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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.

rs530537

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:105027786 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.491866 (130192/264690, TOPMED)
C=0.494623 (69177/139858, GnomAD)
C=0.26343 (7444/28258, 14KJPN) (+ 17 more)
C=0.47374 (8949/18890, ALFA)
C=0.26256 (4400/16758, 8.3KJPN)
C=0.4563 (2922/6404, 1000G_30x)
C=0.4501 (2254/5008, 1000G)
C=0.4739 (2123/4480, Estonian)
C=0.4450 (1715/3854, ALSPAC)
C=0.4577 (1697/3708, TWINSUK)
C=0.2235 (655/2930, KOREAN)
C=0.2112 (387/1832, Korea1K)
C=0.452 (451/998, GoNL)
C=0.467 (280/600, NorthernSweden)
T=0.325 (119/366, SGDP_PRJ)
C=0.451 (148/328, HapMap)
C=0.301 (65/216, Qatari)
C=0.266 (57/214, Vietnamese)
C=0.47 (19/40, GENOME_DK)
T=0.35 (12/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CASP1 : Intron Variant
LOC124902742 : Intron Variant
Publications
3 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 18890 T=0.52626 C=0.47374 0.283854 0.231339 0.484807 4
European Sub 14286 T=0.55201 C=0.44799 0.308694 0.204676 0.48663 1
African Sub 2946 T=0.3951 C=0.6049 0.156823 0.366599 0.476578 0
African Others Sub 114 T=0.316 C=0.684 0.070175 0.438596 0.491228 1
African American Sub 2832 T=0.3983 C=0.6017 0.160311 0.363701 0.475989 0
Asian Sub 112 T=0.688 C=0.312 0.410714 0.035714 0.553571 3
East Asian Sub 86 T=0.69 C=0.31 0.395349 0.023256 0.581395 3
Other Asian Sub 26 T=0.69 C=0.31 0.461538 0.076923 0.461538 0
Latin American 1 Sub 146 T=0.555 C=0.445 0.356164 0.246575 0.39726 2
Latin American 2 Sub 610 T=0.530 C=0.470 0.281967 0.222951 0.495082 0
South Asian Sub 98 T=0.65 C=0.35 0.428571 0.122449 0.44898 0
Other Sub 692 T=0.500 C=0.500 0.257225 0.257225 0.485549 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 T=0.508134 C=0.491866
gnomAD - Genomes Global Study-wide 139858 T=0.505377 C=0.494623
gnomAD - Genomes European Sub 75774 T=0.55200 C=0.44800
gnomAD - Genomes African Sub 41924 T=0.38980 C=0.61020
gnomAD - Genomes American Sub 13584 T=0.51178 C=0.48822
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.6322 C=0.3678
gnomAD - Genomes East Asian Sub 3112 T=0.7478 C=0.2522
gnomAD - Genomes Other Sub 2144 T=0.5289 C=0.4711
14KJPN JAPANESE Study-wide 28258 T=0.73657 C=0.26343
Allele Frequency Aggregator Total Global 18890 T=0.52626 C=0.47374
Allele Frequency Aggregator European Sub 14286 T=0.55201 C=0.44799
Allele Frequency Aggregator African Sub 2946 T=0.3951 C=0.6049
Allele Frequency Aggregator Other Sub 692 T=0.500 C=0.500
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.530 C=0.470
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.555 C=0.445
Allele Frequency Aggregator Asian Sub 112 T=0.688 C=0.312
Allele Frequency Aggregator South Asian Sub 98 T=0.65 C=0.35
8.3KJPN JAPANESE Study-wide 16758 T=0.73744 C=0.26256
1000Genomes_30x Global Study-wide 6404 T=0.5437 C=0.4563
1000Genomes_30x African Sub 1786 T=0.3589 C=0.6411
1000Genomes_30x Europe Sub 1266 T=0.5442 C=0.4558
1000Genomes_30x South Asian Sub 1202 T=0.6364 C=0.3636
1000Genomes_30x East Asian Sub 1170 T=0.7316 C=0.2684
1000Genomes_30x American Sub 980 T=0.542 C=0.458
1000Genomes Global Study-wide 5008 T=0.5499 C=0.4501
1000Genomes African Sub 1322 T=0.3631 C=0.6369
1000Genomes East Asian Sub 1008 T=0.7292 C=0.2708
1000Genomes Europe Sub 1006 T=0.5557 C=0.4443
1000Genomes South Asian Sub 978 T=0.625 C=0.375
1000Genomes American Sub 694 T=0.532 C=0.468
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5261 C=0.4739
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5550 C=0.4450
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5423 C=0.4577
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7765 C=0.2235
Korean Genome Project KOREAN Study-wide 1832 T=0.7888 C=0.2112
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.548 C=0.452
Northern Sweden ACPOP Study-wide 600 T=0.533 C=0.467
SGDP_PRJ Global Study-wide 366 T=0.325 C=0.675
HapMap Global Study-wide 328 T=0.549 C=0.451
HapMap African Sub 120 T=0.392 C=0.608
HapMap American Sub 118 T=0.542 C=0.458
HapMap Asian Sub 90 T=0.77 C=0.23
Qatari Global Study-wide 216 T=0.699 C=0.301
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.734 C=0.266
The Danish reference pan genome Danish Study-wide 40 T=0.53 C=0.47
Siberian Global Study-wide 34 T=0.35 C=0.65
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 11 NC_000011.10:g.105027786T>C
GRCh37.p13 chr 11 NC_000011.9:g.104898513T>C
CASP1 RefSeqGene NG_029124.2:g.12345A>G
Gene: CASP1, caspase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CASP1 transcript variant beta NM_001223.5:c.944-835A>G N/A Intron Variant
CASP1 transcript variant 6 NM_001257118.3:c.1007-835…

NM_001257118.3:c.1007-835A>G

N/A Intron Variant
CASP1 transcript variant 7 NM_001257119.3:c.944-835A…

NM_001257119.3:c.944-835A>G

N/A Intron Variant
CASP1 transcript variant alpha NM_033292.4:c.1007-835A>G N/A Intron Variant
CASP1 transcript variant gamma NM_033293.4:c.728-835A>G N/A Intron Variant
CASP1 transcript variant delta NM_033294.4:c.584-835A>G N/A Intron Variant
CASP1 transcript variant epsilon NM_033295.4:c.59-835A>G N/A Intron Variant
CASP1 transcript variant X1 XM_017018393.2:c.1139-835…

XM_017018393.2:c.1139-835A>G

N/A Intron Variant
CASP1 transcript variant X2 XM_017018394.2:c.1139-835…

XM_017018394.2:c.1139-835A>G

N/A Intron Variant
CASP1 transcript variant X3 XM_017018395.2:c.1076-835…

XM_017018395.2:c.1076-835A>G

N/A Intron Variant
CASP1 transcript variant X5 XM_017018396.2:c.917-835A…

XM_017018396.2:c.917-835A>G

N/A Intron Variant
CASP1 transcript variant X4 XM_047427675.1:c.959-835A…

XM_047427675.1:c.959-835A>G

N/A Intron Variant
Gene: LOC124902742, uncharacterized LOC124902742 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124902742 transcript variant X1 XR_007062869.1: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 T= C
GRCh38.p14 chr 11 NC_000011.10:g.105027786= NC_000011.10:g.105027786T>C
GRCh37.p13 chr 11 NC_000011.9:g.104898513= NC_000011.9:g.104898513T>C
CASP1 RefSeqGene NG_029124.2:g.12345= NG_029124.2:g.12345A>G
CASP1 transcript variant beta NM_001223.4:c.944-835= NM_001223.4:c.944-835A>G
CASP1 transcript variant beta NM_001223.5:c.944-835= NM_001223.5:c.944-835A>G
CASP1 transcript variant 6 NM_001257118.1:c.1007-835= NM_001257118.1:c.1007-835A>G
CASP1 transcript variant 6 NM_001257118.3:c.1007-835= NM_001257118.3:c.1007-835A>G
CASP1 transcript variant 7 NM_001257119.1:c.944-835= NM_001257119.1:c.944-835A>G
CASP1 transcript variant 7 NM_001257119.3:c.944-835= NM_001257119.3:c.944-835A>G
CASP1 transcript variant alpha NM_033292.3:c.1007-835= NM_033292.3:c.1007-835A>G
CASP1 transcript variant alpha NM_033292.4:c.1007-835= NM_033292.4:c.1007-835A>G
CASP1 transcript variant gamma NM_033293.3:c.728-835= NM_033293.3:c.728-835A>G
CASP1 transcript variant gamma NM_033293.4:c.728-835= NM_033293.4:c.728-835A>G
CASP1 transcript variant delta NM_033294.3:c.584-835= NM_033294.3:c.584-835A>G
CASP1 transcript variant delta NM_033294.4:c.584-835= NM_033294.4:c.584-835A>G
CASP1 transcript variant epsilon NM_033295.3:c.59-835= NM_033295.3:c.59-835A>G
CASP1 transcript variant epsilon NM_033295.4:c.59-835= NM_033295.4:c.59-835A>G
CASP1 transcript variant X1 XM_017018393.2:c.1139-835= XM_017018393.2:c.1139-835A>G
CASP1 transcript variant X2 XM_017018394.2:c.1139-835= XM_017018394.2:c.1139-835A>G
CASP1 transcript variant X3 XM_017018395.2:c.1076-835= XM_017018395.2:c.1076-835A>G
CASP1 transcript variant X5 XM_017018396.2:c.917-835= XM_017018396.2:c.917-835A>G
CASP1 transcript variant X4 XM_047427675.1:c.959-835= XM_047427675.1:c.959-835A>G
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#.

68 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss701053 Aug 11, 2000 (83)
2 BCM_SSAHASNP ss10686154 Jul 11, 2003 (116)
3 SSAHASNP ss20794487 Apr 05, 2004 (121)
4 PERLEGEN ss23573806 Sep 20, 2004 (123)
5 HGSV ss80706070 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss88765742 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss97508139 Feb 04, 2009 (130)
8 1000GENOMES ss111008006 Jan 25, 2009 (130)
9 ILLUMINA-UK ss119951584 Dec 01, 2009 (131)
10 ENSEMBL ss132800157 Dec 01, 2009 (131)
11 ENSEMBL ss137869561 Dec 01, 2009 (131)
12 GMI ss156746108 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss168730783 Jul 04, 2010 (132)
14 BUSHMAN ss203159733 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss207572390 Jul 04, 2010 (132)
16 1000GENOMES ss211190984 Jul 14, 2010 (132)
17 1000GENOMES ss225439596 Jul 14, 2010 (132)
18 1000GENOMES ss235703253 Jul 15, 2010 (132)
19 1000GENOMES ss242304661 Jul 15, 2010 (132)
20 BL ss255367531 May 09, 2011 (134)
21 GMI ss281156281 May 04, 2012 (137)
22 PJP ss291131340 May 09, 2011 (134)
23 TISHKOFF ss562799242 Apr 25, 2013 (138)
24 SSMP ss658322268 Apr 25, 2013 (138)
25 EVA-GONL ss988917942 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1078012628 Aug 21, 2014 (142)
27 1000GENOMES ss1342791913 Aug 21, 2014 (142)
28 DDI ss1426748786 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1575928088 Apr 01, 2015 (144)
30 EVA_DECODE ss1598582012 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1627368012 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1670362045 Apr 01, 2015 (144)
33 HAMMER_LAB ss1806977806 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1932280471 Feb 12, 2016 (147)
35 GENOMED ss1967448697 Jul 19, 2016 (147)
36 JJLAB ss2026885145 Sep 14, 2016 (149)
37 USC_VALOUEV ss2155197222 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2185340488 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2627916753 Nov 08, 2017 (151)
40 GRF ss2699503300 Nov 08, 2017 (151)
41 GNOMAD ss2903962128 Nov 08, 2017 (151)
42 SWEGEN ss3008711881 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3027242431 Nov 08, 2017 (151)
44 CSHL ss3349776190 Nov 08, 2017 (151)
45 URBANLAB ss3649696223 Oct 12, 2018 (152)
46 EGCUT_WGS ss3676034826 Jul 13, 2019 (153)
47 EVA_DECODE ss3692516411 Jul 13, 2019 (153)
48 ACPOP ss3738505025 Jul 13, 2019 (153)
49 EVA ss3749759023 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3815092181 Jul 13, 2019 (153)
51 EVA ss3832818571 Apr 26, 2020 (154)
52 SGDP_PRJ ss3877051173 Apr 26, 2020 (154)
53 KRGDB ss3925495073 Apr 26, 2020 (154)
54 KOGIC ss3970664256 Apr 26, 2020 (154)
55 TOPMED ss4898421790 Apr 26, 2021 (155)
56 TOMMO_GENOMICS ss5203696783 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5288752499 Oct 16, 2022 (156)
58 EVA ss5401966805 Oct 16, 2022 (156)
59 HUGCELL_USP ss5483755052 Oct 16, 2022 (156)
60 EVA ss5510505372 Oct 16, 2022 (156)
61 1000G_HIGH_COVERAGE ss5585158685 Oct 16, 2022 (156)
62 SANFORD_IMAGENETICS ss5651988334 Oct 16, 2022 (156)
63 TOMMO_GENOMICS ss5752088165 Oct 16, 2022 (156)
64 YY_MCH ss5812742491 Oct 16, 2022 (156)
65 EVA ss5837170285 Oct 16, 2022 (156)
66 EVA ss5850134051 Oct 16, 2022 (156)
67 EVA ss5921481805 Oct 16, 2022 (156)
68 EVA ss5943312012 Oct 16, 2022 (156)
69 1000Genomes NC_000011.9 - 104898513 Oct 12, 2018 (152)
70 1000Genomes_30x NC_000011.10 - 105027786 Oct 16, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 104898513 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000011.9 - 104898513 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000011.9 - 104898513 Apr 26, 2020 (154)
74 gnomAD - Genomes NC_000011.10 - 105027786 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000011.9 - 104898513 Apr 26, 2020 (154)
76 HapMap NC_000011.10 - 105027786 Apr 26, 2020 (154)
77 KOREAN population from KRGDB NC_000011.9 - 104898513 Apr 26, 2020 (154)
78 Korean Genome Project NC_000011.10 - 105027786 Apr 26, 2020 (154)
79 Northern Sweden NC_000011.9 - 104898513 Jul 13, 2019 (153)
80 Qatari NC_000011.9 - 104898513 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000011.9 - 104898513 Apr 26, 2020 (154)
82 Siberian NC_000011.9 - 104898513 Apr 26, 2020 (154)
83 8.3KJPN NC_000011.9 - 104898513 Apr 26, 2021 (155)
84 14KJPN NC_000011.10 - 105027786 Oct 16, 2022 (156)
85 TopMed NC_000011.10 - 105027786 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000011.9 - 104898513 Oct 12, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000011.9 - 104898513 Jul 13, 2019 (153)
88 ALFA NC_000011.10 - 105027786 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)
rs58364261 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80706070, ss88765742, ss111008006, ss119951584, ss168730783, ss203159733, ss207572390, ss211190984, ss255367531, ss281156281, ss291131340, ss1598582012 NC_000011.8:104403722:T:C NC_000011.10:105027785:T:C (self)
55367734, 30728029, 21773074, 2719029, 13715837, 32672467, 11789890, 14322401, 29068153, 7713576, 61666090, 30728029, 6821454, ss225439596, ss235703253, ss242304661, ss562799242, ss658322268, ss988917942, ss1078012628, ss1342791913, ss1426748786, ss1575928088, ss1627368012, ss1670362045, ss1806977806, ss1932280471, ss1967448697, ss2026885145, ss2155197222, ss2627916753, ss2699503300, ss2903962128, ss3008711881, ss3349776190, ss3676034826, ss3738505025, ss3749759023, ss3832818571, ss3877051173, ss3925495073, ss5203696783, ss5401966805, ss5510505372, ss5651988334, ss5837170285, ss5943312012 NC_000011.9:104898512:T:C NC_000011.10:105027785:T:C (self)
72684620, 390689871, 689493, 27042257, 85925269, 113967446, 8988863075, ss2185340488, ss3027242431, ss3649696223, ss3692516411, ss3815092181, ss3970664256, ss4898421790, ss5288752499, ss5483755052, ss5585158685, ss5752088165, ss5812742491, ss5850134051, ss5921481805 NC_000011.10:105027785:T:C NC_000011.10:105027785:T:C (self)
ss10686154 NT_033899.5:8442354:T:C NC_000011.10:105027785:T:C (self)
ss20794487 NT_033899.6:8442364:T:C NC_000011.10:105027785:T:C (self)
ss701053, ss23573806, ss97508139, ss132800157, ss137869561, ss156746108 NT_033899.8:8460928:T:C NC_000011.10:105027785:T:C (self)
Help

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

3 citations for rs530537
PMID Title Author Year Journal
20184726 Caspase-1 genetic variation is not associated with Alzheimer's disease risk. Vázquez-Higuera JL et al. 2010 BMC medical genetics
24901306 The NOD-like receptor signalling pathway in Helicobacter pylori infection and related gastric cancer: a case-control study and gene expression analyses. Castaño-Rodríguez N et al. 2014 PloS one
34376808 Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus. Miller AK et al. 2021 Oncogene
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