub 48578 A=0.99992 C=0.00008
gnomAD - Exomes American Sub 34528 A=0.99554 C=0.00446
gnomAD - Exomes African Sub 15480 A=0.86486 C=0.13514
gnomAD - Exomes Ashkenazi Jewish Sub 10062 A=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6050 A=0.9967 C=0.0033
Allele Frequency Aggregator Total Global 155712 A=0.991394 C=0.008606
Allele Frequency Aggregator European Sub 132496 A=0.999660 C=0.000340
Allele Frequency Aggregator Other Sub 11098 A=0.99351 C=0.00649
Allele Frequency Aggregator African Sub 9564 A=0.8763 C=0.1237
Allele Frequency Aggregator Latin American 2 Sub 966 A=0.991 C=0.009
Allele Frequency Aggregator Latin American 1 Sub 896 A=0.965 C=0.035
Allele Frequency Aggregator Asian Sub 514 A=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 178 A=1.000 C=0.000
gnomAD - Genomes Global Study-wide 140148 A=0.960206 C=0.039794
gnomAD - Genomes European Sub 75920 A=0.99959 C=0.00041
gnomAD - Genomes African Sub 41972 A=0.87277 C=0.12723
gnomAD - Genomes American Sub 13658 A=0.98960 C=0.01040
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3128 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9702 C=0.0298
ExAC Global Study-wide 120744 A=0.988662 C=0.011338
ExAC Europe Sub 73344 A=0.99969 C=0.00031
ExAC Asian Sub 25136 A=0.99992 C=0.00008
ExAC American Sub 11570 A=0.99533 C=0.00467
ExAC African Sub 9796 A=0.8684 C=0.1316
ExAC Other Sub 898 A=0.999 C=0.001
GO Exome Sequencing Project Global Study-wide 12184 A=0.96315 C=0.03685
GO Exome Sequencing Project European American Sub 8286 A=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 3898 A=0.8848 C=0.1152
1000Genomes_30x Global Study-wide 6404 A=0.9547 C=0.0453
1000Genomes_30x African Sub 1786 A=0.8460 C=0.1540
1000Genomes_30x Europe Sub 1266 A=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 C=0.0000
1000Genomes_30x American Sub 980 A=0.985 C=0.015
1000Genomes Global Study-wide 5008 A=0.9577 C=0.0423
1000Genomes African Sub 1322 A=0.8472 C=0.1528
1000Genomes East Asian Sub 1008 A=1.0000 C=0.0000
1000Genomes Europe Sub 1006 A=1.0000 C=0.0000
1000Genomes South Asian Sub 978 A=1.000 C=0.000
1000Genomes American Sub 694 A=0.986 C=0.014
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9995 C=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 C=0.0000
HapMap Global Study-wide 890 A=0.896 C=0.104
HapMap African Sub 692 A=0.892 C=0.108
HapMap American Sub 198 A=0.909 C=0.091
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.998 C=0.002
Qatari Global Study-wide 216 A=0.972 C=0.028
SGDP_PRJ Global Study-wide 18 A=0.39 C=0.61
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.56361516A>C
GRCh37.p13 chr 12 NC_000012.11:g.56755300A>C
STAT2 RefSeqGene (LRG_1329) NG_046314.1:g.3738T>G
Gene: STAT2, signal transducer and activator of transcription 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
STAT2 transcript variant 3 NM_001385110.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant 4 NM_001385111.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant 5 NM_001385113.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant 6 NM_001385114.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant 7 NM_001385115.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant 1 NM_005419.4:c. N/A Upstream Transcript Variant
STAT2 transcript variant 2 NM_198332.2:c. N/A Upstream Transcript Variant
STAT2 transcript variant X1 XM_011538697.3:c. N/A Upstream Transcript Variant
STAT2 transcript variant X2 XM_011538698.4:c. N/A Upstream Transcript Variant
STAT2 transcript variant X3 XM_011538699.4:c. N/A Upstream Transcript Variant
STAT2 transcript variant X4 XM_047429468.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant X6 XM_047429470.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant X8 XM_047429471.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant X9 XM_047429472.1:c. N/A Upstream Transcript Variant
STAT2 transcript variant X5 XM_047429469.1:c. N/A N/A
STAT2 transcript variant X10 XR_007063122.1:n. N/A Upstream Transcript Variant
STAT2 transcript variant X7 XR_245953.4:n. N/A Upstream Transcript Variant
Gene: APOF, apolipoprotein F (minus strand)
Molecule type Change Amino acid[Codon] SO Term
APOF transcript NM_001638.4:c.690T>G A [GCT] > A [GCG] Coding Sequence Variant
apolipoprotein F preproprotein NP_001629.1:p.Ala230= A (Ala) > A (Ala) Synonymous 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 A= C
GRCh38.p14 chr 12 NC_000012.12:g.56361516= NC_000012.12:g.56361516A>C
GRCh37.p13 chr 12 NC_000012.11:g.56755300= NC_000012.11:g.56755300A>C
STAT2 RefSeqGene (LRG_1329) NG_046314.1:g.3738= NG_046314.1:g.3738T>G
APOF transcript NM_001638.4:c.690= NM_001638.4:c.690T>G
APOF transcript NM_001638.3:c.690= NM_001638.3:c.690T>G
APOF transcript NM_001638.2:c.690= NM_001638.2:c.690T>G
apolipoprotein F preproprotein NP_001629.1:p.Ala230= NP_001629.1:p.Ala230=
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#.

66 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss16361195 Feb 28, 2004 (120)
2 EGP_SNPS ss66857613 Dec 03, 2006 (127)
3 ILLUMINA ss75050159 Dec 07, 2007 (129)
4 KRIBB_YJKIM ss119691174 Dec 01, 2009 (131)
5 ILLUMINA ss159981837 Dec 01, 2009 (131)
6 ILLUMINA ss171303202 Jul 04, 2010 (132)
7 1000GENOMES ss211287983 Jul 14, 2010 (132)
8 1000GENOMES ss225768971 Jul 14, 2010 (132)
9 ILLUMINA ss479529871 May 04, 2012 (137)
10 ILLUMINA ss479533700 May 04, 2012 (137)
11 ILLUMINA ss479993172 Sep 08, 2015 (146)
12 ILLUMINA ss481789655 May 04, 2012 (137)
13 ILLUMINA ss483083521 May 04, 2012 (137)
14 ILLUMINA ss484563901 May 04, 2012 (137)
15 1000GENOMES ss491044997 May 04, 2012 (137)
16 ILLUMINA ss534392934 Sep 08, 2015 (146)
17 NHLBI-ESP ss713099242 Apr 25, 2013 (138)
18 ILLUMINA ss779109130 Aug 21, 2014 (142)
19 ILLUMINA ss781569560 Aug 21, 2014 (142)
20 ILLUMINA ss782728657 Sep 08, 2015 (146)
21 ILLUMINA ss831980373 Sep 08, 2015 (146)
22 ILLUMINA ss834573301 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1067535019 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1078483916 Aug 21, 2014 (142)
25 1000GENOMES ss1345148238 Aug 21, 2014 (142)
26 EVA_UK10K_ALSPAC ss1628656947 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1671650980 Apr 01, 2015 (144)
28 EVA_EXAC ss1690964080 Apr 01, 2015 (144)
29 EVA_MGP ss1711333142 Apr 01, 2015 (144)
30 ILLUMINA ss1752074057 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1932931766 Feb 12, 2016 (147)
32 HUMAN_LONGEVITY ss2190056311 Dec 20, 2016 (150)
33 ILLUMINA ss2632963499 Nov 08, 2017 (151)
34 ILLUMINA ss2632963500 Nov 08, 2017 (151)
35 GNOMAD ss2739903245 Nov 08, 2017 (151)
36 GNOMAD ss2748893061 Nov 08, 2017 (151)
37 GNOMAD ss2910888589 Nov 08, 2017 (151)
38 AFFY ss2984980472 Nov 08, 2017 (151)
39 ILLUMINA ss3626886302 Oct 12, 2018 (152)
40 ILLUMINA ss3630972443 Oct 12, 2018 (152)
41 ILLUMINA ss3633021604 Oct 12, 2018 (152)
42 ILLUMINA ss3633722638 Oct 12, 2018 (152)
43 ILLUMINA ss3634507131 Oct 12, 2018 (152)
44 ILLUMINA ss3635413376 Oct 12, 2018 (152)
45 ILLUMINA ss3636192009 Oct 12, 2018 (152)
46 ILLUMINA ss3637164366 Oct 12, 2018 (152)
47 ILLUMINA ss3637965490 Oct 12, 2018 (152)
48 ILLUMINA ss3640214465 Oct 12, 2018 (152)
49 ILLUMINA ss3642958900 Oct 12, 2018 (152)
50 ILLUMINA ss3653750685 Oct 12, 2018 (152)
51 ILLUMINA ss3744807805 Jul 13, 2019 (153)
52 ILLUMINA ss3772307250 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3815849822 Jul 13, 2019 (153)
54 EVA ss3824740978 Apr 27, 2020 (154)
55 SGDP_PRJ ss3878343137 Apr 27, 2020 (154)
56 FSA-LAB ss3984030576 Apr 26, 2021 (155)
57 EVA ss3986573976 Apr 26, 2021 (155)
58 EVA ss4017590803 Apr 26, 2021 (155)
59 TOPMED ss4919458528 Apr 26, 2021 (155)
60 1000G_HIGH_COVERAGE ss5290927969 Oct 16, 2022 (156)
61 EVA ss5405845425 Oct 16, 2022 (156)
62 HUGCELL_USP ss5485665569 Oct 16, 2022 (156)
63 1000G_HIGH_COVERAGE ss5588470344 Oct 16, 2022 (156)
64 SANFORD_IMAGENETICS ss5653220324 Oct 16, 2022 (156)
65 EVA ss5904524269 Oct 16, 2022 (156)
66 EVA ss5944582791 Oct 16, 2022 (156)
67 1000Genomes NC_000012.11 - 56755300 Oct 12, 2018 (152)
68 1000Genomes_30x NC_000012.12 - 56361516 Oct 16, 2022 (156)
69 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 56755300 Oct 12, 2018 (152)
70 ExAC NC_000012.11 - 56755300 Oct 12, 2018 (152)
71 gnomAD - Genomes NC_000012.12 - 56361516 Apr 26, 2021 (155)
72 gnomAD - Exomes NC_000012.11 - 56755300 Jul 13, 2019 (153)
73 GO Exome Sequencing Project NC_000012.11 - 56755300 Oct 12, 2018 (152)
74 HapMap NC_000012.12 - 56361516 Apr 27, 2020 (154)
75 Medical Genome Project healthy controls from Spanish population NC_000012.11 - 56755300 Apr 27, 2020 (154)
76 Qatari NC_000012.11 - 56755300 Apr 27, 2020 (154)
77 SGDP_PRJ NC_000012.11 - 56755300 Apr 27, 2020 (154)
78 TopMed NC_000012.12 - 56361516 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000012.11 - 56755300 Oct 12, 2018 (152)
80 ALFA NC_000012.12 - 56361516 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
ss159981837, ss211287983, ss479529871, ss483083521, ss3642958900 NC_000012.10:55041566:A:C NC_000012.12:56361515:A:C (self)
57901761, 32148111, 1265481, 9136685, 1198439, 448902, 14973696, 30360117, 32148111, ss225768971, ss479533700, ss479993172, ss481789655, ss484563901, ss491044997, ss534392934, ss713099242, ss779109130, ss781569560, ss782728657, ss831980373, ss834573301, ss1067535019, ss1078483916, ss1345148238, ss1628656947, ss1671650980, ss1690964080, ss1711333142, ss1752074057, ss1932931766, ss2632963499, ss2632963500, ss2739903245, ss2748893061, ss2910888589, ss2984980472, ss3626886302, ss3630972443, ss3633021604, ss3633722638, ss3634507131, ss3635413376, ss3636192009, ss3637164366, ss3637965490, ss3640214465, ss3653750685, ss3744807805, ss3772307250, ss3824740978, ss3878343137, ss3984030576, ss3986573976, ss4017590803, ss5405845425, ss5653220324, ss5944582791 NC_000012.11:56755299:A:C NC_000012.12:56361515:A:C (self)
75996279, 408320970, 822647, 135004185, 153285507, ss2190056311, ss3815849822, ss4919458528, ss5290927969, ss5485665569, ss5588470344, ss5904524269 NC_000012.12:56361515:A:C NC_000012.12:56361515:A:C (self)
ss16361195, ss66857613, ss75050159, ss119691174, ss171303202 NT_029419.12:18898605:A:C NC_000012.12:56361515:A:C (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 rs11575217

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