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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.

rs3766191

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:1082207 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.146534 (38786/264690, TOPMED)
T=0.151854 (21757/143276, ALFA)
T=0.155855 (21853/140214, GnomAD) (+ 17 more)
T=0.09196 (1541/16758, 8.3KJPN)
T=0.1715 (1098/6404, 1000G_30x)
T=0.1711 (857/5008, 1000G)
T=0.1960 (878/4480, Estonian)
T=0.1445 (557/3854, ALSPAC)
T=0.1373 (509/3708, TWINSUK)
T=0.0966 (283/2930, KOREAN)
T=0.1614 (305/1890, HapMap)
T=0.0930 (170/1828, Korea1K)
T=0.160 (160/998, GoNL)
T=0.152 (91/600, NorthernSweden)
T=0.152 (81/534, MGP)
T=0.287 (62/216, Qatari)
T=0.093 (20/214, Vietnamese)
C=0.449 (61/136, SGDP_PRJ)
T=0.20 (8/40, GENOME_DK)
C=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : 3 Prime UTR 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 143276 C=0.848146 T=0.151854
European Sub 122668 C=0.845119 T=0.154881
African Sub 6664 C=0.8469 T=0.1531
African Others Sub 242 C=0.810 T=0.190
African American Sub 6422 C=0.8483 T=0.1517
Asian Sub 628 C=0.869 T=0.131
East Asian Sub 496 C=0.889 T=0.111
Other Asian Sub 132 C=0.795 T=0.205
Latin American 1 Sub 752 C=0.832 T=0.168
Latin American 2 Sub 6310 C=0.9022 T=0.0978
South Asian Sub 184 C=0.848 T=0.152
Other Sub 6070 C=0.8542 T=0.1458


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=0.853466 T=0.146534
Allele Frequency Aggregator Total Global 143276 C=0.848146 T=0.151854
Allele Frequency Aggregator European Sub 122668 C=0.845119 T=0.154881
Allele Frequency Aggregator African Sub 6664 C=0.8469 T=0.1531
Allele Frequency Aggregator Latin American 2 Sub 6310 C=0.9022 T=0.0978
Allele Frequency Aggregator Other Sub 6070 C=0.8542 T=0.1458
Allele Frequency Aggregator Latin American 1 Sub 752 C=0.832 T=0.168
Allele Frequency Aggregator Asian Sub 628 C=0.869 T=0.131
Allele Frequency Aggregator South Asian Sub 184 C=0.848 T=0.152
gnomAD - Genomes Global Study-wide 140214 C=0.844145 T=0.155855
gnomAD - Genomes European Sub 75914 C=0.83855 T=0.16145
gnomAD - Genomes African Sub 42038 C=0.84126 T=0.15874
gnomAD - Genomes American Sub 13660 C=0.88477 T=0.11523
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.7947 T=0.2053
gnomAD - Genomes East Asian Sub 3128 C=0.8865 T=0.1135
gnomAD - Genomes Other Sub 2152 C=0.8546 T=0.1454
8.3KJPN JAPANESE Study-wide 16758 C=0.90804 T=0.09196
1000Genomes_30x Global Study-wide 6404 C=0.8285 T=0.1715
1000Genomes_30x African Sub 1786 C=0.7973 T=0.2027
1000Genomes_30x Europe Sub 1266 C=0.8365 T=0.1635
1000Genomes_30x South Asian Sub 1202 C=0.7712 T=0.2288
1000Genomes_30x East Asian Sub 1170 C=0.8735 T=0.1265
1000Genomes_30x American Sub 980 C=0.892 T=0.108
1000Genomes Global Study-wide 5008 C=0.8289 T=0.1711
1000Genomes African Sub 1322 C=0.7965 T=0.2035
1000Genomes East Asian Sub 1008 C=0.8750 T=0.1250
1000Genomes Europe Sub 1006 C=0.8350 T=0.1650
1000Genomes South Asian Sub 978 C=0.777 T=0.223
1000Genomes American Sub 694 C=0.888 T=0.112
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8040 T=0.1960
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8555 T=0.1445
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8627 T=0.1373
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9034 T=0.0966
HapMap Global Study-wide 1890 C=0.8386 T=0.1614
HapMap American Sub 770 C=0.861 T=0.139
HapMap African Sub 692 C=0.808 T=0.192
HapMap Asian Sub 252 C=0.861 T=0.139
HapMap Europe Sub 176 C=0.830 T=0.170
Korean Genome Project KOREAN Study-wide 1828 C=0.9070 T=0.0930
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.840 T=0.160
Northern Sweden ACPOP Study-wide 600 C=0.848 T=0.152
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.848 T=0.152
Qatari Global Study-wide 216 C=0.713 T=0.287
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.907 T=0.093
SGDP_PRJ Global Study-wide 136 C=0.449 T=0.551
The Danish reference pan genome Danish Study-wide 40 C=0.80 T=0.20
Siberian Global Study-wide 28 C=0.39 T=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 1 NC_000001.11:g.1082207C>G
GRCh38.p14 chr 1 NC_000001.11:g.1082207C>T
GRCh37.p13 chr 1 NC_000001.10:g.1017587C>G
GRCh37.p13 chr 1 NC_000001.10:g.1017587C>T
Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C1orf159 transcript variant 3 NM_001363525.2:c.*686= N/A 3 Prime UTR Variant
C1orf159 transcript variant 1 NM_001330306.2:c.*686= N/A 3 Prime UTR Variant
C1orf159 transcript variant 2 NM_017891.5:c.*686= N/A 3 Prime UTR 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= G T
GRCh38.p14 chr 1 NC_000001.11:g.1082207= NC_000001.11:g.1082207C>G NC_000001.11:g.1082207C>T
GRCh37.p13 chr 1 NC_000001.10:g.1017587= NC_000001.10:g.1017587C>G NC_000001.10:g.1017587C>T
C1orf159 transcript variant 2 NM_017891.5:c.*686= NM_017891.5:c.*686G>C NM_017891.5:c.*686G>A
C1orf159 transcript variant 2 NM_017891.4:c.*686= NM_017891.4:c.*686G>C NM_017891.4:c.*686G>A
C1orf159 transcript variant 1 NM_001330306.2:c.*686= NM_001330306.2:c.*686G>C NM_001330306.2:c.*686G>A
C1orf159 transcript variant 1 NM_001330306.1:c.*686= NM_001330306.1:c.*686G>C NM_001330306.1:c.*686G>A
C1orf159 transcript variant 3 NM_001363525.2:c.*686= NM_001363525.2:c.*686G>C NM_001363525.2:c.*686G>A
C1orf159 transcript variant 3 NM_001363525.1:c.*686= NM_001363525.1:c.*686G>C NM_001363525.1:c.*686G>A
C1orf159 transcript variant 2 NM_001114103.1:c.*686= NM_001114103.1:c.*686G>C NM_001114103.1:c.*686G>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#.

100 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4952233 Aug 28, 2002 (107)
2 CSHL-HAPMAP ss17341268 Feb 27, 2004 (120)
3 PERLEGEN ss24713323 Sep 20, 2004 (123)
4 ABI ss44012866 Mar 14, 2006 (126)
5 SI_EXO ss52077892 Oct 15, 2006 (127)
6 PERLEGEN ss68756309 May 17, 2007 (127)
7 ILLUMINA ss75120839 Dec 06, 2007 (129)
8 HUMANGENOME_JCVI ss99179681 Feb 06, 2009 (130)
9 BGI ss102713553 Dec 01, 2009 (131)
10 KRIBB_YJKIM ss119461346 Dec 01, 2009 (131)
11 ENSEMBL ss131630099 Dec 01, 2009 (131)
12 ILLUMINA ss160638853 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss163706919 Jul 04, 2010 (132)
14 ILLUMINA ss173630699 Jul 04, 2010 (132)
15 1000GENOMES ss218191718 Jul 14, 2010 (132)
16 1000GENOMES ss230396315 Jul 14, 2010 (132)
17 1000GENOMES ss238115878 Jul 15, 2010 (132)
18 GMI ss275682298 May 04, 2012 (137)
19 ILLUMINA ss480823731 May 04, 2012 (137)
20 ILLUMINA ss480839458 May 04, 2012 (137)
21 ILLUMINA ss481770148 Sep 08, 2015 (146)
22 ILLUMINA ss485206660 May 04, 2012 (137)
23 ILLUMINA ss537191171 Sep 08, 2015 (146)
24 TISHKOFF ss553713088 Apr 25, 2013 (138)
25 SSMP ss647518183 Apr 25, 2013 (138)
26 ILLUMINA ss778895359 Sep 08, 2015 (146)
27 ILLUMINA ss783049315 Sep 08, 2015 (146)
28 ILLUMINA ss784007922 Sep 08, 2015 (146)
29 ILLUMINA ss832307141 Sep 08, 2015 (146)
30 ILLUMINA ss834356545 Sep 08, 2015 (146)
31 EVA-GONL ss974771673 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1067613469 Aug 21, 2014 (142)
33 1000GENOMES ss1289348914 Aug 21, 2014 (142)
34 DDI ss1425685716 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1573851880 Apr 01, 2015 (144)
36 EVA_DECODE ss1584131565 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1599381866 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1642375899 Apr 01, 2015 (144)
39 EVA_MGP ss1710883692 Apr 01, 2015 (144)
40 EVA_SVP ss1712305535 Apr 01, 2015 (144)
41 ILLUMINA ss1751859791 Sep 08, 2015 (146)
42 HAMMER_LAB ss1793716461 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1917963538 Feb 12, 2016 (147)
44 JJLAB ss2019499648 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147486323 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2159383293 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624265437 Nov 08, 2017 (151)
48 ILLUMINA ss2632465715 Nov 08, 2017 (151)
49 GRF ss2697377270 Nov 08, 2017 (151)
50 GNOMAD ss2750667917 Nov 08, 2017 (151)
51 SWEGEN ss2986153801 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3023514213 Nov 08, 2017 (151)
53 CSHL ss3343274054 Nov 08, 2017 (151)
54 ILLUMINA ss3626007038 Oct 11, 2018 (152)
55 ILLUMINA ss3630505766 Oct 11, 2018 (152)
56 ILLUMINA ss3632878058 Oct 11, 2018 (152)
57 ILLUMINA ss3633571473 Oct 11, 2018 (152)
58 ILLUMINA ss3634302053 Oct 11, 2018 (152)
59 ILLUMINA ss3635265677 Oct 11, 2018 (152)
60 ILLUMINA ss3635978702 Oct 11, 2018 (152)
61 ILLUMINA ss3637016017 Oct 11, 2018 (152)
62 ILLUMINA ss3637732487 Oct 11, 2018 (152)
63 ILLUMINA ss3640009419 Oct 11, 2018 (152)
64 ILLUMINA ss3640973165 Oct 11, 2018 (152)
65 ILLUMINA ss3641266980 Oct 11, 2018 (152)
66 ILLUMINA ss3642746762 Oct 11, 2018 (152)
67 OMUKHERJEE_ADBS ss3646218954 Oct 11, 2018 (152)
68 URBANLAB ss3646581830 Oct 11, 2018 (152)
69 EGCUT_WGS ss3654264902 Jul 12, 2019 (153)
70 EVA_DECODE ss3685997278 Jul 12, 2019 (153)
71 ACPOP ss3726718418 Jul 12, 2019 (153)
72 ILLUMINA ss3744602984 Jul 12, 2019 (153)
73 EVA ss3745723873 Jul 12, 2019 (153)
74 ILLUMINA ss3772104742 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3798746522 Jul 12, 2019 (153)
76 EVA ss3825549241 Apr 25, 2020 (154)
77 EVA ss3825982469 Apr 25, 2020 (154)
78 SGDP_PRJ ss3848003043 Apr 25, 2020 (154)
79 KRGDB ss3892845578 Apr 25, 2020 (154)
80 KOGIC ss3943635458 Apr 25, 2020 (154)
81 FSA-LAB ss3983910671 Apr 25, 2021 (155)
82 FSA-LAB ss3983910672 Apr 25, 2021 (155)
83 EVA ss3986007849 Apr 25, 2021 (155)
84 EVA ss4016889106 Apr 25, 2021 (155)
85 TOPMED ss4436509958 Apr 25, 2021 (155)
86 TOMMO_GENOMICS ss5142065257 Apr 25, 2021 (155)
87 1000G_HIGH_COVERAGE ss5240872302 Oct 12, 2022 (156)
88 EVA ss5314586033 Oct 12, 2022 (156)
89 EVA ss5316198051 Oct 12, 2022 (156)
90 HUGCELL_USP ss5442119219 Oct 12, 2022 (156)
91 1000G_HIGH_COVERAGE ss5512500550 Oct 12, 2022 (156)
92 SANFORD_IMAGENETICS ss5624754637 Oct 12, 2022 (156)
93 TOMMO_GENOMICS ss5666209139 Oct 12, 2022 (156)
94 TOMMO_GENOMICS ss5666209140 Oct 12, 2022 (156)
95 EVA ss5799472563 Oct 12, 2022 (156)
96 YY_MCH ss5800246039 Oct 12, 2022 (156)
97 EVA ss5831422327 Oct 12, 2022 (156)
98 EVA ss5848749652 Oct 12, 2022 (156)
99 EVA ss5906713601 Oct 12, 2022 (156)
100 EVA ss5936586981 Oct 12, 2022 (156)
101 1000Genomes NC_000001.10 - 1017587 Oct 11, 2018 (152)
102 1000Genomes_30x NC_000001.11 - 1082207 Oct 12, 2022 (156)
103 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1017587 Oct 11, 2018 (152)
104 Genetic variation in the Estonian population NC_000001.10 - 1017587 Oct 11, 2018 (152)
105 The Danish reference pan genome NC_000001.10 - 1017587 Apr 25, 2020 (154)
106 gnomAD - Genomes NC_000001.11 - 1082207 Apr 25, 2021 (155)
107 Genome of the Netherlands Release 5 NC_000001.10 - 1017587 Apr 25, 2020 (154)
108 HapMap NC_000001.11 - 1082207 Apr 25, 2020 (154)
109 KOREAN population from KRGDB NC_000001.10 - 1017587 Apr 25, 2020 (154)
110 Korean Genome Project NC_000001.11 - 1082207 Apr 25, 2020 (154)
111 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 1017587 Apr 25, 2020 (154)
112 Northern Sweden NC_000001.10 - 1017587 Jul 12, 2019 (153)
113 Qatari NC_000001.10 - 1017587 Apr 25, 2020 (154)
114 SGDP_PRJ NC_000001.10 - 1017587 Apr 25, 2020 (154)
115 Siberian NC_000001.10 - 1017587 Apr 25, 2020 (154)
116 8.3KJPN NC_000001.10 - 1017587 Apr 25, 2021 (155)
117 14KJPN

Submission ignored due to conflicting rows:
Row 46243 (NC_000001.11:1082206:C:T 2590/28256)
Row 46244 (NC_000001.11:1082206:C:G 1/28256)

- Oct 12, 2022 (156)
118 14KJPN

Submission ignored due to conflicting rows:
Row 46243 (NC_000001.11:1082206:C:T 2590/28256)
Row 46244 (NC_000001.11:1082206:C:G 1/28256)

- Oct 12, 2022 (156)
119 TopMed NC_000001.11 - 1082207 Apr 25, 2021 (155)
120 UK 10K study - Twins NC_000001.10 - 1017587 Oct 11, 2018 (152)
121 A Vietnamese Genetic Variation Database NC_000001.10 - 1017587 Jul 12, 2019 (153)
122 ALFA NC_000001.11 - 1082207 Apr 25, 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)
rs17232153 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss5666209140 NC_000001.11:1082206:C:G NC_000001.11:1082206:C:G
ss163706919, ss275682298, ss480823731, ss1584131565, ss1712305535, ss3642746762 NC_000001.9:1007449:C:T NC_000001.11:1082206:C:T (self)
14003, 4209, 3150, 1359114, 2046, 22972, 444, 3283, 5468, 20023, 2677, 34564, 4209, 971, ss218191718, ss230396315, ss238115878, ss480839458, ss481770148, ss485206660, ss537191171, ss553713088, ss647518183, ss778895359, ss783049315, ss784007922, ss832307141, ss834356545, ss974771673, ss1067613469, ss1289348914, ss1425685716, ss1573851880, ss1599381866, ss1642375899, ss1710883692, ss1751859791, ss1793716461, ss1917963538, ss2019499648, ss2147486323, ss2624265437, ss2632465715, ss2697377270, ss2750667917, ss2986153801, ss3343274054, ss3626007038, ss3630505766, ss3632878058, ss3633571473, ss3634302053, ss3635265677, ss3635978702, ss3637016017, ss3637732487, ss3640009419, ss3640973165, ss3641266980, ss3646218954, ss3654264902, ss3726718418, ss3744602984, ss3745723873, ss3772104742, ss3825549241, ss3825982469, ss3848003043, ss3892845578, ss3983910671, ss3983910672, ss3986007849, ss4016889106, ss5142065257, ss5314586033, ss5316198051, ss5624754637, ss5799472563, ss5831422327, ss5936586981 NC_000001.10:1017586:C:T NC_000001.11:1082206:C:T (self)
26485, 132601, 179, 13459, 116293, 9489493897, ss2159383293, ss3023514213, ss3646581830, ss3685997278, ss3798746522, ss3943635458, ss4436509958, ss5240872302, ss5442119219, ss5512500550, ss5666209139, ss5800246039, ss5848749652, ss5906713601 NC_000001.11:1082206:C:T NC_000001.11:1082206:C:T (self)
ss4952233, ss24713323, ss44012866, ss68756309, ss75120839, ss99179681, ss102713553, ss119461346, ss131630099, ss160638853, ss173630699 NT_004350.19:496218:C:T NC_000001.11:1082206:C:T (self)
ss17341268 NT_077913.2:21297:C:T NC_000001.11:1082206:C:T (self)
ss52077892 NT_077913.3:496278:C:T NC_000001.11:1082206: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 rs3766191

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