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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.

rs74518378

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:46108044 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.096792 (25620/264690, TOPMED)
T=0.095909 (13123/136828, GnomAD)
T=0.10306 (3159/30652, ALFA) (+ 16 more)
T=0.32911 (9300/28258, 14KJPN)
T=0.32601 (5464/16760, 8.3KJPN)
T=0.1266 (811/6404, 1000G_30x)
T=0.1308 (655/5008, 1000G)
T=0.1362 (610/4480, Estonian)
T=0.0965 (372/3854, ALSPAC)
T=0.1068 (396/3708, TWINSUK)
T=0.2935 (860/2930, KOREAN)
T=0.3524 (640/1816, Korea1K)
T=0.106 (106/998, GoNL)
T=0.108 (65/600, NorthernSweden)
T=0.222 (48/216, Qatari)
T=0.315 (68/216, Vietnamese)
C=0.406 (65/160, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.44 (7/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KANSL1 : 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 30652 C=0.89694 T=0.10306
European Sub 24592 C=0.88960 T=0.11040
African Sub 3138 C=0.9659 T=0.0341
African Others Sub 124 C=0.952 T=0.048
African American Sub 3014 C=0.9665 T=0.0335
Asian Sub 126 C=0.770 T=0.230
East Asian Sub 98 C=0.77 T=0.23
Other Asian Sub 28 C=0.79 T=0.21
Latin American 1 Sub 164 C=0.835 T=0.165
Latin American 2 Sub 684 C=0.887 T=0.113
South Asian Sub 114 C=0.904 T=0.096
Other Sub 1834 C=0.8948 T=0.1052


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=0.903208 T=0.096792
gnomAD - Genomes Global Study-wide 136828 C=0.904091 T=0.095909
gnomAD - Genomes European Sub 73342 C=0.88525 T=0.11475
gnomAD - Genomes African Sub 41880 C=0.96414 T=0.03586
gnomAD - Genomes American Sub 13202 C=0.87252 T=0.12748
gnomAD - Genomes Ashkenazi Jewish Sub 3188 C=0.9046 T=0.0954
gnomAD - Genomes East Asian Sub 3126 C=0.6961 T=0.3039
gnomAD - Genomes Other Sub 2090 C=0.8718 T=0.1282
Allele Frequency Aggregator Total Global 30652 C=0.89694 T=0.10306
Allele Frequency Aggregator European Sub 24592 C=0.88960 T=0.11040
Allele Frequency Aggregator African Sub 3138 C=0.9659 T=0.0341
Allele Frequency Aggregator Other Sub 1834 C=0.8948 T=0.1052
Allele Frequency Aggregator Latin American 2 Sub 684 C=0.887 T=0.113
Allele Frequency Aggregator Latin American 1 Sub 164 C=0.835 T=0.165
Allele Frequency Aggregator Asian Sub 126 C=0.770 T=0.230
Allele Frequency Aggregator South Asian Sub 114 C=0.904 T=0.096
14KJPN JAPANESE Study-wide 28258 C=0.67089 T=0.32911
8.3KJPN JAPANESE Study-wide 16760 C=0.67399 T=0.32601
1000Genomes_30x Global Study-wide 6404 C=0.8734 T=0.1266
1000Genomes_30x African Sub 1786 C=0.9709 T=0.0291
1000Genomes_30x Europe Sub 1266 C=0.8863 T=0.1137
1000Genomes_30x South Asian Sub 1202 C=0.8769 T=0.1231
1000Genomes_30x East Asian Sub 1170 C=0.7000 T=0.3000
1000Genomes_30x American Sub 980 C=0.882 T=0.118
1000Genomes Global Study-wide 5008 C=0.8692 T=0.1308
1000Genomes African Sub 1322 C=0.9690 T=0.0310
1000Genomes East Asian Sub 1008 C=0.6974 T=0.3026
1000Genomes Europe Sub 1006 C=0.8897 T=0.1103
1000Genomes South Asian Sub 978 C=0.883 T=0.117
1000Genomes American Sub 694 C=0.879 T=0.121
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8638 T=0.1362
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9035 T=0.0965
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8932 T=0.1068
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7065 T=0.2935
Korean Genome Project KOREAN Study-wide 1816 C=0.6476 T=0.3524
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.894 T=0.106
Northern Sweden ACPOP Study-wide 600 C=0.892 T=0.108
Qatari Global Study-wide 216 C=0.778 T=0.222
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.685 T=0.315
SGDP_PRJ Global Study-wide 160 C=0.406 T=0.594
The Danish reference pan genome Danish Study-wide 40 C=0.82 T=0.17
Siberian Global Study-wide 16 C=0.44 T=0.56
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 17 NC_000017.11:g.46108044C>T
GRCh37.p13 chr 17 NC_000017.10:g.44185410C>T
KANSL1 RefSeqGene NG_032784.1:g.122331G>A
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5 NT_187663.1:g.810143C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.2:g.678668G>A
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.1:g.680661G>A
Gene: KANSL1, KAT8 regulatory NSL complex subunit 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KANSL1 transcript variant 3 NM_001193465.2:c.1290-133…

NM_001193465.2:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant 1 NM_001193466.2:c.1290-133…

NM_001193466.2:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant 4 NM_001379198.1:c.1290-133…

NM_001379198.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant 2 NM_015443.4:c.1290-13343G…

NM_015443.4:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X1 XM_006721824.5:c.1290-133…

XM_006721824.5:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X2 XM_011524628.4:c.1290-133…

XM_011524628.4:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X8 XM_017024488.3:c.1290-133…

XM_017024488.3:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X1 XM_047435794.1:c.1290-133…

XM_047435794.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X4 XM_047435795.1:c.1290-133…

XM_047435795.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X5 XM_047435796.1:c.1290-133…

XM_047435796.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X6 XM_047435797.1:c.1290-133…

XM_047435797.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X7 XM_047435798.1:c.1290-133…

XM_047435798.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X9 XM_047435799.1:c.1290-133…

XM_047435799.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X3 XM_047435800.1:c.1290-133…

XM_047435800.1:c.1290-13343G>A

N/A Intron Variant
KANSL1 transcript variant X4 XM_047435801.1:c.60-13343…

XM_047435801.1:c.60-13343G>A

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 C= T
GRCh38.p14 chr 17 NC_000017.11:g.46108044= NC_000017.11:g.46108044C>T
GRCh37.p13 chr 17 NC_000017.10:g.44185410= NC_000017.10:g.44185410C>T
KANSL1 RefSeqGene NG_032784.1:g.122331= NG_032784.1:g.122331G>A
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5 NT_187663.1:g.810143= NT_187663.1:g.810143C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.2:g.678668= NT_167251.2:g.678668G>A
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5 NT_167251.1:g.680661= NT_167251.1:g.680661G>A
KANSL1 transcript variant 3 NM_001193465.1:c.1290-13343= NM_001193465.1:c.1290-13343G>A
KANSL1 transcript variant 3 NM_001193465.2:c.1290-13343= NM_001193465.2:c.1290-13343G>A
KANSL1 transcript variant 1 NM_001193466.1:c.1290-13343= NM_001193466.1:c.1290-13343G>A
KANSL1 transcript variant 1 NM_001193466.2:c.1290-13343= NM_001193466.2:c.1290-13343G>A
KANSL1 transcript variant 4 NM_001379198.1:c.1290-13343= NM_001379198.1:c.1290-13343G>A
KANSL1 transcript variant 2 NM_015443.3:c.1290-13343= NM_015443.3:c.1290-13343G>A
KANSL1 transcript variant 2 NM_015443.4:c.1290-13343= NM_015443.4:c.1290-13343G>A
KANSL1 transcript variant X1 XM_005257232.1:c.1290-13343= XM_005257232.1:c.1290-13343G>A
KANSL1 transcript variant X2 XM_005257233.1:c.1290-13343= XM_005257233.1:c.1290-13343G>A
KANSL1 transcript variant X3 XM_005257234.1:c.1290-13343= XM_005257234.1:c.1290-13343G>A
KANSL1 transcript variant X4 XM_005257235.1:c.1290-13343= XM_005257235.1:c.1290-13343G>A
KANSL1 transcript variant X2 XM_005275644.1:c.1290-13033= XM_005275644.1:c.1290-13033G>A
KANSL1 transcript variant X1 XM_005275645.1:c.1290-13033= XM_005275645.1:c.1290-13033G>A
KANSL1 transcript variant X1 XM_006721824.5:c.1290-13343= XM_006721824.5:c.1290-13343G>A
KANSL1 transcript variant X2 XM_011524628.4:c.1290-13343= XM_011524628.4:c.1290-13343G>A
KANSL1 transcript variant X8 XM_017024488.3:c.1290-13343= XM_017024488.3:c.1290-13343G>A
KANSL1 transcript variant X1 XM_047435794.1:c.1290-13343= XM_047435794.1:c.1290-13343G>A
KANSL1 transcript variant X4 XM_047435795.1:c.1290-13343= XM_047435795.1:c.1290-13343G>A
KANSL1 transcript variant X5 XM_047435796.1:c.1290-13343= XM_047435796.1:c.1290-13343G>A
KANSL1 transcript variant X6 XM_047435797.1:c.1290-13343= XM_047435797.1:c.1290-13343G>A
KANSL1 transcript variant X7 XM_047435798.1:c.1290-13343= XM_047435798.1:c.1290-13343G>A
KANSL1 transcript variant X9 XM_047435799.1:c.1290-13343= XM_047435799.1:c.1290-13343G>A
KANSL1 transcript variant X3 XM_047435800.1:c.1290-13343= XM_047435800.1:c.1290-13343G>A
KANSL1 transcript variant X4 XM_047435801.1:c.60-13343= XM_047435801.1:c.60-13343G>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#.

62 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss158054278 Dec 01, 2009 (131)
2 1000GENOMES ss227557440 Jul 14, 2010 (137)
3 1000GENOMES ss237251841 Jul 15, 2010 (137)
4 1000GENOMES ss243546968 Jul 15, 2010 (137)
5 BL ss255653038 May 09, 2011 (137)
6 GMI ss282773600 May 04, 2012 (137)
7 GMI ss287183963 Apr 25, 2013 (138)
8 ILLUMINA ss483353670 May 04, 2012 (137)
9 ILLUMINA ss483629807 May 04, 2012 (137)
10 ILLUMINA ss535567301 Sep 08, 2015 (146)
11 TISHKOFF ss565286586 Apr 25, 2013 (138)
12 SSMP ss661091163 Apr 25, 2013 (138)
13 ILLUMINA ss780245587 Sep 08, 2015 (146)
14 ILLUMINA ss782119957 Sep 08, 2015 (146)
15 ILLUMINA ss835731128 Sep 08, 2015 (146)
16 EVA-GONL ss993132285 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1081074494 Aug 21, 2014 (142)
18 1000GENOMES ss1358752286 Aug 21, 2014 (142)
19 DDI ss1428039047 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1578166884 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1635699493 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1678693526 Apr 01, 2015 (144)
23 EVA_DECODE ss1697175458 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1936593417 Feb 12, 2016 (147)
25 JJLAB ss2029073249 Sep 14, 2016 (149)
26 USC_VALOUEV ss2157546350 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2629031781 Nov 08, 2017 (151)
28 ILLUMINA ss2633399482 Nov 08, 2017 (151)
29 GRF ss2702106602 Nov 08, 2017 (151)
30 SWEGEN ss3015577217 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3028357886 Nov 08, 2017 (151)
32 CSHL ss3351754905 Nov 08, 2017 (151)
33 ILLUMINA ss3627675518 Oct 12, 2018 (152)
34 ILLUMINA ss3631380370 Oct 12, 2018 (152)
35 ILLUMINA ss3641993565 Oct 12, 2018 (152)
36 EGCUT_WGS ss3682459217 Jul 13, 2019 (153)
37 EVA_DECODE ss3700516694 Jul 13, 2019 (153)
38 ACPOP ss3742046997 Jul 13, 2019 (153)
39 EVA ss3754696361 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3819964224 Jul 13, 2019 (153)
41 EVA ss3834880490 Apr 27, 2020 (154)
42 EVA ss3841050912 Apr 27, 2020 (154)
43 EVA ss3846548030 Apr 27, 2020 (154)
44 SGDP_PRJ ss3885800911 Apr 27, 2020 (154)
45 KRGDB ss3935500748 Apr 27, 2020 (154)
46 KOGIC ss3978889673 Apr 27, 2020 (154)
47 VINODS ss4033019524 Apr 26, 2021 (155)
48 TOPMED ss5036842383 Apr 26, 2021 (155)
49 TOMMO_GENOMICS ss5222538130 Apr 26, 2021 (155)
50 1000G_HIGH_COVERAGE ss5303222123 Oct 16, 2022 (156)
51 EVA ss5315888158 Oct 16, 2022 (156)
52 EVA ss5427751927 Oct 16, 2022 (156)
53 HUGCELL_USP ss5496265843 Oct 16, 2022 (156)
54 1000G_HIGH_COVERAGE ss5606983428 Oct 16, 2022 (156)
55 SANFORD_IMAGENETICS ss5660152125 Oct 16, 2022 (156)
56 TOMMO_GENOMICS ss5778788759 Oct 16, 2022 (156)
57 YY_MCH ss5816562006 Oct 16, 2022 (156)
58 EVA ss5834018419 Oct 16, 2022 (156)
59 EVA ss5851816498 Oct 16, 2022 (156)
60 EVA ss5914038930 Oct 16, 2022 (156)
61 EVA ss5951543522 Oct 16, 2022 (156)
62 EVA ss5980969289 Oct 16, 2022 (156)
63 1000Genomes NC_000017.10 - 44185410 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000017.11 - 46108044 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 44185410 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000017.10 - 44185410 Oct 12, 2018 (152)
67 The Danish reference pan genome NC_000017.10 - 44185410 Apr 27, 2020 (154)
68 gnomAD - Genomes NC_000017.11 - 46108044 Apr 26, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000017.10 - 44185410 Apr 27, 2020 (154)
70 KOREAN population from KRGDB NC_000017.10 - 44185410 Apr 27, 2020 (154)
71 Korean Genome Project NC_000017.11 - 46108044 Apr 27, 2020 (154)
72 Northern Sweden NC_000017.10 - 44185410 Jul 13, 2019 (153)
73 Qatari NC_000017.10 - 44185410 Apr 27, 2020 (154)
74 SGDP_PRJ NC_000017.10 - 44185410 Apr 27, 2020 (154)
75 Siberian NC_000017.10 - 44185410 Apr 27, 2020 (154)
76 8.3KJPN NC_000017.10 - 44185410 Apr 26, 2021 (155)
77 14KJPN NC_000017.11 - 46108044 Oct 16, 2022 (156)
78 TopMed NC_000017.11 - 46108044 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000017.10 - 44185410 Oct 12, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000017.10 - 44185410 Jul 13, 2019 (153)
81 ALFA NC_000017.11 - 46108044 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)
rs114387943 May 04, 2012 (137)
rs116932875 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss255653038, ss282773600, ss287183963, ss483629807, ss1697175458 NC_000017.9:41541192:C:T NC_000017.11:46108043:C:T (self)
71997746, 39900738, 28197465, 4368856, 17782856, 42678142, 15331862, 18635339, 37817891, 10062704, 80507437, 39900738, 8826985, ss227557440, ss237251841, ss243546968, ss483353670, ss535567301, ss565286586, ss661091163, ss780245587, ss782119957, ss835731128, ss993132285, ss1081074494, ss1358752286, ss1428039047, ss1578166884, ss1635699493, ss1678693526, ss1936593417, ss2029073249, ss2157546350, ss2629031781, ss2633399482, ss2702106602, ss3015577217, ss3351754905, ss3627675518, ss3631380370, ss3641993565, ss3682459217, ss3742046997, ss3754696361, ss3834880490, ss3841050912, ss3885800911, ss3935500748, ss5222538130, ss5315888158, ss5427751927, ss5660152125, ss5834018419, ss5951543522, ss5980969289 NC_000017.10:44185409:C:T NC_000017.11:46108043:C:T (self)
94509363, 507985743, 35267674, 112625863, 252388045, 3509223668, ss3028357886, ss3700516694, ss3819964224, ss3846548030, ss3978889673, ss5036842383, ss5303222123, ss5496265843, ss5606983428, ss5778788759, ss5816562006, ss5851816498, ss5914038930 NC_000017.11:46108043:C:T NC_000017.11:46108043:C:T (self)
ss158054278 NT_010783.15:9459561:C:T NC_000017.11:46108043:C:T (self)
ss4033019524 NT_187663.1:810142:C:T NC_000017.11:46108043: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 rs74518378

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