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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.

rs2895

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:2529136 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.072122 (19090/264690, TOPMED)
C=0.069357 (9720/140144, GnomAD)
C=0.089767 (11887/132420, ALFA) (+ 20 more)
C=0.00099 (28/28258, 14KJPN)
C=0.00084 (14/16758, 8.3KJPN)
C=0.0440 (282/6404, 1000G_30x)
C=0.0411 (206/5008, 1000G)
C=0.0839 (376/4480, Estonian)
C=0.1051 (405/3854, ALSPAC)
C=0.1011 (375/3708, TWINSUK)
C=0.0007 (2/2920, KOREAN)
C=0.0667 (139/2084, HGDP_Stanford)
C=0.0005 (1/1832, Korea1K)
C=0.0461 (57/1236, HapMap)
C=0.090 (90/998, GoNL)
C=0.192 (120/626, Chileans)
C=0.040 (24/600, NorthernSweden)
C=0.005 (1/216, Qatari)
C=0.009 (2/214, Vietnamese)
C=0.07 (4/56, Ancient Sardinia)
T=0.44 (21/48, SGDP_PRJ)
T=0.5 (5/10, Siberian)
C=0.5 (5/10, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LFNG : 3 Prime UTR 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 132420 T=0.910233 C=0.089767 0.82995 0.009485 0.160565 11
European Sub 108676 T=0.906125 C=0.093875 0.821433 0.009183 0.169384 1
African Sub 6688 T=0.9819 C=0.0181 0.964115 0.000299 0.035586 0
African Others Sub 246 T=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 6442 T=0.9812 C=0.0188 0.962744 0.00031 0.036945 0
Asian Sub 576 T=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 494 T=1.000 C=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 82 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 692 T=0.945 C=0.055 0.895954 0.00578 0.098266 1
Latin American 2 Sub 5598 T=0.8382 C=0.1618 0.707753 0.03144 0.260807 3
South Asian Sub 5036 T=0.9664 C=0.0336 0.936458 0.003574 0.059968 8
Other Sub 5154 T=0.9125 C=0.0875 0.836244 0.011253 0.152503 3


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 T=0.927878 C=0.072122
gnomAD - Genomes Global Study-wide 140144 T=0.930643 C=0.069357
gnomAD - Genomes European Sub 75880 T=0.91173 C=0.08827
gnomAD - Genomes African Sub 42008 T=0.97977 C=0.02023
gnomAD - Genomes American Sub 13650 T=0.86923 C=0.13077
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9323 C=0.0677
gnomAD - Genomes East Asian Sub 3130 T=0.9990 C=0.0010
gnomAD - Genomes Other Sub 2152 T=0.9261 C=0.0739
Allele Frequency Aggregator Total Global 132420 T=0.910233 C=0.089767
Allele Frequency Aggregator European Sub 108676 T=0.906125 C=0.093875
Allele Frequency Aggregator African Sub 6688 T=0.9819 C=0.0181
Allele Frequency Aggregator Latin American 2 Sub 5598 T=0.8382 C=0.1618
Allele Frequency Aggregator Other Sub 5154 T=0.9125 C=0.0875
Allele Frequency Aggregator South Asian Sub 5036 T=0.9664 C=0.0336
Allele Frequency Aggregator Latin American 1 Sub 692 T=0.945 C=0.055
Allele Frequency Aggregator Asian Sub 576 T=1.000 C=0.000
14KJPN JAPANESE Study-wide 28258 T=0.99901 C=0.00099
8.3KJPN JAPANESE Study-wide 16758 T=0.99916 C=0.00084
1000Genomes_30x Global Study-wide 6404 T=0.9560 C=0.0440
1000Genomes_30x African Sub 1786 T=0.9961 C=0.0039
1000Genomes_30x Europe Sub 1266 T=0.9273 C=0.0727
1000Genomes_30x South Asian Sub 1202 T=0.9709 C=0.0291
1000Genomes_30x East Asian Sub 1170 T=0.9940 C=0.0060
1000Genomes_30x American Sub 980 T=0.856 C=0.144
1000Genomes Global Study-wide 5008 T=0.9589 C=0.0411
1000Genomes African Sub 1322 T=0.9947 C=0.0053
1000Genomes East Asian Sub 1008 T=0.9940 C=0.0060
1000Genomes Europe Sub 1006 T=0.9284 C=0.0716
1000Genomes South Asian Sub 978 T=0.975 C=0.025
1000Genomes American Sub 694 T=0.860 C=0.140
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9161 C=0.0839
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8949 C=0.1051
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8989 C=0.1011
KOREAN population from KRGDB KOREAN Study-wide 2920 T=0.9993 C=0.0007
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.9333 C=0.0667
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.996 C=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.981 C=0.019
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.983 C=0.017
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.919 C=0.081
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.569 C=0.431
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.94 C=0.06
Korean Genome Project KOREAN Study-wide 1832 T=0.9995 C=0.0005
HapMap Global Study-wide 1236 T=0.9539 C=0.0461
HapMap American Sub 770 T=0.949 C=0.051
HapMap Europe Sub 176 T=0.903 C=0.097
HapMap Asian Sub 170 T=0.994 C=0.006
HapMap African Sub 120 T=1.000 C=0.000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.910 C=0.090
Chileans Chilean Study-wide 626 T=0.808 C=0.192
Northern Sweden ACPOP Study-wide 600 T=0.960 C=0.040
Qatari Global Study-wide 216 T=0.995 C=0.005
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.991 C=0.009
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 56 T=0.93 C=0.07
SGDP_PRJ Global Study-wide 48 T=0.44 C=0.56
Siberian Global Study-wide 10 T=0.5 C=0.5
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 7 NC_000007.14:g.2529136T>C
GRCh37.p13 chr 7 NC_000007.13:g.2568770T>C
LFNG RefSeqGene NG_008109.2:g.21608T>C
Gene: LFNG, LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LFNG transcript variant 2 NM_001040168.2:c.*250= N/A 3 Prime UTR Variant
LFNG transcript variant 1 NM_001040167.2:c. N/A Genic Downstream Transcript Variant
LFNG transcript variant 3 NM_001166355.2:c. N/A Genic Downstream Transcript Variant
LFNG transcript variant 4 NM_002304.3:c. 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.

Allele: C (allele ID: 1237579 )
ClinVar Accession Disease Names Clinical Significance
RCV001654428.4 not provided Benign
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 T= C
GRCh38.p14 chr 7 NC_000007.14:g.2529136= NC_000007.14:g.2529136T>C
GRCh37.p13 chr 7 NC_000007.13:g.2568770= NC_000007.13:g.2568770T>C
LFNG RefSeqGene NG_008109.2:g.21608= NG_008109.2:g.21608T>C
LFNG transcript variant 2 NM_001040168.2:c.*250= NM_001040168.2:c.*250T>C
LFNG transcript variant 2 NM_001040168.1:c.*250= NM_001040168.1:c.*250T>C
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#.

88 SubSNP, 22 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 WIAF ss2926 Sep 19, 2000 (36)
2 PERLEGEN ss24409653 Sep 20, 2004 (123)
3 ABI ss44810820 Mar 14, 2006 (126)
4 ILLUMINA ss66745325 Nov 30, 2006 (127)
5 ILLUMINA ss67281771 Nov 30, 2006 (127)
6 ILLUMINA ss67683953 Nov 30, 2006 (127)
7 ILLUMINA ss70760283 May 23, 2008 (130)
8 ILLUMINA ss71334022 May 17, 2007 (127)
9 ILLUMINA ss75729933 Dec 06, 2007 (129)
10 ILLUMINA ss79152918 Dec 14, 2007 (130)
11 KRIBB_YJKIM ss83345548 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss93613878 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss98220116 Feb 03, 2009 (130)
14 1000GENOMES ss111392503 Jan 25, 2009 (130)
15 ILLUMINA ss122137917 Dec 01, 2009 (131)
16 ENSEMBL ss142573152 Dec 01, 2009 (131)
17 ILLUMINA ss154244600 Dec 01, 2009 (131)
18 ILLUMINA ss159421478 Dec 01, 2009 (131)
19 ILLUMINA ss160596484 Dec 01, 2009 (131)
20 ILLUMINA ss171470454 Jul 04, 2010 (132)
21 ILLUMINA ss173526949 Jul 04, 2010 (132)
22 1000GENOMES ss233812941 Jul 15, 2010 (132)
23 GMI ss285560376 Apr 25, 2013 (138)
24 ILLUMINA ss410927032 Sep 17, 2011 (135)
25 ILLUMINA ss481600322 Sep 08, 2015 (146)
26 ILLUMINA ss483501080 May 04, 2012 (137)
27 ILLUMINA ss485409910 May 04, 2012 (137)
28 ILLUMINA ss535709172 Sep 08, 2015 (146)
29 SSMP ss654094653 Apr 25, 2013 (138)
30 ILLUMINA ss779508835 Sep 08, 2015 (146)
31 ILLUMINA ss782193951 Sep 08, 2015 (146)
32 ILLUMINA ss825483436 Apr 01, 2015 (144)
33 ILLUMINA ss832933123 Jul 13, 2019 (153)
34 ILLUMINA ss834979163 Sep 08, 2015 (146)
35 EVA-GONL ss983848004 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1074288773 Aug 21, 2014 (142)
37 1000GENOMES ss1323568386 Aug 21, 2014 (142)
38 EVA_UK10K_ALSPAC ss1617388225 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1660382258 Apr 01, 2015 (144)
40 EVA_SVP ss1712924890 Apr 01, 2015 (144)
41 WEILL_CORNELL_DGM ss1927093722 Feb 12, 2016 (147)
42 GENOMED ss1970602370 Jul 19, 2016 (147)
43 JJLAB ss2024214898 Sep 14, 2016 (149)
44 USC_VALOUEV ss2152415090 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2291054108 Dec 20, 2016 (150)
46 ILLUMINA ss2634554153 Nov 08, 2017 (151)
47 ILLUMINA ss2634554154 Nov 08, 2017 (151)
48 GRF ss2708063702 Nov 08, 2017 (151)
49 ILLUMINA ss2711100612 Nov 08, 2017 (151)
50 GNOMAD ss2848759164 Nov 08, 2017 (151)
51 SWEGEN ss3000478218 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3025902135 Nov 08, 2017 (151)
53 CSHL ss3347390976 Nov 08, 2017 (151)
54 ILLUMINA ss3629731290 Oct 12, 2018 (152)
55 ILLUMINA ss3632464673 Oct 12, 2018 (152)
56 ILLUMINA ss3636833333 Oct 12, 2018 (152)
57 ILLUMINA ss3638675468 Oct 12, 2018 (152)
58 ILLUMINA ss3639339569 Oct 12, 2018 (152)
59 ILLUMINA ss3639697277 Oct 12, 2018 (152)
60 ILLUMINA ss3641206735 Oct 12, 2018 (152)
61 ILLUMINA ss3641504081 Oct 12, 2018 (152)
62 ILLUMINA ss3643613349 Oct 12, 2018 (152)
63 URBANLAB ss3648542575 Oct 12, 2018 (152)
64 EGCUT_WGS ss3668409512 Jul 13, 2019 (153)
65 EVA_DECODE ss3718925009 Jul 13, 2019 (153)
66 ACPOP ss3734275285 Jul 13, 2019 (153)
67 EVA ss3766079407 Jul 13, 2019 (153)
68 KHV_HUMAN_GENOMES ss3809241369 Jul 13, 2019 (153)
69 EVA ss3830363674 Apr 26, 2020 (154)
70 HGDP ss3847862689 Apr 26, 2020 (154)
71 SGDP_PRJ ss3866431771 Apr 26, 2020 (154)
72 KRGDB ss3913446665 Apr 26, 2020 (154)
73 KOGIC ss3960713219 Apr 26, 2020 (154)
74 EVA ss3985272666 Apr 26, 2021 (155)
75 EVA ss4017316299 Apr 26, 2021 (155)
76 TOPMED ss4732626548 Apr 26, 2021 (155)
77 TOMMO_GENOMICS ss5181411402 Apr 26, 2021 (155)
78 1000G_HIGH_COVERAGE ss5271505049 Oct 14, 2022 (156)
79 EVA ss5315216309 Oct 14, 2022 (156)
80 EVA ss5371089512 Oct 14, 2022 (156)
81 HUGCELL_USP ss5468830045 Oct 14, 2022 (156)
82 1000G_HIGH_COVERAGE ss5558993226 Oct 14, 2022 (156)
83 SANFORD_IMAGENETICS ss5642154290 Oct 14, 2022 (156)
84 TOMMO_GENOMICS ss5720747983 Oct 14, 2022 (156)
85 EVA ss5822283056 Oct 14, 2022 (156)
86 EVA ss5855723645 Oct 14, 2022 (156)
87 EVA ss5857351042 Oct 14, 2022 (156)
88 EVA ss5971345962 Oct 14, 2022 (156)
89 1000Genomes NC_000007.13 - 2568770 Oct 12, 2018 (152)
90 1000Genomes_30x NC_000007.14 - 2529136 Oct 14, 2022 (156)
91 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 2568770 Oct 12, 2018 (152)
92 Chileans NC_000007.13 - 2568770 Apr 26, 2020 (154)
93 Genetic variation in the Estonian population NC_000007.13 - 2568770 Oct 12, 2018 (152)
94 gnomAD - Genomes NC_000007.14 - 2529136 Apr 26, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000007.13 - 2568770 Apr 26, 2020 (154)
96 HGDP-CEPH-db Supplement 1 NC_000007.12 - 2535296 Apr 26, 2020 (154)
97 HapMap NC_000007.14 - 2529136 Apr 26, 2020 (154)
98 KOREAN population from KRGDB NC_000007.13 - 2568770 Apr 26, 2020 (154)
99 Korean Genome Project NC_000007.14 - 2529136 Apr 26, 2020 (154)
100 Northern Sweden NC_000007.13 - 2568770 Jul 13, 2019 (153)
101 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000007.13 - 2568770 Apr 26, 2021 (155)
102 Qatari NC_000007.13 - 2568770 Apr 26, 2020 (154)
103 SGDP_PRJ NC_000007.13 - 2568770 Apr 26, 2020 (154)
104 Siberian NC_000007.13 - 2568770 Apr 26, 2020 (154)
105 8.3KJPN NC_000007.13 - 2568770 Apr 26, 2021 (155)
106 14KJPN NC_000007.14 - 2529136 Oct 14, 2022 (156)
107 TopMed NC_000007.14 - 2529136 Apr 26, 2021 (155)
108 UK 10K study - Twins NC_000007.13 - 2568770 Oct 12, 2018 (152)
109 A Vietnamese Genetic Variation Database NC_000007.13 - 2568770 Jul 13, 2019 (153)
110 ALFA NC_000007.14 - 2529136 Apr 26, 2021 (155)
111 ClinVar RCV001654428.4 Oct 14, 2022 (156)
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)
rs17801117 Oct 08, 2004 (123)
rs57035648 May 23, 2008 (130)
rs111191609 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639339569, ss3639697277 NC_000007.11:2342010:T:C NC_000007.14:2529135:T:C (self)
540581, ss93613878, ss111392503, ss285560376, ss485409910, ss825483436, ss1712924890, ss3643613349, ss3847862689 NC_000007.12:2535295:T:C NC_000007.14:2529135:T:C (self)
35485185, 19787500, 399212, 14147760, 8810421, 20624059, 7560150, 498593, 9135652, 18448751, 4931444, 39380709, 19787500, 4406259, ss233812941, ss481600322, ss483501080, ss535709172, ss654094653, ss779508835, ss782193951, ss832933123, ss834979163, ss983848004, ss1074288773, ss1323568386, ss1617388225, ss1660382258, ss1927093722, ss1970602370, ss2024214898, ss2152415090, ss2634554153, ss2634554154, ss2708063702, ss2711100612, ss2848759164, ss3000478218, ss3347390976, ss3629731290, ss3632464673, ss3636833333, ss3638675468, ss3641206735, ss3641504081, ss3668409512, ss3734275285, ss3766079407, ss3830363674, ss3866431771, ss3913446665, ss3985272666, ss4017316299, ss5181411402, ss5315216309, ss5371089512, ss5642154290, ss5822283056, ss5971345962 NC_000007.13:2568769:T:C NC_000007.14:2529135:T:C (self)
RCV001654428.4, 46519161, 250356057, 3317930, 17091220, 54585087, 570004107, 9596275875, ss2291054108, ss3025902135, ss3648542575, ss3718925009, ss3809241369, ss3960713219, ss4732626548, ss5271505049, ss5468830045, ss5558993226, ss5720747983, ss5855723645, ss5857351042 NC_000007.14:2529135:T:C NC_000007.14:2529135:T:C (self)
ss2926, ss24409653, ss44810820, ss66745325, ss67281771, ss67683953, ss70760283, ss71334022, ss75729933, ss79152918, ss83345548, ss98220116, ss122137917, ss142573152, ss154244600, ss159421478, ss160596484, ss171470454, ss173526949, ss410927032 NT_007819.17:2558769:T:C NC_000007.14:2529135:T:C (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 rs2895
PMID Title Author Year Journal
34753545 Association between ADRB2 regulatory region polymorphisms and susceptibility to childhood asthma. Cai MX et al. 2021 Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics
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.post825+45319f0