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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.

rs3766186

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1227055 (GRCh38.p13) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.116363 (30800/264690, TOPMED)
A=0.115118 (16135/140160, GnomAD)
A=0.09901 (7101/71722, ALFA) (+ 17 more)
A=0.15712 (2633/16758, 8.3KJPN)
A=0.1258 (630/5008, 1000G)
A=0.1098 (492/4480, Estonian)
A=0.0955 (368/3854, ALSPAC)
A=0.1025 (380/3708, TWINSUK)
A=0.1940 (568/2928, KOREAN)
A=0.1110 (231/2082, HGDP_Stanford)
A=0.1069 (202/1890, HapMap)
A=0.1885 (345/1830, Korea1K)
A=0.113 (68/600, NorthernSweden)
A=0.074 (16/216, Qatari)
A=0.107 (23/214, Vietnamese)
C=0.458 (65/142, SGDP_PRJ)
A=0.10 (4/40, GENOME_DK)
A=0.00 (0/28, Ancient Sardinia)
C=0.50 (10/20, Siberian)
A=0.50 (10/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SDF4 : Intron Variant
Publications
1 citation
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.1227055C>A
GRCh37.p13 chr 1 NC_000001.10:g.1162435C>A
SDF4 RefSeqGene NG_030007.1:g.10013G>T
Gene: SDF4, stromal cell derived factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SDF4 transcript variant 2 NM_016176.6:c.305+1413G>T N/A Intron Variant
SDF4 transcript variant 1 NM_016547.3:c.305+1413G>T N/A Intron Variant
SDF4 transcript variant X2 XM_011541556.1:c.326+1413…

XM_011541556.1:c.326+1413G>T

N/A Intron Variant
SDF4 transcript variant X1 XM_024447473.1:c.326+1413…

XM_024447473.1:c.326+1413G>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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 71722 C=0.90099 A=0.09901
European Sub 59376 C=0.90553 A=0.09447
African Sub 4502 C=0.8239 A=0.1761
African Others Sub 170 C=0.753 A=0.247
African American Sub 4332 C=0.8266 A=0.1734
Asian Sub 186 C=0.849 A=0.151
East Asian Sub 146 C=0.829 A=0.171
Other Asian Sub 40 C=0.93 A=0.07
Latin American 1 Sub 244 C=0.922 A=0.078
Latin American 2 Sub 1224 C=0.9453 A=0.0547
South Asian Sub 4956 C=0.9080 A=0.0920
Other Sub 1234 C=0.8955 A=0.1045


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=0.883637 A=0.116363
gnomAD - Genomes Global Study-wide 140160 C=0.884882 A=0.115118
gnomAD - Genomes European Sub 75906 C=0.90616 A=0.09384
gnomAD - Genomes African Sub 41988 C=0.83183 A=0.16817
gnomAD - Genomes American Sub 13662 C=0.93325 A=0.06675
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9239 A=0.0761
gnomAD - Genomes East Asian Sub 3130 C=0.8236 A=0.1764
gnomAD - Genomes Other Sub 2150 C=0.8912 A=0.1088
8.3KJPN JAPANESE Study-wide 16758 C=0.84288 A=0.15712
1000Genomes Global Study-wide 5008 C=0.8742 A=0.1258
1000Genomes African Sub 1322 C=0.8366 A=0.1634
1000Genomes East Asian Sub 1008 C=0.8403 A=0.1597
1000Genomes Europe Sub 1006 C=0.9125 A=0.0875
1000Genomes South Asian Sub 978 C=0.895 A=0.105
1000Genomes American Sub 694 C=0.911 A=0.089
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8902 A=0.1098
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9045 A=0.0955
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8975 A=0.1025
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.8060 A=0.1940
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 C=0.8890 A=0.1110
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.815 A=0.185
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 412 C=0.930 A=0.070
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.906 A=0.094
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.916 A=0.084
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.777 A=0.223
HGDP-CEPH-db Supplement 1 America Sub 216 C=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.99 A=0.01
HapMap Global Study-wide 1890 C=0.8931 A=0.1069
HapMap American Sub 768 C=0.895 A=0.105
HapMap African Sub 692 C=0.895 A=0.105
HapMap Asian Sub 254 C=0.862 A=0.138
HapMap Europe Sub 176 C=0.926 A=0.074
Korean Genome Project KOREAN Study-wide 1830 C=0.8115 A=0.1885
Northern Sweden ACPOP Study-wide 600 C=0.887 A=0.113
Qatari Global Study-wide 216 C=0.926 A=0.074
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.893 A=0.107
SGDP_PRJ Global Study-wide 142 C=0.458 A=0.542
The Danish reference pan genome Danish Study-wide 40 C=0.90 A=0.10
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 28 C=1.00 A=0.00
Siberian Global Study-wide 20 C=0.50 A=0.50
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= A
GRCh38.p13 chr 1 NC_000001.11:g.1227055= NC_000001.11:g.1227055C>A
GRCh37.p13 chr 1 NC_000001.10:g.1162435= NC_000001.10:g.1162435C>A
SDF4 RefSeqGene NG_030007.1:g.10013= NG_030007.1:g.10013G>T
SDF4 transcript variant 2 NM_016176.3:c.326+1413= NM_016176.3:c.326+1413G>T
SDF4 transcript variant 2 NM_016176.6:c.305+1413= NM_016176.6:c.305+1413G>T
SDF4 transcript variant 1 NM_016547.2:c.326+1413= NM_016547.2:c.326+1413G>T
SDF4 transcript variant 1 NM_016547.3:c.305+1413= NM_016547.3:c.305+1413G>T
SDF4 transcript variant X1 XM_005244756.1:c.326+1413= XM_005244756.1:c.326+1413G>T
SDF4 transcript variant X2 XM_011541556.1:c.326+1413= XM_011541556.1:c.326+1413G>T
SDF4 transcript variant X1 XM_024447473.1:c.326+1413= XM_024447473.1:c.326+1413G>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#.

68 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4952228 Aug 28, 2002 (107)
2 ILLUMINA ss66779003 Dec 02, 2006 (127)
3 ILLUMINA ss67300974 Dec 02, 2006 (127)
4 ILLUMINA ss67705742 Dec 02, 2006 (127)
5 PERLEGEN ss68756328 May 18, 2007 (127)
6 ILLUMINA ss70779609 May 25, 2008 (130)
7 ILLUMINA ss71355916 May 18, 2007 (127)
8 ILLUMINA ss75788035 Dec 06, 2007 (129)
9 ILLUMINA ss79165834 Dec 15, 2007 (130)
10 KRIBB_YJKIM ss84175354 Dec 15, 2007 (130)
11 ILLUMINA ss122214653 Dec 01, 2009 (131)
12 ILLUMINA ss154266930 Dec 01, 2009 (131)
13 ILLUMINA ss159443736 Dec 01, 2009 (131)
14 ILLUMINA ss171640430 Jul 04, 2010 (132)
15 ILLUMINA ss173630697 Jul 04, 2010 (132)
16 BUSHMAN ss197890398 Jul 04, 2010 (132)
17 1000GENOMES ss210449954 Jul 14, 2010 (132)
18 1000GENOMES ss218192526 Jul 14, 2010 (132)
19 1000GENOMES ss230396835 Jul 14, 2010 (132)
20 1000GENOMES ss238116327 Jul 15, 2010 (132)
21 ILLUMINA ss244296707 Jul 04, 2010 (132)
22 GMI ss283988149 Apr 25, 2013 (138)
23 ILLUMINA ss537191170 Sep 08, 2015 (146)
24 TISHKOFF ss553715053 Apr 25, 2013 (138)
25 SSMP ss647519277 Apr 25, 2013 (138)
26 ILLUMINA ss825496352 Apr 01, 2015 (144)
27 ILLUMINA ss832955304 Aug 21, 2014 (142)
28 ILLUMINA ss833546133 Aug 21, 2014 (142)
29 EVA-GONL ss974773150 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067614323 Aug 21, 2014 (142)
31 1000GENOMES ss1289354920 Aug 21, 2014 (142)
32 EVA_GENOME_DK ss1573852458 Apr 01, 2015 (144)
33 EVA_DECODE ss1584133086 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1599384713 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1642378746 Apr 01, 2015 (144)
36 EVA_SVP ss1712305595 Apr 01, 2015 (144)
37 WEILL_CORNELL_DGM ss1917965320 Feb 12, 2016 (147)
38 JJLAB ss2019500483 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147487435 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2159395525 Dec 20, 2016 (150)
41 TOPMED ss2321534832 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624265888 Nov 08, 2017 (151)
43 ILLUMINA ss2634995319 Nov 08, 2017 (151)
44 GRF ss2697378214 Nov 08, 2017 (151)
45 GNOMAD ss2750684603 Nov 08, 2017 (151)
46 SWEGEN ss2986156303 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3023514576 Nov 08, 2017 (151)
48 TOPMED ss3066499412 Nov 08, 2017 (151)
49 CSHL ss3343274975 Nov 08, 2017 (151)
50 ILLUMINA ss3626007324 Oct 11, 2018 (152)
51 ILLUMINA ss3637732566 Oct 11, 2018 (152)
52 ILLUMINA ss3638887886 Oct 11, 2018 (152)
53 ILLUMINA ss3639440652 Oct 11, 2018 (152)
54 ILLUMINA ss3642746843 Oct 11, 2018 (152)
55 EGCUT_WGS ss3654267389 Jul 12, 2019 (153)
56 EVA_DECODE ss3686000288 Jul 12, 2019 (153)
57 ACPOP ss3726719756 Jul 12, 2019 (153)
58 EVA ss3745725684 Jul 12, 2019 (153)
59 KHV_HUMAN_GENOMES ss3798748376 Jul 12, 2019 (153)
60 EVA ss3825983186 Apr 25, 2020 (154)
61 HGDP ss3847322137 Apr 25, 2020 (154)
62 SGDP_PRJ ss3848007049 Apr 25, 2020 (154)
63 KRGDB ss3892850158 Apr 25, 2020 (154)
64 KOGIC ss3943638843 Apr 25, 2020 (154)
65 EVA ss3984774123 Apr 25, 2021 (155)
66 EVA ss4016889170 Apr 25, 2021 (155)
67 TOPMED ss4436553945 Apr 25, 2021 (155)
68 TOMMO_GENOMICS ss5142072464 Apr 25, 2021 (155)
69 1000Genomes NC_000001.10 - 1162435 Oct 11, 2018 (152)
70 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1162435 Oct 11, 2018 (152)
71 Genetic variation in the Estonian population NC_000001.10 - 1162435 Oct 11, 2018 (152)
72 The Danish reference pan genome NC_000001.10 - 1162435 Apr 25, 2020 (154)
73 gnomAD - Genomes NC_000001.11 - 1227055 Apr 25, 2021 (155)
74 HGDP-CEPH-db Supplement 1 NC_000001.9 - 1152298 Apr 25, 2020 (154)
75 HapMap NC_000001.11 - 1227055 Apr 25, 2020 (154)
76 KOREAN population from KRGDB NC_000001.10 - 1162435 Apr 25, 2020 (154)
77 Korean Genome Project NC_000001.11 - 1227055 Apr 25, 2020 (154)
78 Northern Sweden NC_000001.10 - 1162435 Jul 12, 2019 (153)
79 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 1162435 Apr 25, 2021 (155)
80 Qatari NC_000001.10 - 1162435 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 1162435 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 1162435 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 1162435 Apr 25, 2021 (155)
84 TopMed NC_000001.11 - 1227055 Apr 25, 2021 (155)
85 UK 10K study - Twins NC_000001.10 - 1162435 Oct 11, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000001.10 - 1162435 Jul 12, 2019 (153)
87 ALFA NC_000001.11 - 1227055 Apr 25, 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)
rs59853527 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638887886, ss3639440652 NC_000001.8:1202357:C:A NC_000001.11:1227054:C:A (self)
29, ss197890398, ss210449954, ss283988149, ss825496352, ss1584133086, ss1712305595, ss2634995319, ss3642746843, ss3847322137 NC_000001.9:1152297:C:A NC_000001.11:1227054:C:A (self)
20163, 7221, 5637, 1359692, 27552, 4621, 50, 7250, 24029, 3789, 41771, 7221, 1591, ss218192526, ss230396835, ss238116327, ss537191170, ss553715053, ss647519277, ss832955304, ss833546133, ss974773150, ss1067614323, ss1289354920, ss1573852458, ss1599384713, ss1642378746, ss1917965320, ss2019500483, ss2147487435, ss2321534832, ss2624265888, ss2697378214, ss2750684603, ss2986156303, ss3343274975, ss3626007324, ss3637732566, ss3654267389, ss3726719756, ss3745725684, ss3825983186, ss3848007049, ss3892850158, ss3984774123, ss4016889170, ss5142072464 NC_000001.10:1162434:C:A NC_000001.11:1227054:C:A (self)
171092, 309, 16844, 93077, 160280, 15078936280, ss2159395525, ss3023514576, ss3066499412, ss3686000288, ss3798748376, ss3943638843, ss4436553945 NC_000001.11:1227054:C:A NC_000001.11:1227054:C:A (self)
ss4952228, ss66779003, ss67300974, ss67705742, ss68756328, ss70779609, ss71355916, ss75788035, ss79165834, ss84175354, ss122214653, ss154266930, ss159443736, ss171640430, ss173630697, ss244296707 NT_004350.19:641066:C:A NC_000001.11:1227054:C:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs3766186
PMID Title Author Year Journal
20964851 CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies. Lawrence R et al. 2010 BMC bioinformatics
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.post596+ae089ad