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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.

rs6813460

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:176001618 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.187986 (49758/264690, TOPMED)
C=0.178096 (24957/140132, GnomAD)
C=0.23745 (6710/28258, 14KJPN) (+ 18 more)
C=0.23801 (3989/16760, 8.3KJPN)
C=0.1334 (1186/8892, ALFA)
C=0.2633 (1686/6404, 1000G_30x)
C=0.2574 (1289/5008, 1000G)
C=0.0437 (196/4480, Estonian)
C=0.0659 (254/3854, ALSPAC)
C=0.0682 (253/3708, TWINSUK)
C=0.2294 (672/2930, KOREAN)
C=0.2322 (425/1830, Korea1K)
C=0.1567 (178/1136, Daghestan)
C=0.071 (71/998, GoNL)
C=0.023 (14/600, NorthernSweden)
C=0.163 (86/526, SGDP_PRJ)
C=0.268 (88/328, HapMap)
C=0.199 (43/216, Qatari)
C=0.262 (56/214, Vietnamese)
C=0.05 (3/56, Siberian)
C=0.10 (4/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPM6A : 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 8892 C=0.1334 A=0.0000, G=0.8666
European Sub 7484 C=0.0533 A=0.0000, G=0.9467
African Sub 1076 C=0.6403 A=0.0000, G=0.3597
African Others Sub 48 C=0.69 A=0.00, G=0.31
African American Sub 1028 C=0.6381 A=0.0000, G=0.3619
Asian Sub 10 C=0.7 A=0.0, G=0.3
East Asian Sub 6 C=0.7 A=0.0, G=0.3
Other Asian Sub 4 C=0.8 A=0.0, G=0.2
Latin American 1 Sub 8 C=0.5 A=0.0, G=0.5
Latin American 2 Sub 22 C=0.32 A=0.00, G=0.68
South Asian Sub 18 C=0.83 A=0.00, G=0.17
Other Sub 274 C=0.237 A=0.000, G=0.763


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=0.187986 G=0.812014
gnomAD - Genomes Global Study-wide 140132 C=0.178096 G=0.821904
gnomAD - Genomes European Sub 75942 C=0.06526 G=0.93474
gnomAD - Genomes African Sub 41928 C=0.40424 G=0.59576
gnomAD - Genomes American Sub 13660 C=0.11288 G=0.88712
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.1420 G=0.8580
gnomAD - Genomes East Asian Sub 3132 C=0.2162 G=0.7838
gnomAD - Genomes Other Sub 2146 C=0.1682 G=0.8318
14KJPN JAPANESE Study-wide 28258 C=0.23745 G=0.76255
8.3KJPN JAPANESE Study-wide 16760 C=0.23801 G=0.76199
Allele Frequency Aggregator Total Global 8892 C=0.1334 A=0.0000, G=0.8666
Allele Frequency Aggregator European Sub 7484 C=0.0533 A=0.0000, G=0.9467
Allele Frequency Aggregator African Sub 1076 C=0.6403 A=0.0000, G=0.3597
Allele Frequency Aggregator Other Sub 274 C=0.237 A=0.000, G=0.763
Allele Frequency Aggregator Latin American 2 Sub 22 C=0.32 A=0.00, G=0.68
Allele Frequency Aggregator South Asian Sub 18 C=0.83 A=0.00, G=0.17
Allele Frequency Aggregator Asian Sub 10 C=0.7 A=0.0, G=0.3
Allele Frequency Aggregator Latin American 1 Sub 8 C=0.5 A=0.0, G=0.5
1000Genomes_30x Global Study-wide 6404 C=0.2633 G=0.7367
1000Genomes_30x African Sub 1786 C=0.4378 G=0.5622
1000Genomes_30x Europe Sub 1266 C=0.0782 G=0.9218
1000Genomes_30x South Asian Sub 1202 C=0.3344 G=0.6656
1000Genomes_30x East Asian Sub 1170 C=0.2376 G=0.7624
1000Genomes_30x American Sub 980 C=0.128 G=0.872
1000Genomes Global Study-wide 5008 C=0.2574 G=0.7426
1000Genomes African Sub 1322 C=0.4251 G=0.5749
1000Genomes East Asian Sub 1008 C=0.2312 G=0.7688
1000Genomes Europe Sub 1006 C=0.0795 G=0.9205
1000Genomes South Asian Sub 978 C=0.338 G=0.662
1000Genomes American Sub 694 C=0.120 G=0.880
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.0437 G=0.9563
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.0659 G=0.9341
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.0682 G=0.9318
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2294 A=0.0000, G=0.7706, T=0.0000
Korean Genome Project KOREAN Study-wide 1830 C=0.2322 G=0.7678
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.1567 G=0.8433
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.158 G=0.842
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.097 G=0.903
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.164 G=0.836
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.046 G=0.954
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.39 G=0.61
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.06 G=0.94
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.071 G=0.929
Northern Sweden ACPOP Study-wide 600 C=0.023 G=0.977
SGDP_PRJ Global Study-wide 526 C=0.163 G=0.837
HapMap Global Study-wide 328 C=0.268 G=0.732
HapMap African Sub 120 C=0.492 G=0.508
HapMap American Sub 120 C=0.067 G=0.933
HapMap Asian Sub 88 C=0.24 G=0.76
Qatari Global Study-wide 216 C=0.199 G=0.801
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.262 G=0.738
Siberian Global Study-wide 56 C=0.05 G=0.95
The Danish reference pan genome Danish Study-wide 40 C=0.10 G=0.90
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 4 NC_000004.12:g.176001618C>A
GRCh38.p14 chr 4 NC_000004.12:g.176001618C>G
GRCh38.p14 chr 4 NC_000004.12:g.176001618C>T
GRCh37.p13 chr 4 NC_000004.11:g.176922769C>A
GRCh37.p13 chr 4 NC_000004.11:g.176922769C>G
GRCh37.p13 chr 4 NC_000004.11:g.176922769C>T
Gene: GPM6A, glycoprotein M6A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPM6A transcript variant 4 NM_001261447.1:c.282+691G…

NM_001261447.1:c.282+691G>T

N/A Intron Variant
GPM6A transcript variant 1 NM_005277.5:c.-23+691G>T N/A Intron Variant
GPM6A transcript variant 3 NM_201592.3:c.4+691G>T N/A Intron Variant
GPM6A transcript variant 5 NM_001261448.1:c. N/A Genic Upstream Transcript Variant
GPM6A transcript variant 7 NM_001388090.1:c. N/A Genic Upstream Transcript Variant
GPM6A transcript variant 8 NM_001388091.1:c. N/A Genic Upstream Transcript Variant
GPM6A transcript variant 2 NM_201591.3:c. N/A Genic Upstream Transcript Variant
GPM6A transcript variant 6 NR_048571.1: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 C= A G T
GRCh38.p14 chr 4 NC_000004.12:g.176001618= NC_000004.12:g.176001618C>A NC_000004.12:g.176001618C>G NC_000004.12:g.176001618C>T
GRCh37.p13 chr 4 NC_000004.11:g.176922769= NC_000004.11:g.176922769C>A NC_000004.11:g.176922769C>G NC_000004.11:g.176922769C>T
GPM6A transcript variant 4 NM_001261447.1:c.282+691= NM_001261447.1:c.282+691G>T NM_001261447.1:c.282+691G>C NM_001261447.1:c.282+691G>A
GPM6A transcript variant 1 NM_005277.4:c.-23+691= NM_005277.4:c.-23+691G>T NM_005277.4:c.-23+691G>C NM_005277.4:c.-23+691G>A
GPM6A transcript variant 1 NM_005277.5:c.-23+691= NM_005277.5:c.-23+691G>T NM_005277.5:c.-23+691G>C NM_005277.5:c.-23+691G>A
GPM6A transcript variant 3 NM_201592.2:c.4+691= NM_201592.2:c.4+691G>T NM_201592.2:c.4+691G>C NM_201592.2:c.4+691G>A
GPM6A transcript variant 3 NM_201592.3:c.4+691= NM_201592.3:c.4+691G>T NM_201592.3:c.4+691G>C NM_201592.3:c.4+691G>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#.

84 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10106224 Jul 11, 2003 (116)
2 CSHL-HAPMAP ss19571075 Feb 27, 2004 (120)
3 SSAHASNP ss22149642 Apr 05, 2004 (121)
4 ABI ss42342157 Mar 15, 2006 (126)
5 HGSV ss78094602 Dec 07, 2007 (129)
6 HGSV ss81231502 Dec 15, 2007 (130)
7 HUMANGENOME_JCVI ss98890732 Feb 05, 2009 (130)
8 BGI ss105888901 Feb 05, 2009 (130)
9 1000GENOMES ss108611844 Jan 23, 2009 (130)
10 ILLUMINA-UK ss117307073 Feb 14, 2009 (130)
11 ENSEMBL ss134827517 Dec 01, 2009 (131)
12 GMI ss154654668 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162827905 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss167447073 Jul 04, 2010 (132)
15 BUSHMAN ss199575615 Jul 04, 2010 (132)
16 1000GENOMES ss221391477 Jul 14, 2010 (132)
17 1000GENOMES ss232731225 Jul 14, 2010 (132)
18 1000GENOMES ss239949749 Jul 15, 2010 (132)
19 BL ss253765637 May 09, 2011 (134)
20 GMI ss278064401 May 04, 2012 (137)
21 GMI ss285068474 Apr 25, 2013 (138)
22 PJP ss293262449 May 09, 2011 (134)
23 ILLUMINA ss484030126 May 04, 2012 (137)
24 ILLUMINA ss484758047 May 04, 2012 (137)
25 ILLUMINA ss536222027 Sep 08, 2015 (146)
26 TISHKOFF ss558059533 Apr 25, 2013 (138)
27 SSMP ss651892145 Apr 25, 2013 (138)
28 ILLUMINA ss780499823 Aug 21, 2014 (142)
29 ILLUMINA ss782459610 Aug 21, 2014 (142)
30 ILLUMINA ss835990744 Aug 21, 2014 (142)
31 EVA-GONL ss981027175 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1072222086 Aug 21, 2014 (142)
33 1000GENOMES ss1313114751 Aug 21, 2014 (142)
34 HAMMER_LAB ss1397397675 Sep 08, 2015 (146)
35 DDI ss1430161210 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1580915869 Apr 01, 2015 (144)
37 EVA_DECODE ss1590546093 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1611860958 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1654854991 Apr 01, 2015 (144)
40 HAMMER_LAB ss1802659138 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1924269557 Feb 12, 2016 (147)
42 GENOMED ss1969953514 Jul 19, 2016 (147)
43 JJLAB ss2022726218 Sep 14, 2016 (149)
44 USC_VALOUEV ss2150859232 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2269822344 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2625855940 Nov 08, 2017 (151)
47 ILLUMINA ss2634215065 Nov 08, 2017 (151)
48 GRF ss2706364873 Nov 08, 2017 (151)
49 GNOMAD ss2818966439 Nov 08, 2017 (151)
50 SWEGEN ss2996085284 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3025140867 Nov 08, 2017 (151)
52 CSHL ss3346118339 Nov 08, 2017 (151)
53 ILLUMINA ss3629129704 Oct 12, 2018 (152)
54 ILLUMINA ss3632145828 Oct 12, 2018 (152)
55 ILLUMINA ss3642382532 Oct 12, 2018 (152)
56 URBANLAB ss3647927649 Oct 12, 2018 (152)
57 EGCUT_WGS ss3664002075 Jul 13, 2019 (153)
58 EVA_DECODE ss3713699684 Jul 13, 2019 (153)
59 ACPOP ss3731896314 Jul 13, 2019 (153)
60 EVA ss3762808984 Jul 13, 2019 (153)
61 PACBIO ss3784955788 Jul 13, 2019 (153)
62 PACBIO ss3790378996 Jul 13, 2019 (153)
63 PACBIO ss3795254675 Jul 13, 2019 (153)
64 KHV_HUMAN_GENOMES ss3805974635 Jul 13, 2019 (153)
65 EVA ss3828979146 Apr 26, 2020 (154)
66 EVA ss3837942827 Apr 26, 2020 (154)
67 EVA ss3843384498 Apr 26, 2020 (154)
68 SGDP_PRJ ss3860744267 Apr 26, 2020 (154)
69 KRGDB ss3907122191 Apr 26, 2020 (154)
70 KOGIC ss3955726098 Apr 26, 2020 (154)
71 TOPMED ss4643299287 Apr 26, 2021 (155)
72 TOMMO_GENOMICS ss5169469146 Apr 26, 2021 (155)
73 1000G_HIGH_COVERAGE ss5262164444 Oct 13, 2022 (156)
74 EVA ss5315012584 Oct 13, 2022 (156)
75 EVA ss5354370158 Oct 13, 2022 (156)
76 HUGCELL_USP ss5460597522 Oct 13, 2022 (156)
77 1000G_HIGH_COVERAGE ss5544870115 Oct 13, 2022 (156)
78 SANFORD_IMAGENETICS ss5636760569 Oct 13, 2022 (156)
79 TOMMO_GENOMICS ss5704864008 Oct 13, 2022 (156)
80 YY_MCH ss5805825551 Oct 13, 2022 (156)
81 EVA ss5845166557 Oct 13, 2022 (156)
82 EVA ss5854585023 Oct 13, 2022 (156)
83 EVA ss5866802820 Oct 13, 2022 (156)
84 EVA ss5965176655 Oct 13, 2022 (156)
85 1000Genomes NC_000004.11 - 176922769 Oct 12, 2018 (152)
86 1000Genomes_30x NC_000004.12 - 176001618 Oct 13, 2022 (156)
87 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 176922769 Oct 12, 2018 (152)
88 Genome-wide autozygosity in Daghestan NC_000004.10 - 177159763 Apr 26, 2020 (154)
89 Genetic variation in the Estonian population NC_000004.11 - 176922769 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000004.11 - 176922769 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000004.12 - 176001618 Apr 26, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000004.11 - 176922769 Apr 26, 2020 (154)
93 HapMap NC_000004.12 - 176001618 Apr 26, 2020 (154)
94 KOREAN population from KRGDB NC_000004.11 - 176922769 Apr 26, 2020 (154)
95 Korean Genome Project NC_000004.12 - 176001618 Apr 26, 2020 (154)
96 Northern Sweden NC_000004.11 - 176922769 Jul 13, 2019 (153)
97 Qatari NC_000004.11 - 176922769 Apr 26, 2020 (154)
98 SGDP_PRJ NC_000004.11 - 176922769 Apr 26, 2020 (154)
99 Siberian NC_000004.11 - 176922769 Apr 26, 2020 (154)
100 8.3KJPN NC_000004.11 - 176922769 Apr 26, 2021 (155)
101 14KJPN NC_000004.12 - 176001618 Oct 13, 2022 (156)
102 TopMed NC_000004.12 - 176001618 Apr 26, 2021 (155)
103 UK 10K study - Twins NC_000004.11 - 176922769 Oct 12, 2018 (152)
104 A Vietnamese Genetic Variation Database NC_000004.11 - 176922769 Jul 13, 2019 (153)
105 ALFA NC_000004.12 - 176001618 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)
rs60008769 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14299585, ss3907122191 NC_000004.11:176922768:C:A NC_000004.12:176001617:C:A (self)
14348999431 NC_000004.12:176001617:C:A NC_000004.12:176001617:C:A (self)
ss78094602, ss81231502 NC_000004.9:177297917:C:G NC_000004.12:176001617:C:G (self)
372889, ss108611844, ss117307073, ss162827905, ss167447073, ss199575615, ss253765637, ss278064401, ss285068474, ss293262449, ss484758047, ss1397397675, ss1590546093 NC_000004.10:177159762:C:G NC_000004.12:176001617:C:G (self)
24640176, 13709571, 9740323, 7080808, 6076203, 14299585, 5181179, 6311487, 12761247, 3375586, 27438453, 13709571, 3032358, ss221391477, ss232731225, ss239949749, ss484030126, ss536222027, ss558059533, ss651892145, ss780499823, ss782459610, ss835990744, ss981027175, ss1072222086, ss1313114751, ss1430161210, ss1580915869, ss1611860958, ss1654854991, ss1802659138, ss1924269557, ss1969953514, ss2022726218, ss2150859232, ss2625855940, ss2634215065, ss2706364873, ss2818966439, ss2996085284, ss3346118339, ss3629129704, ss3632145828, ss3642382532, ss3664002075, ss3731896314, ss3762808984, ss3784955788, ss3790378996, ss3795254675, ss3828979146, ss3837942827, ss3860744267, ss3907122191, ss5169469146, ss5315012584, ss5354370158, ss5636760569, ss5845166557, ss5965176655 NC_000004.11:176922768:C:G NC_000004.12:176001617:C:G (self)
32396050, 174446936, 2767414, 12104099, 38701112, 480676843, 14348999431, ss2269822344, ss3025140867, ss3647927649, ss3713699684, ss3805974635, ss3843384498, ss3955726098, ss4643299287, ss5262164444, ss5460597522, ss5544870115, ss5704864008, ss5805825551, ss5854585023, ss5866802820 NC_000004.12:176001617:C:G NC_000004.12:176001617:C:G (self)
ss42342157, ss98890732, ss105888901, ss134827517, ss154654668 NT_016354.19:101470489:C:G NC_000004.12:176001617:C:G (self)
ss10106224 NT_022792.15:9334289:C:G NC_000004.12:176001617:C:G (self)
ss19571075, ss22149642 NT_022792.16:9334289:C:G NC_000004.12:176001617:C:G (self)
14299585, ss3907122191 NC_000004.11:176922768:C:T NC_000004.12:176001617: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 rs6813460

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