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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.

rs12461665

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:55353982 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.486157 (128681/264690, TOPMED)
A=0.493801 (68666/139056, GnomAD)
A=0.47508 (37384/78690, PAGE_STUDY) (+ 17 more)
G=0.22843 (5936/25986, 14KJPN)
A=0.43607 (9543/21884, ALFA)
G=0.47974 (8169/17028, ExAC)
G=0.23645 (3412/14430, 8.3KJPN)
A=0.44543 (5183/11636, GO-ESP)
A=0.4900 (3138/6404, 1000G_30x)
A=0.4914 (2461/5008, 1000G)
G=0.4156 (1861/4478, Estonian)
G=0.2396 (690/2880, KOREAN)
G=0.2658 (472/1776, Korea1K)
G=0.353 (212/600, NorthernSweden)
A=0.007 (4/534, MGP)
G=0.285 (111/390, SGDP_PRJ)
A=0.421 (91/216, Qatari)
G=0.332 (71/214, Vietnamese)
G=0.50 (17/34, Siberian)
A=0.50 (17/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COX6B2 : 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 21884 G=0.56393 A=0.43607, C=0.00000, T=0.00000
European Sub 14374 G=0.51113 A=0.48887, C=0.00000, T=0.00000
African Sub 4598 G=0.7486 A=0.2514, C=0.0000, T=0.0000
African Others Sub 142 G=0.866 A=0.134, C=0.000, T=0.000
African American Sub 4456 G=0.7448 A=0.2552, C=0.0000, T=0.0000
Asian Sub 62 G=0.32 A=0.68, C=0.00, T=0.00
East Asian Sub 30 G=0.33 A=0.67, C=0.00, T=0.00
Other Asian Sub 32 G=0.31 A=0.69, C=0.00, T=0.00
Latin American 1 Sub 30 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 96 G=1.00 A=0.00, C=0.00, T=0.00
South Asian Sub 28 G=0.96 A=0.04, C=0.00, T=0.00
Other Sub 2696 G=0.5115 A=0.4885, C=0.0000, T=0.0000


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 G=0.513843 A=0.486157
gnomAD - Genomes Global Study-wide 139056 G=0.506199 A=0.493801
gnomAD - Genomes European Sub 75104 G=0.43665 A=0.56335
gnomAD - Genomes African Sub 41838 G=0.67023 A=0.32977
gnomAD - Genomes American Sub 13582 G=0.45133 A=0.54867
gnomAD - Genomes Ashkenazi Jewish Sub 3284 G=0.4909 A=0.5091
gnomAD - Genomes East Asian Sub 3116 G=0.2522 A=0.7478
gnomAD - Genomes Other Sub 2132 G=0.4817 A=0.5183
The PAGE Study Global Study-wide 78690 G=0.52492 A=0.47508
The PAGE Study AfricanAmerican Sub 32508 G=0.66614 A=0.33386
The PAGE Study Mexican Sub 10808 G=0.40646 A=0.59354
The PAGE Study Asian Sub 8318 G=0.2105 A=0.7895
The PAGE Study PuertoRican Sub 7916 G=0.5472 A=0.4528
The PAGE Study NativeHawaiian Sub 4534 G=0.4292 A=0.5708
The PAGE Study Cuban Sub 4230 G=0.5187 A=0.4813
The PAGE Study Dominican Sub 3828 G=0.5750 A=0.4250
The PAGE Study CentralAmerican Sub 2450 G=0.4090 A=0.5910
The PAGE Study SouthAmerican Sub 1982 G=0.4279 A=0.5721
The PAGE Study NativeAmerican Sub 1260 G=0.4381 A=0.5619
The PAGE Study SouthAsian Sub 856 G=0.505 A=0.495
14KJPN JAPANESE Study-wide 25986 G=0.22843 A=0.77157
Allele Frequency Aggregator Total Global 21884 G=0.56393 A=0.43607, C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 14374 G=0.51113 A=0.48887, C=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 4598 G=0.7486 A=0.2514, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 2696 G=0.5115 A=0.4885, C=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 96 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 62 G=0.32 A=0.68, C=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 30 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 28 G=0.96 A=0.04, C=0.00, T=0.00
ExAC Global Study-wide 17028 G=0.47974 A=0.52026
ExAC Asian Sub 8170 G=0.4891 A=0.5109
ExAC Europe Sub 6916 G=0.4377 A=0.5623
ExAC African Sub 1492 G=0.6381 A=0.3619
ExAC American Sub 292 G=0.418 A=0.582
ExAC Other Sub 158 G=0.456 A=0.544
8.3KJPN JAPANESE Study-wide 14430 G=0.23645 A=0.76355
GO Exome Sequencing Project Global Study-wide 11636 G=0.55457 A=0.44543
GO Exome Sequencing Project European American Sub 7872 G=0.4876 A=0.5124
GO Exome Sequencing Project African American Sub 3764 G=0.6947 A=0.3053
1000Genomes_30x Global Study-wide 6404 G=0.5100 A=0.4900
1000Genomes_30x African Sub 1786 G=0.7105 A=0.2895
1000Genomes_30x Europe Sub 1266 G=0.4613 A=0.5387
1000Genomes_30x South Asian Sub 1202 G=0.5374 A=0.4626
1000Genomes_30x East Asian Sub 1170 G=0.2692 A=0.7308
1000Genomes_30x American Sub 980 G=0.461 A=0.539
1000Genomes Global Study-wide 5008 G=0.5086 A=0.4914
1000Genomes African Sub 1322 G=0.7194 A=0.2806
1000Genomes East Asian Sub 1008 G=0.2728 A=0.7272
1000Genomes Europe Sub 1006 G=0.4632 A=0.5368
1000Genomes South Asian Sub 978 G=0.545 A=0.455
1000Genomes American Sub 694 G=0.464 A=0.536
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.4156 A=0.5844
KOREAN population from KRGDB KOREAN Study-wide 2880 G=0.2396 A=0.7604
Korean Genome Project KOREAN Study-wide 1776 G=0.2658 A=0.7342
Northern Sweden ACPOP Study-wide 600 G=0.353 A=0.647
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.993 A=0.007
SGDP_PRJ Global Study-wide 390 G=0.285 A=0.715
Qatari Global Study-wide 216 G=0.579 A=0.421
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.332 A=0.668
Siberian Global Study-wide 34 G=0.50 A=0.50
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 19 NC_000019.10:g.55353982G>A
GRCh38.p14 chr 19 NC_000019.10:g.55353982G>C
GRCh38.p14 chr 19 NC_000019.10:g.55353982G>T
GRCh37.p13 chr 19 NC_000019.9:g.55865350G>A
GRCh37.p13 chr 19 NC_000019.9:g.55865350G>C
GRCh37.p13 chr 19 NC_000019.9:g.55865350G>T
Gene: COX6B2, cytochrome c oxidase subunit 6B2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COX6B2 transcript variant 1 NM_001369798.1:c.113-16C>T N/A Intron Variant
COX6B2 transcript variant 3 NM_001369799.1:c.113-16C>T N/A Intron Variant
COX6B2 transcript variant 4 NM_001369800.1:c.113-16C>T N/A Intron Variant
COX6B2 transcript variant 2 NM_144613.5:c.113-16C>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 G= A C T
GRCh38.p14 chr 19 NC_000019.10:g.55353982= NC_000019.10:g.55353982G>A NC_000019.10:g.55353982G>C NC_000019.10:g.55353982G>T
GRCh37.p13 chr 19 NC_000019.9:g.55865350= NC_000019.9:g.55865350G>A NC_000019.9:g.55865350G>C NC_000019.9:g.55865350G>T
COX6B2 transcript variant 1 NM_001369798.1:c.113-16= NM_001369798.1:c.113-16C>T NM_001369798.1:c.113-16C>G NM_001369798.1:c.113-16C>A
COX6B2 transcript variant 3 NM_001369799.1:c.113-16= NM_001369799.1:c.113-16C>T NM_001369799.1:c.113-16C>G NM_001369799.1:c.113-16C>A
COX6B2 transcript variant 4 NM_001369800.1:c.113-16= NM_001369800.1:c.113-16C>T NM_001369800.1:c.113-16C>G NM_001369800.1:c.113-16C>A
COX6B2 transcript NM_144613.4:c.113-16= NM_144613.4:c.113-16C>T NM_144613.4:c.113-16C>G NM_144613.4:c.113-16C>A
COX6B2 transcript variant 2 NM_144613.5:c.113-16= NM_144613.5:c.113-16C>T NM_144613.5:c.113-16C>G NM_144613.5:c.113-16C>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#.

79 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19403880 Feb 28, 2004 (120)
2 SSAHASNP ss21529721 Apr 05, 2004 (121)
3 ABI ss44165130 Mar 14, 2006 (126)
4 BCMHGSC_JDW ss91014399 Mar 24, 2008 (129)
5 HUMANGENOME_JCVI ss96316427 Feb 04, 2009 (130)
6 ENSEMBL ss137738175 Dec 01, 2009 (131)
7 ENSEMBL ss161154420 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss168385214 Jul 04, 2010 (132)
9 COMPLETE_GENOMICS ss170185273 Jul 04, 2010 (132)
10 BUSHMAN ss203795226 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss208573554 Jul 04, 2010 (132)
12 1000GENOMES ss228197180 Jul 14, 2010 (132)
13 1000GENOMES ss237720235 Jul 15, 2010 (132)
14 1000GENOMES ss243915721 Jul 15, 2010 (132)
15 GMI ss283258325 May 04, 2012 (137)
16 1000GENOMES ss491168523 May 04, 2012 (137)
17 ILLUMINA ss536258247 Sep 08, 2015 (146)
18 TISHKOFF ss566065010 Apr 25, 2013 (138)
19 SSMP ss661935248 Apr 25, 2013 (138)
20 NHLBI-ESP ss713541240 Apr 25, 2013 (138)
21 EVA-GONL ss994429267 Aug 21, 2014 (142)
22 1000GENOMES ss1363662887 Aug 21, 2014 (142)
23 EVA_EXAC ss1693822056 Apr 01, 2015 (144)
24 EVA_MGP ss1711528035 Apr 01, 2015 (144)
25 HAMMER_LAB ss1809370437 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1937935963 Feb 12, 2016 (147)
27 ILLUMINA ss1959885100 Feb 12, 2016 (147)
28 JJLAB ss2029742415 Sep 14, 2016 (149)
29 USC_VALOUEV ss2158295812 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2226634730 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2629368759 Nov 08, 2017 (151)
32 GRF ss2702912182 Nov 08, 2017 (151)
33 GNOMAD ss2744335166 Nov 08, 2017 (151)
34 GNOMAD ss2750297751 Nov 08, 2017 (151)
35 GNOMAD ss2964301782 Nov 08, 2017 (151)
36 SWEGEN ss3017697016 Nov 08, 2017 (151)
37 ILLUMINA ss3021926659 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3028702906 Nov 08, 2017 (151)
39 CSHL ss3352366369 Nov 08, 2017 (151)
40 ILLUMINA ss3627964186 Oct 12, 2018 (152)
41 OMUKHERJEE_ADBS ss3646543750 Oct 12, 2018 (152)
42 URBANLAB ss3650946668 Oct 12, 2018 (152)
43 ILLUMINA ss3652354540 Oct 12, 2018 (152)
44 EGCUT_WGS ss3684415301 Jul 13, 2019 (153)
45 EVA_DECODE ss3703026885 Jul 13, 2019 (153)
46 ACPOP ss3743153784 Jul 13, 2019 (153)
47 EVA ss3756213852 Jul 13, 2019 (153)
48 PAGE_CC ss3772026499 Jul 13, 2019 (153)
49 PACBIO ss3788568939 Jul 13, 2019 (153)
50 PACBIO ss3793473358 Jul 13, 2019 (153)
51 PACBIO ss3798360473 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3821466599 Jul 13, 2019 (153)
53 EVA ss3825333803 Apr 27, 2020 (154)
54 EVA ss3835530449 Apr 27, 2020 (154)
55 EVA ss3841388092 Apr 27, 2020 (154)
56 EVA ss3846895216 Apr 27, 2020 (154)
57 SGDP_PRJ ss3888509289 Apr 27, 2020 (154)
58 KRGDB ss3938677288 Apr 27, 2020 (154)
59 KOGIC ss3981619194 Apr 27, 2020 (154)
60 FSA-LAB ss3984164817 Apr 27, 2021 (155)
61 EVA ss3986816403 Apr 27, 2021 (155)
62 TOPMED ss5078861652 Apr 27, 2021 (155)
63 TOMMO_GENOMICS ss5228376001 Apr 27, 2021 (155)
64 1000G_HIGH_COVERAGE ss5307723266 Oct 13, 2022 (156)
65 EVA ss5435619154 Oct 13, 2022 (156)
66 HUGCELL_USP ss5500162165 Oct 13, 2022 (156)
67 1000G_HIGH_COVERAGE ss5613640741 Oct 13, 2022 (156)
68 EVA ss5623979760 Oct 13, 2022 (156)
69 EVA ss5624095351 Oct 13, 2022 (156)
70 SANFORD_IMAGENETICS ss5662656924 Oct 13, 2022 (156)
71 TOMMO_GENOMICS ss5787223107 Oct 13, 2022 (156)
72 EVA ss5800226652 Oct 13, 2022 (156)
73 YY_MCH ss5817723643 Oct 13, 2022 (156)
74 EVA ss5840731817 Oct 13, 2022 (156)
75 EVA ss5848504119 Oct 13, 2022 (156)
76 EVA ss5928585950 Oct 13, 2022 (156)
77 EVA ss5936575867 Oct 13, 2022 (156)
78 EVA ss5954054884 Oct 13, 2022 (156)
79 EVA ss5981315145 Oct 13, 2022 (156)
80 1000Genomes NC_000019.9 - 55865350 Oct 12, 2018 (152)
81 1000Genomes_30x NC_000019.10 - 55353982 Oct 13, 2022 (156)
82 Genetic variation in the Estonian population NC_000019.9 - 55865350 Oct 12, 2018 (152)
83 ExAC NC_000019.9 - 55865350 Oct 12, 2018 (152)
84 gnomAD - Genomes NC_000019.10 - 55353982 Apr 27, 2021 (155)
85 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 13651955 (NC_000019.9:55865349:G:G 60272/136124, NC_000019.9:55865349:G:A 75852/136124)
Row 13651956 (NC_000019.9:55865349:G:G 136123/136124, NC_000019.9:55865349:G:T 1/136124)

- Jul 13, 2019 (153)
86 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 13651955 (NC_000019.9:55865349:G:G 60272/136124, NC_000019.9:55865349:G:A 75852/136124)
Row 13651956 (NC_000019.9:55865349:G:G 136123/136124, NC_000019.9:55865349:G:T 1/136124)

- Jul 13, 2019 (153)
87 GO Exome Sequencing Project NC_000019.9 - 55865350 Oct 12, 2018 (152)
88 KOREAN population from KRGDB NC_000019.9 - 55865350 Apr 27, 2020 (154)
89 Korean Genome Project NC_000019.10 - 55353982 Apr 27, 2020 (154)
90 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 55865350 Apr 27, 2020 (154)
91 Northern Sweden NC_000019.9 - 55865350 Jul 13, 2019 (153)
92 The PAGE Study NC_000019.10 - 55353982 Jul 13, 2019 (153)
93 Qatari NC_000019.9 - 55865350 Apr 27, 2020 (154)
94 SGDP_PRJ NC_000019.9 - 55865350 Apr 27, 2020 (154)
95 Siberian NC_000019.9 - 55865350 Apr 27, 2020 (154)
96 8.3KJPN NC_000019.9 - 55865350 Apr 27, 2021 (155)
97 14KJPN NC_000019.10 - 55353982 Oct 13, 2022 (156)
98 TopMed NC_000019.10 - 55353982 Apr 27, 2021 (155)
99 A Vietnamese Genetic Variation Database NC_000019.9 - 55865350 Jul 13, 2019 (153)
100 ALFA NC_000019.10 - 55353982 Apr 27, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91014399, ss168385214, ss170185273, ss203795226, ss208573554, ss283258325 NC_000019.8:60557161:G:A NC_000019.10:55353981:G:A (self)
77088345, 30153549, 4342861, 1790734, 45854682, 643795, 16438649, 19977885, 40526269, 10812166, 86345308, 9420451, ss228197180, ss237720235, ss243915721, ss491168523, ss536258247, ss566065010, ss661935248, ss713541240, ss994429267, ss1363662887, ss1693822056, ss1711528035, ss1809370437, ss1937935963, ss1959885100, ss2029742415, ss2158295812, ss2629368759, ss2702912182, ss2744335166, ss2750297751, ss2964301782, ss3017697016, ss3021926659, ss3352366369, ss3627964186, ss3646543750, ss3652354540, ss3684415301, ss3743153784, ss3756213852, ss3788568939, ss3793473358, ss3798360473, ss3825333803, ss3835530449, ss3841388092, ss3888509289, ss3938677288, ss3984164817, ss3986816403, ss5228376001, ss5435619154, ss5623979760, ss5624095351, ss5662656924, ss5800226652, ss5840731817, ss5848504119, ss5936575867, ss5954054884, ss5981315145 NC_000019.9:55865349:G:A NC_000019.10:55353981:G:A (self)
101166676, 543613038, 37997195, 1247968, 121060211, 294407316, 12868017386, ss2226634730, ss3028702906, ss3650946668, ss3703026885, ss3772026499, ss3821466599, ss3846895216, ss3981619194, ss5078861652, ss5307723266, ss5500162165, ss5613640741, ss5787223107, ss5817723643, ss5928585950 NC_000019.10:55353981:G:A NC_000019.10:55353981:G:A (self)
ss19403880, ss21529721 NT_011109.15:28133539:G:A NC_000019.10:55353981:G:A (self)
ss44165130, ss96316427, ss137738175, ss161154420 NT_011109.16:28133567:G:A NC_000019.10:55353981:G:A (self)
12868017386 NC_000019.10:55353981:G:C NC_000019.10:55353981:G:C (self)
ss2744335166 NC_000019.9:55865349:G:T NC_000019.10:55353981:G:T (self)
12868017386 NC_000019.10:55353981:G:T NC_000019.10:55353981:G: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 rs12461665

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