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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.

rs9886

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:72238621 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.132480 (35066/264690, TOPMED)
C=0.131407 (18409/140092, GnomAD)
C=0.09017 (2548/28258, 14KJPN) (+ 19 more)
C=0.04820 (861/17864, ALFA)
C=0.09148 (1533/16758, 8.3KJPN)
C=0.1602 (1026/6404, 1000G_30x)
C=0.1565 (784/5008, 1000G)
C=0.0946 (424/4480, Estonian)
C=0.0547 (211/3854, ALSPAC)
C=0.0588 (218/3708, TWINSUK)
C=0.1048 (307/2930, KOREAN)
C=0.1223 (224/1832, Korea1K)
C=0.064 (64/998, GoNL)
C=0.058 (35/600, NorthernSweden)
C=0.017 (9/534, MGP)
C=0.168 (55/328, HapMap)
C=0.083 (18/216, Qatari)
C=0.206 (44/214, Vietnamese)
G=0.468 (58/124, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
G=0.5 (5/10, Siberian)
C=0.5 (5/10, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
INPPL1 : 3 Prime UTR Variant
PHOX2A : 500B Downstream 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 17864 G=0.95180 C=0.04820, T=0.00000
European Sub 14632 G=0.95414 C=0.04586, T=0.00000
African Sub 1878 G=0.9127 C=0.0873, T=0.0000
African Others Sub 72 G=0.82 C=0.18, T=0.00
African American Sub 1806 G=0.9164 C=0.0836, T=0.0000
Asian Sub 76 G=0.99 C=0.01, T=0.00
East Asian Sub 56 G=0.98 C=0.02, T=0.00
Other Asian Sub 20 G=1.00 C=0.00, T=0.00
Latin American 1 Sub 124 G=1.000 C=0.000, T=0.000
Latin American 2 Sub 478 G=1.000 C=0.000, T=0.000
South Asian Sub 88 G=1.00 C=0.00, T=0.00
Other Sub 588 G=0.957 C=0.043, T=0.000


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=0.867520 C=0.132480
gnomAD - Genomes Global Study-wide 140092 G=0.868593 C=0.131407
gnomAD - Genomes European Sub 75898 G=0.93167 C=0.06833
gnomAD - Genomes African Sub 41946 G=0.74055 C=0.25945
gnomAD - Genomes American Sub 13650 G=0.90894 C=0.09106
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9116 C=0.0884
gnomAD - Genomes East Asian Sub 3124 G=0.8278 C=0.1722
gnomAD - Genomes Other Sub 2150 G=0.8767 C=0.1233
14KJPN JAPANESE Study-wide 28258 G=0.90983 C=0.09017
Allele Frequency Aggregator Total Global 17864 G=0.95180 C=0.04820, T=0.00000
Allele Frequency Aggregator European Sub 14632 G=0.95414 C=0.04586, T=0.00000
Allele Frequency Aggregator African Sub 1878 G=0.9127 C=0.0873, T=0.0000
Allele Frequency Aggregator Other Sub 588 G=0.957 C=0.043, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 478 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 124 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 88 G=1.00 C=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 76 G=0.99 C=0.01, T=0.00
8.3KJPN JAPANESE Study-wide 16758 G=0.90852 C=0.09148
1000Genomes_30x Global Study-wide 6404 G=0.8398 C=0.1602
1000Genomes_30x African Sub 1786 G=0.6937 C=0.3063
1000Genomes_30x Europe Sub 1266 G=0.9289 C=0.0711
1000Genomes_30x South Asian Sub 1202 G=0.9218 C=0.0782
1000Genomes_30x East Asian Sub 1170 G=0.8521 C=0.1479
1000Genomes_30x American Sub 980 G=0.876 C=0.124
1000Genomes Global Study-wide 5008 G=0.8435 C=0.1565
1000Genomes African Sub 1322 G=0.6997 C=0.3003
1000Genomes East Asian Sub 1008 G=0.8512 C=0.1488
1000Genomes Europe Sub 1006 G=0.9254 C=0.0746
1000Genomes South Asian Sub 978 G=0.916 C=0.084
1000Genomes American Sub 694 G=0.885 C=0.115
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9054 C=0.0946
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9453 C=0.0547
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9412 C=0.0588
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8952 C=0.1048
Korean Genome Project KOREAN Study-wide 1832 G=0.8777 C=0.1223
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.936 C=0.064
Northern Sweden ACPOP Study-wide 600 G=0.942 C=0.058
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.983 C=0.017
HapMap Global Study-wide 328 G=0.832 C=0.168
HapMap African Sub 120 G=0.667 C=0.333
HapMap American Sub 120 G=0.942 C=0.058
HapMap Asian Sub 88 G=0.91 C=0.09
Qatari Global Study-wide 216 G=0.917 C=0.083
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.794 C=0.206
SGDP_PRJ Global Study-wide 124 G=0.468 C=0.532
The Danish reference pan genome Danish Study-wide 40 G=0.93 C=0.07
Siberian Global Study-wide 10 G=0.5 C=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.72238621G>C
GRCh38.p14 chr 11 NC_000011.10:g.72238621G>T
GRCh37.p13 chr 11 NC_000011.9:g.71949665G>C
GRCh37.p13 chr 11 NC_000011.9:g.71949665G>T
INPPL1 RefSeqGene NG_023253.2:g.18784G>C
INPPL1 RefSeqGene NG_023253.2:g.18784G>T
PHOX2A RefSeqGene NG_008169.1:g.10556C>G
PHOX2A RefSeqGene NG_008169.1:g.10556C>A
Gene: INPPL1, inositol polyphosphate phosphatase like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
INPPL1 transcript NM_001567.4:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X1 XM_005273979.5:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X2 XM_047426887.1:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X3 XM_047426888.1:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X4 XM_047426889.1:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X5 XM_011544999.3:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X6 XM_047426890.1:c.*268= N/A 3 Prime UTR Variant
INPPL1 transcript variant X7 XM_047426891.1:c.*356= N/A 3 Prime UTR Variant
INPPL1 transcript variant X8 XM_047426892.1:c.*356= N/A 3 Prime UTR Variant
INPPL1 transcript variant X9 XM_047426893.1:c.*268= N/A 3 Prime UTR Variant
Gene: PHOX2A, paired like homeobox 2A (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
PHOX2A transcript variant 1 NM_005169.4:c. N/A Downstream Transcript Variant
PHOX2A transcript variant X1 XM_047426947.1:c. N/A Downstream Transcript 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.

Allele: C (allele ID: 1267608 )
ClinVar Accession Disease Names Clinical Significance
RCV001687632.1 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 G= C T
GRCh38.p14 chr 11 NC_000011.10:g.72238621= NC_000011.10:g.72238621G>C NC_000011.10:g.72238621G>T
GRCh37.p13 chr 11 NC_000011.9:g.71949665= NC_000011.9:g.71949665G>C NC_000011.9:g.71949665G>T
INPPL1 RefSeqGene NG_023253.2:g.18784= NG_023253.2:g.18784G>C NG_023253.2:g.18784G>T
INPPL1 transcript NM_001567.4:c.*268= NM_001567.4:c.*268G>C NM_001567.4:c.*268G>T
INPPL1 transcript NM_001567.3:c.*268= NM_001567.3:c.*268G>C NM_001567.3:c.*268G>T
PHOX2A RefSeqGene NG_008169.1:g.10556= NG_008169.1:g.10556C>G NG_008169.1:g.10556C>A
INPPL1 transcript variant X1 XM_005273979.5:c.*268= XM_005273979.5:c.*268G>C XM_005273979.5:c.*268G>T
INPPL1 transcript variant X5 XM_005273979.4:c.*268= XM_005273979.4:c.*268G>C XM_005273979.4:c.*268G>T
INPPL1 transcript variant X1 XM_005273979.3:c.*268= XM_005273979.3:c.*268G>C XM_005273979.3:c.*268G>T
INPPL1 transcript variant X2 XM_005273979.2:c.*268= XM_005273979.2:c.*268G>C XM_005273979.2:c.*268G>T
INPPL1 transcript variant X2 XM_005273979.1:c.*268= XM_005273979.1:c.*268G>C XM_005273979.1:c.*268G>T
INPPL1 transcript variant X5 XM_011544999.3:c.*268= XM_011544999.3:c.*268G>C XM_011544999.3:c.*268G>T
INPPL1 transcript variant X6 XM_011544999.2:c.*268= XM_011544999.2:c.*268G>C XM_011544999.2:c.*268G>T
INPPL1 transcript variant X3 XM_011544999.1:c.*268= XM_011544999.1:c.*268G>C XM_011544999.1:c.*268G>T
INPPL1 transcript variant X4 XM_047426889.1:c.*268= XM_047426889.1:c.*268G>C XM_047426889.1:c.*268G>T
INPPL1 transcript variant X2 XM_047426887.1:c.*268= XM_047426887.1:c.*268G>C XM_047426887.1:c.*268G>T
INPPL1 transcript variant X3 XM_047426888.1:c.*268= XM_047426888.1:c.*268G>C XM_047426888.1:c.*268G>T
INPPL1 transcript variant X6 XM_047426890.1:c.*268= XM_047426890.1:c.*268G>C XM_047426890.1:c.*268G>T
INPPL1 transcript variant X7 XM_047426891.1:c.*356= XM_047426891.1:c.*356G>C XM_047426891.1:c.*356G>T
INPPL1 transcript variant X8 XM_047426892.1:c.*356= XM_047426892.1:c.*356G>C XM_047426892.1:c.*356G>T
INPPL1 transcript variant X9 XM_047426893.1:c.*268= XM_047426893.1:c.*268G>C XM_047426893.1:c.*268G>T
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#.

65 SubSNP, 21 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss12008 Sep 19, 2000 (52)
2 YUSUKE ss4936932 Aug 28, 2002 (108)
3 CGAP-GAI ss16247458 Feb 27, 2004 (120)
4 KRIBB_YJKIM ss65835561 Nov 30, 2006 (127)
5 CNG ss95210615 Mar 25, 2008 (129)
6 SHGC ss95216717 Feb 04, 2009 (130)
7 BGI ss102975521 Dec 01, 2009 (131)
8 1000GENOMES ss114773605 Jan 25, 2009 (130)
9 ILLUMINA ss159849474 Dec 01, 2009 (131)
10 ILLUMINA ss169073101 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss170212814 Jul 04, 2010 (132)
12 1000GENOMES ss225307515 Jul 14, 2010 (132)
13 1000GENOMES ss235607522 Jul 15, 2010 (132)
14 1000GENOMES ss242230375 Jul 15, 2010 (132)
15 GMI ss281062110 May 04, 2012 (137)
16 ILLUMINA ss479157981 Sep 08, 2015 (146)
17 ILLUMINA ss535427681 Sep 08, 2015 (146)
18 TISHKOFF ss562643185 Apr 25, 2013 (138)
19 SSMP ss658159562 Apr 25, 2013 (138)
20 EVA-GONL ss988662940 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1077824952 Aug 21, 2014 (142)
22 1000GENOMES ss1341834414 Aug 21, 2014 (142)
23 EVA_GENOME_DK ss1575788442 Apr 01, 2015 (144)
24 EVA_DECODE ss1598323997 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1626868598 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1669862631 Apr 01, 2015 (144)
27 EVA_MGP ss1711301419 Apr 01, 2015 (144)
28 HAMMER_LAB ss1806871589 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1932021658 Feb 12, 2016 (147)
30 GENOMED ss1967389444 Jul 19, 2016 (147)
31 JJLAB ss2026754811 Sep 14, 2016 (149)
32 USC_VALOUEV ss2155064711 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2183433538 Dec 20, 2016 (150)
34 ILLUMINA ss2635027654 Nov 08, 2017 (151)
35 GRF ss2699359921 Nov 08, 2017 (151)
36 GNOMAD ss2901262314 Nov 08, 2017 (151)
37 AFFY ss2984949405 Nov 08, 2017 (151)
38 SWEGEN ss3008326258 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027174861 Nov 08, 2017 (151)
40 ILLUMINA ss3626687432 Oct 12, 2018 (152)
41 ILLUMINA ss3636145793 Oct 12, 2018 (152)
42 ILLUMINA ss3637914735 Oct 12, 2018 (152)
43 OMUKHERJEE_ADBS ss3646429854 Oct 12, 2018 (152)
44 EGCUT_WGS ss3675645032 Jul 13, 2019 (153)
45 EVA_DECODE ss3692057876 Jul 13, 2019 (153)
46 ACPOP ss3738295012 Jul 13, 2019 (153)
47 EVA ss3749466855 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3814804245 Jul 13, 2019 (153)
49 EVA ss3832695067 Apr 26, 2020 (154)
50 SGDP_PRJ ss3876549584 Apr 26, 2020 (154)
51 KRGDB ss3924950181 Apr 26, 2020 (154)
52 KOGIC ss3970207831 Apr 26, 2020 (154)
53 TOPMED ss4890093163 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5202631892 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5287918354 Oct 16, 2022 (156)
56 EVA ss5400460147 Oct 16, 2022 (156)
57 HUGCELL_USP ss5483026462 Oct 16, 2022 (156)
58 1000G_HIGH_COVERAGE ss5583883718 Oct 16, 2022 (156)
59 SANFORD_IMAGENETICS ss5651500437 Oct 16, 2022 (156)
60 TOMMO_GENOMICS ss5750721713 Oct 16, 2022 (156)
61 YY_MCH ss5812537582 Oct 16, 2022 (156)
62 EVA ss5836849763 Oct 16, 2022 (156)
63 EVA ss5850032040 Oct 16, 2022 (156)
64 EVA ss5920528510 Oct 16, 2022 (156)
65 EVA ss5942810496 Oct 16, 2022 (156)
66 1000Genomes NC_000011.9 - 71949665 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000011.10 - 72238621 Oct 16, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 71949665 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000011.9 - 71949665 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000011.9 - 71949665 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000011.10 - 72238621 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000011.9 - 71949665 Apr 26, 2020 (154)
73 HapMap NC_000011.10 - 72238621 Apr 26, 2020 (154)
74 KOREAN population from KRGDB NC_000011.9 - 71949665 Apr 26, 2020 (154)
75 Korean Genome Project NC_000011.10 - 72238621 Apr 26, 2020 (154)
76 Medical Genome Project healthy controls from Spanish population NC_000011.9 - 71949665 Apr 26, 2020 (154)
77 Northern Sweden NC_000011.9 - 71949665 Jul 13, 2019 (153)
78 Qatari NC_000011.9 - 71949665 Apr 26, 2020 (154)
79 SGDP_PRJ NC_000011.9 - 71949665 Apr 26, 2020 (154)
80 Siberian NC_000011.9 - 71949665 Apr 26, 2020 (154)
81 8.3KJPN NC_000011.9 - 71949665 Apr 26, 2021 (155)
82 14KJPN NC_000011.10 - 72238621 Oct 16, 2022 (156)
83 TopMed NC_000011.10 - 72238621 Apr 26, 2021 (155)
84 UK 10K study - Twins NC_000011.9 - 71949665 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000011.9 - 71949665 Jul 13, 2019 (153)
86 ALFA NC_000011.10 - 72238621 Apr 26, 2021 (155)
87 ClinVar RCV001687632.1 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)
rs3750905 Oct 08, 2002 (108)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss114773605, ss159849474, ss170212814, ss281062110, ss1598323997, ss2635027654 NC_000011.8:71627312:G:C NC_000011.10:72238620:G:C (self)
54375483, 30180793, 21383280, 2618960, 13467243, 32127575, 417179, 11579877, 14063588, 28566564, 7581065, 60601199, 30180793, 6696661, ss225307515, ss235607522, ss242230375, ss479157981, ss535427681, ss562643185, ss658159562, ss988662940, ss1077824952, ss1341834414, ss1575788442, ss1626868598, ss1669862631, ss1711301419, ss1806871589, ss1932021658, ss1967389444, ss2026754811, ss2155064711, ss2699359921, ss2901262314, ss2984949405, ss3008326258, ss3626687432, ss3636145793, ss3637914735, ss3646429854, ss3675645032, ss3738295012, ss3749466855, ss3832695067, ss3876549584, ss3924950181, ss5202631892, ss5400460147, ss5651500437, ss5836849763, ss5942810496 NC_000011.9:71949664:G:C NC_000011.10:72238620:G:C (self)
RCV001687632.1, 71409653, 383807206, 635118, 26585832, 84558817, 105638819, 1939279472, ss2183433538, ss3027174861, ss3692057876, ss3814804245, ss3970207831, ss4890093163, ss5287918354, ss5483026462, ss5583883718, ss5750721713, ss5812537582, ss5850032040, ss5920528510 NC_000011.10:72238620:G:C NC_000011.10:72238620:G:C (self)
ss12008, ss4936932, ss16247458, ss65835561, ss95210615, ss95216717, ss102975521, ss169073101 NT_167190.1:17255459:G:C NC_000011.10:72238620:G:C (self)
1939279472 NC_000011.10:72238620:G:T NC_000011.10:72238620: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 rs9886

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