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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.

rs12327656

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:27842481 (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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.229990 (60876/264690, TOPMED)
A=0.242407 (33950/140054, GnomAD)
A=0.07541 (2131/28258, 14KJPN) (+ 16 more)
A=0.23912 (4517/18890, ALFA)
A=0.07393 (1239/16760, 8.3KJPN)
A=0.2277 (1458/6404, 1000G_30x)
A=0.2288 (1146/5008, 1000G)
A=0.2433 (1090/4480, Estonian)
A=0.2449 (944/3854, ALSPAC)
A=0.2505 (929/3708, TWINSUK)
A=0.0464 (136/2930, KOREAN)
A=0.247 (247/998, GoNL)
A=0.288 (173/600, NorthernSweden)
A=0.195 (101/518, SGDP_PRJ)
A=0.085 (28/328, HapMap)
A=0.264 (57/216, Qatari)
A=0.071 (15/212, Vietnamese)
A=0.24 (13/54, Siberian)
A=0.20 (8/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC02987 : 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 18890 A=0.23912 G=0.76088
European Sub 14286 A=0.23856 G=0.76144
African Sub 2946 A=0.2495 G=0.7505
African Others Sub 114 A=0.263 G=0.737
African American Sub 2832 A=0.2489 G=0.7511
Asian Sub 112 A=0.045 G=0.955
East Asian Sub 86 A=0.05 G=0.95
Other Asian Sub 26 A=0.04 G=0.96
Latin American 1 Sub 146 A=0.253 G=0.747
Latin American 2 Sub 610 A=0.203 G=0.797
South Asian Sub 98 A=0.32 G=0.68
Other Sub 692 A=0.256 G=0.744


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=0.229990 G=0.770010
gnomAD - Genomes Global Study-wide 140054 A=0.242407 G=0.757593
gnomAD - Genomes European Sub 75876 A=0.25365 G=0.74635
gnomAD - Genomes African Sub 41944 A=0.25417 G=0.74583
gnomAD - Genomes American Sub 13632 A=0.19594 G=0.80406
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.2121 G=0.7879
gnomAD - Genomes East Asian Sub 3132 A=0.0540 G=0.9460
gnomAD - Genomes Other Sub 2146 A=0.2321 G=0.7679
14KJPN JAPANESE Study-wide 28258 A=0.07541 G=0.92459
Allele Frequency Aggregator Total Global 18890 A=0.23912 G=0.76088
Allele Frequency Aggregator European Sub 14286 A=0.23856 G=0.76144
Allele Frequency Aggregator African Sub 2946 A=0.2495 G=0.7505
Allele Frequency Aggregator Other Sub 692 A=0.256 G=0.744
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.203 G=0.797
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.253 G=0.747
Allele Frequency Aggregator Asian Sub 112 A=0.045 G=0.955
Allele Frequency Aggregator South Asian Sub 98 A=0.32 G=0.68
8.3KJPN JAPANESE Study-wide 16760 A=0.07393 G=0.92607
1000Genomes_30x Global Study-wide 6404 A=0.2277 G=0.7723
1000Genomes_30x African Sub 1786 A=0.2391 G=0.7609
1000Genomes_30x Europe Sub 1266 A=0.1959 G=0.8041
1000Genomes_30x South Asian Sub 1202 A=0.4093 G=0.5907
1000Genomes_30x East Asian Sub 1170 A=0.0624 G=0.9376
1000Genomes_30x American Sub 980 A=0.222 G=0.778
1000Genomes Global Study-wide 5008 A=0.2288 G=0.7712
1000Genomes African Sub 1322 A=0.2398 G=0.7602
1000Genomes East Asian Sub 1008 A=0.0645 G=0.9355
1000Genomes Europe Sub 1006 A=0.2127 G=0.7873
1000Genomes South Asian Sub 978 A=0.406 G=0.594
1000Genomes American Sub 694 A=0.220 G=0.780
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2433 G=0.7567
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2449 G=0.7551
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2505 G=0.7495
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0464 G=0.9536, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.247 G=0.753
Northern Sweden ACPOP Study-wide 600 A=0.288 G=0.712
SGDP_PRJ Global Study-wide 518 A=0.195 G=0.805
HapMap Global Study-wide 328 A=0.085 G=0.915
HapMap African Sub 120 A=0.167 G=0.833
HapMap American Sub 118 A=0.051 G=0.949
HapMap Asian Sub 90 A=0.02 G=0.98
Qatari Global Study-wide 216 A=0.264 G=0.736
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.071 G=0.929
Siberian Global Study-wide 54 A=0.24 G=0.76
The Danish reference pan genome Danish Study-wide 40 A=0.20 G=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 19 NC_000019.10:g.27842481A>G
GRCh38.p14 chr 19 NC_000019.10:g.27842481A>T
GRCh37.p13 chr 19 NC_000019.9:g.28333389A>G
GRCh37.p13 chr 19 NC_000019.9:g.28333389A>T
Gene: LINC02987, long intergenic non-protein coding RNA 2987 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02987 transcript variant 6 NR_146733.1:n. N/A Intron Variant
LINC02987 transcript variant 7 NR_146734.1:n. N/A Intron Variant
LINC02987 transcript variant 8 NR_146735.1:n. N/A Intron Variant
LINC02987 transcript variant 1 NR_110687.1:n. N/A Genic Downstream Transcript Variant
LINC02987 transcript variant 2 NR_110688.2:n. N/A Genic Downstream Transcript Variant
LINC02987 transcript variant 3 NR_110689.2:n. N/A Genic Downstream Transcript Variant
LINC02987 transcript variant 4 NR_110690.1:n. N/A Genic Downstream Transcript Variant
LINC02987 transcript variant 5 NR_110691.2:n. N/A Genic Downstream Transcript Variant
LINC02987 transcript variant 9 NR_146736.1:n. N/A Genic Downstream Transcript 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= G T
GRCh38.p14 chr 19 NC_000019.10:g.27842481= NC_000019.10:g.27842481A>G NC_000019.10:g.27842481A>T
GRCh37.p13 chr 19 NC_000019.9:g.28333389= NC_000019.9:g.28333389A>G NC_000019.9:g.28333389A>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#.

70 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18803405 Feb 28, 2004 (120)
2 SSAHASNP ss21514438 Apr 05, 2004 (121)
3 HGSV ss78292939 Dec 06, 2007 (129)
4 HGSV ss85356442 Dec 14, 2007 (130)
5 BCMHGSC_JDW ss90943816 Mar 24, 2008 (129)
6 BGI ss106050893 Feb 04, 2009 (130)
7 1000GENOMES ss111249098 Jan 25, 2009 (130)
8 ILLUMINA-UK ss117676125 Feb 14, 2009 (130)
9 ENSEMBL ss136288921 Dec 01, 2009 (131)
10 ENSEMBL ss137631446 Dec 01, 2009 (131)
11 GMI ss155784668 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss168035381 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss169464711 Jul 04, 2010 (132)
14 BUSHMAN ss203725687 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss208407764 Jul 04, 2010 (132)
16 1000GENOMES ss237645449 Jul 15, 2010 (132)
17 BL ss255610668 May 09, 2011 (134)
18 GMI ss283175734 May 04, 2012 (137)
19 GMI ss287369458 Apr 25, 2013 (138)
20 PJP ss292234222 May 09, 2011 (134)
21 TISHKOFF ss565926130 Apr 25, 2013 (138)
22 SSMP ss661787577 Apr 25, 2013 (138)
23 EVA-GONL ss994208309 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1081838280 Aug 21, 2014 (142)
25 1000GENOMES ss1362813906 Aug 21, 2014 (142)
26 DDI ss1428377346 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1578604604 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1637784571 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1680778604 Apr 01, 2015 (144)
30 EVA_DECODE ss1698259773 Apr 01, 2015 (144)
31 HAMMER_LAB ss1809266216 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1937699792 Feb 12, 2016 (147)
33 GENOMED ss1968626064 Jul 19, 2016 (147)
34 JJLAB ss2029624954 Sep 14, 2016 (149)
35 USC_VALOUEV ss2158163876 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2629310818 Nov 08, 2017 (151)
37 GRF ss2702770292 Nov 08, 2017 (151)
38 GNOMAD ss2961853151 Nov 08, 2017 (151)
39 SWEGEN ss3017322556 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3028646368 Nov 08, 2017 (151)
41 CSHL ss3352262008 Nov 08, 2017 (151)
42 URBANLAB ss3650897837 Oct 12, 2018 (152)
43 EGCUT_WGS ss3684097811 Jul 13, 2019 (153)
44 EVA_DECODE ss3702589122 Jul 13, 2019 (153)
45 ACPOP ss3742960051 Jul 13, 2019 (153)
46 EVA ss3755953879 Jul 13, 2019 (153)
47 PACBIO ss3788505208 Jul 13, 2019 (153)
48 PACBIO ss3793419929 Jul 13, 2019 (153)
49 PACBIO ss3798306650 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3821205939 Jul 13, 2019 (153)
51 EVA ss3835416827 Apr 27, 2020 (154)
52 EVA ss3841329908 Apr 27, 2020 (154)
53 EVA ss3846835438 Apr 27, 2020 (154)
54 SGDP_PRJ ss3888027220 Apr 27, 2020 (154)
55 KRGDB ss3938104153 Apr 27, 2020 (154)
56 TOPMED ss5071801266 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5227333201 Apr 26, 2021 (155)
58 1000G_HIGH_COVERAGE ss5306930839 Oct 16, 2022 (156)
59 EVA ss5434273244 Oct 16, 2022 (156)
60 HUGCELL_USP ss5499490728 Oct 16, 2022 (156)
61 EVA ss5512076099 Oct 16, 2022 (156)
62 1000G_HIGH_COVERAGE ss5612515327 Oct 16, 2022 (156)
63 SANFORD_IMAGENETICS ss5662217533 Oct 16, 2022 (156)
64 TOMMO_GENOMICS ss5785830329 Oct 16, 2022 (156)
65 YY_MCH ss5817522178 Oct 16, 2022 (156)
66 EVA ss5840427460 Oct 16, 2022 (156)
67 EVA ss5852252694 Oct 16, 2022 (156)
68 EVA ss5927751667 Oct 16, 2022 (156)
69 EVA ss5953626783 Oct 16, 2022 (156)
70 EVA ss5981044885 Oct 16, 2022 (156)
71 1000Genomes NC_000019.9 - 28333389 Oct 12, 2018 (152)
72 1000Genomes_30x NC_000019.10 - 27842481 Oct 16, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 28333389 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000019.9 - 28333389 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000019.9 - 28333389 Apr 27, 2020 (154)
76 gnomAD - Genomes NC_000019.10 - 27842481 Apr 26, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000019.9 - 28333389 Apr 27, 2020 (154)
78 HapMap NC_000019.10 - 27842481 Apr 27, 2020 (154)
79 KOREAN population from KRGDB NC_000019.9 - 28333389 Apr 27, 2020 (154)
80 Northern Sweden NC_000019.9 - 28333389 Jul 13, 2019 (153)
81 Qatari NC_000019.9 - 28333389 Apr 27, 2020 (154)
82 SGDP_PRJ NC_000019.9 - 28333389 Apr 27, 2020 (154)
83 Siberian NC_000019.9 - 28333389 Apr 27, 2020 (154)
84 8.3KJPN NC_000019.9 - 28333389 Apr 26, 2021 (155)
85 14KJPN NC_000019.10 - 27842481 Oct 16, 2022 (156)
86 TopMed NC_000019.10 - 27842481 Apr 26, 2021 (155)
87 UK 10K study - Twins NC_000019.9 - 28333389 Oct 12, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000019.9 - 28333389 Jul 13, 2019 (153)
89 ALFA NC_000019.10 - 27842481 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)
rs57255298 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78292939, ss85356442, ss90943816, ss111249098, ss117676125, ss168035381, ss169464711, ss203725687, ss208407764, ss255610668, ss283175734, ss287369458, ss292234222, ss1698259773 NC_000019.8:33025228:A:G NC_000019.10:27842480:A:G (self)
76208895, 42206878, 29836059, 4788479, 18806054, 45281547, 16244916, 19741714, 40044200, 10680230, 85302508, 42206878, 9325730, ss237645449, ss565926130, ss661787577, ss994208309, ss1081838280, ss1362813906, ss1428377346, ss1578604604, ss1637784571, ss1680778604, ss1809266216, ss1937699792, ss1968626064, ss2029624954, ss2158163876, ss2629310818, ss2702770292, ss2961853151, ss3017322556, ss3352262008, ss3684097811, ss3742960051, ss3755953879, ss3788505208, ss3793419929, ss3798306650, ss3835416827, ss3841329908, ss3888027220, ss3938104153, ss5227333201, ss5434273244, ss5512076099, ss5662217533, ss5840427460, ss5953626783, ss5981044885 NC_000019.9:28333388:A:G NC_000019.10:27842480:A:G (self)
100041262, 537490309, 1681532, 119667433, 287346930, 8675535557, ss3028646368, ss3650897837, ss3702589122, ss3821205939, ss3846835438, ss5071801266, ss5306930839, ss5499490728, ss5612515327, ss5785830329, ss5817522178, ss5852252694, ss5927751667 NC_000019.10:27842480:A:G NC_000019.10:27842480:A:G (self)
ss18803405, ss21514438 NT_011109.15:601606:A:G NC_000019.10:27842480:A:G (self)
ss106050893, ss136288921, ss137631446, ss155784668 NT_011109.16:601606:A:G NC_000019.10:27842480:A:G (self)
45281547, ss3938104153 NC_000019.9:28333388:A:T NC_000019.10:27842480:A: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 rs12327656

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