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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.

rs3131972

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:817341 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.202177 (32358/160048, ALFA)
A=0.332476 (46524/139932, GnomAD)
A=0.30889 (5177/16760, 8.3KJPN) (+ 14 more)
A=0.3466 (1736/5008, 1000G)
A=0.2297 (1029/4480, Estonian)
A=0.1541 (594/3854, ALSPAC)
A=0.1591 (590/3708, TWINSUK)
A=0.3164 (927/2930, KOREAN)
A=0.3916 (741/1892, HapMap)
A=0.206 (206/998, GoNL)
A=0.234 (177/758, PRJEB37584)
A=0.148 (89/600, NorthernSweden)
A=0.322 (172/534, MGP)
A=0.234 (113/482, SGDP_PRJ)
A=0.273 (59/216, Qatari)
A=0.19 (10/52, Siberian)
A=0.05 (2/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FAM87B : 2KB Upstream 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.817341A>C
GRCh38.p13 chr 1 NC_000001.11:g.817341A>G
GRCh38.p13 chr 1 NC_000001.11:g.817341A>T
GRCh37.p13 chr 1 NC_000001.10:g.752721A>C
GRCh37.p13 chr 1 NC_000001.10:g.752721A>G
GRCh37.p13 chr 1 NC_000001.10:g.752721A>T
Gene: FAM87B, family with sequence similarity 87 member B (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
FAM87B transcript NR_103536.1:n. N/A Upstream 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

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 160048 A=0.202177 C=0.000000, G=0.797823
European Sub 139434 A=0.177145 C=0.000000, G=0.822855
African Sub 5928 A=0.6469 C=0.0000, G=0.3531
African Others Sub 214 A=0.743 C=0.000, G=0.257
African American Sub 5714 A=0.6433 C=0.0000, G=0.3567
Asian Sub 406 A=0.229 C=0.000, G=0.771
East Asian Sub 308 A=0.247 C=0.000, G=0.753
Other Asian Sub 98 A=0.17 C=0.00, G=0.83
Latin American 1 Sub 700 A=0.301 C=0.000, G=0.699
Latin American 2 Sub 6086 A=0.2752 C=0.0000, G=0.7248
South Asian Sub 168 A=0.250 C=0.000, G=0.750
Other Sub 7326 A=0.2460 C=0.0000, G=0.7540


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
gnomAD - Genomes Global Study-wide 139932 A=0.332476 G=0.667524
gnomAD - Genomes European Sub 75858 A=0.18117 G=0.81883
gnomAD - Genomes African Sub 41864 A=0.64292 G=0.35708
gnomAD - Genomes American Sub 13650 A=0.27582 G=0.72418
gnomAD - Genomes Ashkenazi Jewish Sub 3312 A=0.2234 G=0.7766
gnomAD - Genomes East Asian Sub 3102 A=0.2324 G=0.7676
gnomAD - Genomes Other Sub 2146 A=0.2982 G=0.7018
8.3KJPN JAPANESE Study-wide 16760 A=0.30889 G=0.69111
1000Genomes Global Study-wide 5008 A=0.3466 G=0.6534
1000Genomes African Sub 1322 A=0.7095 G=0.2905
1000Genomes East Asian Sub 1008 A=0.2341 G=0.7659
1000Genomes Europe Sub 1006 A=0.1610 G=0.8390
1000Genomes South Asian Sub 978 A=0.222 G=0.778
1000Genomes American Sub 694 A=0.264 G=0.736
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2297 G=0.7703
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1541 G=0.8459
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1591 G=0.8409
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3164 C=0.0000, G=0.6836, T=0.0000
HapMap Global Study-wide 1892 A=0.3916 G=0.6084
HapMap American Sub 770 A=0.247 G=0.753
HapMap African Sub 692 A=0.679 G=0.321
HapMap Asian Sub 254 A=0.220 G=0.780
HapMap Europe Sub 176 A=0.142 G=0.858
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.206 G=0.794
CNV burdens in cranial meningiomas Global Study-wide 758 A=0.234 G=0.766
CNV burdens in cranial meningiomas CRM Sub 758 A=0.234 G=0.766
Northern Sweden ACPOP Study-wide 600 A=0.148 G=0.852
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.322 G=0.678
SGDP_PRJ Global Study-wide 482 A=0.234 G=0.766
Qatari Global Study-wide 216 A=0.273 G=0.727
Siberian Global Study-wide 52 A=0.19 G=0.81
The Danish reference pan genome Danish Study-wide 40 A=0.05 G=0.95
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 T
GRCh38.p13 chr 1 NC_000001.11:g.817341= NC_000001.11:g.817341A>C NC_000001.11:g.817341A>G NC_000001.11:g.817341A>T
GRCh37.p13 chr 1 NC_000001.10:g.752721= NC_000001.10:g.752721A>C NC_000001.10:g.752721A>G NC_000001.10:g.752721A>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#.

106 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4379448 Mar 26, 2002 (103)
2 ILLUMINA ss74993256 Dec 06, 2007 (129)
3 HGSV ss78643137 Dec 06, 2007 (129)
4 BCMHGSC_JDW ss87155630 Mar 23, 2008 (129)
5 HUMANGENOME_JCVI ss97913182 Feb 06, 2009 (130)
6 BGI ss105111646 Dec 01, 2009 (131)
7 1000GENOMES ss107938263 Jan 22, 2009 (130)
8 1000GENOMES ss109937164 Jan 24, 2009 (130)
9 ILLUMINA-UK ss118438193 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119455365 Dec 01, 2009 (131)
11 ENSEMBL ss138899069 Dec 01, 2009 (131)
12 GMI ss154522302 Dec 01, 2009 (131)
13 ILLUMINA ss160613670 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162980826 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss163702698 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss165981005 Jul 04, 2010 (132)
17 ILLUMINA ss173568268 Jul 04, 2010 (132)
18 BUSHMAN ss197885385 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss205098301 Jul 04, 2010 (132)
20 1000GENOMES ss218190360 Jul 14, 2010 (132)
21 1000GENOMES ss230395425 Jul 14, 2010 (132)
22 1000GENOMES ss238114952 Jul 15, 2010 (132)
23 BL ss252864064 May 09, 2011 (134)
24 GMI ss275680743 May 04, 2012 (137)
25 GMI ss283987353 Apr 25, 2013 (138)
26 PJP ss290493765 May 09, 2011 (134)
27 ILLUMINA ss480760791 May 04, 2012 (137)
28 ILLUMINA ss480776595 May 04, 2012 (137)
29 ILLUMINA ss481669009 Sep 08, 2015 (146)
30 ILLUMINA ss485175110 May 04, 2012 (137)
31 ILLUMINA ss537165056 Sep 08, 2015 (146)
32 TISHKOFF ss553710353 Apr 25, 2013 (138)
33 SSMP ss647516067 Apr 25, 2013 (138)
34 ILLUMINA ss778889095 Aug 21, 2014 (142)
35 ILLUMINA ss783033737 Sep 08, 2015 (146)
36 ILLUMINA ss783993352 Aug 21, 2014 (142)
37 ILLUMINA ss832291380 Sep 08, 2015 (146)
38 ILLUMINA ss834350188 Aug 21, 2014 (142)
39 EVA-GONL ss974769212 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1067612324 Aug 21, 2014 (142)
41 1000GENOMES ss1289338800 Aug 21, 2014 (142)
42 DDI ss1425684786 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1573851123 Apr 01, 2015 (144)
44 EVA_DECODE ss1584129425 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1599378264 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1642372297 Apr 01, 2015 (144)
47 EVA_MGP ss1710883345 Apr 01, 2015 (144)
48 EVA_SVP ss1712305455 Apr 01, 2015 (144)
49 ILLUMINA ss1751932614 Sep 08, 2015 (146)
50 HAMMER_LAB ss1793705632 Sep 08, 2015 (146)
51 WEILL_CORNELL_DGM ss1917960119 Feb 12, 2016 (147)
52 ILLUMINA ss1945981588 Feb 12, 2016 (147)
53 ILLUMINA ss1958229939 Feb 12, 2016 (147)
54 GENOMED ss1966667312 Jul 19, 2016 (147)
55 JJLAB ss2019498334 Sep 14, 2016 (149)
56 EGCUT_WGS ss2137543936 Jul 12, 2019 (153)
57 USC_VALOUEV ss2147484246 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2159368076 Dec 20, 2016 (150)
59 TOPMED ss2321502631 Dec 20, 2016 (150)
60 SYSTEMSBIOZJU ss2624264743 Nov 08, 2017 (151)
61 ILLUMINA ss2632465441 Nov 08, 2017 (151)
62 GRF ss2697374432 Nov 08, 2017 (151)
63 ILLUMINA ss2710663539 Nov 08, 2017 (151)
64 GNOMAD ss2750636448 Nov 08, 2017 (151)
65 AFFY ss2984840981 Nov 08, 2017 (151)
66 AFFY ss2985494976 Nov 08, 2017 (151)
67 SWEGEN ss2986148520 Nov 08, 2017 (151)
68 ILLUMINA ss3021042976 Nov 08, 2017 (151)
69 BIOINF_KMB_FNS_UNIBA ss3023513705 Nov 08, 2017 (151)
70 TOPMED ss3066395646 Nov 08, 2017 (151)
71 CSHL ss3343272378 Nov 08, 2017 (151)
72 ILLUMINA ss3625523486 Oct 11, 2018 (152)
73 ILLUMINA ss3626006469 Oct 11, 2018 (152)
74 ILLUMINA ss3630505567 Oct 11, 2018 (152)
75 ILLUMINA ss3632878027 Oct 11, 2018 (152)
76 ILLUMINA ss3633571433 Oct 11, 2018 (152)
77 ILLUMINA ss3634301812 Oct 11, 2018 (152)
78 ILLUMINA ss3635265639 Oct 11, 2018 (152)
79 ILLUMINA ss3635978593 Oct 11, 2018 (152)
80 ILLUMINA ss3637015977 Oct 11, 2018 (152)
81 ILLUMINA ss3637732355 Oct 11, 2018 (152)
82 ILLUMINA ss3640009178 Oct 11, 2018 (152)
83 ILLUMINA ss3642746657 Oct 11, 2018 (152)
84 ILLUMINA ss3644477460 Oct 11, 2018 (152)
85 URBANLAB ss3646581172 Oct 11, 2018 (152)
86 ILLUMINA ss3651365029 Oct 11, 2018 (152)
87 ILLUMINA ss3653614732 Oct 11, 2018 (152)
88 EVA_DECODE ss3685991930 Jul 12, 2019 (153)
89 ILLUMINA ss3724988048 Jul 12, 2019 (153)
90 ACPOP ss3726716173 Jul 12, 2019 (153)
91 ILLUMINA ss3744040762 Jul 12, 2019 (153)
92 ILLUMINA ss3744602744 Jul 12, 2019 (153)
93 EVA ss3745720826 Jul 12, 2019 (153)
94 ILLUMINA ss3772104509 Jul 12, 2019 (153)
95 PACBIO ss3783302092 Jul 12, 2019 (153)
96 PACBIO ss3788979962 Jul 12, 2019 (153)
97 PACBIO ss3793852499 Jul 12, 2019 (153)
98 KHV_HUMAN_GENOMES ss3798743422 Jul 12, 2019 (153)
99 EVA ss3825981415 Apr 25, 2020 (154)
100 EVA ss3836378356 Apr 25, 2020 (154)
101 EVA ss3841782358 Apr 25, 2020 (154)
102 SGDP_PRJ ss3847994711 Apr 25, 2020 (154)
103 KRGDB ss3892835085 Apr 25, 2020 (154)
104 EVA ss3984450705 Apr 25, 2021 (155)
105 EVA ss4016889033 Apr 25, 2021 (155)
106 TOMMO_GENOMICS ss5142050934 Apr 25, 2021 (155)
107 1000Genomes NC_000001.10 - 752721 Oct 11, 2018 (152)
108 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 752721 Oct 11, 2018 (152)
109 Genetic variation in the Estonian population NC_000001.10 - 752721 Oct 11, 2018 (152)
110 The Danish reference pan genome NC_000001.10 - 752721 Apr 25, 2020 (154)
111 gnomAD - Genomes NC_000001.11 - 817341 Apr 25, 2021 (155)
112 Genome of the Netherlands Release 5 NC_000001.10 - 752721 Apr 25, 2020 (154)
113 HapMap NC_000001.11 - 817341 Apr 25, 2020 (154)
114 KOREAN population from KRGDB NC_000001.10 - 752721 Apr 25, 2020 (154)
115 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 752721 Apr 25, 2020 (154)
116 Northern Sweden NC_000001.10 - 752721 Jul 12, 2019 (153)
117 CNV burdens in cranial meningiomas NC_000001.10 - 752721 Apr 25, 2021 (155)
118 Qatari NC_000001.10 - 752721 Apr 25, 2020 (154)
119 SGDP_PRJ NC_000001.10 - 752721 Apr 25, 2020 (154)
120 Siberian NC_000001.10 - 752721 Apr 25, 2020 (154)
121 8.3KJPN NC_000001.10 - 752721 Apr 25, 2021 (155)
122 UK 10K study - Twins NC_000001.10 - 752721 Oct 11, 2018 (152)
123 ALFA NC_000001.11 - 817341 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
12479, ss3892835085 NC_000001.10:752720:A:C NC_000001.11:817340:A:C (self)
10360428774 NC_000001.11:817340:A:C NC_000001.11:817340:A:C
ss78643137 NC_000001.8:792583:A:G NC_000001.11:817340:A:G (self)
ss87155630, ss107938263, ss109937164, ss118438193, ss160613670, ss162980826, ss163702698, ss165981005, ss197885385, ss205098301, ss252864064, ss275680743, ss283987353, ss290493765, ss480760791, ss1584129425, ss1712305455, ss3642746657 NC_000001.9:742583:A:G NC_000001.11:817340:A:G (self)
3512, 150, 1, 1358357, 290, 12479, 97, 1038, 4, 2049, 11691, 600, 20241, 150, ss218190360, ss230395425, ss238114952, ss480776595, ss481669009, ss485175110, ss537165056, ss553710353, ss647516067, ss778889095, ss783033737, ss783993352, ss832291380, ss834350188, ss974769212, ss1067612324, ss1289338800, ss1425684786, ss1573851123, ss1599378264, ss1642372297, ss1710883345, ss1751932614, ss1793705632, ss1917960119, ss1945981588, ss1958229939, ss1966667312, ss2019498334, ss2137543936, ss2147484246, ss2321502631, ss2624264743, ss2632465441, ss2697374432, ss2710663539, ss2750636448, ss2984840981, ss2985494976, ss2986148520, ss3021042976, ss3343272378, ss3625523486, ss3626006469, ss3630505567, ss3632878027, ss3633571433, ss3634301812, ss3635265639, ss3635978593, ss3637015977, ss3637732355, ss3640009178, ss3644477460, ss3651365029, ss3653614732, ss3726716173, ss3744040762, ss3744602744, ss3745720826, ss3772104509, ss3783302092, ss3788979962, ss3793852499, ss3825981415, ss3836378356, ss3847994711, ss3892835085, ss3984450705, ss4016889033, ss5142050934 NC_000001.10:752720:A:G NC_000001.11:817340:A:G (self)
60712, 41, 10360428774, ss2159368076, ss3023513705, ss3066395646, ss3646581172, ss3685991930, ss3724988048, ss3798743422, ss3841782358 NC_000001.11:817340:A:G NC_000001.11:817340:A:G (self)
ss4379448, ss74993256, ss97913182, ss105111646, ss119455365, ss138899069, ss154522302, ss173568268 NT_004350.19:231352:A:G NC_000001.11:817340:A:G (self)
12479, ss3892835085 NC_000001.10:752720:A:T NC_000001.11:817340: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 rs3131972

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