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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.

rs6046408

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:19883711 (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 / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.00000 (0/28258, 14KJPN)
A=0.00000 (0/16760, 8.3KJPN) (+ 15 more)
A=0.0000 (0/7840, ALFA)
C=0.0000 (0/7840, ALFA)
A=0.0000 (0/6404, 1000G_30x)
A=0.0000 (0/5008, 1000G)
A=0.0000 (0/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0000 (0/2930, KOREAN)
T=0.0000 (0/2930, KOREAN)
A=0.0000 (0/1832, Korea1K)
A=0.000 (0/600, NorthernSweden)
A=0.000 (0/556, SGDP_PRJ)
A=0.000 (0/216, Qatari)
A=0.000 (0/212, Vietnamese)
A=0.00 (0/56, Siberian)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RIN2 : 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 7840 A=0.0000 C=0.0000, G=1.0000
European Sub 7190 A=0.0000 C=0.0000, G=1.0000
African Sub 604 A=0.000 C=0.000, G=1.000
African Others Sub 30 A=0.00 C=0.00, G=1.00
African American Sub 574 A=0.000 C=0.000, G=1.000
Asian Sub 4 A=0.0 C=0.0, G=1.0
East Asian Sub 2 A=0.0 C=0.0, G=1.0
Other Asian Sub 2 A=0.0 C=0.0, G=1.0
Latin American 1 Sub 0 A=0 C=0, G=0
Latin American 2 Sub 0 A=0 C=0, G=0
South Asian Sub 4 A=0.0 C=0.0, G=1.0
Other Sub 38 A=0.00 C=0.00, G=1.00


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=0.000011 G=0.999989
14KJPN JAPANESE Study-wide 28258 A=0.00000 G=1.00000
8.3KJPN JAPANESE Study-wide 16760 A=0.00000 G=1.00000
Allele Frequency Aggregator Total Global 7840 A=0.0000 C=0.0000, G=1.0000
Allele Frequency Aggregator European Sub 7190 A=0.0000 C=0.0000, G=1.0000
Allele Frequency Aggregator African Sub 604 A=0.000 C=0.000, G=1.000
Allele Frequency Aggregator Other Sub 38 A=0.00 C=0.00, G=1.00
Allele Frequency Aggregator South Asian Sub 4 A=0.0 C=0.0, G=1.0
Allele Frequency Aggregator Asian Sub 4 A=0.0 C=0.0, G=1.0
Allele Frequency Aggregator Latin American 1 Sub 0 A=0 C=0, G=0
Allele Frequency Aggregator Latin American 2 Sub 0 A=0 C=0, G=0
1000Genomes_30x Global Study-wide 6404 A=0.0000 G=1.0000
1000Genomes_30x African Sub 1786 A=0.0000 G=1.0000
1000Genomes_30x Europe Sub 1266 A=0.0000 G=1.0000
1000Genomes_30x South Asian Sub 1202 A=0.0000 G=1.0000
1000Genomes_30x East Asian Sub 1170 A=0.0000 G=1.0000
1000Genomes_30x American Sub 980 A=0.000 G=1.000
1000Genomes Global Study-wide 5008 A=0.0000 G=1.0000
1000Genomes African Sub 1322 A=0.0000 G=1.0000
1000Genomes East Asian Sub 1008 A=0.0000 G=1.0000
1000Genomes Europe Sub 1006 A=0.0000 G=1.0000
1000Genomes South Asian Sub 978 A=0.000 G=1.000
1000Genomes American Sub 694 A=0.000 G=1.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0000 G=1.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0000 G=1.0000
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0000 G=1.0000, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0000 G=1.0000
Northern Sweden ACPOP Study-wide 600 A=0.000 G=1.000
SGDP_PRJ Global Study-wide 556 A=0.000 G=1.000
Qatari Global Study-wide 216 A=0.000 G=1.000
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.000 G=1.000
Siberian Global Study-wide 56 A=0.00 G=1.00
The Danish reference pan genome Danish Study-wide 40 A=0.00 G=1.00
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.19883711A>C
GRCh38.p14 chr 20 NC_000020.11:g.19883711A>G
GRCh38.p14 chr 20 NC_000020.11:g.19883711A>T
GRCh37.p13 chr 20 NC_000020.10:g.19864355A>C
GRCh37.p13 chr 20 NC_000020.10:g.19864355A>G
GRCh37.p13 chr 20 NC_000020.10:g.19864355A>T
Gene: RIN2, Ras and Rab interactor 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RIN2 transcript variant 4 NM_001378238.1:c.-581-585…

NM_001378238.1:c.-581-5855A>C

N/A Intron Variant
RIN2 transcript variant 2 NM_018993.4:c.-36-5855A>C N/A Intron Variant
RIN2 transcript variant 1 NM_001242581.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X3 XM_017027887.2:c.-33-2926…

XM_017027887.2:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X6 XM_017027888.2:c.-33-2926…

XM_017027888.2:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X2 XM_047440209.1:c.-33-2926…

XM_047440209.1:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X4 XM_047440210.1:c.-33-2926…

XM_047440210.1:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X5 XM_047440211.1:c.-33-2926…

XM_047440211.1:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X7 XM_047440212.1:c.-33-2926…

XM_047440212.1:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X8 XM_047440213.1:c.-33-2926…

XM_047440213.1:c.-33-2926A>C

N/A Intron Variant
RIN2 transcript variant X10 XM_047440214.1:c.-106-300…

XM_047440214.1:c.-106-3000A>C

N/A Intron Variant
RIN2 transcript variant X11 XM_047440215.1:c.-36-5855…

XM_047440215.1:c.-36-5855A>C

N/A Intron Variant
RIN2 transcript variant X13 XM_006723577.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X1 XM_011529255.3:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X15 XM_011529259.3:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X9 XM_017027889.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X12 XM_017027890.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X16 XM_017027892.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X17 XM_017027893.2:c. N/A Genic Upstream Transcript Variant
RIN2 transcript variant X14 XM_047440216.1:c. N/A Genic Upstream Transcript 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 G T
GRCh38.p14 chr 20 NC_000020.11:g.19883711= NC_000020.11:g.19883711A>C NC_000020.11:g.19883711A>G NC_000020.11:g.19883711A>T
GRCh37.p13 chr 20 NC_000020.10:g.19864355= NC_000020.10:g.19864355A>C NC_000020.10:g.19864355A>G NC_000020.10:g.19864355A>T
RIN2 transcript variant 4 NM_001378238.1:c.-581-5855= NM_001378238.1:c.-581-5855A>C NM_001378238.1:c.-581-5855A>G NM_001378238.1:c.-581-5855A>T
RIN2 transcript variant 2 NM_018993.4:c.-36-5855= NM_018993.4:c.-36-5855A>C NM_018993.4:c.-36-5855A>G NM_018993.4:c.-36-5855A>T
RIN2 transcript variant X3 XM_005260731.1:c.-36-5855= XM_005260731.1:c.-36-5855A>C XM_005260731.1:c.-36-5855A>G XM_005260731.1:c.-36-5855A>T
RIN2 transcript variant X3 XM_017027887.2:c.-33-2926= XM_017027887.2:c.-33-2926A>C XM_017027887.2:c.-33-2926A>G XM_017027887.2:c.-33-2926A>T
RIN2 transcript variant X6 XM_017027888.2:c.-33-2926= XM_017027888.2:c.-33-2926A>C XM_017027888.2:c.-33-2926A>G XM_017027888.2:c.-33-2926A>T
RIN2 transcript variant X2 XM_047440209.1:c.-33-2926= XM_047440209.1:c.-33-2926A>C XM_047440209.1:c.-33-2926A>G XM_047440209.1:c.-33-2926A>T
RIN2 transcript variant X4 XM_047440210.1:c.-33-2926= XM_047440210.1:c.-33-2926A>C XM_047440210.1:c.-33-2926A>G XM_047440210.1:c.-33-2926A>T
RIN2 transcript variant X5 XM_047440211.1:c.-33-2926= XM_047440211.1:c.-33-2926A>C XM_047440211.1:c.-33-2926A>G XM_047440211.1:c.-33-2926A>T
RIN2 transcript variant X7 XM_047440212.1:c.-33-2926= XM_047440212.1:c.-33-2926A>C XM_047440212.1:c.-33-2926A>G XM_047440212.1:c.-33-2926A>T
RIN2 transcript variant X8 XM_047440213.1:c.-33-2926= XM_047440213.1:c.-33-2926A>C XM_047440213.1:c.-33-2926A>G XM_047440213.1:c.-33-2926A>T
RIN2 transcript variant X10 XM_047440214.1:c.-106-3000= XM_047440214.1:c.-106-3000A>C XM_047440214.1:c.-106-3000A>G XM_047440214.1:c.-106-3000A>T
RIN2 transcript variant X11 XM_047440215.1:c.-36-5855= XM_047440215.1:c.-36-5855A>C XM_047440215.1:c.-36-5855A>G XM_047440215.1:c.-36-5855A>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#.

71 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8357311 Apr 21, 2003 (114)
2 WI_SSAHASNP ss12493877 Jul 11, 2003 (117)
3 CSHL-HAPMAP ss16900003 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19479895 Feb 27, 2004 (120)
5 SSAHASNP ss21759229 Apr 05, 2004 (121)
6 BCMHGSC_JDW ss91662791 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96190076 Feb 05, 2009 (130)
8 1000GENOMES ss111842097 Jan 25, 2009 (130)
9 1000GENOMES ss113183071 Jan 25, 2009 (130)
10 ILLUMINA-UK ss117508957 Feb 14, 2009 (130)
11 ENSEMBL ss135746846 Dec 01, 2009 (131)
12 ENSEMBL ss138221854 Dec 01, 2009 (131)
13 GMI ss156254759 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss167959117 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss169294404 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss171985448 Jul 04, 2010 (132)
17 BUSHMAN ss203853307 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss208719305 Jul 04, 2010 (132)
19 1000GENOMES ss228296450 Jul 14, 2010 (132)
20 1000GENOMES ss237793495 Jul 15, 2010 (132)
21 1000GENOMES ss243973130 Jul 15, 2010 (132)
22 BL ss255532620 May 09, 2011 (134)
23 GMI ss283328770 May 04, 2012 (137)
24 GMI ss287435859 Apr 25, 2013 (138)
25 PJP ss292627761 May 09, 2011 (134)
26 TISHKOFF ss566181749 Apr 25, 2013 (138)
27 SSMP ss662056930 Apr 25, 2013 (138)
28 JMKIDD_LAB ss1082130496 Aug 21, 2014 (142)
29 1000GENOMES ss1364339159 Aug 21, 2014 (142)
30 DDI ss1429019305 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1579468816 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1638563213 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1681557246 Apr 01, 2015 (144)
34 HAMMER_LAB ss1809454097 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1938122708 Feb 12, 2016 (147)
36 GENOMED ss1969110132 Jul 19, 2016 (147)
37 JJLAB ss2029846799 Sep 14, 2016 (149)
38 USC_VALOUEV ss2158399200 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2241896940 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2629418630 Nov 08, 2017 (151)
41 GRF ss2704074689 Nov 08, 2017 (151)
42 GNOMAD ss2966197077 Nov 08, 2017 (151)
43 SWEGEN ss3017979795 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3028756877 Nov 08, 2017 (151)
45 CSHL ss3352454194 Nov 08, 2017 (151)
46 URBANLAB ss3650987780 Oct 12, 2018 (152)
47 EVA_DECODE ss3706697615 Jul 13, 2019 (153)
48 ACPOP ss3743312165 Jul 13, 2019 (153)
49 EVA ss3758511797 Jul 13, 2019 (153)
50 PACBIO ss3788618846 Jul 13, 2019 (153)
51 PACBIO ss3793516478 Jul 13, 2019 (153)
52 PACBIO ss3798403657 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3821681082 Jul 13, 2019 (153)
54 EVA ss3835625729 Apr 27, 2020 (154)
55 EVA ss3841439064 Apr 27, 2020 (154)
56 EVA ss3846947158 Apr 27, 2020 (154)
57 SGDP_PRJ ss3888876846 Apr 27, 2020 (154)
58 KRGDB ss3939079053 Apr 27, 2020 (154)
59 KOGIC ss3981950684 Apr 27, 2020 (154)
60 TOPMED ss5084652934 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5229146001 Apr 26, 2021 (155)
62 EVA ss5436702811 Oct 13, 2022 (156)
63 HUGCELL_USP ss5500703789 Oct 13, 2022 (156)
64 1000G_HIGH_COVERAGE ss5614526174 Oct 13, 2022 (156)
65 SANFORD_IMAGENETICS ss5663002758 Oct 13, 2022 (156)
66 TOMMO_GENOMICS ss5788218168 Oct 13, 2022 (156)
67 YY_MCH ss5817878396 Oct 13, 2022 (156)
68 EVA ss5845542225 Oct 13, 2022 (156)
69 EVA ss5853100183 Oct 13, 2022 (156)
70 EVA ss5922952713 Oct 13, 2022 (156)
71 EVA ss5957915524 Oct 13, 2022 (156)
72 1000Genomes NC_000020.10 - 19864355 Oct 12, 2018 (152)
73 1000Genomes_30x NC_000020.11 - 19883711 Oct 13, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 19864355 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000020.10 - 19864355 Apr 27, 2020 (154)
76 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 548430856 (NC_000020.11:19883710:A:C 1/140168)
Row 548430857 (NC_000020.11:19883710:A:G 140162/140168)

- Apr 26, 2021 (155)
77 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 548430856 (NC_000020.11:19883710:A:C 1/140168)
Row 548430857 (NC_000020.11:19883710:A:G 140162/140168)

- Apr 26, 2021 (155)
78 KOREAN population from KRGDB NC_000020.10 - 19864355 Apr 27, 2020 (154)
79 Korean Genome Project NC_000020.11 - 19883711 Apr 27, 2020 (154)
80 Northern Sweden NC_000020.10 - 19864355 Jul 13, 2019 (153)
81 Qatari NC_000020.10 - 19864355 Apr 27, 2020 (154)
82 SGDP_PRJ NC_000020.10 - 19864355 Apr 27, 2020 (154)
83 Siberian NC_000020.10 - 19864355 Apr 27, 2020 (154)
84 8.3KJPN NC_000020.10 - 19864355 Apr 26, 2021 (155)
85 14KJPN NC_000020.11 - 19883711 Oct 13, 2022 (156)
86 TopMed NC_000020.11 - 19883711 Apr 26, 2021 (155)
87 UK 10K study - Twins NC_000020.10 - 19864355 Oct 12, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000020.10 - 19864355 Jul 13, 2019 (153)
89 ALFA NC_000020.11 - 19883711 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)
rs8123570 Aug 26, 2003 (117)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2966197077 NC_000020.10:19864354:A:C NC_000020.11:19883710:A:C (self)
11677585017 NC_000020.11:19883710:A:C NC_000020.11:19883710:A:C (self)
ss91662791, ss111842097, ss113183071, ss117508957, ss167959117, ss169294404, ss171985448, ss203853307, ss208719305, ss255532620, ss283328770, ss287435859, ss292627761 NC_000020.9:19812354:A:G NC_000020.11:19883710:A:G (self)
77788334, 43070266, 5633755, 46256447, 16597030, 20164630, 40893826, 10915554, 87115308, 43070266, 9511024, ss228296450, ss237793495, ss243973130, ss566181749, ss662056930, ss1082130496, ss1364339159, ss1429019305, ss1579468816, ss1638563213, ss1681557246, ss1809454097, ss1938122708, ss1969110132, ss2029846799, ss2158399200, ss2629418630, ss2704074689, ss2966197077, ss3017979795, ss3352454194, ss3743312165, ss3758511797, ss3788618846, ss3793516478, ss3798403657, ss3835625729, ss3841439064, ss3888876846, ss3939079053, ss5229146001, ss5436702811, ss5663002758, ss5845542225, ss5957915524 NC_000020.10:19864354:A:G NC_000020.11:19883710:A:G (self)
102052109, 38328685, 122055272, 359761879, 11677585017, ss2241896940, ss3028756877, ss3650987780, ss3706697615, ss3821681082, ss3846947158, ss3981950684, ss5084652934, ss5500703789, ss5614526174, ss5788218168, ss5817878396, ss5853100183, ss5922952713 NC_000020.11:19883710:A:G NC_000020.11:19883710:A:G (self)
ss8357311, ss12493877, ss16900003, ss19479895, ss21759229, ss96190076, ss135746846, ss138221854, ss156254759 NT_011387.8:19804354:A:G NC_000020.11:19883710:A:G (self)
46256447, ss3939079053 NC_000020.10:19864354:A:T NC_000020.11:19883710:A: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 rs6046408

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