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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.

rs1050244

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:47238926 (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=0.028917 (7654/264690, TOPMED)
T=0.031707 (4431/139748, GnomAD)
T=0.03426 (2018/58908, ALFA) (+ 19 more)
T=0.03511 (992/28258, 14KJPN)
T=0.03533 (592/16758, 8.3KJPN)
T=0.0472 (302/6404, 1000G_30x)
T=0.0489 (245/5008, 1000G)
T=0.0337 (154/4566, GO-ESP)
T=0.0578 (259/4480, Estonian)
T=0.0389 (150/3854, ALSPAC)
T=0.0275 (102/3708, TWINSUK)
T=0.0291 (85/2922, KOREAN)
T=0.0322 (59/1832, Korea1K)
T=0.028 (28/998, GoNL)
T=0.047 (28/600, NorthernSweden)
T=0.026 (14/534, MGP)
T=0.042 (9/216, Qatari)
T=0.034 (7/208, Vietnamese)
T=0.009 (1/108, HapMap)
C=0.48 (20/42, SGDP_PRJ)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DDB2 : Non Coding Transcript Variant
ACP2 : 500B Downstream Variant
Publications
3 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 58908 C=0.96574 T=0.03426
European Sub 43092 C=0.96289 T=0.03711
African Sub 5174 C=0.9735 T=0.0265
African Others Sub 190 C=0.963 T=0.037
African American Sub 4984 C=0.9739 T=0.0261
Asian Sub 454 C=0.938 T=0.062
East Asian Sub 386 C=0.948 T=0.052
Other Asian Sub 68 C=0.88 T=0.12
Latin American 1 Sub 596 C=0.982 T=0.018
Latin American 2 Sub 4994 C=0.9828 T=0.0172
South Asian Sub 178 C=0.860 T=0.140
Other Sub 4420 C=0.9701 T=0.0299


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=0.971083 T=0.028917
gnomAD - Genomes Global Study-wide 139748 C=0.968293 T=0.031707
gnomAD - Genomes European Sub 75742 C=0.96079 T=0.03921
gnomAD - Genomes African Sub 41854 C=0.97666 T=0.02334
gnomAD - Genomes American Sub 13574 C=0.98298 T=0.01702
gnomAD - Genomes Ashkenazi Jewish Sub 3316 C=0.9843 T=0.0157
gnomAD - Genomes East Asian Sub 3118 C=0.9586 T=0.0414
gnomAD - Genomes Other Sub 2144 C=0.9664 T=0.0336
Allele Frequency Aggregator Total Global 58908 C=0.96574 T=0.03426
Allele Frequency Aggregator European Sub 43092 C=0.96289 T=0.03711
Allele Frequency Aggregator African Sub 5174 C=0.9735 T=0.0265
Allele Frequency Aggregator Latin American 2 Sub 4994 C=0.9828 T=0.0172
Allele Frequency Aggregator Other Sub 4420 C=0.9701 T=0.0299
Allele Frequency Aggregator Latin American 1 Sub 596 C=0.982 T=0.018
Allele Frequency Aggregator Asian Sub 454 C=0.938 T=0.062
Allele Frequency Aggregator South Asian Sub 178 C=0.860 T=0.140
14KJPN JAPANESE Study-wide 28258 C=0.96489 T=0.03511
8.3KJPN JAPANESE Study-wide 16758 C=0.96467 T=0.03533
1000Genomes_30x Global Study-wide 6404 C=0.9528 T=0.0472
1000Genomes_30x African Sub 1786 C=0.9871 T=0.0129
1000Genomes_30x Europe Sub 1266 C=0.9645 T=0.0355
1000Genomes_30x South Asian Sub 1202 C=0.8644 T=0.1356
1000Genomes_30x East Asian Sub 1170 C=0.9462 T=0.0538
1000Genomes_30x American Sub 980 C=0.992 T=0.008
1000Genomes Global Study-wide 5008 C=0.9511 T=0.0489
1000Genomes African Sub 1322 C=0.9864 T=0.0136
1000Genomes East Asian Sub 1008 C=0.9494 T=0.0506
1000Genomes Europe Sub 1006 C=0.9622 T=0.0378
1000Genomes South Asian Sub 978 C=0.864 T=0.136
1000Genomes American Sub 694 C=0.993 T=0.007
GO Exome Sequencing Project Global Study-wide 4566 C=0.9663 T=0.0337
GO Exome Sequencing Project European American Sub 3182 C=0.9623 T=0.0377
GO Exome Sequencing Project African American Sub 1384 C=0.9754 T=0.0246
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9422 T=0.0578
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9611 T=0.0389
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9725 T=0.0275
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9709 T=0.0291
Korean Genome Project KOREAN Study-wide 1832 C=0.9678 T=0.0322
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.972 T=0.028
Northern Sweden ACPOP Study-wide 600 C=0.953 T=0.047
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.974 T=0.026
Qatari Global Study-wide 216 C=0.958 T=0.042
A Vietnamese Genetic Variation Database Global Study-wide 208 C=0.966 T=0.034
HapMap Global Study-wide 108 C=0.991 T=0.009
HapMap African Sub 108 C=0.991 T=0.009
SGDP_PRJ Global Study-wide 42 C=0.48 T=0.52
Siberian Global Study-wide 6 C=0.5 T=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 11 NC_000011.10:g.47238926C>T
GRCh37.p13 chr 11 NC_000011.9:g.47260477C>T
DDB2 RefSeqGene (LRG_467) NG_009365.1:g.28985C>T
ACP2 RefSeqGene NG_023296.1:g.14981G>A
Gene: DDB2, damage specific DNA binding protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDB2 transcript variant WT NM_000107.3:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant D1 NM_001300734.2:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant 6 NM_001399878.1:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant 5 NM_001399876.1:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant 4 NM_001399875.1:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant 3 NM_001399874.1:c.*77= N/A 3 Prime UTR Variant
DDB2 transcript variant 7 NR_174610.1:n.1612C>T N/A Non Coding Transcript Variant
DDB2 transcript variant 8 NR_174611.1:n.1590C>T N/A Non Coding Transcript Variant
DDB2 transcript variant X1 XM_047426487.1:c. N/A Genic Downstream Transcript Variant
Gene: ACP2, acid phosphatase 2, lysosomal (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
ACP2 transcript variant 3 NM_001302489.2:c. N/A Downstream Transcript Variant
ACP2 transcript variant 4 NM_001302490.2:c. N/A Downstream Transcript Variant
ACP2 transcript variant 5 NM_001302491.2:c. N/A Downstream Transcript Variant
ACP2 transcript variant 6 NM_001302492.2:c. N/A Downstream Transcript Variant
ACP2 transcript variant 1 NM_001357016.2:c. N/A Downstream Transcript Variant
ACP2 transcript variant 1 NM_001610.4:c. N/A Downstream Transcript Variant
ACP2 transcript variant X1 XR_007062487.1:n. N/A N/A
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.

Allele: T (allele ID: 327904 )
ClinVar Accession Disease Names Clinical Significance
RCV000393317.3 Xeroderma pigmentosum, group E Benign
RCV001612962.3 not provided Benign
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 11 NC_000011.10:g.47238926= NC_000011.10:g.47238926C>T
GRCh37.p13 chr 11 NC_000011.9:g.47260477= NC_000011.9:g.47260477C>T
DDB2 RefSeqGene (LRG_467) NG_009365.1:g.28985= NG_009365.1:g.28985C>T
DDB2 transcript variant WT NM_000107.3:c.*77= NM_000107.3:c.*77C>T
DDB2 transcript variant WT NM_000107.2:c.*77= NM_000107.2:c.*77C>T
DDB2 transcript variant D1 NM_001300734.2:c.*77= NM_001300734.2:c.*77C>T
DDB2 transcript variant D1 NM_001300734.1:c.*77= NM_001300734.1:c.*77C>T
DDB2 transcript variant 3 NM_001399874.1:c.*77= NM_001399874.1:c.*77C>T
DDB2 transcript variant 4 NM_001399875.1:c.*77= NM_001399875.1:c.*77C>T
DDB2 transcript variant 7 NR_174610.1:n.1612= NR_174610.1:n.1612C>T
DDB2 transcript variant 8 NR_174611.1:n.1590= NR_174611.1:n.1590C>T
DDB2 transcript variant 6 NM_001399878.1:c.*77= NM_001399878.1:c.*77C>T
DDB2 transcript variant 5 NM_001399876.1:c.*77= NM_001399876.1:c.*77C>T
ACP2 RefSeqGene NG_023296.1:g.14981= NG_023296.1:g.14981G>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#.

75 SubSNP, 21 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 LEE ss1524711 Oct 05, 2000 (86)
2 EGP_SNPS ss6313618 Feb 20, 2003 (111)
3 SC_SNP ss16025802 Feb 27, 2004 (120)
4 PERLEGEN ss24697579 Sep 20, 2004 (123)
5 HGSV ss78862761 Dec 07, 2007 (129)
6 ILLUMINA-UK ss119833083 Dec 01, 2009 (131)
7 ILLUMINA ss159904017 Dec 01, 2009 (131)
8 1000GENOMES ss225236311 Jul 14, 2010 (132)
9 1000GENOMES ss235551269 Jul 15, 2010 (132)
10 1000GENOMES ss242186737 Jul 15, 2010 (132)
11 ILLUMINA ss410791717 Sep 17, 2011 (135)
12 ILLUMINA ss479681930 Sep 08, 2015 (146)
13 ILLUMINA ss482845660 May 04, 2012 (137)
14 ILLUMINA ss484085241 May 04, 2012 (137)
15 ILLUMINA ss536275477 Sep 08, 2015 (146)
16 TISHKOFF ss562553282 Apr 25, 2013 (138)
17 SSMP ss658048102 Apr 25, 2013 (138)
18 NHLBI-ESP ss713010159 Apr 25, 2013 (138)
19 ILLUMINA ss779525006 Sep 08, 2015 (146)
20 ILLUMINA ss782487562 Sep 08, 2015 (146)
21 ILLUMINA ss834995516 Sep 08, 2015 (146)
22 EVA-GONL ss988494777 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1077713972 Aug 21, 2014 (142)
24 1000GENOMES ss1341163315 Aug 21, 2014 (142)
25 DDI ss1426624314 Apr 01, 2015 (144)
26 EVA_DECODE ss1598170562 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1626546760 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1669540793 Apr 01, 2015 (144)
29 EVA_MGP ss1711289717 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1931851391 Feb 12, 2016 (147)
31 JJLAB ss2026673083 Sep 14, 2016 (149)
32 USC_VALOUEV ss2154965382 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2182352051 Dec 20, 2016 (150)
34 ILLUMINA ss2632834271 Nov 08, 2017 (151)
35 GRF ss2699249020 Nov 08, 2017 (151)
36 GNOMAD ss2899274256 Nov 08, 2017 (151)
37 SWEGEN ss3008024822 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3027136137 Nov 08, 2017 (151)
39 CSHL ss3349578977 Nov 08, 2017 (151)
40 ILLUMINA ss3626656369 Oct 12, 2018 (152)
41 ILLUMINA ss3630851662 Oct 12, 2018 (152)
42 ILLUMINA ss3636138237 Oct 12, 2018 (152)
43 OMUKHERJEE_ADBS ss3646424992 Oct 12, 2018 (152)
44 EGCUT_WGS ss3675434127 Jul 13, 2019 (153)
45 EVA_DECODE ss3691731608 Jul 13, 2019 (153)
46 ACPOP ss3738156579 Jul 13, 2019 (153)
47 EVA ss3749266349 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3814613236 Jul 13, 2019 (153)
49 EVA ss3824611896 Apr 26, 2020 (154)
50 SGDP_PRJ ss3876193421 Apr 26, 2020 (154)
51 KRGDB ss3924469000 Apr 26, 2020 (154)
52 KOGIC ss3969718315 Apr 26, 2020 (154)
53 FSA-LAB ss3984001032 Apr 26, 2021 (155)
54 EVA ss3986054627 Apr 26, 2021 (155)
55 EVA ss3986522977 Apr 26, 2021 (155)
56 TOPMED ss4884335453 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5201846938 Apr 26, 2021 (155)
58 CPQ_GEN_INCA ss5236853700 Apr 26, 2021 (155)
59 CPQ_GEN_INCA ss5236856244 Apr 26, 2021 (155)
60 CPQ_GEN_INCA ss5236856245 Apr 26, 2021 (155)
61 EVA ss5237214028 Apr 26, 2021 (155)
62 1000G_HIGH_COVERAGE ss5287311084 Oct 16, 2022 (156)
63 EVA ss5315546572 Oct 16, 2022 (156)
64 EVA ss5399408583 Oct 16, 2022 (156)
65 HUGCELL_USP ss5482524587 Oct 16, 2022 (156)
66 EVA ss5510353316 Oct 16, 2022 (156)
67 1000G_HIGH_COVERAGE ss5582920338 Oct 16, 2022 (156)
68 SANFORD_IMAGENETICS ss5651165556 Oct 16, 2022 (156)
69 TOMMO_GENOMICS ss5748932162 Oct 16, 2022 (156)
70 YY_MCH ss5812359633 Oct 16, 2022 (156)
71 EVA ss5836621700 Oct 16, 2022 (156)
72 EVA ss5848323236 Oct 16, 2022 (156)
73 EVA ss5849972568 Oct 16, 2022 (156)
74 EVA ss5919878949 Oct 16, 2022 (156)
75 EVA ss5942485239 Oct 16, 2022 (156)
76 1000Genomes NC_000011.9 - 47260477 Oct 12, 2018 (152)
77 1000Genomes_30x NC_000011.10 - 47238926 Oct 16, 2022 (156)
78 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 47260477 Oct 12, 2018 (152)
79 Genetic variation in the Estonian population NC_000011.9 - 47260477 Oct 12, 2018 (152)
80 gnomAD - Genomes NC_000011.10 - 47238926 Apr 26, 2021 (155)
81 GO Exome Sequencing Project NC_000011.9 - 47260477 Oct 12, 2018 (152)
82 Genome of the Netherlands Release 5 NC_000011.9 - 47260477 Apr 26, 2020 (154)
83 HapMap NC_000011.10 - 47238926 Apr 26, 2020 (154)
84 KOREAN population from KRGDB NC_000011.9 - 47260477 Apr 26, 2020 (154)
85 Korean Genome Project NC_000011.10 - 47238926 Apr 26, 2020 (154)
86 Medical Genome Project healthy controls from Spanish population NC_000011.9 - 47260477 Apr 26, 2020 (154)
87 Northern Sweden NC_000011.9 - 47260477 Jul 13, 2019 (153)
88 Qatari NC_000011.9 - 47260477 Apr 26, 2020 (154)
89 SGDP_PRJ NC_000011.9 - 47260477 Apr 26, 2020 (154)
90 Siberian NC_000011.9 - 47260477 Apr 26, 2020 (154)
91 8.3KJPN NC_000011.9 - 47260477 Apr 26, 2021 (155)
92 14KJPN NC_000011.10 - 47238926 Oct 16, 2022 (156)
93 TopMed NC_000011.10 - 47238926 Apr 26, 2021 (155)
94 UK 10K study - Twins NC_000011.9 - 47260477 Oct 12, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000011.9 - 47260477 Jul 13, 2019 (153)
96 ALFA NC_000011.10 - 47238926 Apr 26, 2021 (155)
97 ClinVar RCV000393317.3 Oct 16, 2022 (156)
98 ClinVar RCV001612962.3 Oct 16, 2022 (156)
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)
rs17726331 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78862761, ss119833083, ss482845660, ss1598170562 NC_000011.8:47217052:C:T NC_000011.10:47238925:C:T (self)
53684329, 29827934, 21172375, 1069489, 13306835, 31646394, 405477, 11441444, 13893321, 28210401, 7481736, 59816245, 29827934, 6626580, ss225236311, ss235551269, ss242186737, ss479681930, ss484085241, ss536275477, ss562553282, ss658048102, ss713010159, ss779525006, ss782487562, ss834995516, ss988494777, ss1077713972, ss1341163315, ss1426624314, ss1626546760, ss1669540793, ss1711289717, ss1931851391, ss2026673083, ss2154965382, ss2632834271, ss2699249020, ss2899274256, ss3008024822, ss3349578977, ss3626656369, ss3630851662, ss3636138237, ss3646424992, ss3675434127, ss3738156579, ss3749266349, ss3824611896, ss3876193421, ss3924469000, ss3984001032, ss3986054627, ss3986522977, ss5201846938, ss5236853700, ss5236856244, ss5236856245, ss5315546572, ss5399408583, ss5510353316, ss5651165556, ss5836621700, ss5848323236, ss5942485239 NC_000011.9:47260476:C:T NC_000011.10:47238925:C:T (self)
RCV000393317.3, RCV001612962.3, 70446273, 378892013, 610375, 26096316, 82769266, 99881109, 693260098, ss2182352051, ss3027136137, ss3691731608, ss3814613236, ss3969718315, ss4884335453, ss5237214028, ss5287311084, ss5482524587, ss5582920338, ss5748932162, ss5812359633, ss5849972568, ss5919878949 NC_000011.10:47238925:C:T NC_000011.10:47238925:C:T (self)
ss16025802 NT_009237.16:46024416:C:T NC_000011.10:47238925:C:T (self)
ss1524711, ss6313618, ss24697579, ss159904017, ss410791717 NT_009237.18:47200476:C:T NC_000011.10:47238925: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.

3 citations for rs1050244
PMID Title Author Year Journal
17357082 Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. Melquist S et al. 2007 American journal of human genetics
21692063 Comprehensive pathway-based interrogation of genetic variations in the nucleotide excision DNA repair pathway and risk of bladder cancer. Xing J et al. 2012 Cancer
32090112 Association between Single-Nucleotide Polymorphism in MicroRNA Target Site of DDB2 and Risk of Hepatocellular Carcinoma in a Southern Chinese Population. Qiu M et al. 2020 BioMed research international
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