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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.

rs2742686

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3082370 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.103517 (27400/264690, TOPMED)
T=0.107830 (15118/140202, GnomAD)
T=0.13526 (3164/23392, ALFA) (+ 14 more)
T=0.00788 (132/16756, 8.3KJPN)
T=0.0601 (301/5008, 1000G)
T=0.1451 (650/4480, Estonian)
T=0.1619 (624/3854, ALSPAC)
T=0.1624 (602/3708, TWINSUK)
T=0.0140 (41/2930, KOREAN)
T=0.0175 (32/1832, Korea1K)
T=0.170 (170/998, GoNL)
T=0.110 (66/600, NorthernSweden)
T=0.059 (33/558, SGDP_PRJ)
T=0.028 (6/216, Qatari)
T=0.047 (10/214, Vietnamese)
T=0.16 (9/56, Siberian)
T=0.28 (11/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRDM16 : 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 23392 T=0.13526 C=0.86474
European Sub 18752 T=0.15614 C=0.84386
African Sub 2946 T=0.0309 C=0.9691
African Others Sub 114 T=0.000 C=1.000
African American Sub 2832 T=0.0321 C=0.9679
Asian Sub 112 T=0.036 C=0.964
East Asian Sub 86 T=0.03 C=0.97
Other Asian Sub 26 T=0.04 C=0.96
Latin American 1 Sub 146 T=0.034 C=0.966
Latin American 2 Sub 610 T=0.082 C=0.918
South Asian Sub 98 T=0.03 C=0.97
Other Sub 728 T=0.114 C=0.886


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 T=0.103517 C=0.896483
gnomAD - Genomes Global Study-wide 140202 T=0.107830 C=0.892170
gnomAD - Genomes European Sub 75904 T=0.15371 C=0.84629
gnomAD - Genomes African Sub 42030 T=0.02907 C=0.97093
gnomAD - Genomes American Sub 13658 T=0.10536 C=0.89464
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.1474 C=0.8526
gnomAD - Genomes East Asian Sub 3132 T=0.0243 C=0.9757
gnomAD - Genomes Other Sub 2154 T=0.1040 C=0.8960
8.3KJPN JAPANESE Study-wide 16756 T=0.00788 C=0.99212
1000Genomes Global Study-wide 5008 T=0.0601 C=0.9399
1000Genomes African Sub 1322 T=0.0083 C=0.9917
1000Genomes East Asian Sub 1008 T=0.0317 C=0.9683
1000Genomes Europe Sub 1006 T=0.1521 C=0.8479
1000Genomes South Asian Sub 978 T=0.034 C=0.966
1000Genomes American Sub 694 T=0.104 C=0.896
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.1451 C=0.8549
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1619 C=0.8381
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1624 C=0.8376
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0140 A=0.0000, C=0.9860, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.0175 C=0.9825
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.170 C=0.830
Northern Sweden ACPOP Study-wide 600 T=0.110 C=0.890
SGDP_PRJ Global Study-wide 558 T=0.059 C=0.941
Qatari Global Study-wide 216 T=0.028 C=0.972
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.047 C=0.953
Siberian Global Study-wide 56 T=0.16 C=0.84
The Danish reference pan genome Danish Study-wide 40 T=0.28 C=0.72
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.3082370T>A
GRCh38.p13 chr 1 NC_000001.11:g.3082370T>C
GRCh38.p13 chr 1 NC_000001.11:g.3082370T>G
GRCh37.p13 chr 1 NC_000001.10:g.2998934T>A
GRCh37.p13 chr 1 NC_000001.10:g.2998934T>C
GRCh37.p13 chr 1 NC_000001.10:g.2998934T>G
PRDM16 RefSeqGene NG_029576.2:g.18193T>A
PRDM16 RefSeqGene NG_029576.2:g.18193T>C
PRDM16 RefSeqGene NG_029576.2:g.18193T>G
Gene: PRDM16, PR/SET domain 16 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRDM16 transcript variant 1 NM_022114.4:c.37+13074T>A N/A Intron Variant
PRDM16 transcript variant 2 NM_199454.3:c.37+13074T>A 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 T= A C G
GRCh38.p13 chr 1 NC_000001.11:g.3082370= NC_000001.11:g.3082370T>A NC_000001.11:g.3082370T>C NC_000001.11:g.3082370T>G
GRCh37.p13 chr 1 NC_000001.10:g.2998934= NC_000001.10:g.2998934T>A NC_000001.10:g.2998934T>C NC_000001.10:g.2998934T>G
PRDM16 RefSeqGene NG_029576.2:g.18193= NG_029576.2:g.18193T>A NG_029576.2:g.18193T>C NG_029576.2:g.18193T>G
PRDM16 transcript variant 1 NM_022114.3:c.37+13074= NM_022114.3:c.37+13074T>A NM_022114.3:c.37+13074T>C NM_022114.3:c.37+13074T>G
PRDM16 transcript variant 1 NM_022114.4:c.37+13074= NM_022114.4:c.37+13074T>A NM_022114.4:c.37+13074T>C NM_022114.4:c.37+13074T>G
PRDM16 transcript variant 2 NM_199454.2:c.37+13074= NM_199454.2:c.37+13074T>A NM_199454.2:c.37+13074T>C NM_199454.2:c.37+13074T>G
PRDM16 transcript variant 2 NM_199454.3:c.37+13074= NM_199454.3:c.37+13074T>A NM_199454.3:c.37+13074T>C NM_199454.3:c.37+13074T>G
PRDM16 transcript variant X1 XM_005244772.1:c.37+13074= XM_005244772.1:c.37+13074T>A XM_005244772.1:c.37+13074T>C XM_005244772.1:c.37+13074T>G
PRDM16 transcript variant X2 XM_005244773.1:c.37+13074= XM_005244773.1:c.37+13074T>A XM_005244773.1:c.37+13074T>C XM_005244773.1:c.37+13074T>G
PRDM16 transcript variant X3 XM_005244774.1:c.37+13074= XM_005244774.1:c.37+13074T>A XM_005244774.1:c.37+13074T>C XM_005244774.1:c.37+13074T>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#.

76 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3871066 Sep 28, 2001 (100)
2 WI_SSAHASNP ss6396354 Feb 20, 2003 (111)
3 CSHL-HAPMAP ss16410253 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19844212 Feb 27, 2004 (120)
5 SSAHASNP ss20490450 Apr 05, 2004 (121)
6 ABI ss44062652 Mar 14, 2006 (126)
7 HGSV ss84405369 Dec 15, 2007 (130)
8 HGSV ss85229109 Dec 15, 2007 (130)
9 HGSV ss85977490 Dec 15, 2007 (130)
10 HGSV ss86179404 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss87170121 Mar 23, 2008 (129)
12 HUMANGENOME_JCVI ss99180699 Feb 05, 2009 (130)
13 BGI ss105114163 Dec 01, 2009 (131)
14 1000GENOMES ss107944641 Jan 22, 2009 (130)
15 1000GENOMES ss109958578 Jan 24, 2009 (130)
16 ILLUMINA-UK ss118447791 Feb 14, 2009 (130)
17 ENSEMBL ss131779602 Dec 01, 2009 (131)
18 ENSEMBL ss137760996 Dec 01, 2009 (131)
19 GMI ss154550838 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162998022 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss163728555 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss166000034 Jul 04, 2010 (132)
23 BUSHMAN ss197914280 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss205285875 Jul 04, 2010 (132)
25 1000GENOMES ss218199091 Jul 14, 2010 (132)
26 1000GENOMES ss230401350 Jul 14, 2010 (132)
27 1000GENOMES ss238120549 Jul 15, 2010 (132)
28 BL ss252875800 May 09, 2011 (134)
29 GMI ss275689002 May 04, 2012 (137)
30 GMI ss283990137 Apr 25, 2013 (138)
31 PJP ss290497063 May 09, 2011 (134)
32 ILLUMINA ss482310533 May 04, 2012 (137)
33 ILLUMINA ss483424416 May 04, 2012 (137)
34 TISHKOFF ss553728096 Apr 25, 2013 (138)
35 SSMP ss647531318 Apr 25, 2013 (138)
36 ILLUMINA ss782155467 Sep 08, 2015 (146)
37 EVA-GONL ss974788738 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1067622754 Aug 21, 2014 (142)
39 1000GENOMES ss1289423457 Aug 21, 2014 (142)
40 DDI ss1425690774 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1573857518 Apr 01, 2015 (144)
42 EVA_DECODE ss1584148222 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1599413282 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1642407315 Apr 01, 2015 (144)
45 HAMMER_LAB ss1793760259 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1917983862 Feb 12, 2016 (147)
47 JJLAB ss2019508065 Sep 14, 2016 (149)
48 USC_VALOUEV ss2147498151 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2159516690 Dec 20, 2016 (150)
50 TOPMED ss2321672312 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624269995 Nov 08, 2017 (151)
52 ILLUMINA ss2632467557 Nov 08, 2017 (151)
53 GRF ss2697391793 Nov 08, 2017 (151)
54 GNOMAD ss2750896797 Nov 08, 2017 (151)
55 SWEGEN ss2986190227 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3023517783 Nov 08, 2017 (151)
57 TOPMED ss3066961984 Nov 08, 2017 (151)
58 CSHL ss3343285308 Nov 08, 2017 (151)
59 ILLUMINA ss3641567258 Oct 11, 2018 (152)
60 URBANLAB ss3646585407 Oct 11, 2018 (152)
61 EGCUT_WGS ss3654291253 Jul 12, 2019 (153)
62 EVA_DECODE ss3686033238 Jul 12, 2019 (153)
63 ACPOP ss3726733703 Jul 12, 2019 (153)
64 EVA ss3745745884 Jul 12, 2019 (153)
65 PACBIO ss3783307309 Jul 12, 2019 (153)
66 PACBIO ss3788984337 Jul 12, 2019 (153)
67 PACBIO ss3793856962 Jul 12, 2019 (153)
68 KHV_HUMAN_GENOMES ss3798768102 Jul 12, 2019 (153)
69 EVA ss3825990517 Apr 25, 2020 (154)
70 EVA ss3836382534 Apr 25, 2020 (154)
71 EVA ss3841786668 Apr 25, 2020 (154)
72 SGDP_PRJ ss3848053067 Apr 25, 2020 (154)
73 KRGDB ss3892912890 Apr 25, 2020 (154)
74 KOGIC ss3943676293 Apr 25, 2020 (154)
75 TOPMED ss4437090470 Apr 25, 2021 (155)
76 TOMMO_GENOMICS ss5142169255 Apr 25, 2021 (155)
77 1000Genomes NC_000001.10 - 2998934 Oct 11, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2998934 Oct 11, 2018 (152)
79 Genetic variation in the Estonian population NC_000001.10 - 2998934 Oct 11, 2018 (152)
80 The Danish reference pan genome NC_000001.10 - 2998934 Apr 25, 2020 (154)
81 gnomAD - Genomes NC_000001.11 - 3082370 Apr 25, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000001.10 - 2998934 Apr 25, 2020 (154)
83 KOREAN population from KRGDB NC_000001.10 - 2998934 Apr 25, 2020 (154)
84 Korean Genome Project NC_000001.11 - 3082370 Apr 25, 2020 (154)
85 Northern Sweden NC_000001.10 - 2998934 Jul 12, 2019 (153)
86 Qatari NC_000001.10 - 2998934 Apr 25, 2020 (154)
87 SGDP_PRJ NC_000001.10 - 2998934 Apr 25, 2020 (154)
88 Siberian NC_000001.10 - 2998934 Apr 25, 2020 (154)
89 8.3KJPN NC_000001.10 - 2998934 Apr 25, 2021 (155)
90 TopMed NC_000001.11 - 3082370 Apr 25, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 2998934 Oct 11, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000001.10 - 2998934 Jul 12, 2019 (153)
93 ALFA NC_000001.11 - 3082370 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)
rs59998571 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
90284, ss3892912890 NC_000001.10:2998933:T:A NC_000001.11:3082369:T:A (self)
ss84405369, ss85229109, ss85977490, ss86179404 NC_000001.8:3022090:T:C NC_000001.11:3082369:T:C (self)
ss87170121, ss107944641, ss109958578, ss118447791, ss162998022, ss163728555, ss166000034, ss197914280, ss205285875, ss252875800, ss275689002, ss283990137, ss290497063, ss482310533, ss1584148222 NC_000001.9:2988793:T:C NC_000001.11:3082369:T:C (self)
90613, 38398, 29501, 1364752, 16165, 90284, 18568, 25792, 70047, 14505, 138562, 38398, 7895, ss218199091, ss230401350, ss238120549, ss483424416, ss553728096, ss647531318, ss782155467, ss974788738, ss1067622754, ss1289423457, ss1425690774, ss1573857518, ss1599413282, ss1642407315, ss1793760259, ss1917983862, ss2019508065, ss2147498151, ss2321672312, ss2624269995, ss2632467557, ss2697391793, ss2750896797, ss2986190227, ss3343285308, ss3641567258, ss3654291253, ss3726733703, ss3745745884, ss3783307309, ss3788984337, ss3793856962, ss3825990517, ss3836382534, ss3848053067, ss3892912890, ss5142169255 NC_000001.10:2998933:T:C NC_000001.11:3082369:T:C (self)
680237, 54294, 430236, 696805, 5773503277, ss2159516690, ss3023517783, ss3066961984, ss3646585407, ss3686033238, ss3798768102, ss3841786668, ss3943676293, ss4437090470 NC_000001.11:3082369:T:C NC_000001.11:3082369:T:C (self)
ss16410253, ss19844212, ss20490450 NT_004321.15:305708:T:C NC_000001.11:3082369:T:C (self)
ss3871066, ss6396354, ss44062652, ss99180699, ss105114163, ss131779602, ss137760996, ss154550838 NT_004350.19:2477565:T:C NC_000001.11:3082369:T:C (self)
90284, ss3892912890 NC_000001.10:2998933:T:G NC_000001.11:3082369:T: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 rs2742686

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.post629+eb05767