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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.

rs13407683

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:34252371 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.292108 (77318/264690, TOPMED)
G=0.302866 (42417/140052, GnomAD)
G=0.288546 (31122/107858, ALFA) (+ 20 more)
G=0.03217 (909/28258, 14KJPN)
G=0.03222 (540/16760, 8.3KJPN)
G=0.2353 (1507/6404, 1000G_30x)
G=0.2336 (1170/5008, 1000G)
G=0.2679 (1200/4480, Estonian)
G=0.2774 (1069/3854, ALSPAC)
G=0.2813 (1043/3708, TWINSUK)
G=0.0457 (134/2930, KOREAN)
G=0.2056 (428/2082, HGDP_Stanford)
G=0.2603 (492/1890, HapMap)
G=0.0529 (97/1832, Korea1K)
G=0.285 (284/998, GoNL)
G=0.043 (34/790, PRJEB37584)
G=0.288 (173/600, NorthernSweden)
G=0.154 (80/520, SGDP_PRJ)
G=0.278 (60/216, Qatari)
G=0.028 (6/214, Vietnamese)
G=0.35 (32/92, Ancient Sardinia)
G=0.19 (10/52, Siberian)
G=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01317 : 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 107858 G=0.288546 A=0.711454
European Sub 88500 G=0.29164 A=0.70836
African Sub 6718 G=0.3733 A=0.6267
African Others Sub 246 G=0.374 A=0.626
African American Sub 6472 G=0.3733 A=0.6267
Asian Sub 532 G=0.041 A=0.959
East Asian Sub 450 G=0.042 A=0.958
Other Asian Sub 82 G=0.04 A=0.96
Latin American 1 Sub 636 G=0.314 A=0.686
Latin American 2 Sub 1558 G=0.1938 A=0.8062
South Asian Sub 5036 G=0.1767 A=0.8233
Other Sub 4878 G=0.2850 A=0.7150


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=0.292108 A=0.707892
gnomAD - Genomes Global Study-wide 140052 G=0.302866 A=0.697134
gnomAD - Genomes European Sub 75858 G=0.29090 A=0.70910
gnomAD - Genomes African Sub 41942 G=0.36651 A=0.63349
gnomAD - Genomes American Sub 13644 G=0.21541 A=0.78459
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.3889 A=0.6111
gnomAD - Genomes East Asian Sub 3134 G=0.0348 A=0.9652
gnomAD - Genomes Other Sub 2152 G=0.2965 A=0.7035
Allele Frequency Aggregator Total Global 107858 G=0.288546 A=0.711454
Allele Frequency Aggregator European Sub 88500 G=0.29164 A=0.70836
Allele Frequency Aggregator African Sub 6718 G=0.3733 A=0.6267
Allele Frequency Aggregator South Asian Sub 5036 G=0.1767 A=0.8233
Allele Frequency Aggregator Other Sub 4878 G=0.2850 A=0.7150
Allele Frequency Aggregator Latin American 2 Sub 1558 G=0.1938 A=0.8062
Allele Frequency Aggregator Latin American 1 Sub 636 G=0.314 A=0.686
Allele Frequency Aggregator Asian Sub 532 G=0.041 A=0.959
14KJPN JAPANESE Study-wide 28258 G=0.03217 A=0.96783
8.3KJPN JAPANESE Study-wide 16760 G=0.03222 A=0.96778
1000Genomes_30x Global Study-wide 6404 G=0.2353 A=0.7647
1000Genomes_30x African Sub 1786 G=0.3779 A=0.6221
1000Genomes_30x Europe Sub 1266 G=0.3112 A=0.6888
1000Genomes_30x South Asian Sub 1202 G=0.1539 A=0.8461
1000Genomes_30x East Asian Sub 1170 G=0.0504 A=0.9496
1000Genomes_30x American Sub 980 G=0.198 A=0.802
1000Genomes Global Study-wide 5008 G=0.2336 A=0.7664
1000Genomes African Sub 1322 G=0.3933 A=0.6067
1000Genomes East Asian Sub 1008 G=0.0456 A=0.9544
1000Genomes Europe Sub 1006 G=0.3141 A=0.6859
1000Genomes South Asian Sub 978 G=0.157 A=0.843
1000Genomes American Sub 694 G=0.193 A=0.807
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2679 A=0.7321
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2774 A=0.7226
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2813 A=0.7187
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0457 A=0.9543
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 G=0.2056 A=0.7944
HGDP-CEPH-db Supplement 1 Est_Asia Sub 468 G=0.073 A=0.927
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.184 A=0.816
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.346 A=0.654
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.316 A=0.684
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.314 A=0.686
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.037 A=0.963
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.17 A=0.83
HapMap Global Study-wide 1890 G=0.2603 A=0.7397
HapMap American Sub 768 G=0.223 A=0.777
HapMap African Sub 692 G=0.363 A=0.637
HapMap Asian Sub 254 G=0.055 A=0.945
HapMap Europe Sub 176 G=0.318 A=0.682
Korean Genome Project KOREAN Study-wide 1832 G=0.0529 A=0.9471
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.285 A=0.715
CNV burdens in cranial meningiomas Global Study-wide 790 G=0.043 A=0.957
CNV burdens in cranial meningiomas CRM Sub 790 G=0.043 A=0.957
Northern Sweden ACPOP Study-wide 600 G=0.288 A=0.712
SGDP_PRJ Global Study-wide 520 G=0.154 A=0.846
Qatari Global Study-wide 216 G=0.278 A=0.722
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.028 A=0.972
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 92 G=0.35 A=0.65
Siberian Global Study-wide 52 G=0.19 A=0.81
The Danish reference pan genome Danish Study-wide 40 G=0.38 A=0.62
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.34252371G>A
GRCh37.p13 chr 2 NC_000002.11:g.34477438G>A
Gene: LINC01317, long intergenic non-protein coding RNA 1317 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01317 transcript NR_126403.1:n. 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
GRCh38.p14 chr 2 NC_000002.12:g.34252371= NC_000002.12:g.34252371G>A
GRCh37.p13 chr 2 NC_000002.11:g.34477438= NC_000002.11:g.34477438G>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#.

109 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 WUGSC_SSAHASNP ss23082554 Apr 05, 2004 (121)
2 ILLUMINA ss66769379 Nov 29, 2006 (127)
3 ILLUMINA ss67078801 Nov 29, 2006 (127)
4 ILLUMINA ss67410545 Nov 29, 2006 (127)
5 ILLUMINA ss70423961 May 16, 2007 (127)
6 ILLUMINA ss70605071 May 27, 2008 (130)
7 ILLUMINA ss71151458 May 16, 2007 (127)
8 ILLUMINA ss75785745 Dec 07, 2007 (129)
9 HGSV ss78546078 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss85320696 Dec 16, 2007 (130)
11 BCMHGSC_JDW ss91113592 Mar 24, 2008 (129)
12 HUMANGENOME_JCVI ss97026381 Feb 06, 2009 (130)
13 BGI ss106080618 Feb 06, 2009 (130)
14 1000GENOMES ss109392785 Jan 24, 2009 (130)
15 ILLUMINA-UK ss117650885 Feb 14, 2009 (130)
16 ILLUMINA ss121646858 Dec 01, 2009 (131)
17 ENSEMBL ss138418480 Dec 01, 2009 (131)
18 ILLUMINA ss153370973 Dec 01, 2009 (131)
19 GMI ss156889932 Dec 01, 2009 (131)
20 ILLUMINA ss159256520 Dec 01, 2009 (131)
21 ILLUMINA ss160336237 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss164140378 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss166400870 Jul 04, 2010 (132)
24 ILLUMINA ss170375201 Jul 04, 2010 (132)
25 ILLUMINA ss172414699 Jul 04, 2010 (132)
26 BUSHMAN ss200254948 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss205672034 Jul 04, 2010 (132)
28 1000GENOMES ss210859426 Jul 14, 2010 (132)
29 1000GENOMES ss219162427 Jul 14, 2010 (132)
30 1000GENOMES ss231106817 Jul 14, 2010 (132)
31 1000GENOMES ss238675025 Jul 15, 2010 (132)
32 BL ss253022067 May 09, 2011 (134)
33 GMI ss276412431 May 04, 2012 (137)
34 GMI ss284321337 Apr 25, 2013 (138)
35 PJP ss292541480 May 09, 2011 (134)
36 ILLUMINA ss480563416 Sep 08, 2015 (146)
37 ILLUMINA ss484069190 May 04, 2012 (137)
38 ILLUMINA ss484346648 May 04, 2012 (137)
39 ILLUMINA ss536529445 Sep 08, 2015 (146)
40 TISHKOFF ss555464860 Apr 25, 2013 (138)
41 SSMP ss649048341 Apr 25, 2013 (138)
42 ILLUMINA ss780619260 Sep 08, 2015 (146)
43 ILLUMINA ss782619570 Sep 08, 2015 (146)
44 ILLUMINA ss825393235 Apr 01, 2015 (144)
45 ILLUMINA ss832768761 Jul 13, 2019 (153)
46 ILLUMINA ss836112824 Sep 08, 2015 (146)
47 EVA-GONL ss976669198 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1068992887 Aug 21, 2014 (142)
49 1000GENOMES ss1296603964 Aug 21, 2014 (142)
50 DDI ss1428530104 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1578813440 Apr 01, 2015 (144)
52 EVA_DECODE ss1586076772 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1603179602 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1646173635 Apr 01, 2015 (144)
55 EVA_SVP ss1712444268 Apr 01, 2015 (144)
56 HAMMER_LAB ss1796529580 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1919901979 Feb 12, 2016 (147)
58 GENOMED ss1968733769 Jul 19, 2016 (147)
59 JJLAB ss2020480672 Sep 14, 2016 (149)
60 USC_VALOUEV ss2148525514 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2228960488 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2624753723 Nov 08, 2017 (151)
63 ILLUMINA ss2633594588 Nov 08, 2017 (151)
64 GRF ss2703086554 Nov 08, 2017 (151)
65 GNOMAD ss2771683002 Nov 08, 2017 (151)
66 SWEGEN ss2989256350 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3024006699 Nov 08, 2017 (151)
68 CSHL ss3344155556 Nov 08, 2017 (151)
69 ILLUMINA ss3628031093 Oct 11, 2018 (152)
70 ILLUMINA ss3631562764 Oct 11, 2018 (152)
71 ILLUMINA ss3636445422 Oct 11, 2018 (152)
72 ILLUMINA ss3638252045 Oct 11, 2018 (152)
73 ILLUMINA ss3639130752 Oct 11, 2018 (152)
74 ILLUMINA ss3639576864 Oct 11, 2018 (152)
75 ILLUMINA ss3642086530 Oct 11, 2018 (152)
76 ILLUMINA ss3643222824 Oct 11, 2018 (152)
77 URBANLAB ss3647001966 Oct 11, 2018 (152)
78 EGCUT_WGS ss3657214896 Jul 13, 2019 (153)
79 EVA_DECODE ss3703590759 Jul 13, 2019 (153)
80 ACPOP ss3728302705 Jul 13, 2019 (153)
81 EVA ss3756567939 Jul 13, 2019 (153)
82 PACBIO ss3783825164 Jul 13, 2019 (153)
83 PACBIO ss3789418921 Jul 13, 2019 (153)
84 PACBIO ss3794291703 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3800946074 Jul 13, 2019 (153)
86 EVA ss3826906923 Apr 25, 2020 (154)
87 EVA ss3836861565 Apr 25, 2020 (154)
88 EVA ss3842276367 Apr 25, 2020 (154)
89 HGDP ss3847612481 Apr 25, 2020 (154)
90 SGDP_PRJ ss3851948497 Apr 25, 2020 (154)
91 KRGDB ss3897374974 Apr 25, 2020 (154)
92 KOGIC ss3947456347 Apr 25, 2020 (154)
93 EVA ss3984480210 Apr 26, 2021 (155)
94 EVA ss3984884056 Apr 26, 2021 (155)
95 EVA ss4016988611 Apr 26, 2021 (155)
96 TOPMED ss4500150051 Apr 26, 2021 (155)
97 TOMMO_GENOMICS ss5150650046 Apr 26, 2021 (155)
98 1000G_HIGH_COVERAGE ss5247518489 Oct 12, 2022 (156)
99 EVA ss5314723418 Oct 12, 2022 (156)
100 EVA ss5327926112 Oct 12, 2022 (156)
101 HUGCELL_USP ss5447771754 Oct 12, 2022 (156)
102 1000G_HIGH_COVERAGE ss5522445920 Oct 12, 2022 (156)
103 SANFORD_IMAGENETICS ss5628435719 Oct 12, 2022 (156)
104 TOMMO_GENOMICS ss5679069482 Oct 12, 2022 (156)
105 YY_MCH ss5802071257 Oct 12, 2022 (156)
106 EVA ss5819889176 Oct 12, 2022 (156)
107 EVA ss5852460158 Oct 12, 2022 (156)
108 EVA ss5929729067 Oct 12, 2022 (156)
109 EVA ss5954644209 Oct 12, 2022 (156)
110 1000Genomes NC_000002.11 - 34477438 Oct 11, 2018 (152)
111 1000Genomes_30x NC_000002.12 - 34252371 Oct 12, 2022 (156)
112 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 34477438 Oct 11, 2018 (152)
113 Genetic variation in the Estonian population NC_000002.11 - 34477438 Oct 11, 2018 (152)
114 The Danish reference pan genome NC_000002.11 - 34477438 Apr 25, 2020 (154)
115 gnomAD - Genomes NC_000002.12 - 34252371 Apr 26, 2021 (155)
116 Genome of the Netherlands Release 5 NC_000002.11 - 34477438 Apr 25, 2020 (154)
117 HGDP-CEPH-db Supplement 1 NC_000002.10 - 34330942 Apr 25, 2020 (154)
118 HapMap NC_000002.12 - 34252371 Apr 25, 2020 (154)
119 KOREAN population from KRGDB NC_000002.11 - 34477438 Apr 25, 2020 (154)
120 Korean Genome Project NC_000002.12 - 34252371 Apr 25, 2020 (154)
121 Northern Sweden NC_000002.11 - 34477438 Jul 13, 2019 (153)
122 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 34477438 Apr 26, 2021 (155)
123 CNV burdens in cranial meningiomas NC_000002.11 - 34477438 Apr 26, 2021 (155)
124 Qatari NC_000002.11 - 34477438 Apr 25, 2020 (154)
125 SGDP_PRJ NC_000002.11 - 34477438 Apr 25, 2020 (154)
126 Siberian NC_000002.11 - 34477438 Apr 25, 2020 (154)
127 8.3KJPN NC_000002.11 - 34477438 Apr 26, 2021 (155)
128 14KJPN NC_000002.12 - 34252371 Oct 12, 2022 (156)
129 TopMed NC_000002.12 - 34252371 Apr 26, 2021 (155)
130 UK 10K study - Twins NC_000002.11 - 34477438 Oct 11, 2018 (152)
131 A Vietnamese Genetic Variation Database NC_000002.11 - 34477438 Jul 13, 2019 (153)
132 ALFA NC_000002.12 - 34252371 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)
rs61688695 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78546078, ss3639130752, ss3639576864 NC_000002.9:34389088:G:A NC_000002.12:34252370:G:A (self)
290373, ss91113592, ss109392785, ss117650885, ss164140378, ss166400870, ss200254948, ss205672034, ss210859426, ss253022067, ss276412431, ss284321337, ss292541480, ss484069190, ss825393235, ss1586076772, ss1712444268, ss3643222824, ss3847612481 NC_000002.10:34330941:G:A NC_000002.12:34252370:G:A (self)
7529181, 4181923, 2953144, 4988512, 1837182, 4552368, 1587570, 109983, 29536, 1943909, 3965477, 1041868, 8619353, 4181923, 909059, ss219162427, ss231106817, ss238675025, ss480563416, ss484346648, ss536529445, ss555464860, ss649048341, ss780619260, ss782619570, ss832768761, ss836112824, ss976669198, ss1068992887, ss1296603964, ss1428530104, ss1578813440, ss1603179602, ss1646173635, ss1796529580, ss1919901979, ss1968733769, ss2020480672, ss2148525514, ss2624753723, ss2633594588, ss2703086554, ss2771683002, ss2989256350, ss3344155556, ss3628031093, ss3631562764, ss3636445422, ss3638252045, ss3642086530, ss3657214896, ss3728302705, ss3756567939, ss3783825164, ss3789418921, ss3794291703, ss3826906923, ss3836861565, ss3851948497, ss3897374974, ss3984480210, ss3984884056, ss4016988611, ss5150650046, ss5314723418, ss5327926112, ss5628435719, ss5819889176, ss5954644209 NC_000002.11:34477437:G:A NC_000002.12:34252370:G:A (self)
9971855, 53461436, 1768137, 3834348, 12906586, 303972930, 10706133698, ss2228960488, ss3024006699, ss3647001966, ss3703590759, ss3800946074, ss3842276367, ss3947456347, ss4500150051, ss5247518489, ss5447771754, ss5522445920, ss5679069482, ss5802071257, ss5852460158, ss5929729067 NC_000002.12:34252370:G:A NC_000002.12:34252370:G:A (self)
ss23082554 NT_022184.13:13293370:G:A NC_000002.12:34252370:G:A (self)
ss66769379, ss67078801, ss67410545, ss70423961, ss70605071, ss71151458, ss75785745, ss85320696, ss97026381, ss106080618, ss121646858, ss138418480, ss153370973, ss156889932, ss159256520, ss160336237, ss170375201, ss172414699 NT_022184.15:13299324:G:A NC_000002.12:34252370:G:A (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 rs13407683

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