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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.

rs230490

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:102466262 (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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.342907 (90764/264690, TOPMED)
A=0.394877 (59846/151556, ALFA)
A=0.339382 (47464/139854, GnomAD) (+ 15 more)
G=0.28067 (4704/16760, 8.3KJPN)
A=0.3746 (1876/5008, 1000G)
A=0.3980 (1783/4480, Estonian)
A=0.4235 (1632/3854, ALSPAC)
A=0.4226 (1567/3708, TWINSUK)
G=0.3355 (983/2930, KOREAN)
G=0.3450 (632/1832, Korea1K)
A=0.431 (430/998, GoNL)
A=0.407 (244/600, NorthernSweden)
A=0.363 (119/328, HapMap)
G=0.346 (106/306, SGDP_PRJ)
A=0.213 (46/216, Qatari)
G=0.458 (98/214, Vietnamese)
A=0.45 (18/40, GENOME_DK)
G=0.40 (16/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105377621 : Intron Variant
Publications
3 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 4 NC_000004.12:g.102466262G>A
GRCh38.p13 chr 4 NC_000004.12:g.102466262G>C
GRCh38.p13 chr 4 NC_000004.12:g.102466262G>T
GRCh37.p13 chr 4 NC_000004.11:g.103387419G>A
GRCh37.p13 chr 4 NC_000004.11:g.103387419G>C
GRCh37.p13 chr 4 NC_000004.11:g.103387419G>T
Gene: LOC105377621, uncharacterized LOC105377621 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105377621 transcript NR_136202.1: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 151556 G=0.605123 A=0.394877
European Sub 130060 G=0.596986 A=0.403014
African Sub 7792 G=0.8378 A=0.1622
African Others Sub 284 G=0.873 A=0.127
African American Sub 7508 G=0.8364 A=0.1636
Asian Sub 378 G=0.376 A=0.624
East Asian Sub 278 G=0.371 A=0.629
Other Asian Sub 100 G=0.39 A=0.61
Latin American 1 Sub 702 G=0.652 A=0.348
Latin American 2 Sub 6076 G=0.4937 A=0.5063
South Asian Sub 168 G=0.714 A=0.286
Other Sub 6380 G=0.5984 A=0.4016


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=0.657093 A=0.342907
gnomAD - Genomes Global Study-wide 139854 G=0.660618 A=0.339382
gnomAD - Genomes European Sub 75766 G=0.59263 A=0.40737
gnomAD - Genomes African Sub 41894 G=0.83907 A=0.16093
gnomAD - Genomes American Sub 13604 G=0.55006 A=0.44994
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.6523 A=0.3477
gnomAD - Genomes East Asian Sub 3124 G=0.4286 A=0.5714
gnomAD - Genomes Other Sub 2150 G=0.6288 A=0.3712
8.3KJPN JAPANESE Study-wide 16760 G=0.28067 A=0.71933
1000Genomes Global Study-wide 5008 G=0.6254 A=0.3746
1000Genomes African Sub 1322 G=0.8608 A=0.1392
1000Genomes East Asian Sub 1008 G=0.4464 A=0.5536
1000Genomes Europe Sub 1006 G=0.6113 A=0.3887
1000Genomes South Asian Sub 978 G=0.584 A=0.416
1000Genomes American Sub 694 G=0.516 A=0.484
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6020 A=0.3980
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5765 A=0.4235
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5774 A=0.4226
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.3355 A=0.6645, C=0.0000, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.3450 A=0.6550
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.569 A=0.431
Northern Sweden ACPOP Study-wide 600 G=0.593 A=0.407
HapMap Global Study-wide 328 G=0.637 A=0.363
HapMap African Sub 120 G=0.867 A=0.133
HapMap American Sub 120 G=0.625 A=0.375
HapMap Asian Sub 88 G=0.34 A=0.66
SGDP_PRJ Global Study-wide 306 G=0.346 A=0.654
Qatari Global Study-wide 216 G=0.787 A=0.213
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.458 A=0.542
The Danish reference pan genome Danish Study-wide 40 G=0.55 A=0.45
Siberian Global Study-wide 40 G=0.40 A=0.60
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 C T
GRCh38.p13 chr 4 NC_000004.12:g.102466262= NC_000004.12:g.102466262G>A NC_000004.12:g.102466262G>C NC_000004.12:g.102466262G>T
GRCh37.p13 chr 4 NC_000004.11:g.103387419= NC_000004.11:g.103387419G>A NC_000004.11:g.103387419G>C NC_000004.11:g.103387419G>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#.

94 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss298175 Jul 12, 2000 (79)
2 KWOK ss1043234 Oct 04, 2000 (86)
3 KWOK ss1949112 Oct 18, 2000 (89)
4 SC_JCM ss4126901 Nov 05, 2001 (101)
5 BCM_SSAHASNP ss10140543 Jul 11, 2003 (116)
6 CSHL-HAPMAP ss17822017 Feb 27, 2004 (120)
7 SSAHASNP ss22193667 Apr 05, 2004 (121)
8 ABI ss44543662 Mar 15, 2006 (126)
9 ILLUMINA ss65718059 Oct 16, 2006 (127)
10 HGSV ss77449926 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss80750573 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss92710621 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss98849757 Feb 04, 2009 (130)
14 BGI ss105849498 Feb 04, 2009 (130)
15 1000GENOMES ss108187969 Jan 23, 2009 (130)
16 1000GENOMES ss110324108 Jan 24, 2009 (130)
17 ILLUMINA-UK ss117122404 Feb 14, 2009 (130)
18 ILLUMINA ss120240166 Dec 01, 2009 (131)
19 ENSEMBL ss135200600 Dec 01, 2009 (131)
20 ILLUMINA ss160534404 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss162399830 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss163959731 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss166968680 Jul 04, 2010 (132)
24 BUSHMAN ss198948825 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss206290625 Jul 04, 2010 (132)
26 1000GENOMES ss221111164 Jul 14, 2010 (132)
27 1000GENOMES ss232524168 Jul 14, 2010 (132)
28 1000GENOMES ss239786860 Jul 15, 2010 (132)
29 ILLUMINA ss244256726 Jul 04, 2010 (132)
30 BL ss253387268 May 09, 2011 (134)
31 GMI ss277853021 May 04, 2012 (137)
32 GMI ss284971963 Apr 25, 2013 (138)
33 PJP ss293151873 May 09, 2011 (134)
34 ILLUMINA ss480525019 May 04, 2012 (137)
35 ILLUMINA ss480541076 May 04, 2012 (137)
36 ILLUMINA ss481352003 Sep 08, 2015 (146)
37 ILLUMINA ss485059738 May 04, 2012 (137)
38 ILLUMINA ss537075446 Sep 08, 2015 (146)
39 TISHKOFF ss557735786 Apr 25, 2013 (138)
40 SSMP ss651539143 Apr 25, 2013 (138)
41 ILLUMINA ss778864875 Aug 21, 2014 (142)
42 ILLUMINA ss782976111 Aug 21, 2014 (142)
43 ILLUMINA ss783937268 Aug 21, 2014 (142)
44 ILLUMINA ss832232559 Apr 01, 2015 (144)
45 ILLUMINA ss834325709 Aug 21, 2014 (142)
46 EVA-GONL ss980475182 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1071805541 Aug 21, 2014 (142)
48 1000GENOMES ss1311066223 Aug 21, 2014 (142)
49 HAMMER_LAB ss1397384124 Sep 08, 2015 (146)
50 DDI ss1429990346 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1580697091 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1610785605 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1653779638 Apr 01, 2015 (144)
54 ILLUMINA ss1752490122 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1923714479 Feb 12, 2016 (147)
56 GENOMED ss1969822294 Jul 19, 2016 (147)
57 JJLAB ss2022443299 Sep 14, 2016 (149)
58 USC_VALOUEV ss2150572510 Dec 20, 2016 (150)
59 HUMAN_LONGEVITY ss2265608808 Dec 20, 2016 (150)
60 TOPMED ss2433430065 Dec 20, 2016 (150)
61 SYSTEMSBIOZJU ss2625720158 Nov 08, 2017 (151)
62 ILLUMINA ss2634157379 Nov 08, 2017 (151)
63 GRF ss2706049631 Nov 08, 2017 (151)
64 ILLUMINA ss2711012242 Nov 08, 2017 (151)
65 GNOMAD ss2813102570 Nov 08, 2017 (151)
66 SWEGEN ss2995246806 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3024997274 Nov 08, 2017 (151)
68 CSHL ss3345872765 Nov 08, 2017 (151)
69 TOPMED ss3437813366 Nov 08, 2017 (151)
70 ILLUMINA ss3629030234 Oct 12, 2018 (152)
71 ILLUMINA ss3632091586 Oct 12, 2018 (152)
72 ILLUMINA ss3633343990 Oct 12, 2018 (152)
73 ILLUMINA ss3634063314 Oct 12, 2018 (152)
74 ILLUMINA ss3634964253 Oct 12, 2018 (152)
75 ILLUMINA ss3635746030 Oct 12, 2018 (152)
76 ILLUMINA ss3636668685 Oct 12, 2018 (152)
77 ILLUMINA ss3637498571 Oct 12, 2018 (152)
78 ILLUMINA ss3640671546 Oct 12, 2018 (152)
79 EGCUT_WGS ss3663144624 Jul 13, 2019 (153)
80 EVA_DECODE ss3712700510 Jul 13, 2019 (153)
81 ACPOP ss3731442111 Jul 13, 2019 (153)
82 ILLUMINA ss3745264510 Jul 13, 2019 (153)
83 EVA ss3762192349 Jul 13, 2019 (153)
84 ILLUMINA ss3772759040 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3805340835 Jul 13, 2019 (153)
86 EVA ss3828715419 Apr 26, 2020 (154)
87 EVA ss3837798910 Apr 26, 2020 (154)
88 EVA ss3843237434 Apr 26, 2020 (154)
89 SGDP_PRJ ss3859656604 Apr 26, 2020 (154)
90 KRGDB ss3905935242 Apr 26, 2020 (154)
91 KOGIC ss3954780356 Apr 26, 2020 (154)
92 EVA ss4017160604 Apr 26, 2021 (155)
93 TOPMED ss4625411336 Apr 26, 2021 (155)
94 TOMMO_GENOMICS ss5167171951 Apr 26, 2021 (155)
95 1000Genomes NC_000004.11 - 103387419 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 103387419 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000004.11 - 103387419 Oct 12, 2018 (152)
98 The Danish reference pan genome NC_000004.11 - 103387419 Apr 26, 2020 (154)
99 gnomAD - Genomes NC_000004.12 - 102466262 Apr 26, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000004.11 - 103387419 Apr 26, 2020 (154)
101 HapMap NC_000004.12 - 102466262 Apr 26, 2020 (154)
102 KOREAN population from KRGDB NC_000004.11 - 103387419 Apr 26, 2020 (154)
103 Korean Genome Project NC_000004.12 - 102466262 Apr 26, 2020 (154)
104 Northern Sweden NC_000004.11 - 103387419 Jul 13, 2019 (153)
105 Qatari NC_000004.11 - 103387419 Apr 26, 2020 (154)
106 SGDP_PRJ NC_000004.11 - 103387419 Apr 26, 2020 (154)
107 Siberian NC_000004.11 - 103387419 Apr 26, 2020 (154)
108 8.3KJPN NC_000004.11 - 103387419 Apr 26, 2021 (155)
109 TopMed NC_000004.12 - 102466262 Apr 26, 2021 (155)
110 UK 10K study - Twins NC_000004.11 - 103387419 Oct 12, 2018 (152)
111 A Vietnamese Genetic Variation Database NC_000004.11 - 103387419 Jul 13, 2019 (153)
112 ALFA NC_000004.12 - 102466262 Apr 26, 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)
rs1313893 Nov 09, 2000 (89)
rs57119528 May 23, 2008 (130)
rs386564470 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77449926 NC_000004.9:103744597:A:A NC_000004.12:102466261:G:A (self)
ss92710621, ss108187969, ss110324108, ss117122404, ss160534404, ss162399830, ss163959731, ss166968680, ss198948825, ss206290625, ss244256726, ss253387268, ss277853021, ss284971963, ss293151873, ss480525019, ss1397384124 NC_000004.10:103606442:A:A NC_000004.12:102466261:G:A (self)
22511702, 12526334, 8882872, 6862030, 5538195, 13112636, 4726976, 5756409, 11673584, 3088864, 25141258, 12526334, 2755320, ss221111164, ss232524168, ss239786860, ss480541076, ss481352003, ss485059738, ss537075446, ss557735786, ss651539143, ss778864875, ss782976111, ss783937268, ss832232559, ss834325709, ss980475182, ss1071805541, ss1311066223, ss1429990346, ss1580697091, ss1610785605, ss1653779638, ss1752490122, ss1923714479, ss1969822294, ss2022443299, ss2150572510, ss2433430065, ss2625720158, ss2634157379, ss2706049631, ss2711012242, ss2813102570, ss2995246806, ss3345872765, ss3629030234, ss3632091586, ss3633343990, ss3634063314, ss3634964253, ss3635746030, ss3636668685, ss3637498571, ss3640671546, ss3663144624, ss3731442111, ss3745264510, ss3762192349, ss3772759040, ss3828715419, ss3837798910, ss3859656604, ss3905935242, ss4017160604, ss5167171951 NC_000004.11:103387418:G:A NC_000004.12:102466261:G:A (self)
159471590, 2674302, 11158357, 289289617, 462788892, 3212776132, ss2265608808, ss3024997274, ss3437813366, ss3712700510, ss3805340835, ss3843237434, ss3954780356, ss4625411336 NC_000004.12:102466261:G:A NC_000004.12:102466261:G:A (self)
ss10140543 NT_016354.15:27882123:A:A NC_000004.12:102466261:G:A (self)
ss17822017, ss22193667 NT_016354.16:27882123:A:A NC_000004.12:102466261:G:A (self)
ss298175, ss1043234, ss1949112, ss4126901, ss44543662, ss65718059, ss80750573, ss98849757, ss105849498, ss120240166, ss135200600 NT_016354.19:27935139:G:A NC_000004.12:102466261:G:A (self)
13112636, ss3905935242 NC_000004.11:103387418:G:C NC_000004.12:102466261:G:C (self)
13112636, ss3905935242 NC_000004.11:103387418:G:T NC_000004.12:102466261:G:T (self)
Help

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

3 citations for rs230490
PMID Title Author Year Journal
19001172 Analyses of the National Institute on Aging Late-Onset Alzheimer's Disease Family Study: implication of additional loci. Lee JH et al. 2008 Archives of neurology
23002237 IκBKβ and NFκB1, NSAID use and risk of colorectal cancer in the Colon Cancer Family Registry. Seufert BL et al. 2013 Carcinogenesis
24889212 Systematic review: interactions between aspirin, and other nonsteroidal anti-inflammatory drugs, and polymorphisms in relation to colorectal cancer. Andersen V et al. 2014 Alimentary pharmacology & therapeutics
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