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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.

rs223201

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:18295492 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.216261 (57242/264690, TOPMED)
T=0.216591 (30311/139946, GnomAD)
T=0.17966 (14926/83078, ALFA) (+ 15 more)
T=0.02924 (490/16760, 8.3KJPN)
T=0.1789 (896/5008, 1000G)
T=0.1719 (770/4480, Estonian)
T=0.1850 (713/3854, ALSPAC)
T=0.1888 (700/3708, TWINSUK)
T=0.0321 (94/2930, KOREAN)
T=0.1411 (294/2084, HGDP_Stanford)
T=0.2019 (382/1892, HapMap)
T=0.197 (197/998, GoNL)
T=0.195 (117/600, NorthernSweden)
T=0.157 (34/216, Qatari)
C=0.395 (45/114, SGDP_PRJ)
T=0.06 (4/68, Ancient Sardinia)
T=0.25 (10/40, GENOME_DK)
C=0.43 (6/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IGSF21 : 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.18295492C>T
GRCh37.p13 chr 1 NC_000001.10:g.18621986C>T
IGSF21 RefSeqGene NG_027535.2:g.192747C>T
Gene: IGSF21, immunoglobin superfamily member 21 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
IGSF21 transcript NM_032880.5:c.305+3505C>T N/A Intron Variant
IGSF21 transcript variant X4 XM_011542319.3:c.305+3505…

XM_011542319.3:c.305+3505C>T

N/A Intron Variant
IGSF21 transcript variant X1 XM_017002604.2:c.287+3505…

XM_017002604.2:c.287+3505C>T

N/A Intron Variant
IGSF21 transcript variant X3 XM_017002605.1:c.74+3505C…

XM_017002605.1:c.74+3505C>T

N/A Intron Variant
IGSF21 transcript variant X2 XM_024450444.1:c.146+3505…

XM_024450444.1:c.146+3505C>T

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 83078 C=0.82034 T=0.17966
European Sub 69228 C=0.82350 T=0.17650
African Sub 4724 C=0.6713 T=0.3287
African Others Sub 180 C=0.628 T=0.372
African American Sub 4544 C=0.6730 T=0.3270
Asian Sub 202 C=0.965 T=0.035
East Asian Sub 160 C=0.969 T=0.031
Other Asian Sub 42 C=0.95 T=0.05
Latin American 1 Sub 268 C=0.795 T=0.205
Latin American 2 Sub 1316 C=0.8716 T=0.1284
South Asian Sub 4972 C=0.8880 T=0.1120
Other Sub 2368 C=0.8454 T=0.1546


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=0.783739 T=0.216261
gnomAD - Genomes Global Study-wide 139946 C=0.783409 T=0.216591
gnomAD - Genomes European Sub 75854 C=0.82461 T=0.17539
gnomAD - Genomes African Sub 41860 C=0.66522 T=0.33478
gnomAD - Genomes American Sub 13638 C=0.83891 T=0.16109
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.9154 T=0.0846
gnomAD - Genomes East Asian Sub 3122 C=0.9731 T=0.0269
gnomAD - Genomes Other Sub 2152 C=0.7997 T=0.2003
8.3KJPN JAPANESE Study-wide 16760 C=0.97076 T=0.02924
1000Genomes Global Study-wide 5008 C=0.8211 T=0.1789
1000Genomes African Sub 1322 C=0.6263 T=0.3737
1000Genomes East Asian Sub 1008 C=0.9653 T=0.0347
1000Genomes Europe Sub 1006 C=0.8390 T=0.1610
1000Genomes South Asian Sub 978 C=0.894 T=0.106
1000Genomes American Sub 694 C=0.854 T=0.146
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8281 T=0.1719
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8150 T=0.1850
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8112 T=0.1888
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9679 T=0.0321
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.8589 T=0.1411
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.936 T=0.064
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.874 T=0.126
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.866 T=0.134
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.800 T=0.200
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.661 T=0.339
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.912 T=0.088
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=1.00 T=0.00
HapMap Global Study-wide 1892 C=0.7981 T=0.2019
HapMap American Sub 770 C=0.856 T=0.144
HapMap African Sub 692 C=0.655 T=0.345
HapMap Asian Sub 254 C=0.965 T=0.035
HapMap Europe Sub 176 C=0.869 T=0.131
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.803 T=0.197
Northern Sweden ACPOP Study-wide 600 C=0.805 T=0.195
Qatari Global Study-wide 216 C=0.843 T=0.157
SGDP_PRJ Global Study-wide 114 C=0.395 T=0.605
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 68 C=0.94 T=0.06
The Danish reference pan genome Danish Study-wide 40 C=0.75 T=0.25
Siberian Global Study-wide 14 C=0.43 T=0.57
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= T
GRCh38.p13 chr 1 NC_000001.11:g.18295492= NC_000001.11:g.18295492C>T
GRCh37.p13 chr 1 NC_000001.10:g.18621986= NC_000001.10:g.18621986C>T
IGSF21 RefSeqGene NG_027535.2:g.192747= NG_027535.2:g.192747C>T
IGSF21 transcript NM_032880.4:c.305+3505= NM_032880.4:c.305+3505C>T
IGSF21 transcript NM_032880.5:c.305+3505= NM_032880.5:c.305+3505C>T
IGSF21 transcript variant X4 XM_011542319.3:c.305+3505= XM_011542319.3:c.305+3505C>T
IGSF21 transcript variant X1 XM_017002604.2:c.287+3505= XM_017002604.2:c.287+3505C>T
IGSF21 transcript variant X3 XM_017002605.1:c.74+3505= XM_017002605.1:c.74+3505C>T
IGSF21 transcript variant X2 XM_024450444.1:c.146+3505= XM_024450444.1:c.146+3505C>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#.

100 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss289814 Jul 12, 2000 (79)
2 SC_JCM ss481404 Jul 16, 2000 (80)
3 KWOK ss1225756 Oct 04, 2000 (86)
4 KWOK ss1227240 Oct 04, 2000 (86)
5 KWOK ss1959555 Oct 18, 2000 (87)
6 KWOK ss1959718 Oct 18, 2000 (87)
7 TSC-CSHL ss2400401 Oct 23, 2000 (88)
8 TSC-CSHL ss5176799 Oct 08, 2002 (108)
9 PERLEGEN ss23686784 Sep 20, 2004 (123)
10 ABI ss44131878 Mar 14, 2006 (126)
11 ILLUMINA ss65718009 Oct 13, 2006 (127)
12 ILLUMINA ss66742240 Nov 29, 2006 (127)
13 ILLUMINA ss67235677 Nov 29, 2006 (127)
14 ILLUMINA ss67631793 Nov 29, 2006 (127)
15 PERLEGEN ss68760094 May 16, 2007 (127)
16 ILLUMINA ss70714006 May 26, 2008 (130)
17 ILLUMINA ss71281706 May 16, 2007 (127)
18 ILLUMINA ss75689720 Dec 06, 2007 (129)
19 ILLUMINA ss79121806 Dec 15, 2007 (130)
20 KRIBB_YJKIM ss83392293 Dec 15, 2007 (130)
21 HGSV ss85069687 Dec 15, 2007 (130)
22 HUMANGENOME_JCVI ss99190975 Feb 06, 2009 (130)
23 1000GENOMES ss108030373 Jan 22, 2009 (130)
24 ILLUMINA-UK ss118535564 Feb 14, 2009 (130)
25 ILLUMINA ss120244564 Dec 01, 2009 (131)
26 ILLUMINA ss121957683 Dec 01, 2009 (131)
27 ENSEMBL ss131722898 Dec 01, 2009 (131)
28 ILLUMINA ss153888566 Dec 01, 2009 (131)
29 ILLUMINA ss159370221 Dec 01, 2009 (131)
30 COMPLETE_GENOMICS ss163909221 Jul 04, 2010 (132)
31 ILLUMINA ss171105575 Jul 04, 2010 (132)
32 ILLUMINA ss173195619 Jul 04, 2010 (132)
33 BUSHMAN ss198106174 Jul 04, 2010 (132)
34 BCM-HGSC-SUB ss205290758 Jul 04, 2010 (132)
35 1000GENOMES ss210478646 Jul 14, 2010 (132)
36 1000GENOMES ss218263454 Jul 14, 2010 (132)
37 1000GENOMES ss230446958 Jul 14, 2010 (132)
38 1000GENOMES ss238158101 Jul 15, 2010 (132)
39 ILLUMINA ss244255242 Jul 04, 2010 (132)
40 GMI ss275738335 May 04, 2012 (137)
41 GMI ss284011243 Apr 25, 2013 (138)
42 PJP ss290704237 May 09, 2011 (134)
43 ILLUMINA ss482169097 May 04, 2012 (137)
44 ILLUMINA ss483846991 May 04, 2012 (137)
45 ILLUMINA ss536042826 Sep 08, 2015 (146)
46 TISHKOFF ss553849099 Apr 25, 2013 (138)
47 SSMP ss647614529 Apr 25, 2013 (138)
48 ILLUMINA ss780430603 Sep 08, 2015 (146)
49 ILLUMINA ss782367064 Sep 08, 2015 (146)
50 ILLUMINA ss825452324 Apr 01, 2015 (144)
51 ILLUMINA ss832882049 Aug 21, 2014 (142)
52 ILLUMINA ss833472879 Aug 21, 2014 (142)
53 ILLUMINA ss835920066 Sep 08, 2015 (146)
54 EVA-GONL ss974907799 Aug 21, 2014 (142)
55 JMKIDD_LAB ss1067707218 Aug 21, 2014 (142)
56 1000GENOMES ss1289887996 Aug 21, 2014 (142)
57 DDI ss1425732507 Apr 01, 2015 (144)
58 EVA_GENOME_DK ss1573917718 Apr 01, 2015 (144)
59 EVA_DECODE ss1584265189 Apr 01, 2015 (144)
60 EVA_UK10K_ALSPAC ss1599648193 Apr 01, 2015 (144)
61 EVA_UK10K_TWINSUK ss1642642226 Apr 01, 2015 (144)
62 EVA_SVP ss1712314965 Apr 01, 2015 (144)
63 HAMMER_LAB ss1793999031 Sep 08, 2015 (146)
64 WEILL_CORNELL_DGM ss1918118343 Feb 12, 2016 (147)
65 JJLAB ss2019570627 Sep 14, 2016 (149)
66 USC_VALOUEV ss2147573099 Dec 20, 2016 (150)
67 HUMAN_LONGEVITY ss2160424109 Dec 20, 2016 (150)
68 TOPMED ss2322604684 Dec 20, 2016 (150)
69 ILLUMINA ss2632484428 Nov 08, 2017 (151)
70 GRF ss2697477325 Nov 08, 2017 (151)
71 GNOMAD ss2752250454 Nov 08, 2017 (151)
72 SWEGEN ss2986404789 Nov 08, 2017 (151)
73 BIOINF_KMB_FNS_UNIBA ss3023549971 Nov 08, 2017 (151)
74 TOPMED ss3069978293 Nov 08, 2017 (151)
75 CSHL ss3343348572 Nov 08, 2017 (151)
76 ILLUMINA ss3626038721 Oct 11, 2018 (152)
77 ILLUMINA ss3630522389 Oct 11, 2018 (152)
78 ILLUMINA ss3637740513 Oct 11, 2018 (152)
79 ILLUMINA ss3638891300 Oct 11, 2018 (152)
80 ILLUMINA ss3639442643 Oct 11, 2018 (152)
81 ILLUMINA ss3640975837 Oct 11, 2018 (152)
82 ILLUMINA ss3641269700 Oct 11, 2018 (152)
83 ILLUMINA ss3641575492 Oct 11, 2018 (152)
84 ILLUMINA ss3642754063 Oct 11, 2018 (152)
85 URBANLAB ss3646613496 Oct 11, 2018 (152)
86 EGCUT_WGS ss3654474246 Jul 12, 2019 (153)
87 EVA_DECODE ss3686269273 Jul 12, 2019 (153)
88 ACPOP ss3726836404 Jul 12, 2019 (153)
89 EVA ss3745893315 Jul 12, 2019 (153)
90 KHV_HUMAN_GENOMES ss3798914735 Jul 12, 2019 (153)
91 EVA ss3826050471 Apr 25, 2020 (154)
92 EVA ss3836413404 Apr 25, 2020 (154)
93 EVA ss3841817745 Apr 25, 2020 (154)
94 HGDP ss3847326072 Apr 25, 2020 (154)
95 SGDP_PRJ ss3848328113 Apr 25, 2020 (154)
96 KRGDB ss3893232749 Apr 25, 2020 (154)
97 EVA ss3984781703 Apr 27, 2021 (155)
98 EVA ss4016896104 Apr 27, 2021 (155)
99 TOPMED ss4440883304 Apr 27, 2021 (155)
100 TOMMO_GENOMICS ss5142755376 Apr 27, 2021 (155)
101 1000Genomes NC_000001.10 - 18621986 Oct 11, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 18621986 Oct 11, 2018 (152)
103 Genetic variation in the Estonian population NC_000001.10 - 18621986 Oct 11, 2018 (152)
104 The Danish reference pan genome NC_000001.10 - 18621986 Apr 25, 2020 (154)
105 gnomAD - Genomes NC_000001.11 - 18295492 Apr 27, 2021 (155)
106 Genome of the Netherlands Release 5 NC_000001.10 - 18621986 Apr 25, 2020 (154)
107 HGDP-CEPH-db Supplement 1 NC_000001.9 - 18494573 Apr 25, 2020 (154)
108 HapMap NC_000001.11 - 18295492 Apr 25, 2020 (154)
109 KOREAN population from KRGDB NC_000001.10 - 18621986 Apr 25, 2020 (154)
110 Northern Sweden NC_000001.10 - 18621986 Jul 12, 2019 (153)
111 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 18621986 Apr 27, 2021 (155)
112 Qatari NC_000001.10 - 18621986 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000001.10 - 18621986 Apr 25, 2020 (154)
114 Siberian NC_000001.10 - 18621986 Apr 25, 2020 (154)
115 8.3KJPN NC_000001.10 - 18621986 Apr 27, 2021 (155)
116 TopMed NC_000001.11 - 18295492 Apr 27, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 18621986 Oct 11, 2018 (152)
118 ALFA NC_000001.11 - 18295492 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).

Associated ID History Updated (Build)
rs60993430 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85069687, ss3638891300, ss3639442643 NC_000001.8:18367291:C:T NC_000001.11:18295491:C:T (self)
3964, ss108030373, ss118535564, ss163909221, ss198106174, ss205290758, ss210478646, ss275738335, ss284011243, ss290704237, ss482169097, ss825452324, ss1584265189, ss1712314965, ss3642754063, ss3847326072 NC_000001.9:18494572:C:T NC_000001.11:18295491:C:T (self)
571023, 296967, 212494, 1410427, 129493, 410143, 121269, 7630, 160273, 345093, 89453, 724683, 296967, ss218263454, ss230446958, ss238158101, ss483846991, ss536042826, ss553849099, ss647614529, ss780430603, ss782367064, ss832882049, ss833472879, ss835920066, ss974907799, ss1067707218, ss1289887996, ss1425732507, ss1573917718, ss1599648193, ss1642642226, ss1793999031, ss1918118343, ss2019570627, ss2147573099, ss2322604684, ss2632484428, ss2697477325, ss2752250454, ss2986404789, ss3343348572, ss3626038721, ss3630522389, ss3637740513, ss3640975837, ss3641269700, ss3641575492, ss3654474246, ss3726836404, ss3745893315, ss3826050471, ss3836413404, ss3848328113, ss3893232749, ss3984781703, ss4016896104, ss5142755376 NC_000001.10:18621985:C:T NC_000001.11:18295491:C:T (self)
3986994, 22841, 2818955, 4489639, 11988333827, ss2160424109, ss3023549971, ss3069978293, ss3646613496, ss3686269273, ss3798914735, ss3841817745, ss4440883304 NC_000001.11:18295491:C:T NC_000001.11:18295491:C:T (self)
ss289814, ss481404, ss1225756, ss1227240, ss1959555, ss1959718, ss2400401, ss5176799, ss23686784, ss44131878, ss65718009, ss66742240, ss67235677, ss67631793, ss68760094, ss70714006, ss71281706, ss75689720, ss79121806, ss83392293, ss99190975, ss120244564, ss121957683, ss131722898, ss153888566, ss159370221, ss171105575, ss173195619, ss244255242 NT_004610.19:5302073:C:T NC_000001.11:18295491: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 rs223201

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