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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.

rs11240777

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:863579 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.380487 (100711/264690, TOPMED)
A=0.243319 (59696/245340, ALFA)
A=0.369721 (51707/139854, GnomAD) (+ 13 more)
A=0.45292 (7591/16760, 8.3KJPN)
A=0.4099 (2053/5008, 1000G)
A=0.1998 (770/3854, ALSPAC)
A=0.2098 (778/3708, TWINSUK)
A=0.3949 (1157/2930, KOREAN)
G=0.4804 (737/1534, HapMap)
A=0.2708 (299/1104, Daghestan)
A=0.231 (231/998, GoNL)
A=0.347 (261/752, PRJEB37584)
A=0.168 (101/600, NorthernSweden)
G=0.346 (124/358, SGDP_PRJ)
A=0.435 (94/216, Qatari)
G=0.38 (10/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107984850 : 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.863579G>A
GRCh37.p13 chr 1 NC_000001.10:g.798959G>A
Gene: LOC107984850, uncharacterized LOC107984850 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107984850 transcript variant X1 XR_001737607.2:n. N/A Intron Variant
LOC107984850 transcript variant X2 XR_001737608.2: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

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 245340 G=0.756681 A=0.243319
European Sub 214188 G=0.780973 A=0.219027
African Sub 8156 G=0.3367 A=0.6633
African Others Sub 304 G=0.224 A=0.776
African American Sub 7852 G=0.3411 A=0.6589
Asian Sub 3874 G=0.6141 A=0.3859
East Asian Sub 3110 G=0.6125 A=0.3875
Other Asian Sub 764 G=0.620 A=0.380
Latin American 1 Sub 1170 G=0.6479 A=0.3521
Latin American 2 Sub 8734 G=0.6932 A=0.3068
South Asian Sub 378 G=0.698 A=0.302
Other Sub 8840 G=0.6977 A=0.3023


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 G=0.619513 A=0.380487
gnomAD - Genomes Global Study-wide 139854 G=0.630279 A=0.369721
gnomAD - Genomes European Sub 75762 G=0.77458 A=0.22542
gnomAD - Genomes African Sub 41894 G=0.33313 A=0.66687
gnomAD - Genomes American Sub 13630 G=0.69222 A=0.30778
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.8015 A=0.1985
gnomAD - Genomes East Asian Sub 3102 G=0.6564 A=0.3436
gnomAD - Genomes Other Sub 2146 G=0.6407 A=0.3593
8.3KJPN JAPANESE Study-wide 16760 G=0.54708 A=0.45292
1000Genomes Global Study-wide 5008 G=0.5901 A=0.4099
1000Genomes African Sub 1322 G=0.2572 A=0.7428
1000Genomes East Asian Sub 1008 G=0.6478 A=0.3522
1000Genomes Europe Sub 1006 G=0.7952 A=0.2048
1000Genomes South Asian Sub 978 G=0.679 A=0.321
1000Genomes American Sub 694 G=0.718 A=0.282
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8002 A=0.1998
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7902 A=0.2098
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6051 A=0.3949
HapMap Global Study-wide 1534 G=0.4804 A=0.5196
HapMap African Sub 684 G=0.228 A=0.772
HapMap American Sub 594 G=0.665 A=0.335
HapMap Europe Sub 176 G=0.812 A=0.188
HapMap Asian Sub 80 G=0.54 A=0.46
Genome-wide autozygosity in Daghestan Global Study-wide 1104 G=0.7292 A=0.2708
Genome-wide autozygosity in Daghestan Daghestan Sub 618 G=0.756 A=0.244
Genome-wide autozygosity in Daghestan Near_East Sub 136 G=0.632 A=0.368
Genome-wide autozygosity in Daghestan Central Asia Sub 114 G=0.711 A=0.289
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.722 A=0.278
Genome-wide autozygosity in Daghestan South Asian Sub 92 G=0.68 A=0.32
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.83 A=0.17
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.769 A=0.231
CNV burdens in cranial meningiomas Global Study-wide 752 G=0.653 A=0.347
CNV burdens in cranial meningiomas CRM Sub 752 G=0.653 A=0.347
Northern Sweden ACPOP Study-wide 600 G=0.832 A=0.168
SGDP_PRJ Global Study-wide 358 G=0.346 A=0.654
Qatari Global Study-wide 216 G=0.565 A=0.435
Siberian Global Study-wide 26 G=0.38 A=0.62
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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.863579= NC_000001.11:g.863579G>A
GRCh37.p13 chr 1 NC_000001.10:g.798959= NC_000001.10:g.798959G>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#.

85 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18273122 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss19853484 Feb 27, 2004 (120)
3 PERLEGEN ss24152258 Sep 20, 2004 (123)
4 SSAHASNP ss35124991 May 24, 2005 (125)
5 PERLEGEN ss68756307 May 16, 2007 (127)
6 AFFY ss76654462 Dec 05, 2007 (129)
7 HGSV ss85876064 Dec 16, 2007 (130)
8 KRIBB_YJKIM ss105027838 Feb 06, 2009 (130)
9 ILLUMINA-UK ss118438425 Feb 14, 2009 (130)
10 ENSEMBL ss137752342 Dec 01, 2009 (131)
11 GMI ss154522465 Dec 01, 2009 (131)
12 ILLUMINA ss159973853 Dec 01, 2009 (131)
13 ILLUMINA ss171207637 Jul 04, 2010 (132)
14 BUSHMAN ss197885517 Jul 04, 2010 (132)
15 1000GENOMES ss210446476 Jul 14, 2010 (132)
16 1000GENOMES ss230395507 Jul 14, 2010 (132)
17 GMI ss275680966 May 04, 2012 (137)
18 ILLUMINA ss479508485 May 04, 2012 (137)
19 ILLUMINA ss479512442 May 04, 2012 (137)
20 ILLUMINA ss479961175 Sep 08, 2015 (146)
21 ILLUMINA ss484553510 May 04, 2012 (137)
22 ILLUMINA ss536690617 Sep 08, 2015 (146)
23 SSMP ss647516444 Apr 25, 2013 (138)
24 ILLUMINA ss778757199 Sep 08, 2015 (146)
25 ILLUMINA ss782723416 Sep 08, 2015 (146)
26 ILLUMINA ss783690912 Sep 08, 2015 (146)
27 ILLUMINA ss831975042 Sep 08, 2015 (146)
28 ILLUMINA ss834216922 Sep 08, 2015 (146)
29 EVA-GONL ss974769608 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067612430 Aug 21, 2014 (142)
31 1000GENOMES ss1289340259 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397238520 Sep 08, 2015 (146)
33 DDI ss1425684944 Apr 01, 2015 (144)
34 EVA_DECODE ss1584129639 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1599378555 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1642372588 Apr 01, 2015 (144)
37 EVA_SVP ss1712305467 Apr 01, 2015 (144)
38 ILLUMINA ss1751934175 Sep 08, 2015 (146)
39 HAMMER_LAB ss1793706222 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1917960782 Feb 12, 2016 (147)
41 ILLUMINA ss1945981590 Feb 12, 2016 (147)
42 ILLUMINA ss1958229992 Feb 12, 2016 (147)
43 GENOMED ss1966667361 Jul 19, 2016 (147)
44 JJLAB ss2019498494 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147484470 Dec 20, 2016 (150)
46 TOPMED ss2321505196 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624264826 Nov 08, 2017 (151)
48 ILLUMINA ss2632465466 Nov 08, 2017 (151)
49 GRF ss2697374860 Nov 08, 2017 (151)
50 ILLUMINA ss2710663541 Nov 08, 2017 (151)
51 GNOMAD ss2750641672 Nov 08, 2017 (151)
52 SWEGEN ss2986149484 Nov 08, 2017 (151)
53 ILLUMINA ss3021043024 Nov 08, 2017 (151)
54 TOPMED ss3066406113 Nov 08, 2017 (151)
55 CSHL ss3343272692 Nov 08, 2017 (151)
56 ILLUMINA ss3625523487 Oct 11, 2018 (152)
57 ILLUMINA ss3626006538 Oct 11, 2018 (152)
58 ILLUMINA ss3630505590 Oct 11, 2018 (152)
59 ILLUMINA ss3632878030 Oct 11, 2018 (152)
60 ILLUMINA ss3633571436 Oct 11, 2018 (152)
61 ILLUMINA ss3634301816 Oct 11, 2018 (152)
62 ILLUMINA ss3635265641 Oct 11, 2018 (152)
63 ILLUMINA ss3635978609 Oct 11, 2018 (152)
64 ILLUMINA ss3637015980 Oct 11, 2018 (152)
65 ILLUMINA ss3637732370 Oct 11, 2018 (152)
66 ILLUMINA ss3640009182 Oct 11, 2018 (152)
67 ILLUMINA ss3644477462 Oct 11, 2018 (152)
68 ILLUMINA ss3651365075 Oct 11, 2018 (152)
69 EVA_DECODE ss3685992502 Jul 12, 2019 (153)
70 ILLUMINA ss3724988062 Jul 12, 2019 (153)
71 ACPOP ss3726716523 Jul 12, 2019 (153)
72 ILLUMINA ss3744040763 Jul 12, 2019 (153)
73 ILLUMINA ss3744602748 Jul 12, 2019 (153)
74 EVA ss3745721199 Jul 12, 2019 (153)
75 ILLUMINA ss3772104513 Jul 12, 2019 (153)
76 KHV_HUMAN_GENOMES ss3798743871 Jul 12, 2019 (153)
77 EVA ss3825981516 Apr 25, 2020 (154)
78 EVA ss3836378468 Apr 25, 2020 (154)
79 EVA ss3841782471 Apr 25, 2020 (154)
80 SGDP_PRJ ss3847996158 Apr 25, 2020 (154)
81 KRGDB ss3892836408 Apr 25, 2020 (154)
82 EVA ss3984450707 Apr 25, 2021 (155)
83 EVA ss4016889042 Apr 25, 2021 (155)
84 TOPMED ss4436440182 Apr 25, 2021 (155)
85 TOMMO_GENOMICS ss5142053347 Apr 25, 2021 (155)
86 1000Genomes NC_000001.10 - 798959 Oct 11, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 798959 Oct 11, 2018 (152)
88 Genome-wide autozygosity in Daghestan NC_000001.9 - 788822 Apr 25, 2020 (154)
89 gnomAD - Genomes NC_000001.11 - 863579 Apr 25, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000001.10 - 798959 Apr 25, 2020 (154)
91 HapMap NC_000001.11 - 863579 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000001.10 - 798959 Apr 25, 2020 (154)
93 Northern Sweden NC_000001.10 - 798959 Jul 12, 2019 (153)
94 CNV burdens in cranial meningiomas NC_000001.10 - 798959 Apr 25, 2021 (155)
95 Qatari NC_000001.10 - 798959 Apr 25, 2020 (154)
96 SGDP_PRJ NC_000001.10 - 798959 Apr 25, 2020 (154)
97 Siberian NC_000001.10 - 798959 Apr 25, 2020 (154)
98 8.3KJPN NC_000001.10 - 798959 Apr 25, 2021 (155)
99 TopMed NC_000001.11 - 863579 Apr 25, 2021 (155)
100 UK 10K study - Twins NC_000001.10 - 798959 Oct 11, 2018 (152)
101 ALFA NC_000001.11 - 863579 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)
rs61165853 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35124991, ss85876064 NC_000001.8:838821:G:A NC_000001.11:863578:G:A (self)
7, ss76654462, ss118438425, ss197885517, ss210446476, ss275680966, ss479508485, ss1397238520, ss1584129639, ss1712305467 NC_000001.9:788821:G:A NC_000001.11:863578:G:A (self)
5026, 519, 635, 13802, 1388, 6, 2712, 13138, 824, 22654, 519, ss230395507, ss479512442, ss479961175, ss484553510, ss536690617, ss647516444, ss778757199, ss782723416, ss783690912, ss831975042, ss834216922, ss974769608, ss1067612430, ss1289340259, ss1425684944, ss1599378555, ss1642372588, ss1751934175, ss1793706222, ss1917960782, ss1945981590, ss1958229992, ss1966667361, ss2019498494, ss2147484470, ss2321505196, ss2624264826, ss2632465466, ss2697374860, ss2710663541, ss2750641672, ss2986149484, ss3021043024, ss3343272692, ss3625523487, ss3626006538, ss3630505590, ss3632878030, ss3633571436, ss3634301816, ss3635265641, ss3635978609, ss3637015980, ss3637732370, ss3640009182, ss3644477462, ss3651365075, ss3726716523, ss3744040763, ss3744602748, ss3745721199, ss3772104513, ss3825981516, ss3836378468, ss3847996158, ss3892836408, ss3984450707, ss4016889042, ss5142053347 NC_000001.10:798958:G:A NC_000001.11:863578:G:A (self)
71360, 84, 21438, 46517, 2979200241, ss3066406113, ss3685992502, ss3724988062, ss3798743871, ss3841782471, ss4436440182 NC_000001.11:863578:G:A NC_000001.11:863578:G:A (self)
ss24152258, ss68756307, ss105027838, ss137752342, ss154522465, ss159973853, ss171207637 NT_004350.19:277590:G:A NC_000001.11:863578:G:A (self)
ss18273122, ss19853484 NT_034471.3:277590:G:A NC_000001.11:863578:G:A (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 rs11240777

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