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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.

rs4040617

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:843942 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.234467 (62061/264690, TOPMED)
G=0.236256 (33099/140098, GnomAD)
G=0.16691 (6726/40298, ALFA) (+ 16 more)
G=0.15033 (4248/28258, 14KJPN)
G=0.14952 (2506/16760, 8.3KJPN)
G=0.2347 (1503/6404, 1000G_30x)
G=0.2264 (1134/5008, 1000G)
G=0.1222 (471/3854, ALSPAC)
G=0.1276 (473/3708, TWINSUK)
G=0.1529 (448/2930, KOREAN)
G=0.2476 (465/1878, HapMap)
G=0.1567 (287/1832, Korea1K)
G=0.144 (144/998, GoNL)
G=0.135 (81/600, NorthernSweden)
G=0.185 (40/216, Qatari)
G=0.075 (16/214, Vietnamese)
A=0.450 (81/180, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
A=0.39 (7/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : Intron Variant
Publications
1 citation
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 40392 A=0.83309 G=0.16691
European Sub 34540 A=0.85950 G=0.14050
African Sub 3166 A=0.5644 G=0.4356
African Others Sub 128 A=0.555 G=0.445
African American Sub 3038 A=0.5648 G=0.4352
Asian Sub 134 A=0.903 G=0.097
East Asian Sub 106 A=0.906 G=0.094
Other Asian Sub 28 A=0.89 G=0.11
Latin American 1 Sub 178 A=0.719 G=0.281
Latin American 2 Sub 738 A=0.833 G=0.167
South Asian Sub 114 A=0.860 G=0.140
Other Sub 1522 A=0.7976 G=0.2024


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=0.765533 G=0.234467
gnomAD - Genomes Global Study-wide 140098 A=0.763744 G=0.236256
gnomAD - Genomes European Sub 75888 A=0.85158 G=0.14842
gnomAD - Genomes African Sub 41966 A=0.56715 G=0.43285
gnomAD - Genomes American Sub 13648 A=0.82173 G=0.17827
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.8494 G=0.1506
gnomAD - Genomes East Asian Sub 3126 A=0.9021 G=0.0979
gnomAD - Genomes Other Sub 2150 A=0.7991 G=0.2009
Allele Frequency Aggregator Total Global 40298 A=0.83309 G=0.16691
Allele Frequency Aggregator European Sub 34464 A=0.85956 G=0.14044
Allele Frequency Aggregator African Sub 3166 A=0.5644 G=0.4356
Allele Frequency Aggregator Other Sub 1504 A=0.7972 G=0.2028
Allele Frequency Aggregator Latin American 2 Sub 738 A=0.833 G=0.167
Allele Frequency Aggregator Latin American 1 Sub 178 A=0.719 G=0.281
Allele Frequency Aggregator Asian Sub 134 A=0.903 G=0.097
Allele Frequency Aggregator South Asian Sub 114 A=0.860 G=0.140
14KJPN JAPANESE Study-wide 28258 A=0.84967 G=0.15033
8.3KJPN JAPANESE Study-wide 16760 A=0.85048 G=0.14952
1000Genomes_30x Global Study-wide 6404 A=0.7653 G=0.2347
1000Genomes_30x African Sub 1786 A=0.5224 G=0.4776
1000Genomes_30x Europe Sub 1266 A=0.8831 G=0.1169
1000Genomes_30x South Asian Sub 1202 A=0.8245 G=0.1755
1000Genomes_30x East Asian Sub 1170 A=0.8855 G=0.1145
1000Genomes_30x American Sub 980 A=0.840 G=0.160
1000Genomes Global Study-wide 5008 A=0.7736 G=0.2264
1000Genomes African Sub 1322 A=0.5272 G=0.4728
1000Genomes East Asian Sub 1008 A=0.8879 G=0.1121
1000Genomes Europe Sub 1006 A=0.8817 G=0.1183
1000Genomes South Asian Sub 978 A=0.827 G=0.173
1000Genomes American Sub 694 A=0.844 G=0.156
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8778 G=0.1222
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8724 G=0.1276
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.8471 G=0.1529
HapMap Global Study-wide 1878 A=0.7524 G=0.2476
HapMap American Sub 770 A=0.825 G=0.175
HapMap African Sub 680 A=0.575 G=0.425
HapMap Asian Sub 252 A=0.897 G=0.103
HapMap Europe Sub 176 A=0.915 G=0.085
Korean Genome Project KOREAN Study-wide 1832 A=0.8433 G=0.1567
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.856 G=0.144
Northern Sweden ACPOP Study-wide 600 A=0.865 G=0.135
Qatari Global Study-wide 216 A=0.815 G=0.185
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.925 G=0.075
SGDP_PRJ Global Study-wide 180 A=0.450 G=0.550
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
Siberian Global Study-wide 18 A=0.39 G=0.61
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 1 NC_000001.11:g.843942A>G
GRCh37.p13 chr 1 NC_000001.10:g.779322A>G
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n. N/A Intron Variant
LINC01128 transcript variant 3 NR_047521.1:n. N/A Intron Variant
LINC01128 transcript variant 5 NR_047523.1:n. N/A Intron Variant
LINC01128 transcript variant 7 NR_047524.1:n. N/A Intron Variant
LINC01128 transcript variant 8 NR_047525.1:n. N/A Intron Variant
LINC01128 transcript variant 9 NR_047526.1: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
GRCh38.p14 chr 1 NC_000001.11:g.843942= NC_000001.11:g.843942A>G
GRCh37.p13 chr 1 NC_000001.10:g.779322= NC_000001.10:g.779322A>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#.

71 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5397759 Oct 10, 2002 (108)
2 SC_JCM ss6221804 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9878998 Jul 11, 2003 (117)
4 ABI ss46530420 Mar 15, 2006 (126)
5 AFFY ss66273559 Dec 02, 2006 (127)
6 ILLUMINA ss75251476 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss81989376 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss87155937 Mar 23, 2008 (129)
9 ENSEMBL ss137752282 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss165981035 Jul 04, 2010 (132)
11 ILLUMINA ss173681057 Jul 04, 2010 (132)
12 1000GENOMES ss218190426 Jul 14, 2010 (132)
13 GMI ss275680877 May 04, 2012 (137)
14 ILLUMINA ss482403659 May 04, 2012 (137)
15 ILLUMINA ss483501648 May 04, 2012 (137)
16 ILLUMINA ss535709683 Sep 08, 2015 (146)
17 TISHKOFF ss553710509 Apr 25, 2013 (138)
18 ILLUMINA ss780301317 Aug 21, 2014 (142)
19 ILLUMINA ss782194227 Aug 21, 2014 (142)
20 ILLUMINA ss835788050 Aug 21, 2014 (142)
21 EVA-GONL ss974769456 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1067612366 Aug 21, 2014 (142)
23 1000GENOMES ss1289339620 Aug 21, 2014 (142)
24 DDI ss1425684887 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1573851176 Apr 01, 2015 (144)
26 EVA_DECODE ss1584129527 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1599378441 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1642372474 Apr 01, 2015 (144)
29 EVA_SVP ss1712305463 Apr 01, 2015 (144)
30 HAMMER_LAB ss1793705865 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1917960510 Feb 12, 2016 (147)
32 GENOMED ss1966667337 Jul 19, 2016 (147)
33 JJLAB ss2019498438 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147484423 Dec 20, 2016 (150)
35 ILLUMINA ss2632465454 Nov 08, 2017 (151)
36 GRF ss2697374718 Nov 08, 2017 (151)
37 GNOMAD ss2750639640 Nov 08, 2017 (151)
38 AFFY ss2984840985 Nov 08, 2017 (151)
39 AFFY ss2985494978 Nov 08, 2017 (151)
40 SWEGEN ss2986149183 Nov 08, 2017 (151)
41 CSHL ss3343272617 Nov 08, 2017 (151)
42 ILLUMINA ss3626006510 Oct 11, 2018 (152)
43 ILLUMINA ss3630505579 Oct 11, 2018 (152)
44 ILLUMINA ss3637732365 Oct 11, 2018 (152)
45 ILLUMINA ss3641566152 Oct 11, 2018 (152)
46 ILLUMINA ss3642746668 Oct 11, 2018 (152)
47 ILLUMINA ss3653614736 Oct 11, 2018 (152)
48 EVA_DECODE ss3685992233 Jul 12, 2019 (153)
49 ACPOP ss3726716419 Jul 12, 2019 (153)
50 EVA ss3745721052 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3798743689 Jul 12, 2019 (153)
52 EVA ss3825981479 Apr 25, 2020 (154)
53 EVA ss3836378431 Apr 25, 2020 (154)
54 EVA ss3841782431 Apr 25, 2020 (154)
55 SGDP_PRJ ss3847995679 Apr 25, 2020 (154)
56 KRGDB ss3892835980 Apr 25, 2020 (154)
57 KOGIC ss3943629767 Apr 25, 2020 (154)
58 EVA ss4016889039 Apr 25, 2021 (155)
59 TOPMED ss4436435228 Apr 25, 2021 (155)
60 TOMMO_GENOMICS ss5142052492 Apr 25, 2021 (155)
61 1000G_HIGH_COVERAGE ss5240863690 Oct 12, 2022 (156)
62 EVA ss5314585876 Oct 12, 2022 (156)
63 EVA ss5316183753 Oct 12, 2022 (156)
64 HUGCELL_USP ss5442112364 Oct 12, 2022 (156)
65 1000G_HIGH_COVERAGE ss5512488424 Oct 12, 2022 (156)
66 SANFORD_IMAGENETICS ss5624749478 Oct 12, 2022 (156)
67 TOMMO_GENOMICS ss5666191877 Oct 12, 2022 (156)
68 YY_MCH ss5800243813 Oct 12, 2022 (156)
69 EVA ss5831418452 Oct 12, 2022 (156)
70 EVA ss5906704882 Oct 12, 2022 (156)
71 EVA ss5936582757 Oct 12, 2022 (156)
72 1000Genomes NC_000001.10 - 779322 Oct 11, 2018 (152)
73 1000Genomes_30x NC_000001.11 - 843942 Oct 12, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 779322 Oct 11, 2018 (152)
75 The Danish reference pan genome NC_000001.10 - 779322 Apr 25, 2020 (154)
76 gnomAD - Genomes NC_000001.11 - 843942 Apr 25, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000001.10 - 779322 Apr 25, 2020 (154)
78 HapMap NC_000001.11 - 843942 Apr 25, 2020 (154)
79 KOREAN population from KRGDB NC_000001.10 - 779322 Apr 25, 2020 (154)
80 Korean Genome Project NC_000001.11 - 843942 Apr 25, 2020 (154)
81 Northern Sweden NC_000001.10 - 779322 Jul 12, 2019 (153)
82 Qatari NC_000001.10 - 779322 Apr 25, 2020 (154)
83 SGDP_PRJ NC_000001.10 - 779322 Apr 25, 2020 (154)
84 Siberian NC_000001.10 - 779322 Apr 25, 2020 (154)
85 8.3KJPN NC_000001.10 - 779322 Apr 25, 2021 (155)
86 14KJPN NC_000001.11 - 843942 Oct 12, 2022 (156)
87 TopMed NC_000001.11 - 843942 Apr 25, 2021 (155)
88 UK 10K study - Twins NC_000001.10 - 779322 Oct 11, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000001.10 - 779322 Jul 12, 2019 (153)
90 ALFA NC_000001.11 - 843942 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)
rs6691036 Aug 27, 2003 (117)
rs56714435 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66273559, ss87155937, ss165981035, ss275680877, ss482403659, ss1584129527, ss1712305463, ss3642746668 NC_000001.9:769184:A:G NC_000001.11:843941:A:G (self)
4360, 370, 1358410, 495, 13374, 1284, 2440, 12659, 777, 21799, 370, 78, ss218190426, ss483501648, ss535709683, ss553710509, ss780301317, ss782194227, ss835788050, ss974769456, ss1067612366, ss1289339620, ss1425684887, ss1573851176, ss1599378441, ss1642372474, ss1793705865, ss1917960510, ss1966667337, ss2019498438, ss2147484423, ss2632465454, ss2697374718, ss2750639640, ss2984840985, ss2985494978, ss2986149183, ss3343272617, ss3626006510, ss3630505579, ss3637732365, ss3641566152, ss3653614736, ss3726716419, ss3745721052, ss3825981479, ss3836378431, ss3847995679, ss3892835980, ss4016889039, ss5142052492, ss5314585876, ss5316183753, ss5624749478, ss5831418452, ss5936582757 NC_000001.10:779321:A:G NC_000001.11:843941:A:G (self)
14359, 67149, 68, 7768, 28981, 41563, 4615089899, ss3685992233, ss3798743689, ss3841782431, ss3943629767, ss4436435228, ss5240863690, ss5442112364, ss5512488424, ss5666191877, ss5800243813, ss5906704882 NC_000001.11:843941:A:G NC_000001.11:843941:A:G (self)
ss5397759, ss6221804, ss46530420, ss75251476, ss81989376, ss137752282, ss173681057 NT_004350.19:257953:A:G NC_000001.11:843941:A:G (self)
ss9878998 NT_034471.3:257953:A:G NC_000001.11:843941:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs4040617
PMID Title Author Year Journal
21159730 Damming the genomic data flood using a comprehensive analysis and storage data structure. Bouffard M et al. 2010 Database
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