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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.

rs3758815

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:44613215 (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>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.233832 (61893/264690, TOPMED)
T=0.243252 (34081/140106, GnomAD)
T=0.10195 (2881/28258, 14KJPN) (+ 16 more)
T=0.26855 (5073/18890, ALFA)
T=0.10282 (1723/16758, 8.3KJPN)
T=0.1996 (1278/6404, 1000G_30x)
T=0.1969 (986/5008, 1000G)
T=0.3058 (1370/4480, Estonian)
T=0.2852 (1099/3854, ALSPAC)
T=0.2737 (1015/3708, TWINSUK)
T=0.1266 (371/2930, KOREAN)
T=0.301 (300/998, GoNL)
T=0.305 (183/600, NorthernSweden)
T=0.132 (69/524, SGDP_PRJ)
T=0.182 (57/314, HapMap)
T=0.167 (36/216, Qatari)
T=0.106 (23/216, Vietnamese)
T=0.23 (12/52, Siberian)
T=0.30 (12/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CD82 : 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 18890 T=0.26855 A=0.73145
European Sub 14286 T=0.29441 A=0.70559
African Sub 2946 T=0.1602 A=0.8398
African Others Sub 114 T=0.123 A=0.877
African American Sub 2832 T=0.1617 A=0.8383
Asian Sub 112 T=0.009 A=0.991
East Asian Sub 86 T=0.01 A=0.99
Other Asian Sub 26 T=0.00 A=1.00
Latin American 1 Sub 146 T=0.301 A=0.699
Latin American 2 Sub 610 T=0.261 A=0.739
South Asian Sub 98 T=0.31 A=0.69
Other Sub 692 T=0.233 A=0.767


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=0.233832 A=0.766168
gnomAD - Genomes Global Study-wide 140106 T=0.243252 A=0.756748
gnomAD - Genomes European Sub 75860 T=0.29672 A=0.70328
gnomAD - Genomes African Sub 42004 T=0.14930 A=0.85070
gnomAD - Genomes American Sub 13636 T=0.26298 A=0.73702
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.2708 A=0.7292
gnomAD - Genomes East Asian Sub 3132 T=0.0894 A=0.9106
gnomAD - Genomes Other Sub 2150 T=0.2488 A=0.7512
14KJPN JAPANESE Study-wide 28258 T=0.10195 A=0.89805
Allele Frequency Aggregator Total Global 18890 T=0.26855 A=0.73145
Allele Frequency Aggregator European Sub 14286 T=0.29441 A=0.70559
Allele Frequency Aggregator African Sub 2946 T=0.1602 A=0.8398
Allele Frequency Aggregator Other Sub 692 T=0.233 A=0.767
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.261 A=0.739
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.301 A=0.699
Allele Frequency Aggregator Asian Sub 112 T=0.009 A=0.991
Allele Frequency Aggregator South Asian Sub 98 T=0.31 A=0.69
8.3KJPN JAPANESE Study-wide 16758 T=0.10282 A=0.89718
1000Genomes_30x Global Study-wide 6404 T=0.1996 A=0.8004
1000Genomes_30x African Sub 1786 T=0.1355 A=0.8645
1000Genomes_30x Europe Sub 1266 T=0.3081 A=0.6919
1000Genomes_30x South Asian Sub 1202 T=0.2080 A=0.7920
1000Genomes_30x East Asian Sub 1170 T=0.0974 A=0.9026
1000Genomes_30x American Sub 980 T=0.288 A=0.712
1000Genomes Global Study-wide 5008 T=0.1969 A=0.8031
1000Genomes African Sub 1322 T=0.1392 A=0.8608
1000Genomes East Asian Sub 1008 T=0.0952 A=0.9048
1000Genomes Europe Sub 1006 T=0.3022 A=0.6978
1000Genomes South Asian Sub 978 T=0.213 A=0.787
1000Genomes American Sub 694 T=0.280 A=0.720
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.3058 A=0.6942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.2852 A=0.7148
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.2737 A=0.7263
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.1266 A=0.8734, C=0.0000, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.301 A=0.699
Northern Sweden ACPOP Study-wide 600 T=0.305 A=0.695
SGDP_PRJ Global Study-wide 524 T=0.132 A=0.868
HapMap Global Study-wide 314 T=0.182 A=0.818
HapMap American Sub 120 T=0.325 A=0.675
HapMap African Sub 106 T=0.094 A=0.906
HapMap Asian Sub 88 T=0.09 A=0.91
Qatari Global Study-wide 216 T=0.167 A=0.833
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.106 A=0.894
Siberian Global Study-wide 52 T=0.23 A=0.77
The Danish reference pan genome Danish Study-wide 40 T=0.30 A=0.70
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.44613215T>A
GRCh38.p14 chr 11 NC_000011.10:g.44613215T>C
GRCh38.p14 chr 11 NC_000011.10:g.44613215T>G
GRCh37.p13 chr 11 NC_000011.9:g.44634765T>A
GRCh37.p13 chr 11 NC_000011.9:g.44634765T>C
GRCh37.p13 chr 11 NC_000011.9:g.44634765T>G
CD82 RefSeqGene NG_023234.1:g.52625T>A
CD82 RefSeqGene NG_023234.1:g.52625T>C
CD82 RefSeqGene NG_023234.1:g.52625T>G
Gene: CD82, CD82 molecule (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CD82 transcript variant 2 NM_001024844.2:c.262-2057…

NM_001024844.2:c.262-2057T>A

N/A Intron Variant
CD82 transcript variant 1 NM_002231.4:c.337-2057T>A N/A Intron Variant
CD82 transcript variant X5 XM_011520067.3:c.244-2057…

XM_011520067.3:c.244-2057T>A

N/A Intron Variant
CD82 transcript variant X1 XM_047426900.1:c.460-2057…

XM_047426900.1:c.460-2057T>A

N/A Intron Variant
CD82 transcript variant X2 XM_047426901.1:c.337-2057…

XM_047426901.1:c.337-2057T>A

N/A Intron Variant
CD82 transcript variant X3 XM_047426903.1:c.337-2057…

XM_047426903.1:c.337-2057T>A

N/A Intron Variant
CD82 transcript variant X4 XM_047426904.1:c.337-2057…

XM_047426904.1:c.337-2057T>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 T= A C G
GRCh38.p14 chr 11 NC_000011.10:g.44613215= NC_000011.10:g.44613215T>A NC_000011.10:g.44613215T>C NC_000011.10:g.44613215T>G
GRCh37.p13 chr 11 NC_000011.9:g.44634765= NC_000011.9:g.44634765T>A NC_000011.9:g.44634765T>C NC_000011.9:g.44634765T>G
CD82 RefSeqGene NG_023234.1:g.52625= NG_023234.1:g.52625T>A NG_023234.1:g.52625T>C NG_023234.1:g.52625T>G
CD82 transcript variant 2 NM_001024844.1:c.262-2057= NM_001024844.1:c.262-2057T>A NM_001024844.1:c.262-2057T>C NM_001024844.1:c.262-2057T>G
CD82 transcript variant 2 NM_001024844.2:c.262-2057= NM_001024844.2:c.262-2057T>A NM_001024844.2:c.262-2057T>C NM_001024844.2:c.262-2057T>G
CD82 transcript variant 1 NM_002231.3:c.337-2057= NM_002231.3:c.337-2057T>A NM_002231.3:c.337-2057T>C NM_002231.3:c.337-2057T>G
CD82 transcript variant 1 NM_002231.4:c.337-2057= NM_002231.4:c.337-2057T>A NM_002231.4:c.337-2057T>C NM_002231.4:c.337-2057T>G
CD82 transcript variant X5 XM_011520067.3:c.244-2057= XM_011520067.3:c.244-2057T>A XM_011520067.3:c.244-2057T>C XM_011520067.3:c.244-2057T>G
CD82 transcript variant X1 XM_047426900.1:c.460-2057= XM_047426900.1:c.460-2057T>A XM_047426900.1:c.460-2057T>C XM_047426900.1:c.460-2057T>G
CD82 transcript variant X2 XM_047426901.1:c.337-2057= XM_047426901.1:c.337-2057T>A XM_047426901.1:c.337-2057T>C XM_047426901.1:c.337-2057T>G
CD82 transcript variant X3 XM_047426903.1:c.337-2057= XM_047426903.1:c.337-2057T>A XM_047426903.1:c.337-2057T>C XM_047426903.1:c.337-2057T>G
CD82 transcript variant X4 XM_047426904.1:c.337-2057= XM_047426904.1:c.337-2057T>A XM_047426904.1:c.337-2057T>C XM_047426904.1:c.337-2057T>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#.

87 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4944847 Aug 28, 2002 (107)
2 SSAHASNP ss20800798 Apr 05, 2004 (121)
3 ABI ss38657636 Mar 15, 2006 (126)
4 HGSV ss85094110 Dec 16, 2007 (130)
5 BCMHGSC_JDW ss88564361 Mar 23, 2008 (129)
6 HUMANGENOME_JCVI ss97384019 Feb 06, 2009 (130)
7 BGI ss106741977 Feb 06, 2009 (130)
8 1000GENOMES ss114562122 Jan 25, 2009 (130)
9 ILLUMINA-UK ss119826937 Dec 01, 2009 (131)
10 ENSEMBL ss132474961 Dec 01, 2009 (131)
11 ENSEMBL ss137718939 Dec 01, 2009 (131)
12 GMI ss156238238 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss168315038 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss169817534 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss175123690 Jul 04, 2010 (132)
16 BUSHMAN ss202662784 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss207836629 Jul 04, 2010 (132)
18 1000GENOMES ss225228112 Jul 14, 2010 (132)
19 1000GENOMES ss235545362 Jul 15, 2010 (132)
20 1000GENOMES ss242182323 Jul 15, 2010 (132)
21 BL ss255092641 May 09, 2011 (134)
22 GMI ss280985541 May 04, 2012 (137)
23 GMI ss286366252 Apr 25, 2013 (138)
24 PJP ss291234188 May 09, 2011 (134)
25 ILLUMINA ss482840230 May 04, 2012 (137)
26 ILLUMINA ss483986610 May 04, 2012 (137)
27 ILLUMINA ss536179967 Sep 08, 2015 (146)
28 TISHKOFF ss562543294 Apr 25, 2013 (138)
29 SSMP ss658037343 Apr 25, 2013 (138)
30 ILLUMINA ss780483261 Sep 08, 2015 (146)
31 ILLUMINA ss782437524 Sep 08, 2015 (146)
32 ILLUMINA ss835973836 Sep 08, 2015 (146)
33 EVA-GONL ss988477124 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1077701676 Aug 21, 2014 (142)
35 1000GENOMES ss1341093094 Aug 21, 2014 (142)
36 DDI ss1426620035 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1575685056 Apr 01, 2015 (144)
38 EVA_DECODE ss1598153019 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1626509485 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1669503518 Apr 01, 2015 (144)
41 HAMMER_LAB ss1806805738 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1931834385 Feb 12, 2016 (147)
43 GENOMED ss1967357701 Jul 19, 2016 (147)
44 JJLAB ss2026665158 Sep 14, 2016 (149)
45 USC_VALOUEV ss2154956082 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2182201797 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2627806659 Nov 08, 2017 (151)
48 ILLUMINA ss2632832040 Nov 08, 2017 (151)
49 ILLUMINA ss2635025546 Nov 08, 2017 (151)
50 GRF ss2699240150 Nov 08, 2017 (151)
51 GNOMAD ss2899070992 Nov 08, 2017 (151)
52 SWEGEN ss3007997431 Nov 08, 2017 (151)
53 ILLUMINA ss3021330521 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3027132170 Nov 08, 2017 (151)
55 CSHL ss3349572154 Nov 08, 2017 (151)
56 ILLUMINA ss3626652328 Oct 12, 2018 (152)
57 ILLUMINA ss3630849575 Oct 12, 2018 (152)
58 ILLUMINA ss3641733638 Oct 12, 2018 (152)
59 URBANLAB ss3649596465 Oct 12, 2018 (152)
60 ILLUMINA ss3651694193 Oct 12, 2018 (152)
61 EGCUT_WGS ss3675405952 Jul 13, 2019 (153)
62 EVA_DECODE ss3691698018 Jul 13, 2019 (153)
63 ILLUMINA ss3725236869 Jul 13, 2019 (153)
64 ACPOP ss3738143039 Jul 13, 2019 (153)
65 EVA ss3749245251 Jul 13, 2019 (153)
66 PACBIO ss3786942542 Jul 13, 2019 (153)
67 PACBIO ss3792086662 Jul 13, 2019 (153)
68 PACBIO ss3796968882 Jul 13, 2019 (153)
69 KHV_HUMAN_GENOMES ss3814594032 Jul 13, 2019 (153)
70 EVA ss3832608876 Apr 26, 2020 (154)
71 SGDP_PRJ ss3876159580 Apr 26, 2020 (154)
72 KRGDB ss3924428333 Apr 26, 2020 (154)
73 TOPMED ss4883705902 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5201767329 Apr 26, 2021 (155)
75 1000G_HIGH_COVERAGE ss5287250566 Oct 16, 2022 (156)
76 EVA ss5315545322 Oct 16, 2022 (156)
77 EVA ss5399293777 Oct 16, 2022 (156)
78 HUGCELL_USP ss5482469431 Oct 16, 2022 (156)
79 1000G_HIGH_COVERAGE ss5582828917 Oct 16, 2022 (156)
80 SANFORD_IMAGENETICS ss5651132616 Oct 16, 2022 (156)
81 TOMMO_GENOMICS ss5748826780 Oct 16, 2022 (156)
82 YY_MCH ss5812346549 Oct 16, 2022 (156)
83 EVA ss5836599437 Oct 16, 2022 (156)
84 EVA ss5849966276 Oct 16, 2022 (156)
85 EVA ss5919807573 Oct 16, 2022 (156)
86 EVA ss5942450226 Oct 16, 2022 (156)
87 EVA ss5980674360 Oct 16, 2022 (156)
88 1000Genomes NC_000011.9 - 44634765 Oct 12, 2018 (152)
89 1000Genomes_30x NC_000011.10 - 44613215 Oct 16, 2022 (156)
90 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 44634765 Oct 12, 2018 (152)
91 Genetic variation in the Estonian population NC_000011.9 - 44634765 Oct 12, 2018 (152)
92 The Danish reference pan genome NC_000011.9 - 44634765 Apr 26, 2020 (154)
93 gnomAD - Genomes NC_000011.10 - 44613215 Apr 26, 2021 (155)
94 Genome of the Netherlands Release 5 NC_000011.9 - 44634765 Apr 26, 2020 (154)
95 HapMap NC_000011.10 - 44613215 Apr 26, 2020 (154)
96 KOREAN population from KRGDB NC_000011.9 - 44634765 Apr 26, 2020 (154)
97 Northern Sweden NC_000011.9 - 44634765 Jul 13, 2019 (153)
98 Qatari NC_000011.9 - 44634765 Apr 26, 2020 (154)
99 SGDP_PRJ NC_000011.9 - 44634765 Apr 26, 2020 (154)
100 Siberian NC_000011.9 - 44634765 Apr 26, 2020 (154)
101 8.3KJPN NC_000011.9 - 44634765 Apr 26, 2021 (155)
102 14KJPN NC_000011.10 - 44613215 Oct 16, 2022 (156)
103 TopMed NC_000011.10 - 44613215 Apr 26, 2021 (155)
104 UK 10K study - Twins NC_000011.9 - 44634765 Oct 12, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000011.9 - 44634765 Jul 13, 2019 (153)
106 ALFA NC_000011.10 - 44613215 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)
rs61444802 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85094110, ss88564361, ss114562122, ss119826937, ss168315038, ss169817534, ss175123690, ss202662784, ss207836629, ss255092641, ss280985541, ss286366252, ss291234188, ss482840230, ss1598153019, ss2635025546 NC_000011.8:44591340:T:A NC_000011.10:44613214:T:A (self)
53611849, 29787055, 21144200, 2549982, 13289725, 31605727, 11427904, 13876315, 28176560, 7472436, 59736636, 29787055, 6619095, ss225228112, ss235545362, ss242182323, ss483986610, ss536179967, ss562543294, ss658037343, ss780483261, ss782437524, ss835973836, ss988477124, ss1077701676, ss1341093094, ss1426620035, ss1575685056, ss1626509485, ss1669503518, ss1806805738, ss1931834385, ss1967357701, ss2026665158, ss2154956082, ss2627806659, ss2632832040, ss2699240150, ss2899070992, ss3007997431, ss3021330521, ss3349572154, ss3626652328, ss3630849575, ss3641733638, ss3651694193, ss3675405952, ss3738143039, ss3749245251, ss3786942542, ss3792086662, ss3796968882, ss3832608876, ss3876159580, ss3924428333, ss5201767329, ss5315545322, ss5399293777, ss5651132616, ss5836599437, ss5942450226, ss5980674360 NC_000011.9:44634764:T:A NC_000011.10:44613214:T:A (self)
70354852, 378371309, 607081, 82663884, 99251558, 2785655041, ss2182201797, ss3027132170, ss3649596465, ss3691698018, ss3725236869, ss3814594032, ss4883705902, ss5287250566, ss5482469431, ss5582828917, ss5748826780, ss5812346549, ss5849966276, ss5919807573 NC_000011.10:44613214:T:A NC_000011.10:44613214:T:A (self)
ss20800798 NT_009237.16:43398704:T:A NC_000011.10:44613214:T:A (self)
ss4944847, ss38657636, ss97384019, ss106741977, ss132474961, ss137718939, ss156238238 NT_009237.18:44574764:T:A NC_000011.10:44613214:T:A (self)
31605727, ss3924428333 NC_000011.9:44634764:T:C NC_000011.10:44613214:T:C (self)
31605727, ss3924428333 NC_000011.9:44634764:T:G NC_000011.10:44613214:T:G (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 rs3758815

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