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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.

rs2840531

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:2354969 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.151638 (40137/264690, TOPMED)
T=0.163619 (24090/147232, ALFA)
T=0.148983 (20880/140150, GnomAD) (+ 18 more)
T=0.21044 (3527/16760, 8.3KJPN)
T=0.1795 (899/5008, 1000G)
T=0.2047 (917/4480, Estonian)
T=0.1619 (624/3854, ALSPAC)
T=0.1580 (586/3708, TWINSUK)
T=0.1959 (574/2930, KOREAN)
T=0.1339 (253/1890, HapMap)
T=0.1889 (346/1832, Korea1K)
T=0.166 (166/998, GoNL)
T=0.363 (227/626, Chileans)
T=0.248 (149/600, NorthernSweden)
T=0.069 (15/216, Qatari)
T=0.200 (42/210, Vietnamese)
C=0.409 (76/186, SGDP_PRJ)
T=0.10 (6/60, Ancient Sardinia)
T=0.12 (5/40, GENOME_DK)
C=0.50 (13/26, Siberian)
T=0.50 (13/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MORN1 : 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.2354969C>T
GRCh37.p13 chr 1 NC_000001.10:g.2286408C>T
Gene: MORN1, MORN repeat containing 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MORN1 transcript variant 1 NM_024848.3:c.1036+2463G>A N/A Intron Variant
MORN1 transcript variant 2 NM_001301060.2:c. N/A Genic Downstream Transcript Variant
MORN1 transcript variant 3 NR_125361.2: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

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 147232 C=0.836381 T=0.163619
European Sub 124066 C=0.847339 T=0.152661
African Sub 6210 C=0.9452 T=0.0548
African Others Sub 220 C=0.968 T=0.032
African American Sub 5990 C=0.9444 T=0.0556
Asian Sub 670 C=0.790 T=0.210
East Asian Sub 506 C=0.804 T=0.196
Other Asian Sub 164 C=0.744 T=0.256
Latin American 1 Sub 884 C=0.835 T=0.165
Latin American 2 Sub 8426 C=0.6145 T=0.3855
South Asian Sub 194 C=0.784 T=0.216
Other Sub 6782 C=0.8182 T=0.1818


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 C=0.848362 T=0.151638
gnomAD - Genomes Global Study-wide 140150 C=0.851017 T=0.148983
gnomAD - Genomes European Sub 75888 C=0.82576 T=0.17424
gnomAD - Genomes African Sub 42020 C=0.94462 T=0.05538
gnomAD - Genomes American Sub 13646 C=0.68753 T=0.31247
gnomAD - Genomes Ashkenazi Jewish Sub 3316 C=0.9530 T=0.0470
gnomAD - Genomes East Asian Sub 3128 C=0.8098 T=0.1902
gnomAD - Genomes Other Sub 2152 C=0.8536 T=0.1464
8.3KJPN JAPANESE Study-wide 16760 C=0.78956 T=0.21044
1000Genomes Global Study-wide 5008 C=0.8205 T=0.1795
1000Genomes African Sub 1322 C=0.9713 T=0.0287
1000Genomes East Asian Sub 1008 C=0.7907 T=0.2093
1000Genomes Europe Sub 1006 C=0.8380 T=0.1620
1000Genomes South Asian Sub 978 C=0.770 T=0.230
1000Genomes American Sub 694 C=0.622 T=0.378
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7953 T=0.2047
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8381 T=0.1619
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8420 T=0.1580
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8041 T=0.1959
HapMap Global Study-wide 1890 C=0.8661 T=0.1339
HapMap American Sub 770 C=0.782 T=0.218
HapMap African Sub 690 C=0.974 T=0.026
HapMap Asian Sub 254 C=0.803 T=0.197
HapMap Europe Sub 176 C=0.903 T=0.097
Korean Genome Project KOREAN Study-wide 1832 C=0.8111 T=0.1889
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.834 T=0.166
Chileans Chilean Study-wide 626 C=0.637 T=0.363
Northern Sweden ACPOP Study-wide 600 C=0.752 T=0.248
Qatari Global Study-wide 216 C=0.931 T=0.069
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.800 T=0.200
SGDP_PRJ Global Study-wide 186 C=0.409 T=0.591
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 60 C=0.90 T=0.10
The Danish reference pan genome Danish Study-wide 40 C=0.88 T=0.12
Siberian Global Study-wide 26 C=0.50 T=0.50
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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.2354969= NC_000001.11:g.2354969C>T
GRCh37.p13 chr 1 NC_000001.10:g.2286408= NC_000001.10:g.2286408C>T
MORN1 transcript NM_024848.1:c.1036+2463= NM_024848.1:c.1036+2463G>A
MORN1 transcript variant 1 NM_024848.3:c.1036+2463= NM_024848.3:c.1036+2463G>A
MORN1 transcript variant X1 XM_005244797.1:c.985+2463= XM_005244797.1:c.985+2463G>A
MORN1 transcript variant X2 XM_005244798.1:c.964+2463= XM_005244798.1:c.964+2463G>A
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#.

82 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4022000 Sep 28, 2001 (100)
2 SC_SNP ss12992989 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss19098168 Feb 27, 2004 (120)
4 PERLEGEN ss24237906 Sep 20, 2004 (123)
5 ABI ss43990115 Mar 14, 2006 (126)
6 ILLUMINA ss65718325 Oct 13, 2006 (127)
7 AFFY ss76634938 Dec 07, 2007 (129)
8 BGI ss102714199 Dec 01, 2009 (131)
9 KRIBB_YJKIM ss104881919 Feb 05, 2009 (130)
10 ILLUMINA ss120244549 Dec 01, 2009 (131)
11 ILLUMINA ss160587436 Dec 01, 2009 (131)
12 ENSEMBL ss161226705 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss163720663 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165993864 Jul 04, 2010 (132)
15 1000GENOMES ss218195988 Jul 14, 2010 (132)
16 1000GENOMES ss230399410 Jul 14, 2010 (132)
17 1000GENOMES ss238118670 Jul 15, 2010 (132)
18 ILLUMINA ss244255174 Jul 04, 2010 (132)
19 BL ss252871807 May 09, 2011 (134)
20 GMI ss275686225 May 04, 2012 (137)
21 ILLUMINA ss480689055 May 04, 2012 (137)
22 ILLUMINA ss480704556 May 04, 2012 (137)
23 ILLUMINA ss481564068 Sep 08, 2015 (146)
24 ILLUMINA ss485139355 May 04, 2012 (137)
25 ILLUMINA ss537136305 Sep 08, 2015 (146)
26 TISHKOFF ss553723620 Apr 25, 2013 (138)
27 SSMP ss647526627 Apr 25, 2013 (138)
28 ILLUMINA ss778881688 Aug 21, 2014 (142)
29 ILLUMINA ss783015967 Sep 08, 2015 (146)
30 ILLUMINA ss783976091 Aug 21, 2014 (142)
31 ILLUMINA ss832273414 Sep 08, 2015 (146)
32 ILLUMINA ss834342697 Aug 21, 2014 (142)
33 EVA-GONL ss974783017 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067619494 Aug 21, 2014 (142)
35 1000GENOMES ss1289398031 Aug 21, 2014 (142)
36 DDI ss1425688941 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1573855492 Apr 01, 2015 (144)
38 EVA_DECODE ss1584142610 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1599402190 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1642396223 Apr 01, 2015 (144)
41 EVA_SVP ss1712306034 Apr 01, 2015 (144)
42 ILLUMINA ss1751903370 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1917976973 Feb 12, 2016 (147)
44 GENOMED ss1966669232 Jul 19, 2016 (147)
45 JJLAB ss2019505054 Sep 14, 2016 (149)
46 USC_VALOUEV ss2147493699 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2159470300 Dec 20, 2016 (150)
48 TOPMED ss2321624049 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624268452 Nov 08, 2017 (151)
50 ILLUMINA ss2632466873 Nov 08, 2017 (151)
51 GRF ss2697385567 Nov 08, 2017 (151)
52 GNOMAD ss2750814102 Nov 08, 2017 (151)
53 SWEGEN ss2986175158 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3023516497 Nov 08, 2017 (151)
55 TOPMED ss3066791845 Nov 08, 2017 (151)
56 CSHL ss3343280608 Nov 08, 2017 (151)
57 ILLUMINA ss3626009152 Oct 11, 2018 (152)
58 ILLUMINA ss3630506583 Oct 11, 2018 (152)
59 ILLUMINA ss3632878237 Oct 11, 2018 (152)
60 ILLUMINA ss3633571743 Oct 11, 2018 (152)
61 ILLUMINA ss3634302766 Oct 11, 2018 (152)
62 ILLUMINA ss3635265934 Oct 11, 2018 (152)
63 ILLUMINA ss3635979153 Oct 11, 2018 (152)
64 ILLUMINA ss3637016280 Oct 11, 2018 (152)
65 ILLUMINA ss3640010131 Oct 11, 2018 (152)
66 ILLUMINA ss3640973381 Oct 11, 2018 (152)
67 ILLUMINA ss3641267192 Oct 11, 2018 (152)
68 EGCUT_WGS ss3654282160 Jul 12, 2019 (153)
69 EVA_DECODE ss3686021937 Jul 12, 2019 (153)
70 ACPOP ss3726728254 Jul 12, 2019 (153)
71 ILLUMINA ss3744603692 Jul 12, 2019 (153)
72 EVA ss3745738275 Jul 12, 2019 (153)
73 ILLUMINA ss3772105430 Jul 12, 2019 (153)
74 KHV_HUMAN_GENOMES ss3798761151 Jul 12, 2019 (153)
75 EVA ss3825987807 Apr 25, 2020 (154)
76 SGDP_PRJ ss3848035355 Apr 25, 2020 (154)
77 KRGDB ss3892883373 Apr 25, 2020 (154)
78 KOGIC ss3943666410 Apr 25, 2020 (154)
79 EVA ss3984774352 Apr 25, 2021 (155)
80 EVA ss4016889546 Apr 25, 2021 (155)
81 TOPMED ss4436905945 Apr 25, 2021 (155)
82 TOMMO_GENOMICS ss5142129821 Apr 25, 2021 (155)
83 1000Genomes NC_000001.10 - 2286408 Oct 11, 2018 (152)
84 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2286408 Oct 11, 2018 (152)
85 Chileans NC_000001.10 - 2286408 Apr 25, 2020 (154)
86 Genetic variation in the Estonian population NC_000001.10 - 2286408 Oct 11, 2018 (152)
87 The Danish reference pan genome NC_000001.10 - 2286408 Apr 25, 2020 (154)
88 gnomAD - Genomes NC_000001.11 - 2354969 Apr 25, 2021 (155)
89 Genome of the Netherlands Release 5 NC_000001.10 - 2286408 Apr 25, 2020 (154)
90 HapMap NC_000001.11 - 2354969 Apr 25, 2020 (154)
91 KOREAN population from KRGDB NC_000001.10 - 2286408 Apr 25, 2020 (154)
92 Korean Genome Project NC_000001.11 - 2354969 Apr 25, 2020 (154)
93 Northern Sweden NC_000001.10 - 2286408 Jul 12, 2019 (153)
94 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 2286408 Apr 25, 2021 (155)
95 Qatari NC_000001.10 - 2286408 Apr 25, 2020 (154)
96 SGDP_PRJ NC_000001.10 - 2286408 Apr 25, 2020 (154)
97 Siberian NC_000001.10 - 2286408 Apr 25, 2020 (154)
98 8.3KJPN NC_000001.10 - 2286408 Apr 25, 2021 (155)
99 TopMed NC_000001.11 - 2354969 Apr 25, 2021 (155)
100 UK 10K study - Twins NC_000001.10 - 2286408 Oct 11, 2018 (152)
101 A Vietnamese Genetic Variation Database NC_000001.10 - 2286408 Jul 12, 2019 (153)
102 ALFA NC_000001.11 - 2354969 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)
rs17373065 Oct 07, 2004 (123)
rs386575014 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss76634938, ss163720663, ss165993864, ss252871807, ss275686225, ss480689055, ss1584142610, ss1712306034 NC_000001.9:2276267:C:T NC_000001.11:2354968:C:T (self)
64689, 26548, 58, 20408, 1362726, 11236, 60767, 13119, 279, 18903, 52335, 10053, 99128, 26548, 5417, ss218195988, ss230399410, ss238118670, ss480704556, ss481564068, ss485139355, ss537136305, ss553723620, ss647526627, ss778881688, ss783015967, ss783976091, ss832273414, ss834342697, ss974783017, ss1067619494, ss1289398031, ss1425688941, ss1573855492, ss1599402190, ss1642396223, ss1751903370, ss1917976973, ss1966669232, ss2019505054, ss2147493699, ss2321624049, ss2624268452, ss2632466873, ss2697385567, ss2750814102, ss2986175158, ss3343280608, ss3626009152, ss3630506583, ss3632878237, ss3633571743, ss3634302766, ss3635265934, ss3635979153, ss3637016280, ss3640010131, ss3640973381, ss3641267192, ss3654282160, ss3726728254, ss3744603692, ss3745738275, ss3772105430, ss3825987807, ss3848035355, ss3892883373, ss3984774352, ss4016889546, ss5142129821 NC_000001.10:2286407:C:T NC_000001.11:2354968:C:T (self)
484271, 1103, 44411, 314649, 512280, 13656216273, ss2159470300, ss3023516497, ss3066791845, ss3686021937, ss3798761151, ss3943666410, ss4436905945 NC_000001.11:2354968:C:T NC_000001.11:2354968:C:T (self)
ss12992989 NT_004350.15:33998:C:T NC_000001.11:2354968:C:T (self)
ss19098168 NT_004350.16:264069:C:T NC_000001.11:2354968:C:T (self)
ss4022000, ss24237906, ss43990115, ss65718325, ss102714199, ss104881919, ss120244549, ss160587436, ss161226705, ss244255174 NT_004350.19:1765039:C:T NC_000001.11:2354968:C: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 rs2840531

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