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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.

rs5030655

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:42129084 (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
delA
Variation Type
Deletion
Frequency
delA=0.007114 (1883/264690, TOPMED)
delA=0.007918 (1935/244380, GnomAD_exome)
delA=0.008828 (1233/139672, GnomAD) (+ 8 more)
delA=0.007929 (808/101902, ExAC)
delA=0.00177 (164/92826, ALFA)
delA=0.00665 (80/12024, GO-ESP)
delA=0.0048 (31/6404, 1000G_30x)
delA=0.0048 (24/5008, 1000G)
delA=0.0112 (43/3854, ALSPAC)
delA=0.0100 (37/3708, TWINSUK)
delA=0.003 (2/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP2D6 : Frameshift Variant
LOC102723722 : 2KB Upstream Variant
Publications
30 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 92826 A=0.99823 =0.00177 0.996553 8.6e-05 0.003361 32
European Sub 79814 A=0.99833 =0.00167 0.996742 0.000075 0.003182 32
African Sub 4282 A=0.9979 =0.0021 0.996263 0.000467 0.00327 32
African Others Sub 174 A=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 4108 A=0.9978 =0.0022 0.996105 0.000487 0.003408 32
Asian Sub 3330 A=1.0000 =0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2674 A=1.0000 =0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 656 A=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 434 A=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 924 A=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 274 A=1.000 =0.000 1.0 0.0 0.0 N/A
Other Sub 3768 A=0.9942 =0.0058 0.988323 0.0 0.011677 0


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=0.992886 delA=0.007114
gnomAD - Exomes Global Study-wide 244380 A=0.992082 delA=0.007918
gnomAD - Exomes European Sub 131600 A=0.987766 delA=0.012234
gnomAD - Exomes Asian Sub 48160 A=0.99896 delA=0.00104
gnomAD - Exomes American Sub 34122 A=0.99631 delA=0.00369
gnomAD - Exomes African Sub 14646 A=0.99788 delA=0.00212
gnomAD - Exomes Ashkenazi Jewish Sub 9932 A=0.9916 delA=0.0084
gnomAD - Exomes Other Sub 5920 A=0.9941 delA=0.0059
gnomAD - Genomes Global Study-wide 139672 A=0.991172 delA=0.008828
gnomAD - Genomes European Sub 75768 A=0.98666 delA=0.01334
gnomAD - Genomes African Sub 41696 A=0.99770 delA=0.00230
gnomAD - Genomes American Sub 13616 A=0.99434 delA=0.00566
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9883 delA=0.0117
gnomAD - Genomes East Asian Sub 3122 A=1.0000 delA=0.0000
gnomAD - Genomes Other Sub 2146 A=0.9953 delA=0.0047
ExAC Global Study-wide 101902 A=0.992071 delA=0.007929
ExAC Europe Sub 61446 A=0.98822 delA=0.01178
ExAC Asian Sub 22650 A=0.99916 delA=0.00084
ExAC American Sub 9768 A=0.9958 delA=0.0042
ExAC African Sub 7304 A=0.9971 delA=0.0029
ExAC Other Sub 734 A=0.996 delA=0.004
Allele Frequency Aggregator Total Global 92826 A=0.99823 delA=0.00177
Allele Frequency Aggregator European Sub 79814 A=0.99833 delA=0.00167
Allele Frequency Aggregator African Sub 4282 A=0.9979 delA=0.0021
Allele Frequency Aggregator Other Sub 3768 A=0.9942 delA=0.0058
Allele Frequency Aggregator Asian Sub 3330 A=1.0000 delA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 924 A=1.000 delA=0.000
Allele Frequency Aggregator Latin American 1 Sub 434 A=1.000 delA=0.000
Allele Frequency Aggregator South Asian Sub 274 A=1.000 delA=0.000
GO Exome Sequencing Project Global Study-wide 12024 A=0.99335 delA=0.00665
GO Exome Sequencing Project European American Sub 8028 A=0.9910 delA=0.0090
GO Exome Sequencing Project African American Sub 3996 A=0.9980 delA=0.0020
1000Genomes_30x Global Study-wide 6404 A=0.9952 delA=0.0048
1000Genomes_30x African Sub 1786 A=0.9994 delA=0.0006
1000Genomes_30x Europe Sub 1266 A=0.9803 delA=0.0197
1000Genomes_30x South Asian Sub 1202 A=0.9983 delA=0.0017
1000Genomes_30x East Asian Sub 1170 A=1.0000 delA=0.0000
1000Genomes_30x American Sub 980 A=0.997 delA=0.003
1000Genomes Global Study-wide 5008 A=0.9952 delA=0.0048
1000Genomes African Sub 1322 A=0.9992 delA=0.0008
1000Genomes East Asian Sub 1008 A=1.0000 delA=0.0000
1000Genomes Europe Sub 1006 A=0.9801 delA=0.0199
1000Genomes South Asian Sub 978 A=0.999 delA=0.001
1000Genomes American Sub 694 A=0.997 delA=0.003
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9888 delA=0.0112
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9900 delA=0.0100
Northern Sweden ACPOP Study-wide 600 A=0.997 delA=0.003
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 22 NC_000022.11:g.42129084del
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.6727del
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.6825del
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.22673del
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.14650del
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.51411del
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.51425del
GRCh37.p13 chr 22 NC_000022.10:g.42525086del
Gene: CYP2D6, cytochrome P450 family 2 subfamily D member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP2D6 transcript variant 2 NM_001025161.3:c.353-140d…

NM_001025161.3:c.353-140del

N/A Intron Variant
CYP2D6 transcript variant 1 NM_000106.6:c.454del W [TGG] > G [GG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Trp152fs W (Trp) > G (Gly) Frameshift 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.

Allele: delA (allele ID: 31930 )
ClinVar Accession Disease Names Clinical Significance
RCV000018387.28 Debrisoquine, poor metabolism of Drug-Response
RCV000734613.5 not provided Likely-Benign,Other
RCV001030443.2 Deutetrabenazine response Drug-Response
RCV001093716.2 Tamoxifen response Drug-Response
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= delA
GRCh38.p14 chr 22 NC_000022.11:g.42129084= NC_000022.11:g.42129084del
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.6727= NG_008376.4:g.6727del
CYP2D6 transcript variant 1 NM_000106.6:c.454= NM_000106.6:c.454del
CYP2D6 transcript variant 1 NM_000106.5:c.454= NM_000106.5:c.454del
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.6825= NW_015148968.1:g.6825del
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.22673= NW_014040931.1:g.22673del
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.14650= NW_009646208.1:g.14650del
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.51411= NW_004504305.1:g.51411del
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.51425= NT_187682.1:g.51425del
GRCh37.p13 chr 22 NC_000022.10:g.42525086= NC_000022.10:g.42525086del
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Trp152= NP_000097.3:p.Trp152fs
CYP2D6 transcript variant 2 NM_001025161.2:c.353-140= NM_001025161.2:c.353-140del
CYP2D6 transcript variant 2 NM_001025161.3:c.353-140= NM_001025161.3:c.353-140del
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#.

40 SubSNP, 11 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss7985784 Mar 31, 2003 (113)
2 BIOVENTURES ss32476043 May 24, 2005 (126)
3 PHARMGKB_COBRA ss69365828 May 17, 2007 (127)
4 1000GENOMES ss499881210 May 04, 2012 (137)
5 OMIM-CURATED-RECORDS ss825077089 Jun 20, 2013 (137)
6 EVA-GONL ss995393811 Aug 21, 2014 (142)
7 1000GENOMES ss1379076283 Aug 21, 2014 (142)
8 EVA_DECODE ss1699465074 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1709606615 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1709606802 Apr 01, 2015 (144)
11 EVA_EXAC ss1712254308 Apr 01, 2015 (144)
12 ILLUMINA ss1959984047 Feb 12, 2016 (147)
13 ILLUMINA ss2710959489 Nov 08, 2017 (151)
14 GNOMAD ss2745191909 Nov 08, 2017 (151)
15 GNOMAD ss2750571749 Nov 08, 2017 (151)
16 GNOMAD ss2974893683 Nov 08, 2017 (151)
17 AFFY ss2985240507 Nov 08, 2017 (151)
18 AFFY ss2985857671 Nov 08, 2017 (151)
19 SWEGEN ss3019375541 Nov 08, 2017 (151)
20 ILLUMINA ss3022190901 Nov 08, 2017 (151)
21 ILLUMINA ss3022190902 Nov 08, 2017 (151)
22 ILLUMINA ss3652655253 Oct 12, 2018 (152)
23 ILLUMINA ss3652655254 Oct 12, 2018 (152)
24 ILLUMINA ss3654008761 Oct 12, 2018 (152)
25 EVA_DECODE ss3708287362 Jul 13, 2019 (153)
26 ILLUMINA ss3725972593 Jul 13, 2019 (153)
27 ACPOP ss3743969270 Jul 13, 2019 (153)
28 EVA ss3825454861 Apr 27, 2020 (154)
29 EVA ss3836012235 Apr 27, 2020 (154)
30 EVA ss3986866475 Apr 26, 2021 (155)
31 TOPMED ss5110780740 Apr 26, 2021 (155)
32 EVA ss5237676622 Oct 16, 2022 (156)
33 1000G_HIGH_COVERAGE ss5311255665 Oct 16, 2022 (156)
34 HUGCELL_USP ss5503082686 Oct 16, 2022 (156)
35 1000G_HIGH_COVERAGE ss5618884821 Oct 16, 2022 (156)
36 SANFORD_IMAGENETICS ss5624504245 Oct 16, 2022 (156)
37 SANFORD_IMAGENETICS ss5664576735 Oct 16, 2022 (156)
38 EVA ss5822131245 Oct 16, 2022 (156)
39 EVA ss5848570319 Oct 16, 2022 (156)
40 EVA ss5959434922 Oct 16, 2022 (156)
41 1000Genomes NC_000022.10 - 42525086 Oct 12, 2018 (152)
42 1000Genomes_30x NC_000022.11 - 42129084 Oct 16, 2022 (156)
43 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 42525086 Oct 12, 2018 (152)
44 ExAC NC_000022.10 - 42525086 Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000022.11 - 42129084 Apr 26, 2021 (155)
46 gnomAD - Exomes NC_000022.10 - 42525086 Jul 13, 2019 (153)
47 GO Exome Sequencing Project NC_000022.10 - 42525086 Oct 12, 2018 (152)
48 Northern Sweden NC_000022.10 - 42525086 Jul 13, 2019 (153)
49 TopMed NC_000022.11 - 42129084 Apr 26, 2021 (155)
50 UK 10K study - Twins NC_000022.10 - 42525086 Oct 12, 2018 (152)
51 ALFA NC_000022.11 - 42129084 Apr 26, 2021 (155)
52 ClinVar RCV000018387.28 Oct 12, 2018 (152)
53 ClinVar RCV000734613.5 Oct 16, 2022 (156)
54 ClinVar RCV001030443.2 Oct 16, 2022 (156)
55 ClinVar RCV001093716.2 Oct 16, 2022 (156)
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)
rs11568727 Apr 05, 2004 (121)
rs28371709 Mar 10, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1699465074 NC_000022.9:40855029:A: NC_000022.11:42129083:A: (self)
80894572, 44747537, 5962776, 14524690, 1911690, 17254135, 44747537, ss499881210, ss995393811, ss1379076283, ss1709606615, ss1709606802, ss1712254308, ss1959984047, ss2710959489, ss2745191909, ss2750571749, ss2974893683, ss2985240507, ss2985857671, ss3019375541, ss3022190901, ss3022190902, ss3652655253, ss3652655254, ss3654008761, ss3743969270, ss3825454861, ss3836012235, ss3986866475, ss5624504245, ss5664576735, ss5822131245, ss5848570319, ss5959434922 NC_000022.10:42525085:A: NC_000022.11:42129083:A: (self)
RCV000018387.28, RCV000734613.5, RCV001030443.2, RCV001093716.2, 106410756, 571270028, 385889687, 5988074168, ss825077089, ss3708287362, ss3725972593, ss5110780740, ss5237676622, ss5311255665, ss5503082686, ss5618884821 NC_000022.11:42129083:A: NC_000022.11:42129083:A: (self)
ss7985784, ss32476043, ss69365828 NT_011520.12:21915654:A: NC_000022.11:42129083:A: (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

30 citations for rs5030655
PMID Title Author Year Journal
7951238 Identification of a new variant CYP2D6 allele with a single base deletion in exon 3 and its association with the poor metabolizer phenotype. Saxena R et al. 1994 Human molecular genetics
19639055
20174590 Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. Van Nieuwerburgh FC et al. 2009 International journal of psychiatry in clinical practice
20548328 High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues. Sikora MJ et al. 2011 The pharmacogenomics journal
20847277 Genotyping of DNA samples isolated from formalin-fixed paraffin-embedded tissues using preamplification. Baak-Pablo R et al. 2010 The Journal of molecular diagnostics
21480951 Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients. Lim JS et al. 2011 British journal of clinical pharmacology
21790905 CYP2B6 SNPs are associated with methadone dose required for effective treatment of opioid addiction. Levran O et al. 2013 Addiction biology
22482072 Genomics of Dementia: APOE- and CYP2D6-Related Pharmacogenetics. Cacabelos R et al. 2012 International journal of Alzheimer's disease
23226064 Pharmacogenomic considerations in opioid analgesia. Vuilleumier PH et al. 2012 Pharmacogenomics and personalized medicine
24151610 Polymorphisms in the human cytochrome P450 and arylamine N-acetyltransferase: susceptibility to head and neck cancers. Khlifi R et al. 2013 BioMed research international
24779372 Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. Yang HC et al. 2014 BMC genomics
24944790 Screening for 392 polymorphisms in 141 pharmacogenes. Kim JY et al. 2014 Biomedical reports
25047911 Response to CYP2D6 substrate antidepressants is predicted by a CYP2D6 composite phenotype based on genotype and comedications with CYP2D6 inhibitors. Gressier F et al. 2015 Journal of neural transmission (Vienna, Austria
26369774 Impact of New Genomic Technologies on Understanding Adverse Drug Reactions. Maggo SD et al. 2016 Clinical pharmacokinetics
26785747 Polymorphisms in genes involved in the absorption, distribution, metabolism, and excretion of drugs in the Kazakhs of Kazakhstan. Iskakova AN et al. 2016 BMC genetics
26793106 CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping. Riffel AK et al. 2015 Frontiers in pharmacology
26858644 Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX(®) ADME PGx Panel for Pharmacogenomic Profiling. Chua EW et al. 2016 Frontiers in pharmacology
27108086 Multiplex SNaPshot-a new simple and efficient CYP2D6 and ADRB1 genotyping method. Ben S et al. 2016 Human genomics
27171561 Liver Function Test Abnormalities in Depressed Patients Treated with Antidepressants: A Real-World Systematic Observational Study in Psychiatric Settings. Voican CS et al. 2016 PloS one
27536078 Factors affecting the development of adverse drug reactions to β-blockers in hospitalized cardiac patient population. Mugoša S et al. 2016 Patient preference and adherence
27785397 CYP2D6 allele distribution in Macedonians, Albanians and Romanies in the Republic of Macedonia. Kuzmanovska M et al. 2015 Balkan journal of medical genetics
29193749 Clinical Implementation of Pharmacogenetic Testing in a Hospital of the Spanish National Health System: Strategy and Experience Over 3 Years. Borobia AM et al. 2018 Clinical and translational science
29681089 Genetic variation in biotransformation enzymes, air pollution exposures, and risk of spina bifida. Padula AM et al. 2018 American journal of medical genetics. Part A
30093869 Biological Predictors of Clozapine Response: A Systematic Review. Samanaite R et al. 2018 Frontiers in psychiatry
31019283 Secondary actionable findings identified by exome sequencing: expected impact on the organisation of care from the study of 700 consecutive tests. Thauvin-Robinet C et al. 2019 European journal of human genetics
31086207 Implications of genetic variation of common Drug Metabolizing Enzymes and ABC Transporters among the Pakistani Population. Afsar NA et al. 2019 Scientific reports
33519226 Genetic Diversity of Drug-Related Genes in Native Americans of the Brazilian Amazon. Fernandes MR et al. 2021 Pharmacogenomics and personalized medicine
34385834 Individualized Drugs' Selection by Evaluation of Drug Properties, Pharmacogenomics and Clinical Parameters: Performance of a Bioinformatic Tool Compared to a Clinically Established Counselling Process. Borro M et al. 2021 Pharmacogenomics and personalized medicine
34621706 Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform. Kim B et al. 2021 Translational and clinical pharmacology
34958284 Warfarin Pharmacogenomics for Precision Medicine in Real-Life Clinical Practice in Southern Africa: Harnessing 73 Variants in 29 Pharmacogenes. Muyambo S et al. 2022 Omics
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.post820+afb47a3d