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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs9786184

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:3019783 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.47797 (17206/35998, ALFA)
A=0.1770 (283/1599, 1000G_30x)
A=0.0014 (2/1398, KOREAN) (+ 7 more)
A=0.1744 (215/1233, 1000G)
A=0.000 (0/328, SGDP_PRJ)
A=0.00 (0/53, Qatari)
A=0.00 (0/48, Vietnamese)
A=0.43 (18/42, Ancient Sardinia)
A=0.00 (0/30, Siberian)
A=0.20 (4/20, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC00278 : Intron Variant
Publications
2 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 35998 A=0.52203 C=0.47797
European Sub 33834 A=0.54173 C=0.45827
African Sub 528 A=0.199 C=0.801
African Others Sub 24 A=0.00 C=1.00
African American Sub 504 A=0.208 C=0.792
Asian Sub 560 A=0.005 C=0.995
East Asian Sub 486 A=0.006 C=0.994
Other Asian Sub 74 A=0.00 C=1.00
Latin American 1 Sub 124 A=0.226 C=0.774
Latin American 2 Sub 148 A=0.480 C=0.520
South Asian Sub 114 A=0.053 C=0.947
Other Sub 690 A=0.362 C=0.638


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
Allele Frequency Aggregator Total Global 35998 A=0.52203 C=0.47797
Allele Frequency Aggregator European Sub 33834 A=0.54173 C=0.45827
Allele Frequency Aggregator Other Sub 690 A=0.362 C=0.638
Allele Frequency Aggregator Asian Sub 560 A=0.005 C=0.995
Allele Frequency Aggregator African Sub 528 A=0.199 C=0.801
Allele Frequency Aggregator Latin American 2 Sub 148 A=0.480 C=0.520
Allele Frequency Aggregator Latin American 1 Sub 124 A=0.226 C=0.774
Allele Frequency Aggregator South Asian Sub 114 A=0.053 C=0.947
1000Genomes_30x Global Study-wide 1599 A=0.1770 C=0.8230
1000Genomes_30x African Sub 458 A=0.033 C=0.967
1000Genomes_30x South Asian Sub 319 A=0.003 C=0.997
1000Genomes_30x Europe Sub 305 A=0.564 C=0.436
1000Genomes_30x East Asian Sub 292 A=0.003 C=0.997
1000Genomes_30x American Sub 225 A=0.418 C=0.582
KOREAN population from KRGDB KOREAN Study-wide 1398 A=0.0014 C=0.9986, G=0.0000
1000Genomes Global Study-wide 1233 A=0.1744 C=0.8256
1000Genomes African Sub 319 A=0.038 C=0.962
1000Genomes South Asian Sub 260 A=0.004 C=0.996
1000Genomes East Asian Sub 244 A=0.004 C=0.996
1000Genomes Europe Sub 240 A=0.533 C=0.467
1000Genomes American Sub 170 A=0.429 C=0.571
SGDP_PRJ Global Study-wide 328 A=0.000 C=1.000
Qatari Global Study-wide 53 A=0.00 C=1.00
A Vietnamese Genetic Variation Database Global Study-wide 48 A=0.00 C=1.00
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 42 A=0.43 C=0.57
Siberian Global Study-wide 30 A=0.00 C=1.00
The Danish reference pan genome Danish Study-wide 20 A=0.20 C=0.80
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 Y NC_000024.10:g.3019783A>C
GRCh38.p14 chr Y NC_000024.10:g.3019783A>G
GRCh37.p13 chr Y NC_000024.9:g.2887824A>C
GRCh37.p13 chr Y NC_000024.9:g.2887824A>G
Gene: LINC00278, long intergenic non-protein coding RNA 278 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC00278 transcript NR_046502.1: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 A= C G
GRCh38.p14 chr Y NC_000024.10:g.3019783= NC_000024.10:g.3019783A>C NC_000024.10:g.3019783A>G
GRCh37.p13 chr Y NC_000024.9:g.2887824= NC_000024.9:g.2887824A>C NC_000024.9:g.2887824A>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#.

55 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13606479 Dec 05, 2003 (119)
2 BGI ss105777452 Feb 05, 2009 (130)
3 ILLUMINA-UK ss115580870 Feb 05, 2009 (130)
4 GMI ss157810014 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss162979330 Jul 04, 2010 (132)
6 BUSHMAN ss204405234 Jul 04, 2010 (132)
7 BCM-HGSC-SUB ss208949040 Jul 04, 2010 (132)
8 GMI ss283910371 May 04, 2012 (137)
9 ILLUMINA ss537626609 Jul 19, 2016 (147)
10 TISHKOFF ss567111071 Apr 25, 2013 (138)
11 SSMP ss663091617 Apr 25, 2013 (138)
12 ILLUMINA ss778717363 Aug 21, 2014 (142)
13 ILLUMINA ss834176695 Aug 21, 2014 (142)
14 CDBUSTAMANTE ss947849441 Aug 21, 2014 (142)
15 DDI ss1432149057 Apr 01, 2015 (144)
16 1000GENOMES ss1556728518 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1583553677 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1939857773 Feb 12, 2016 (147)
19 ILLUMINA ss1945966922 Feb 12, 2016 (147)
20 ILLUMINA ss1958165951 Feb 12, 2016 (147)
21 ILLUMINA ss1958165952 Feb 12, 2016 (147)
22 USC_VALOUEV ss2159309107 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2321362529 Dec 20, 2016 (150)
24 SYSTEMSBIOZJU ss2629802241 Nov 08, 2017 (151)
25 ILLUMINA ss2634992486 Nov 08, 2017 (151)
26 GRF ss2710421420 Nov 08, 2017 (151)
27 SWEGEN ss3020838676 Nov 08, 2017 (151)
28 ILLUMINA ss3023048974 Nov 08, 2017 (151)
29 ILLUMINA ss3023048975 Nov 08, 2017 (151)
30 ILLUMINA ss3626004544 Oct 12, 2018 (152)
31 ILLUMINA ss3630503339 Oct 12, 2018 (152)
32 ILLUMINA ss3632875924 Oct 12, 2018 (152)
33 ILLUMINA ss3641265455 Oct 12, 2018 (152)
34 ILLUMINA ss3641563514 Oct 12, 2018 (152)
35 ILLUMINA ss3645020537 Oct 12, 2018 (152)
36 ILLUMINA ss3653607370 Oct 12, 2018 (152)
37 ILLUMINA ss3653607371 Oct 12, 2018 (152)
38 ILLUMINA ss3726711692 Jul 14, 2019 (153)
39 ILLUMINA ss3744335372 Jul 14, 2019 (153)
40 PACBIO ss3788973789 Jul 14, 2019 (153)
41 PACBIO ss3793842898 Jul 14, 2019 (153)
42 PACBIO ss3798727865 Jul 14, 2019 (153)
43 KHV_HUMAN_GENOMES ss3823530899 Jul 14, 2019 (153)
44 EVA ss3836370357 Apr 27, 2020 (154)
45 SGDP_PRJ ss3892554024 Apr 27, 2020 (154)
46 KRGDB ss3943290904 Apr 27, 2020 (154)
47 EVA ss3984770970 Apr 27, 2021 (155)
48 EVA ss3985975616 Apr 27, 2021 (155)
49 ESTONIANBIOCENTRE ss5237677972 Oct 13, 2022 (156)
50 EVA ss5316103432 Oct 13, 2022 (156)
51 1000G_HIGH_COVERAGE ss5623743779 Oct 13, 2022 (156)
52 SANFORD_IMAGENETICS ss5666110411 Oct 13, 2022 (156)
53 YY_MCH ss5819461300 Oct 13, 2022 (156)
54 EVA ss5857244282 Oct 13, 2022 (156)
55 EVA ss5979924893 Oct 13, 2022 (156)
56 1000Genomes NC_000024.9 - 2887824 Oct 12, 2018 (152)
57 1000Genomes_30x NC_000024.10 - 3019783 Oct 13, 2022 (156)
58 The Danish reference pan genome NC_000024.9 - 2887824 Apr 27, 2020 (154)
59 KOREAN population from KRGDB NC_000024.9 - 2887824 Apr 27, 2020 (154)
60 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 2887824 Apr 27, 2021 (155)
61 Qatari NC_000024.9 - 2887824 Apr 27, 2020 (154)
62 SGDP_PRJ NC_000024.9 - 2887824 Apr 27, 2020 (154)
63 Siberian NC_000024.9 - 2887824 Apr 27, 2020 (154)
64 A Vietnamese Genetic Variation Database NC_000024.9 - 2887824 Jul 14, 2019 (153)
65 ALFA NC_000024.10 - 3019783 Apr 27, 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
ss162979330, ss204405234, ss208949040, ss283910371 NC_000024.8:2947823:A:C NC_000024.10:3019782:A:C (self)
84681506, 9718614, 50468298, 1201543, 21899695, 44571004, 11825461, 10242387, ss537626609, ss567111071, ss663091617, ss778717363, ss834176695, ss947849441, ss1432149057, ss1556728518, ss1583553677, ss1939857773, ss1945966922, ss1958165951, ss1958165952, ss2159309107, ss2629802241, ss2634992486, ss2710421420, ss3020838676, ss3023048974, ss3023048975, ss3626004544, ss3630503339, ss3632875924, ss3641265455, ss3641563514, ss3645020537, ss3653607370, ss3653607371, ss3744335372, ss3788973789, ss3793842898, ss3798727865, ss3836370357, ss3892554024, ss3943290904, ss3984770970, ss3985975616, ss5237677972, ss5316103432, ss5666110411, ss5979924893 NC_000024.9:2887823:A:C NC_000024.10:3019782:A:C (self)
111269714, 12361961587, ss2321362529, ss3726711692, ss3823530899, ss5623743779, ss5819461300, ss5857244282 NC_000024.10:3019782:A:C NC_000024.10:3019782:A:C (self)
ss13606479, ss105777452, ss115580870, ss157810014 NT_011896.9:238303:A:C NC_000024.10:3019782:A:C (self)
50468298, ss3943290904 NC_000024.9:2887823:A:G NC_000024.10:3019782: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.

2 citations for rs9786184
PMID Title Author Year Journal
22271044 Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry. Wang Z et al. 2012 Human genetics
35176104 Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel. Rauf S et al. 2022 PloS one
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