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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.

rs3785874

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:47219747 (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
T=0.111515 (29517/264690, TOPMED)
T=0.099999 (14014/140142, GnomAD)
T=0.10136 (6669/65796, ALFA) (+ 20 more)
T=0.47296 (13365/28258, 14KJPN)
T=0.47082 (7891/16760, 8.3KJPN)
T=0.1955 (1252/6404, 1000G_30x)
T=0.2043 (1023/5008, 1000G)
T=0.0980 (439/4480, Estonian)
T=0.0968 (373/3854, ALSPAC)
T=0.0974 (361/3708, TWINSUK)
G=0.4717 (1382/2930, KOREAN)
T=0.1809 (377/2084, HGDP_Stanford)
T=0.1919 (363/1892, HapMap)
G=0.4700 (861/1832, Korea1K)
T=0.082 (82/998, GoNL)
T=0.163 (98/600, NorthernSweden)
T=0.006 (3/534, MGP)
T=0.079 (17/216, Qatari)
T=0.368 (78/212, Vietnamese)
G=0.418 (71/170, SGDP_PRJ)
T=0.03 (2/70, Ancient Sardinia)
T=0.17 (7/40, GENOME_DK)
G=0.46 (11/24, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MYL4 : 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 65796 G=0.89864 T=0.10136
European Sub 53532 G=0.90680 T=0.09320
African Sub 4500 G=0.9227 T=0.0773
African Others Sub 170 G=0.906 T=0.094
African American Sub 4330 G=0.9233 T=0.0767
Asian Sub 186 G=0.543 T=0.457
East Asian Sub 146 G=0.514 T=0.486
Other Asian Sub 40 G=0.65 T=0.35
Latin American 1 Sub 246 G=0.919 T=0.081
Latin American 2 Sub 1226 G=0.8809 T=0.1191
South Asian Sub 4948 G=0.8110 T=0.1890
Other Sub 1158 G=0.8739 T=0.1261


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=0.888485 T=0.111515
gnomAD - Genomes Global Study-wide 140142 G=0.900001 T=0.099999
gnomAD - Genomes European Sub 75902 G=0.90641 T=0.09359
gnomAD - Genomes African Sub 42006 G=0.92642 T=0.07358
gnomAD - Genomes American Sub 13644 G=0.86272 T=0.13728
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9133 T=0.0867
gnomAD - Genomes East Asian Sub 3118 G=0.5411 T=0.4589
gnomAD - Genomes Other Sub 2150 G=0.8944 T=0.1056
Allele Frequency Aggregator Total Global 65796 G=0.89864 T=0.10136
Allele Frequency Aggregator European Sub 53532 G=0.90680 T=0.09320
Allele Frequency Aggregator South Asian Sub 4948 G=0.8110 T=0.1890
Allele Frequency Aggregator African Sub 4500 G=0.9227 T=0.0773
Allele Frequency Aggregator Latin American 2 Sub 1226 G=0.8809 T=0.1191
Allele Frequency Aggregator Other Sub 1158 G=0.8739 T=0.1261
Allele Frequency Aggregator Latin American 1 Sub 246 G=0.919 T=0.081
Allele Frequency Aggregator Asian Sub 186 G=0.543 T=0.457
14KJPN JAPANESE Study-wide 28258 G=0.52704 T=0.47296
8.3KJPN JAPANESE Study-wide 16760 G=0.52918 T=0.47082
1000Genomes_30x Global Study-wide 6404 G=0.8045 T=0.1955
1000Genomes_30x African Sub 1786 G=0.9093 T=0.0907
1000Genomes_30x Europe Sub 1266 G=0.9013 T=0.0987
1000Genomes_30x South Asian Sub 1202 G=0.7654 T=0.2346
1000Genomes_30x East Asian Sub 1170 G=0.5496 T=0.4504
1000Genomes_30x American Sub 980 G=0.841 T=0.159
1000Genomes Global Study-wide 5008 G=0.7957 T=0.2043
1000Genomes African Sub 1322 G=0.9092 T=0.0908
1000Genomes East Asian Sub 1008 G=0.5476 T=0.4524
1000Genomes Europe Sub 1006 G=0.8946 T=0.1054
1000Genomes South Asian Sub 978 G=0.771 T=0.229
1000Genomes American Sub 694 G=0.831 T=0.169
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9020 T=0.0980
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9032 T=0.0968
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9026 T=0.0974
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4717 C=0.0000, T=0.5283
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8191 T=0.1809
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.585 T=0.415
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.809 T=0.191
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.951 T=0.049
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.912 T=0.087
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.930 T=0.070
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.856 T=0.144
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.86 T=0.14
HapMap Global Study-wide 1892 G=0.8081 T=0.1919
HapMap American Sub 770 G=0.766 T=0.234
HapMap African Sub 692 G=0.938 T=0.062
HapMap Asian Sub 254 G=0.504 T=0.496
HapMap Europe Sub 176 G=0.920 T=0.080
Korean Genome Project KOREAN Study-wide 1832 G=0.4700 T=0.5300
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.918 T=0.082
Northern Sweden ACPOP Study-wide 600 G=0.837 T=0.163
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.994 T=0.006
Qatari Global Study-wide 216 G=0.921 T=0.079
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.632 T=0.368
SGDP_PRJ Global Study-wide 170 G=0.418 T=0.582
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 70 G=0.97 T=0.03
The Danish reference pan genome Danish Study-wide 40 G=0.82 T=0.17
Siberian Global Study-wide 24 G=0.46 T=0.54
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 17 NC_000017.11:g.47219747G>C
GRCh38.p14 chr 17 NC_000017.11:g.47219747G>T
GRCh37.p13 chr 17 NC_000017.10:g.45297113G>C
GRCh37.p13 chr 17 NC_000017.10:g.45297113G>T
MYL4 RefSeqGene NG_052847.1:g.15731G>C
MYL4 RefSeqGene NG_052847.1:g.15731G>T
Gene: MYL4, myosin light chain 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MYL4 transcript variant 1 NM_001002841.2:c.164-157G…

NM_001002841.2:c.164-157G>C

N/A Intron Variant
MYL4 transcript variant 2 NM_002476.2:c.164-157G>C N/A Intron Variant
MYL4 transcript variant X4 XM_005257391.6:c.164-157G…

XM_005257391.6:c.164-157G>C

N/A Intron Variant
MYL4 transcript variant X1 XM_011524839.3:c.257-157G…

XM_011524839.3:c.257-157G>C

N/A Intron Variant
MYL4 transcript variant X2 XM_017024683.2:c.257-157G…

XM_017024683.2:c.257-157G>C

N/A Intron Variant
MYL4 transcript variant X3 XM_024450766.2:c.257-157G…

XM_024450766.2:c.257-157G>C

N/A Intron Variant
MYL4 transcript variant X5 XM_047436131.1:c.257-157G…

XM_047436131.1:c.257-157G>C

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.

Allele: T (allele ID: 1213425 )
ClinVar Accession Disease Names Clinical Significance
RCV001599016.3 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 G= C T
GRCh38.p14 chr 17 NC_000017.11:g.47219747= NC_000017.11:g.47219747G>C NC_000017.11:g.47219747G>T
GRCh37.p13 chr 17 NC_000017.10:g.45297113= NC_000017.10:g.45297113G>C NC_000017.10:g.45297113G>T
MYL4 RefSeqGene NG_052847.1:g.15731= NG_052847.1:g.15731G>C NG_052847.1:g.15731G>T
MYL4 transcript variant 1 NM_001002841.1:c.164-157= NM_001002841.1:c.164-157G>C NM_001002841.1:c.164-157G>T
MYL4 transcript variant 1 NM_001002841.2:c.164-157= NM_001002841.2:c.164-157G>C NM_001002841.2:c.164-157G>T
MYL4 transcript variant 2 NM_002476.2:c.164-157= NM_002476.2:c.164-157G>C NM_002476.2:c.164-157G>T
MYL4 transcript variant X1 XM_005257391.1:c.164-157= XM_005257391.1:c.164-157G>C XM_005257391.1:c.164-157G>T
MYL4 transcript variant X4 XM_005257391.6:c.164-157= XM_005257391.6:c.164-157G>C XM_005257391.6:c.164-157G>T
MYL4 transcript variant X2 XM_005257392.1:c.164-157= XM_005257392.1:c.164-157G>C XM_005257392.1:c.164-157G>T
MYL4 transcript variant X1 XM_011524839.3:c.257-157= XM_011524839.3:c.257-157G>C XM_011524839.3:c.257-157G>T
MYL4 transcript variant X2 XM_017024683.2:c.257-157= XM_017024683.2:c.257-157G>C XM_017024683.2:c.257-157G>T
MYL4 transcript variant X3 XM_024450766.2:c.257-157= XM_024450766.2:c.257-157G>C XM_024450766.2:c.257-157G>T
MYL4 transcript variant X5 XM_047436131.1:c.257-157= XM_047436131.1:c.257-157G>C XM_047436131.1:c.257-157G>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#.

73 SubSNP, 23 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4972233 Aug 28, 2002 (107)
2 ABI ss43971260 Mar 14, 2006 (126)
3 ILLUMINA ss70781652 May 24, 2008 (130)
4 ILLUMINA ss71358128 May 17, 2007 (127)
5 ILLUMINA ss75637771 Dec 06, 2007 (129)
6 BGI ss106508643 Feb 04, 2009 (130)
7 1000GENOMES ss109781246 Jan 24, 2009 (130)
8 ILLUMINA ss154269134 Dec 01, 2009 (131)
9 GMI ss158059373 Dec 01, 2009 (131)
10 ILLUMINA ss159445910 Dec 01, 2009 (131)
11 ILLUMINA ss173638746 Jul 04, 2010 (132)
12 BUSHMAN ss202555079 Jul 04, 2010 (132)
13 1000GENOMES ss211801542 Jul 14, 2010 (132)
14 1000GENOMES ss227559182 Jul 14, 2010 (132)
15 1000GENOMES ss237253918 Jul 15, 2010 (132)
16 1000GENOMES ss243547880 Jul 15, 2010 (132)
17 GMI ss282775472 May 04, 2012 (137)
18 GMI ss287184756 Apr 25, 2013 (138)
19 TISHKOFF ss565288868 Apr 25, 2013 (138)
20 SSMP ss661095054 Apr 25, 2013 (138)
21 ILLUMINA ss832957472 Jul 13, 2019 (153)
22 EVA-GONL ss993137597 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1081077631 Aug 21, 2014 (142)
24 1000GENOMES ss1358772340 Aug 21, 2014 (142)
25 DDI ss1428040202 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1578169128 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1635706988 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1678701021 Apr 01, 2015 (144)
29 EVA_DECODE ss1697180193 Apr 01, 2015 (144)
30 EVA_MGP ss1711463988 Apr 01, 2015 (144)
31 EVA_SVP ss1713584395 Apr 01, 2015 (144)
32 WEILL_CORNELL_DGM ss1936599880 Feb 12, 2016 (147)
33 GENOMED ss1968395372 Jul 19, 2016 (147)
34 JJLAB ss2029076307 Sep 14, 2016 (149)
35 USC_VALOUEV ss2157550111 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2217061918 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2629033232 Nov 08, 2017 (151)
38 GRF ss2702109850 Nov 08, 2017 (151)
39 GNOMAD ss2950235591 Nov 08, 2017 (151)
40 SWEGEN ss3015589246 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3028359643 Nov 08, 2017 (151)
42 CSHL ss3351756822 Nov 08, 2017 (151)
43 ILLUMINA ss3638163391 Oct 12, 2018 (152)
44 ILLUMINA ss3643141692 Oct 12, 2018 (152)
45 EGCUT_WGS ss3682465088 Jul 13, 2019 (153)
46 EVA_DECODE ss3700527723 Jul 13, 2019 (153)
47 ACPOP ss3742052221 Jul 13, 2019 (153)
48 EVA ss3754702500 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3819970283 Jul 13, 2019 (153)
50 EVA ss3834883385 Apr 27, 2020 (154)
51 EVA ss3841053161 Apr 27, 2020 (154)
52 EVA ss3846550096 Apr 27, 2020 (154)
53 HGDP ss3847564720 Apr 27, 2020 (154)
54 SGDP_PRJ ss3885816491 Apr 27, 2020 (154)
55 KRGDB ss3935519875 Apr 27, 2020 (154)
56 KOGIC ss3978895915 Apr 27, 2020 (154)
57 FSA-LAB ss3984117404 Apr 27, 2021 (155)
58 EVA ss3985792467 Apr 27, 2021 (155)
59 EVA ss4017768452 Apr 27, 2021 (155)
60 TOPMED ss5037014689 Apr 27, 2021 (155)
61 TOMMO_GENOMICS ss5222572481 Apr 27, 2021 (155)
62 1000G_HIGH_COVERAGE ss5303242954 Oct 16, 2022 (156)
63 EVA ss5427785231 Oct 16, 2022 (156)
64 HUGCELL_USP ss5496280368 Oct 16, 2022 (156)
65 EVA ss5511775530 Oct 16, 2022 (156)
66 1000G_HIGH_COVERAGE ss5607014952 Oct 16, 2022 (156)
67 SANFORD_IMAGENETICS ss5660164012 Oct 16, 2022 (156)
68 TOMMO_GENOMICS ss5778833295 Oct 16, 2022 (156)
69 YY_MCH ss5816566552 Oct 16, 2022 (156)
70 EVA ss5834026812 Oct 16, 2022 (156)
71 EVA ss5851817959 Oct 16, 2022 (156)
72 EVA ss5914051579 Oct 16, 2022 (156)
73 EVA ss5951552487 Oct 16, 2022 (156)
74 1000Genomes NC_000017.10 - 45297113 Oct 12, 2018 (152)
75 1000Genomes_30x NC_000017.11 - 47219747 Oct 16, 2022 (156)
76 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 45297113 Oct 12, 2018 (152)
77 Genetic variation in the Estonian population NC_000017.10 - 45297113 Oct 12, 2018 (152)
78 The Danish reference pan genome NC_000017.10 - 45297113 Apr 27, 2020 (154)
79 gnomAD - Genomes NC_000017.11 - 47219747 Apr 27, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000017.10 - 45297113 Apr 27, 2020 (154)
81 HGDP-CEPH-db Supplement 1 NC_000017.9 - 42652112 Apr 27, 2020 (154)
82 HapMap NC_000017.11 - 47219747 Apr 27, 2020 (154)
83 KOREAN population from KRGDB NC_000017.10 - 45297113 Apr 27, 2020 (154)
84 Korean Genome Project NC_000017.11 - 47219747 Apr 27, 2020 (154)
85 Medical Genome Project healthy controls from Spanish population NC_000017.10 - 45297113 Apr 27, 2020 (154)
86 Northern Sweden NC_000017.10 - 45297113 Jul 13, 2019 (153)
87 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000017.10 - 45297113 Apr 27, 2021 (155)
88 Qatari NC_000017.10 - 45297113 Apr 27, 2020 (154)
89 SGDP_PRJ NC_000017.10 - 45297113 Apr 27, 2020 (154)
90 Siberian NC_000017.10 - 45297113 Apr 27, 2020 (154)
91 8.3KJPN NC_000017.10 - 45297113 Apr 27, 2021 (155)
92 14KJPN NC_000017.11 - 47219747 Oct 16, 2022 (156)
93 TopMed NC_000017.11 - 47219747 Apr 27, 2021 (155)
94 UK 10K study - Twins NC_000017.10 - 45297113 Oct 12, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000017.10 - 45297113 Jul 13, 2019 (153)
96 ALFA NC_000017.11 - 47219747 Apr 27, 2021 (155)
97 ClinVar RCV001599016.3 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
42697269, ss3935519875 NC_000017.10:45297112:G:C NC_000017.11:47219746:G:C (self)
242612, ss109781246, ss202555079, ss211801542, ss282775472, ss287184756, ss1697180193, ss1713584395, ss3643141692, ss3847564720 NC_000017.9:42652111:G:T NC_000017.11:47219746:G:T (self)
72018686, 39909497, 28203336, 4370987, 17787831, 42697269, 579748, 15337086, 1018394, 18641802, 37833471, 10066465, 80541788, 39909497, 8828761, ss227559182, ss237253918, ss243547880, ss565288868, ss661095054, ss832957472, ss993137597, ss1081077631, ss1358772340, ss1428040202, ss1578169128, ss1635706988, ss1678701021, ss1711463988, ss1936599880, ss1968395372, ss2029076307, ss2157550111, ss2629033232, ss2702109850, ss2950235591, ss3015589246, ss3351756822, ss3638163391, ss3682465088, ss3742052221, ss3754702500, ss3834883385, ss3841053161, ss3885816491, ss3935519875, ss3984117404, ss3985792467, ss4017768452, ss5222572481, ss5427785231, ss5511775530, ss5660164012, ss5834026812, ss5951552487 NC_000017.10:45297112:G:T NC_000017.11:47219746:G:T (self)
RCV001599016.3, 94540887, 508159450, 1492825, 35273916, 112670399, 252560351, 15159506222, ss2217061918, ss3028359643, ss3700527723, ss3819970283, ss3846550096, ss3978895915, ss5037014689, ss5303242954, ss5496280368, ss5607014952, ss5778833295, ss5816566552, ss5851817959, ss5914051579 NC_000017.11:47219746:G:T NC_000017.11:47219746:G:T (self)
ss4972233, ss43971260, ss70781652, ss71358128, ss75637771, ss106508643, ss154269134, ss158059373, ss159445910, ss173638746 NT_010783.15:10571264:G:T NC_000017.11:47219746: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 rs3785874

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