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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.

rs11516185

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:908025 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.369459 (97792/264690, TOPMED)
G=0.374313 (52454/140134, GnomAD)
G=0.36208 (28190/77856, PAGE_STUDY) (+ 16 more)
G=0.38208 (8943/23406, ALFA)
G=0.39433 (6609/16760, 8.3KJPN)
G=0.3754 (1880/5008, 1000G)
G=0.4301 (1927/4480, Estonian)
G=0.3848 (1483/3854, ALSPAC)
G=0.3743 (1388/3708, TWINSUK)
G=0.4751 (1392/2930, KOREAN)
G=0.4934 (904/1832, Korea1K)
G=0.380 (379/998, GoNL)
G=0.388 (233/600, NorthernSweden)
A=0.340 (125/368, SGDP_PRJ)
G=0.250 (54/216, Qatari)
G=0.410 (87/212, Vietnamese)
A=0.50 (20/40, GENOME_DK)
G=0.50 (20/40, GENOME_DK)
A=0.37 (11/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC284600 : Intron Variant
Publications
0 citations
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.908025A>G
GRCh37.p13 chr 1 NC_000001.10:g.843405A>G
Gene: LOC284600, uncharacterized LOC284600 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC284600 transcript XR_002958526.1: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

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 23406 A=0.61792 G=0.38208
European Sub 18766 A=0.61121 G=0.38879
African Sub 2946 A=0.6568 G=0.3432
African Others Sub 114 A=0.667 G=0.333
African American Sub 2832 A=0.6564 G=0.3436
Asian Sub 112 A=0.518 G=0.482
East Asian Sub 86 A=0.53 G=0.47
Other Asian Sub 26 A=0.46 G=0.54
Latin American 1 Sub 146 A=0.692 G=0.308
Latin American 2 Sub 610 A=0.630 G=0.370
South Asian Sub 98 A=0.63 G=0.37
Other Sub 728 A=0.622 G=0.378


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 A=0.630541 G=0.369459
gnomAD - Genomes Global Study-wide 140134 A=0.625687 G=0.374313
gnomAD - Genomes European Sub 75884 A=0.61308 G=0.38692
gnomAD - Genomes African Sub 41998 A=0.65603 G=0.34397
gnomAD - Genomes American Sub 13656 A=0.60054 G=0.39946
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.7214 G=0.2786
gnomAD - Genomes East Asian Sub 3124 A=0.5323 G=0.4677
gnomAD - Genomes Other Sub 2148 A=0.6252 G=0.3748
The PAGE Study Global Study-wide 77856 A=0.63792 G=0.36208
The PAGE Study AfricanAmerican Sub 32358 A=0.66073 G=0.33927
The PAGE Study Mexican Sub 10764 A=0.62783 G=0.37217
The PAGE Study PuertoRican Sub 7904 A=0.6383 G=0.3617
The PAGE Study Asian Sub 7818 A=0.5945 G=0.4055
The PAGE Study NativeHawaiian Sub 4454 A=0.6194 G=0.3806
The PAGE Study Cuban Sub 4212 A=0.6064 G=0.3936
The PAGE Study Dominican Sub 3818 A=0.6461 G=0.3539
The PAGE Study CentralAmerican Sub 2448 A=0.6176 G=0.3824
The PAGE Study SouthAmerican Sub 1974 A=0.6363 G=0.3637
The PAGE Study NativeAmerican Sub 1260 A=0.6262 G=0.3738
The PAGE Study SouthAsian Sub 846 A=0.589 G=0.411
8.3KJPN JAPANESE Study-wide 16760 A=0.60567 G=0.39433
1000Genomes Global Study-wide 5008 A=0.6246 G=0.3754
1000Genomes African Sub 1322 A=0.6483 G=0.3517
1000Genomes East Asian Sub 1008 A=0.5794 G=0.4206
1000Genomes Europe Sub 1006 A=0.6243 G=0.3757
1000Genomes South Asian Sub 978 A=0.646 G=0.354
1000Genomes American Sub 694 A=0.615 G=0.385
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5699 G=0.4301
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6152 G=0.3848
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6257 G=0.3743
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5249 G=0.4751
Korean Genome Project KOREAN Study-wide 1832 A=0.5066 G=0.4934
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.620 G=0.380
Northern Sweden ACPOP Study-wide 600 A=0.612 G=0.388
SGDP_PRJ Global Study-wide 368 A=0.340 G=0.660
Qatari Global Study-wide 216 A=0.750 G=0.250
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.590 G=0.410
The Danish reference pan genome Danish Study-wide 40 A=0.50 G=0.50
Siberian Global Study-wide 30 A=0.37 G=0.63
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.908025= NC_000001.11:g.908025A>G
GRCh37.p13 chr 1 NC_000001.10:g.843405= NC_000001.10:g.843405A>G
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#.

64 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15865755 Feb 28, 2004 (120)
2 BCMHGSC_JDW ss87156563 Mar 23, 2008 (129)
3 BGI ss102713446 Dec 01, 2009 (131)
4 1000GENOMES ss107938320 Jan 22, 2009 (130)
5 ILLUMINA-UK ss118438719 Feb 14, 2009 (130)
6 ENSEMBL ss137753421 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss163703132 Jul 04, 2010 (132)
8 BUSHMAN ss197886092 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss205213601 Jul 04, 2010 (132)
10 1000GENOMES ss218190863 Jul 14, 2010 (132)
11 1000GENOMES ss230395775 Jul 14, 2010 (132)
12 1000GENOMES ss238115343 Jul 15, 2010 (132)
13 GMI ss275681663 May 04, 2012 (137)
14 GMI ss283987750 Apr 25, 2013 (138)
15 PJP ss290493965 May 09, 2011 (134)
16 ILLUMINA ss479445972 May 04, 2012 (137)
17 ILLUMINA ss482416572 May 04, 2012 (137)
18 TISHKOFF ss553710868 Apr 25, 2013 (138)
19 SSMP ss647516905 Apr 25, 2013 (138)
20 ILLUMINA ss780983360 Sep 08, 2015 (146)
21 EVA-GONL ss974769950 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1067612591 Aug 21, 2014 (142)
23 1000GENOMES ss1289341565 Aug 21, 2014 (142)
24 DDI ss1425685150 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1573851335 Apr 01, 2015 (144)
26 EVA_DECODE ss1584129865 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1599378957 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1642372990 Apr 01, 2015 (144)
29 HAMMER_LAB ss1793709630 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1917961330 Feb 12, 2016 (147)
31 ILLUMINA ss1958230122 Feb 12, 2016 (147)
32 GENOMED ss1966667453 Jul 19, 2016 (147)
33 JJLAB ss2019498666 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147485217 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2159368921 Dec 20, 2016 (150)
36 TOPMED ss2321507608 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2624264907 Nov 08, 2017 (151)
38 ILLUMINA ss2632465510 Nov 08, 2017 (151)
39 GRF ss2697376165 Nov 08, 2017 (151)
40 GNOMAD ss2750646677 Nov 08, 2017 (151)
41 SWEGEN ss2986150691 Nov 08, 2017 (151)
42 ILLUMINA ss3021043138 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023513798 Nov 08, 2017 (151)
44 TOPMED ss3066415288 Nov 08, 2017 (151)
45 CSHL ss3343273113 Nov 08, 2017 (151)
46 ILLUMINA ss3641566193 Oct 11, 2018 (152)
47 ILLUMINA ss3651365189 Oct 11, 2018 (152)
48 EGCUT_WGS ss3654261905 Jul 12, 2019 (153)
49 EVA_DECODE ss3685993150 Jul 12, 2019 (153)
50 ACPOP ss3726716814 Jul 12, 2019 (153)
51 EVA ss3745721581 Jul 12, 2019 (153)
52 PAGE_CC ss3770778546 Jul 12, 2019 (153)
53 PACBIO ss3783302483 Jul 12, 2019 (153)
54 PACBIO ss3788980143 Jul 12, 2019 (153)
55 PACBIO ss3793852703 Jul 12, 2019 (153)
56 KHV_HUMAN_GENOMES ss3798744312 Jul 12, 2019 (153)
57 EVA ss3825981648 Apr 25, 2020 (154)
58 EVA ss3836378535 Apr 25, 2020 (154)
59 EVA ss3841782551 Apr 25, 2020 (154)
60 SGDP_PRJ ss3847997492 Apr 25, 2020 (154)
61 KRGDB ss3892839487 Apr 25, 2020 (154)
62 KOGIC ss3943631051 Apr 25, 2020 (154)
63 TOPMED ss4436450356 Apr 25, 2021 (155)
64 TOMMO_GENOMICS ss5142055752 Apr 25, 2021 (155)
65 1000Genomes NC_000001.10 - 843405 Oct 11, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 843405 Oct 11, 2018 (152)
67 Genetic variation in the Estonian population NC_000001.10 - 843405 Oct 11, 2018 (152)
68 The Danish reference pan genome NC_000001.10 - 843405 Apr 25, 2020 (154)
69 gnomAD - Genomes NC_000001.11 - 908025 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 843405 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000001.10 - 843405 Apr 25, 2020 (154)
72 Korean Genome Project NC_000001.11 - 908025 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 843405 Jul 12, 2019 (153)
74 The PAGE Study NC_000001.11 - 908025 Jul 12, 2019 (153)
75 Qatari NC_000001.10 - 843405 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000001.10 - 843405 Apr 25, 2020 (154)
77 Siberian NC_000001.10 - 843405 Apr 25, 2020 (154)
78 8.3KJPN NC_000001.10 - 843405 Apr 25, 2021 (155)
79 TopMed NC_000001.11 - 908025 Apr 25, 2021 (155)
80 UK 10K study - Twins NC_000001.10 - 843405 Oct 11, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000001.10 - 843405 Jul 12, 2019 (153)
82 ALFA NC_000001.11 - 908025 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87156563, ss107938320, ss118438719, ss163703132, ss197886092, ss205213601, ss275681663, ss283987750, ss290493965, ss482416572, ss1584129865 NC_000001.9:833267:A:G NC_000001.11:908024:A:G (self)
6387, 997, 153, 1358569, 905, 16881, 1679, 3260, 14472, 1571, 25059, 997, 210, ss218190863, ss230395775, ss238115343, ss479445972, ss553710868, ss647516905, ss780983360, ss974769950, ss1067612591, ss1289341565, ss1425685150, ss1573851335, ss1599378957, ss1642372990, ss1793709630, ss1917961330, ss1958230122, ss1966667453, ss2019498666, ss2147485217, ss2321507608, ss2624264907, ss2632465510, ss2697376165, ss2750646677, ss2986150691, ss3021043138, ss3343273113, ss3641566193, ss3651365189, ss3654261905, ss3726716814, ss3745721581, ss3783302483, ss3788980143, ss3793852703, ss3825981648, ss3836378535, ss3847997492, ss3892839487, ss5142055752 NC_000001.10:843404:A:G NC_000001.11:908024:A:G (self)
80738, 9052, 15, 27593, 56691, 3282658671, ss2159368921, ss3023513798, ss3066415288, ss3685993150, ss3770778546, ss3798744312, ss3841782551, ss3943631051, ss4436450356 NC_000001.11:908024:A:G NC_000001.11:908024:A:G (self)
ss102713446, ss137753421 NT_004350.19:322036:A:G NC_000001.11:908024:A:G (self)
ss15865755 NT_079624.1:33645:A:G NC_000001.11:908024:A:G (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 rs11516185

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