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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.

rs12714254

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:21042065 (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
G=0.00221 (67/30338, ALFA)
G=0.0448 (287/6404, 1000G_30x)
G=0.0455 (228/5008, 1000G) (+ 9 more)
G=0.0008 (3/3854, ALSPAC)
G=0.0011 (4/3708, TWINSUK)
G=0.0904 (265/2930, KOREAN)
G=0.013 (8/600, NorthernSweden)
G=0.044 (16/360, PharmGKB)
G=0.019 (4/216, Qatari)
T=0.46 (34/74, SGDP_PRJ)
T=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
APOB : 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 30338 T=0.99776 A=0.00000, C=0.00003, G=0.00221
European Sub 24712 T=0.99879 A=0.00000, C=0.00000, G=0.00121
African Sub 2780 T=0.9960 A=0.0000, C=0.0000, G=0.0040
African Others Sub 104 T=0.981 A=0.000, C=0.000, G=0.019
African American Sub 2676 T=0.9966 A=0.0000, C=0.0000, G=0.0034
Asian Sub 110 T=1.000 A=0.000, C=0.000, G=0.000
East Asian Sub 90 T=1.00 A=0.00, C=0.00, G=0.00
Other Asian Sub 20 T=1.00 A=0.00, C=0.00, G=0.00
Latin American 1 Sub 162 T=1.000 A=0.000, C=0.000, G=0.000
Latin American 2 Sub 646 T=0.998 A=0.000, C=0.000, G=0.002
South Asian Sub 112 T=1.000 A=0.000, C=0.000, G=0.000
Other Sub 1816 T=0.9857 A=0.0000, C=0.0006, G=0.0138


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
Allele Frequency Aggregator Total Global 30338 T=0.99776 A=0.00000, C=0.00003, G=0.00221
Allele Frequency Aggregator European Sub 24712 T=0.99879 A=0.00000, C=0.00000, G=0.00121
Allele Frequency Aggregator African Sub 2780 T=0.9960 A=0.0000, C=0.0000, G=0.0040
Allele Frequency Aggregator Other Sub 1816 T=0.9857 A=0.0000, C=0.0006, G=0.0138
Allele Frequency Aggregator Latin American 2 Sub 646 T=0.998 A=0.000, C=0.000, G=0.002
Allele Frequency Aggregator Latin American 1 Sub 162 T=1.000 A=0.000, C=0.000, G=0.000
Allele Frequency Aggregator South Asian Sub 112 T=1.000 A=0.000, C=0.000, G=0.000
Allele Frequency Aggregator Asian Sub 110 T=1.000 A=0.000, C=0.000, G=0.000
1000Genomes_30x Global Study-wide 6404 T=0.9507 C=0.0045, G=0.0448
1000Genomes_30x African Sub 1786 T=0.9138 C=0.0000, G=0.0862
1000Genomes_30x Europe Sub 1266 T=0.9976 C=0.0000, G=0.0024
1000Genomes_30x South Asian Sub 1202 T=0.9892 C=0.0000, G=0.0108
1000Genomes_30x East Asian Sub 1170 T=0.9068 C=0.0248, G=0.0684
1000Genomes_30x American Sub 980 T=0.962 C=0.000, G=0.038
1000Genomes Global Study-wide 5008 T=0.9495 C=0.0050, G=0.0455
1000Genomes African Sub 1322 T=0.9100 C=0.0000, G=0.0900
1000Genomes East Asian Sub 1008 T=0.9067 C=0.0248, G=0.0685
1000Genomes Europe Sub 1006 T=0.9970 C=0.0000, G=0.0030
1000Genomes South Asian Sub 978 T=0.989 C=0.000, G=0.011
1000Genomes American Sub 694 T=0.963 C=0.000, G=0.037
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9992 G=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9989 G=0.0011
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8768 C=0.0328, G=0.0904
Northern Sweden ACPOP Study-wide 600 T=0.987 G=0.013
PharmGKB Aggregated Global Study-wide 360 T=0.956 G=0.044
PharmGKB Aggregated PA128749333 Sub 94 T=0.96 G=0.04
PharmGKB Aggregated PA128749605 Sub 94 T=0.96 G=0.04
PharmGKB Aggregated PA151853697 Sub 86 T=0.95 G=0.05
PharmGKB Aggregated PA151853969 Sub 86 T=0.95 G=0.05
Qatari Global Study-wide 216 T=0.981 G=0.019
SGDP_PRJ Global Study-wide 74 T=0.46 G=0.54
Siberian Global Study-wide 2 T=0.5 G=0.5
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 2 NC_000002.12:g.21042065T>A
GRCh38.p14 chr 2 NC_000002.12:g.21042065T>C
GRCh38.p14 chr 2 NC_000002.12:g.21042065T>G
GRCh37.p13 chr 2 NC_000002.11:g.21264937T>A
GRCh37.p13 chr 2 NC_000002.11:g.21264937T>C
GRCh37.p13 chr 2 NC_000002.11:g.21264937T>G
LOC106560211 genomic region NG_042873.1:g.1078T>A
LOC106560211 genomic region NG_042873.1:g.1078T>C
LOC106560211 genomic region NG_042873.1:g.1078T>G
APOB RefSeqGene NG_011793.1:g.7009A>T
APOB RefSeqGene NG_011793.1:g.7009A>G
APOB RefSeqGene NG_011793.1:g.7009A>C
GRCh38.p14 chr 2 fix patch HG2231_HG2496_PATCH NW_025791767.1:g.92733T>A
GRCh38.p14 chr 2 fix patch HG2231_HG2496_PATCH NW_025791767.1:g.92733T>C
GRCh38.p14 chr 2 fix patch HG2231_HG2496_PATCH NW_025791767.1:g.92733T>G
Gene: APOB, apolipoprotein B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
APOB transcript NM_000384.3:c.237+296A>T 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 2 NC_000002.12:g.21042065= NC_000002.12:g.21042065T>A NC_000002.12:g.21042065T>C NC_000002.12:g.21042065T>G
GRCh37.p13 chr 2 NC_000002.11:g.21264937= NC_000002.11:g.21264937T>A NC_000002.11:g.21264937T>C NC_000002.11:g.21264937T>G
LOC106560211 genomic region NG_042873.1:g.1078= NG_042873.1:g.1078T>A NG_042873.1:g.1078T>C NG_042873.1:g.1078T>G
APOB RefSeqGene NG_011793.1:g.7009= NG_011793.1:g.7009A>T NG_011793.1:g.7009A>G NG_011793.1:g.7009A>C
GRCh38.p14 chr 2 fix patch HG2231_HG2496_PATCH NW_025791767.1:g.92733= NW_025791767.1:g.92733T>A NW_025791767.1:g.92733T>C NW_025791767.1:g.92733T>G
APOB transcript NM_000384.2:c.237+296= NM_000384.2:c.237+296A>T NM_000384.2:c.237+296A>G NM_000384.2:c.237+296A>C
APOB transcript NM_000384.3:c.237+296= NM_000384.3:c.237+296A>T NM_000384.3:c.237+296A>G NM_000384.3:c.237+296A>C
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#.

66 SubSNP, 26 Frequency submissions
No Submitter Submission ID Date (Build)
1 PARC ss23143746 Sep 20, 2004 (126)
2 PHARMGKB_PARC ss69369340 May 16, 2007 (127)
3 PHARMGKB_PARC ss69369341 May 16, 2007 (127)
4 PHARMGKB_PARC ss84143816 Dec 15, 2007 (130)
5 PHARMGKB_PARC ss84143822 Dec 15, 2007 (130)
6 BGI ss103464824 Dec 01, 2009 (131)
7 BUSHMAN ss200138530 Jul 04, 2010 (132)
8 1000GENOMES ss210842073 Jul 14, 2010 (132)
9 1000GENOMES ss219112810 Jul 14, 2010 (132)
10 1000GENOMES ss238648610 Jul 15, 2010 (132)
11 ILLUMINA ss410831626 Sep 17, 2011 (135)
12 GMI ss475606045 May 04, 2012 (137)
13 ILLUMINA ss480521437 May 04, 2012 (137)
14 ILLUMINA ss484003848 May 04, 2012 (137)
15 ILLUMINA ss533792370 Sep 08, 2015 (146)
16 TISHKOFF ss555407876 Apr 25, 2013 (138)
17 SSMP ss648986522 Apr 25, 2013 (138)
18 ILLUMINA ss779760214 Sep 08, 2015 (146)
19 ILLUMINA ss781252138 Sep 08, 2015 (146)
20 ILLUMINA ss835235486 Sep 08, 2015 (146)
21 JMKIDD_LAB ss1068922841 Aug 21, 2014 (142)
22 1000GENOMES ss1296219065 Aug 21, 2014 (142)
23 1000GENOMES ss1296219066 Aug 21, 2014 (142)
24 DDI ss1428503023 Apr 01, 2015 (144)
25 EVA_DECODE ss1585973034 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1602976120 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1645970153 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1919804751 Feb 12, 2016 (147)
29 JJLAB ss2020429561 Sep 14, 2016 (149)
30 USC_VALOUEV ss2148474119 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2228150513 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2624731662 Nov 08, 2017 (151)
33 ILLUMINA ss2633582650 Nov 08, 2017 (151)
34 GRF ss2703034119 Nov 08, 2017 (151)
35 GNOMAD ss2770590067 Nov 08, 2017 (151)
36 SWEGEN ss2989102326 Nov 08, 2017 (151)
37 ILLUMINA ss3628009367 Oct 11, 2018 (152)
38 ILLUMINA ss3631551432 Oct 11, 2018 (152)
39 ILLUMINA ss3642081320 Oct 11, 2018 (152)
40 EGCUT_WGS ss3657054902 Jul 12, 2019 (153)
41 EGCUT_WGS ss3657054903 Jul 12, 2019 (153)
42 EVA_DECODE ss3703404059 Jul 12, 2019 (153)
43 ACPOP ss3728221304 Jul 12, 2019 (153)
44 EVA ss3756451877 Jul 12, 2019 (153)
45 KHV_HUMAN_GENOMES ss3800835689 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3800835690 Jul 12, 2019 (153)
47 EVA ss3826860051 Apr 25, 2020 (154)
48 SGDP_PRJ ss3851756324 Apr 25, 2020 (154)
49 KRGDB ss3897153139 Apr 25, 2020 (154)
50 KOGIC ss3947261994 Apr 25, 2020 (154)
51 KOGIC ss3947261995 Apr 25, 2020 (154)
52 TOPMED ss4496804679 Apr 26, 2021 (155)
53 TOPMED ss4496804680 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5150214046 Apr 26, 2021 (155)
55 TOMMO_GENOMICS ss5150214047 Apr 26, 2021 (155)
56 1000G_HIGH_COVERAGE ss5247184165 Oct 12, 2022 (156)
57 1000G_HIGH_COVERAGE ss5247184166 Oct 12, 2022 (156)
58 EVA ss5314716539 Oct 12, 2022 (156)
59 HUGCELL_USP ss5447469713 Oct 12, 2022 (156)
60 HUGCELL_USP ss5447469714 Oct 12, 2022 (156)
61 1000G_HIGH_COVERAGE ss5521944166 Oct 12, 2022 (156)
62 SANFORD_IMAGENETICS ss5628249049 Oct 12, 2022 (156)
63 TOMMO_GENOMICS ss5678502256 Oct 12, 2022 (156)
64 TOMMO_GENOMICS ss5678502257 Oct 12, 2022 (156)
65 YY_MCH ss5801993924 Oct 12, 2022 (156)
66 EVA ss5954446894 Oct 12, 2022 (156)
67 1000Genomes NC_000002.11 - 21264937 Oct 11, 2018 (152)
68 1000Genomes_30x NC_000002.12 - 21042065 Oct 12, 2022 (156)
69 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 21264937 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population

Submission ignored due to conflicting rows:
Row 2793150 (NC_000002.11:21264936:T:T 4449/4450, NC_000002.11:21264936:T:C 1/4450)
Row 2793151 (NC_000002.11:21264936:T:T 4463/4478, NC_000002.11:21264936:T:G 15/4478)

- Oct 11, 2018 (152)
71 Genetic variation in the Estonian population

Submission ignored due to conflicting rows:
Row 2793150 (NC_000002.11:21264936:T:T 4449/4450, NC_000002.11:21264936:T:C 1/4450)
Row 2793151 (NC_000002.11:21264936:T:T 4463/4478, NC_000002.11:21264936:T:G 15/4478)

- Oct 11, 2018 (152)
72 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 50656854 (NC_000002.12:21042064:T:A 1/140258)
Row 50656855 (NC_000002.12:21042064:T:C 102/140258)
Row 50656856 (NC_000002.12:21042064:T:G 3579/140248)

- Apr 26, 2021 (155)
73 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 50656854 (NC_000002.12:21042064:T:A 1/140258)
Row 50656855 (NC_000002.12:21042064:T:C 102/140258)
Row 50656856 (NC_000002.12:21042064:T:G 3579/140248)

- Apr 26, 2021 (155)
74 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 50656854 (NC_000002.12:21042064:T:A 1/140258)
Row 50656855 (NC_000002.12:21042064:T:C 102/140258)
Row 50656856 (NC_000002.12:21042064:T:G 3579/140248)

- Apr 26, 2021 (155)
75 KOREAN population from KRGDB NC_000002.11 - 21264937 Apr 25, 2020 (154)
76 Korean Genome Project

Submission ignored due to conflicting rows:
Row 3639995 (NC_000002.12:21042064:T:G 190/1832)
Row 3639996 (NC_000002.12:21042064:T:C 63/1832)

- Apr 25, 2020 (154)
77 Korean Genome Project

Submission ignored due to conflicting rows:
Row 3639995 (NC_000002.12:21042064:T:G 190/1832)
Row 3639996 (NC_000002.12:21042064:T:C 63/1832)

- Apr 25, 2020 (154)
78 Northern Sweden NC_000002.11 - 21264937 Jul 12, 2019 (153)
79 PharmGKB Aggregated NC_000002.12 - 21042065 Apr 25, 2020 (154)
80 Qatari NC_000002.11 - 21264937 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000002.11 - 21264937 Apr 25, 2020 (154)
82 Siberian NC_000002.11 - 21264937 Apr 25, 2020 (154)
83 8.3KJPN

Submission ignored due to conflicting rows:
Row 8183353 (NC_000002.11:21264936:T:G 1830/16760)
Row 8183354 (NC_000002.11:21264936:T:C 733/16760)

- Apr 26, 2021 (155)
84 8.3KJPN

Submission ignored due to conflicting rows:
Row 8183353 (NC_000002.11:21264936:T:G 1830/16760)
Row 8183354 (NC_000002.11:21264936:T:C 733/16760)

- Apr 26, 2021 (155)
85 14KJPN

Submission ignored due to conflicting rows:
Row 12339360 (NC_000002.12:21042064:T:G 3049/28258)
Row 12339361 (NC_000002.12:21042064:T:C 1241/28258)

- Oct 12, 2022 (156)
86 14KJPN

Submission ignored due to conflicting rows:
Row 12339360 (NC_000002.12:21042064:T:G 3049/28258)
Row 12339361 (NC_000002.12:21042064:T:C 1241/28258)

- Oct 12, 2022 (156)
87 TopMed

Submission ignored due to conflicting rows:
Row 300627558 (NC_000002.12:21042064:T:A 1/264690)
Row 300627559 (NC_000002.12:21042064:T:G 8376/264690)

- Apr 26, 2021 (155)
88 TopMed

Submission ignored due to conflicting rows:
Row 300627558 (NC_000002.12:21042064:T:A 1/264690)
Row 300627559 (NC_000002.12:21042064:T:G 8376/264690)

- Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000002.11 - 21264937 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database

Submission ignored due to conflicting rows:
Row 864878 (NC_000002.11:21264936:T:T 193/198, NC_000002.11:21264936:T:C 5/198)
Row 864879 (NC_000002.11:21264936:T:T 193/209, NC_000002.11:21264936:T:G 16/209)

- Jul 12, 2019 (153)
91 A Vietnamese Genetic Variation Database

Submission ignored due to conflicting rows:
Row 864878 (NC_000002.11:21264936:T:T 193/198, NC_000002.11:21264936:T:C 5/198)
Row 864879 (NC_000002.11:21264936:T:T 193/209, NC_000002.11:21264936:T:G 16/209)

- Jul 12, 2019 (153)
92 ALFA NC_000002.12 - 21042065 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)
rs17246828 Mar 10, 2006 (126)
rs58834038 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
2059133268, ss4496804679 NC_000002.12:21042064:T:A NC_000002.12:21042064:T:A (self)
7131118, 4330533, ss1296219065, ss1428503023, ss2703034119, ss2770590067, ss3657054902, ss3897153139, ss5150214047, ss5628249049 NC_000002.11:21264936:T:C NC_000002.12:21042064:T:C (self)
9470101, 2059133268, ss2228150513, ss3800835690, ss3947261995, ss5247184166, ss5447469714, ss5521944166, ss5678502257, ss5801993924 NC_000002.12:21042064:T:C NC_000002.12:21042064:T:C (self)
ss200138530, ss210842073, ss475606045, ss484003848, ss1585973034 NC_000002.10:21118441:T:G NC_000002.12:21042064:T:G (self)
7131118, 3958732, 4330533, 1506169, 1846681, 3773304, 990473, 3958732, ss219112810, ss238648610, ss480521437, ss533792370, ss555407876, ss648986522, ss779760214, ss781252138, ss835235486, ss1068922841, ss1296219066, ss1602976120, ss1645970153, ss1919804751, ss2020429561, ss2148474119, ss2624731662, ss2633582650, ss2770590067, ss2989102326, ss3628009367, ss3631551432, ss3642081320, ss3657054903, ss3728221304, ss3756451877, ss3826860051, ss3851756324, ss3897153139, ss5150214046, ss5314716539, ss5628249049, ss5954446894 NC_000002.11:21264936:T:G NC_000002.12:21042064:T:G (self)
9470101, 6139, 2059133268, ss2228150513, ss3703404059, ss3800835689, ss3947261994, ss4496804680, ss5247184165, ss5447469713, ss5521944166, ss5678502256, ss5801993924 NC_000002.12:21042064:T:G NC_000002.12:21042064:T:G (self)
ss23143746, ss69369340, ss69369341, ss84143816, ss84143822, ss103464824, ss410831626 NT_022184.15:86823:T:G NC_000002.12:21042064: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 rs12714254

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