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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.

rs4801131

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:55085469 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.397174 (105128/264690, TOPMED)
T=0.393864 (55122/139952, GnomAD)
T=0.40880 (32172/78698, PAGE_STUDY) (+ 21 more)
C=0.37650 (10639/28258, 14KJPN)
T=0.39352 (7229/18370, ALFA)
C=0.37763 (6329/16760, 8.3KJPN)
T=0.3904 (2500/6404, 1000G_30x)
T=0.3936 (1971/5008, 1000G)
T=0.4324 (1937/4480, Estonian)
T=0.3972 (1531/3854, ALSPAC)
T=0.3892 (1443/3708, TWINSUK)
C=0.4212 (1234/2930, KOREAN)
C=0.4279 (784/1832, Korea1K)
T=0.3838 (436/1136, Daghestan)
T=0.398 (397/998, GoNL)
C=0.380 (298/784, PRJEB37584)
T=0.485 (291/600, NorthernSweden)
C=0.371 (126/340, SGDP_PRJ)
T=0.457 (150/328, HapMap)
T=0.412 (89/216, Qatari)
C=0.340 (72/212, Vietnamese)
T=0.42 (17/40, GENOME_DK)
C=0.33 (12/36, Siberian)
T=0.45 (10/22, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC03035 : Non Coding Transcript Variant
Publications
0 citations
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 18370 C=0.60648 A=0.00000, T=0.39352
European Sub 13942 C=0.59798 A=0.00000, T=0.40202
African Sub 2674 C=0.6687 A=0.0000, T=0.3313
African Others Sub 100 C=0.66 A=0.00, T=0.34
African American Sub 2574 C=0.6690 A=0.0000, T=0.3310
Asian Sub 146 C=0.349 A=0.000, T=0.651
East Asian Sub 120 C=0.317 A=0.000, T=0.683
Other Asian Sub 26 C=0.50 A=0.00, T=0.50
Latin American 1 Sub 146 C=0.658 A=0.000, T=0.342
Latin American 2 Sub 610 C=0.582 A=0.000, T=0.418
South Asian Sub 104 C=0.683 A=0.000, T=0.317
Other Sub 748 C=0.592 A=0.000, T=0.408


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=0.602826 T=0.397174
gnomAD - Genomes Global Study-wide 139952 C=0.606136 T=0.393864
gnomAD - Genomes European Sub 75824 C=0.58955 T=0.41045
gnomAD - Genomes African Sub 41892 C=0.65454 T=0.34546
gnomAD - Genomes American Sub 13640 C=0.59406 T=0.40594
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.6301 T=0.3699
gnomAD - Genomes East Asian Sub 3124 C=0.3864 T=0.6136
gnomAD - Genomes Other Sub 2152 C=0.6069 T=0.3931
The PAGE Study Global Study-wide 78698 C=0.59120 T=0.40880
The PAGE Study AfricanAmerican Sub 32516 C=0.64716 T=0.35284
The PAGE Study Mexican Sub 10808 C=0.56541 T=0.43459
The PAGE Study Asian Sub 8318 C=0.3795 T=0.6205
The PAGE Study PuertoRican Sub 7916 C=0.6210 T=0.3790
The PAGE Study NativeHawaiian Sub 4534 C=0.5227 T=0.4773
The PAGE Study Cuban Sub 4230 C=0.6213 T=0.3787
The PAGE Study Dominican Sub 3828 C=0.6343 T=0.3657
The PAGE Study CentralAmerican Sub 2450 C=0.5837 T=0.4163
The PAGE Study SouthAmerican Sub 1982 C=0.5656 T=0.4344
The PAGE Study NativeAmerican Sub 1260 C=0.5849 T=0.4151
The PAGE Study SouthAsian Sub 856 C=0.683 T=0.317
14KJPN JAPANESE Study-wide 28258 C=0.37650 T=0.62350
Allele Frequency Aggregator Total Global 18370 C=0.60648 A=0.00000, T=0.39352
Allele Frequency Aggregator European Sub 13942 C=0.59798 A=0.00000, T=0.40202
Allele Frequency Aggregator African Sub 2674 C=0.6687 A=0.0000, T=0.3313
Allele Frequency Aggregator Other Sub 748 C=0.592 A=0.000, T=0.408
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.582 A=0.000, T=0.418
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.658 A=0.000, T=0.342
Allele Frequency Aggregator Asian Sub 146 C=0.349 A=0.000, T=0.651
Allele Frequency Aggregator South Asian Sub 104 C=0.683 A=0.000, T=0.317
8.3KJPN JAPANESE Study-wide 16760 C=0.37763 T=0.62237
1000Genomes_30x Global Study-wide 6404 C=0.6096 T=0.3904
1000Genomes_30x African Sub 1786 C=0.6954 T=0.3046
1000Genomes_30x Europe Sub 1266 C=0.6051 T=0.3949
1000Genomes_30x South Asian Sub 1202 C=0.7121 T=0.2879
1000Genomes_30x East Asian Sub 1170 C=0.4085 T=0.5915
1000Genomes_30x American Sub 980 C=0.573 T=0.427
1000Genomes Global Study-wide 5008 C=0.6064 T=0.3936
1000Genomes African Sub 1322 C=0.6823 T=0.3177
1000Genomes East Asian Sub 1008 C=0.4018 T=0.5982
1000Genomes Europe Sub 1006 C=0.6143 T=0.3857
1000Genomes South Asian Sub 978 C=0.719 T=0.281
1000Genomes American Sub 694 C=0.589 T=0.411
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5676 T=0.4324
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6028 T=0.3972
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6108 T=0.3892
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4212 T=0.5788
Korean Genome Project KOREAN Study-wide 1832 C=0.4279 T=0.5721
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.6162 T=0.3838
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.605 T=0.395
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.681 T=0.319
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.533 T=0.467
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.648 T=0.352
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.67 T=0.33
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.58 T=0.42
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.602 T=0.398
CNV burdens in cranial meningiomas Global Study-wide 784 C=0.380 T=0.620
CNV burdens in cranial meningiomas CRM Sub 784 C=0.380 T=0.620
Northern Sweden ACPOP Study-wide 600 C=0.515 T=0.485
SGDP_PRJ Global Study-wide 340 C=0.371 T=0.629
HapMap Global Study-wide 328 C=0.543 T=0.457
HapMap African Sub 120 C=0.692 T=0.308
HapMap American Sub 120 C=0.542 T=0.458
HapMap Asian Sub 88 C=0.34 T=0.66
Qatari Global Study-wide 216 C=0.588 T=0.412
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.340 T=0.660
The Danish reference pan genome Danish Study-wide 40 C=0.57 T=0.42
Siberian Global Study-wide 36 C=0.33 T=0.67
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 22 C=0.55 T=0.45
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 18 NC_000018.10:g.55085469C>A
GRCh38.p14 chr 18 NC_000018.10:g.55085469C>T
GRCh37.p13 chr 18 NC_000018.9:g.52752700C>A
GRCh37.p13 chr 18 NC_000018.9:g.52752700C>T
Gene: LINC03035, uncharacterized LINC03035 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC03035 transcript XR_935478.3:n.124G>T N/A Non Coding Transcript Variant
LINC03035 transcript XR_935478.3:n.124G>A N/A Non Coding 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 C= A T
GRCh38.p14 chr 18 NC_000018.10:g.55085469= NC_000018.10:g.55085469C>A NC_000018.10:g.55085469C>T
GRCh37.p13 chr 18 NC_000018.9:g.52752700= NC_000018.9:g.52752700C>A NC_000018.9:g.52752700C>T
LINC03035 transcript XR_935478.3:n.124= XR_935478.3:n.124G>T XR_935478.3:n.124G>A
LOC105372125 transcript XR_935478.2:n.165= XR_935478.2:n.165G>T XR_935478.2:n.165G>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#.

83 SubSNP, 24 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6626665 Feb 20, 2003 (111)
2 CSHL-HAPMAP ss17599875 Feb 27, 2004 (120)
3 SSAHASNP ss21491246 Apr 05, 2004 (121)
4 ABI ss44085340 Mar 13, 2006 (126)
5 HGSV ss78049278 Dec 06, 2007 (129)
6 HUMANGENOME_JCVI ss96513944 Feb 05, 2009 (130)
7 1000GENOMES ss110592598 Jan 25, 2009 (130)
8 1000GENOMES ss114439809 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117888221 Feb 14, 2009 (130)
10 ENSEMBL ss136400000 Dec 01, 2009 (131)
11 GMI ss155217436 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss168286526 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss169902720 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss171828817 Jul 04, 2010 (132)
15 BUSHMAN ss203313683 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss208125054 Jul 04, 2010 (132)
17 1000GENOMES ss227888327 Jul 14, 2010 (132)
18 1000GENOMES ss237487584 Jul 15, 2010 (132)
19 1000GENOMES ss243732629 Jul 15, 2010 (132)
20 BL ss255688755 May 09, 2011 (134)
21 GMI ss283010184 May 04, 2012 (137)
22 GMI ss287291969 Apr 25, 2013 (138)
23 PJP ss292078865 May 09, 2011 (134)
24 TISHKOFF ss565673809 Apr 25, 2013 (138)
25 SSMP ss661509176 Apr 25, 2013 (138)
26 EVA-GONL ss993783566 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1081541544 Aug 21, 2014 (142)
28 1000GENOMES ss1361240803 Aug 21, 2014 (142)
29 HAMMER_LAB ss1397747133 Sep 08, 2015 (146)
30 DDI ss1428234772 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1578427052 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1636992211 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1679986244 Apr 01, 2015 (144)
34 HAMMER_LAB ss1809074414 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1937251833 Feb 12, 2016 (147)
36 ILLUMINA ss1959808128 Feb 12, 2016 (147)
37 GENOMED ss1968536674 Jul 19, 2016 (147)
38 JJLAB ss2029395825 Sep 14, 2016 (149)
39 USC_VALOUEV ss2157903113 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2222020226 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2629196208 Nov 08, 2017 (151)
42 GRF ss2702493727 Nov 08, 2017 (151)
43 GNOMAD ss2957291864 Nov 08, 2017 (151)
44 SWEGEN ss3016613596 Nov 08, 2017 (151)
45 ILLUMINA ss3021847777 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3028527569 Nov 08, 2017 (151)
47 CSHL ss3352048049 Nov 08, 2017 (151)
48 URBANLAB ss3650801753 Oct 12, 2018 (152)
49 ILLUMINA ss3652269909 Oct 12, 2018 (152)
50 EGCUT_WGS ss3683458800 Jul 13, 2019 (153)
51 ILLUMINA ss3725680807 Jul 13, 2019 (153)
52 ACPOP ss3742590091 Jul 13, 2019 (153)
53 EVA ss3755458117 Jul 13, 2019 (153)
54 PAGE_CC ss3771974887 Jul 13, 2019 (153)
55 PACBIO ss3788385864 Jul 13, 2019 (153)
56 PACBIO ss3793315183 Jul 13, 2019 (153)
57 PACBIO ss3798201619 Jul 13, 2019 (153)
58 KHV_HUMAN_GENOMES ss3820715029 Jul 13, 2019 (153)
59 EVA ss3835196741 Apr 27, 2020 (154)
60 EVA ss3841216410 Apr 27, 2020 (154)
61 EVA ss3846718790 Apr 27, 2020 (154)
62 SGDP_PRJ ss3887129987 Apr 27, 2020 (154)
63 KRGDB ss3937014461 Apr 27, 2020 (154)
64 KOGIC ss3980250602 Apr 27, 2020 (154)
65 EVA ss3984733644 Apr 27, 2021 (155)
66 EVA ss3985829453 Apr 27, 2021 (155)
67 TOPMED ss5058600625 Apr 27, 2021 (155)
68 TOMMO_GENOMICS ss5225412283 Apr 27, 2021 (155)
69 1000G_HIGH_COVERAGE ss5305479192 Oct 16, 2022 (156)
70 HUGCELL_USP ss5498228568 Oct 16, 2022 (156)
71 EVA ss5511960005 Oct 16, 2022 (156)
72 1000G_HIGH_COVERAGE ss5610419810 Oct 16, 2022 (156)
73 SANFORD_IMAGENETICS ss5624415385 Oct 16, 2022 (156)
74 SANFORD_IMAGENETICS ss5661401655 Oct 16, 2022 (156)
75 TOMMO_GENOMICS ss5783272879 Oct 16, 2022 (156)
76 YY_MCH ss5817145938 Oct 16, 2022 (156)
77 EVA ss5827618517 Oct 16, 2022 (156)
78 EVA ss5847487401 Oct 16, 2022 (156)
79 EVA ss5847823132 Oct 16, 2022 (156)
80 EVA ss5852076183 Oct 16, 2022 (156)
81 EVA ss5874301129 Oct 16, 2022 (156)
82 EVA ss5952823004 Oct 16, 2022 (156)
83 EVA ss5979529309 Oct 16, 2022 (156)
84 1000Genomes NC_000018.9 - 52752700 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000018.10 - 55085469 Oct 16, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 52752700 Oct 12, 2018 (152)
87 Genome-wide autozygosity in Daghestan NC_000018.8 - 50903698 Apr 27, 2020 (154)
88 Genetic variation in the Estonian population NC_000018.9 - 52752700 Oct 12, 2018 (152)
89 The Danish reference pan genome NC_000018.9 - 52752700 Apr 27, 2020 (154)
90 gnomAD - Genomes NC_000018.10 - 55085469 Apr 27, 2021 (155)
91 Genome of the Netherlands Release 5 NC_000018.9 - 52752700 Apr 27, 2020 (154)
92 HapMap NC_000018.10 - 55085469 Apr 27, 2020 (154)
93 KOREAN population from KRGDB NC_000018.9 - 52752700 Apr 27, 2020 (154)
94 Korean Genome Project NC_000018.10 - 55085469 Apr 27, 2020 (154)
95 Northern Sweden NC_000018.9 - 52752700 Jul 13, 2019 (153)
96 The PAGE Study NC_000018.10 - 55085469 Jul 13, 2019 (153)
97 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000018.9 - 52752700 Apr 27, 2021 (155)
98 CNV burdens in cranial meningiomas NC_000018.9 - 52752700 Apr 27, 2021 (155)
99 Qatari NC_000018.9 - 52752700 Apr 27, 2020 (154)
100 SGDP_PRJ NC_000018.9 - 52752700 Apr 27, 2020 (154)
101 Siberian NC_000018.9 - 52752700 Apr 27, 2020 (154)
102 8.3KJPN NC_000018.9 - 52752700 Apr 27, 2021 (155)
103 14KJPN NC_000018.10 - 55085469 Oct 16, 2022 (156)
104 TopMed NC_000018.10 - 55085469 Apr 27, 2021 (155)
105 UK 10K study - Twins NC_000018.9 - 52752700 Oct 12, 2018 (152)
106 A Vietnamese Genetic Variation Database NC_000018.9 - 52752700 Jul 13, 2019 (153)
107 ALFA NC_000018.10 - 55085469 Apr 27, 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
1431563973 NC_000018.10:55085468:C:A NC_000018.10:55085468:C:A (self)
216811, ss78049278, ss110592598, ss114439809, ss117888221, ss168286526, ss169902720, ss171828817, ss203313683, ss208125054, ss255688755, ss283010184, ss287291969, ss292078865, ss1397747133 NC_000018.8:50903697:C:T NC_000018.10:55085468:C:T (self)
74577267, 41326802, 29197048, 4618131, 18410138, 44191855, 15874956, 1055380, 283196, 19293755, 39146967, 10419467, 83381590, 41326802, 9131304, ss227888327, ss237487584, ss243732629, ss565673809, ss661509176, ss993783566, ss1081541544, ss1361240803, ss1428234772, ss1578427052, ss1636992211, ss1679986244, ss1809074414, ss1937251833, ss1959808128, ss1968536674, ss2029395825, ss2157903113, ss2629196208, ss2702493727, ss2957291864, ss3016613596, ss3021847777, ss3352048049, ss3652269909, ss3683458800, ss3742590091, ss3755458117, ss3788385864, ss3793315183, ss3798201619, ss3835196741, ss3841216410, ss3887129987, ss3937014461, ss3984733644, ss3985829453, ss5225412283, ss5511960005, ss5624415385, ss5661401655, ss5827618517, ss5847487401, ss5847823132, ss5952823004, ss5979529309 NC_000018.9:52752699:C:T NC_000018.10:55085468:C:T (self)
97945745, 526088754, 1612974, 36628603, 1196356, 117109983, 274146288, 1431563973, ss2222020226, ss3028527569, ss3650801753, ss3725680807, ss3771974887, ss3820715029, ss3846718790, ss3980250602, ss5058600625, ss5305479192, ss5498228568, ss5610419810, ss5783272879, ss5817145938, ss5852076183, ss5874301129 NC_000018.10:55085468:C:T NC_000018.10:55085468:C:T (self)
ss17599875, ss21491246 NT_025028.13:543563:C:T NC_000018.10:55085468:C:T (self)
ss6626665, ss44085340, ss96513944, ss136400000, ss155217436 NT_025028.14:543563:C:T NC_000018.10:55085468: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 rs4801131

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