Name: rs13147359
Published: September 21, 2022
License: Open Access

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.

rs13147359

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:122676016 (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=0.020012 (5297/264690, TOPMED)
C=0.024013 (3367/140218, GnomAD)
C=0.03540 (683/19296, ALFA) (+ 13 more)
C=0.0089 (57/6404, 1000G_30x)
C=0.0096 (48/5008, 1000G)
C=0.0658 (295/4480, Estonian)
C=0.0402 (155/3854, ALSPAC)
C=0.0329 (122/3708, TWINSUK)
C=0.0337 (38/1128, Daghestan)
C=0.037 (37/998, GoNL)
C=0.063 (38/600, NorthernSweden)
C=0.021 (7/330, HapMap)
C=0.014 (3/216, Qatari)
C=0.07 (3/40, GENOME_DK)
T=0.45 (9/20, SGDP_PRJ)
T=0.0 (0/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: IL21-AS1 : 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	19296	T=0.96460	C=0.03540
European	Sub	14370	T=0.95672	C=0.04328
African	Sub	2974	T=0.9923	C=0.0077
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2860	T=0.9920	C=0.0080
Asian	Sub	118	T=1.000	C=0.000
East Asian	Sub	90	T=1.00	C=0.00
Other Asian	Sub	28	T=1.00	C=0.00
Latin American 1	Sub	154	T=0.994	C=0.006
Latin American 2	Sub	616	T=0.982	C=0.018
South Asian	Sub	100	T=0.97	C=0.03
Other	Sub	964	T=0.976	C=0.024

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.979988	C=0.020012
gnomAD - Genomes	Global	Study-wide	140218	T=0.975987	C=0.024013
gnomAD - Genomes	European	Sub	75932	T=0.96197	C=0.03803
gnomAD - Genomes	African	Sub	42030	T=0.99427	C=0.00573
gnomAD - Genomes	American	Sub	13648	T=0.98740	C=0.01260
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9928	C=0.0072
gnomAD - Genomes	East Asian	Sub	3132	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2152	T=0.9805	C=0.0195
Allele Frequency Aggregator	Total	Global	19296	T=0.96460	C=0.03540
Allele Frequency Aggregator	European	Sub	14370	T=0.95672	C=0.04328
Allele Frequency Aggregator	African	Sub	2974	T=0.9923	C=0.0077
Allele Frequency Aggregator	Other	Sub	964	T=0.976	C=0.024
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.982	C=0.018
Allele Frequency Aggregator	Latin American 1	Sub	154	T=0.994	C=0.006
Allele Frequency Aggregator	Asian	Sub	118	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	100	T=0.97	C=0.03
1000Genomes_30x	Global	Study-wide	6404	T=0.9911	C=0.0089
1000Genomes_30x	African	Sub	1786	T=0.9978	C=0.0022
1000Genomes_30x	Europe	Sub	1266	T=0.9731	C=0.0269
1000Genomes_30x	South Asian	Sub	1202	T=0.9875	C=0.0125
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.996	C=0.004
1000Genomes	Global	Study-wide	5008	T=0.9904	C=0.0096
1000Genomes	African	Sub	1322	T=0.9977	C=0.0023
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9722	C=0.0278
1000Genomes	South Asian	Sub	978	T=0.986	C=0.014
1000Genomes	American	Sub	694	T=0.996	C=0.004
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9342	C=0.0658
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9598	C=0.0402
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9671	C=0.0329
Genome-wide autozygosity in Daghestan	Global	Study-wide	1128	T=0.9663	C=0.0337
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	T=0.960	C=0.040
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	T=0.965	C=0.035
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.984	C=0.016
Genome-wide autozygosity in Daghestan	Europe	Sub	106	T=0.962	C=0.038
Genome-wide autozygosity in Daghestan	South Asian	Sub	96	T=1.00	C=0.00
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.94	C=0.06
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.963	C=0.037
Northern Sweden	ACPOP	Study-wide	600	T=0.937	C=0.063
HapMap	Global	Study-wide	330	T=0.979	C=0.021
HapMap	African	Sub	120	T=1.000	C=0.000
HapMap	American	Sub	120	T=0.942	C=0.058
HapMap	Asian	Sub	90	T=1.00	C=0.00
Qatari	Global	Study-wide	216	T=0.986	C=0.014
The Danish reference pan genome	Danish	Study-wide	40	T=0.93	C=0.07
SGDP_PRJ	Global	Study-wide	20	T=0.45	C=0.55
Siberian	Global	Study-wide	4	T=0.0	C=1.0

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 4	NC_000004.12:g.122676016T>C
GRCh37.p13 chr 4	NC_000004.11:g.123597171T>C

Gene: IL21-AS1, IL21 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IL21-AS1 transcript	NR_104126.1:n.	N/A	Intron Variant

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

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 4	NC_000004.12:g.122676016=	NC_000004.12:g.122676016T>C
GRCh37.p13 chr 4	NC_000004.11:g.123597171=	NC_000004.11:g.123597171T>C

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#.

43 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss22198421	Apr 05, 2004 (121)
2	ABI	ss44582037	Mar 13, 2006 (126)
3	VANHEEL_LAB_LONDON	ss120248426	Dec 01, 2009 (131)
4	BCM-HGSC-SUB	ss206400107	Jul 04, 2010 (132)
5	1000GENOMES	ss232578779	Jul 14, 2010 (132)
6	ILLUMINA	ss536499398	Sep 08, 2015 (146)
7	EVA-GONL	ss980623345	Aug 21, 2014 (142)
8	1000GENOMES	ss1311616589	Aug 21, 2014 (142)
9	HAMMER_LAB	ss1397387814	Sep 08, 2015 (146)
10	EVA_GENOME_DK	ss1580755259	Apr 01, 2015 (144)
11	EVA_DECODE	ss1590131163	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1611072932	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1654066965	Apr 01, 2015 (144)
14	WEILL_CORNELL_DGM	ss1923866136	Feb 12, 2016 (147)
15	JJLAB	ss2022516397	Sep 14, 2016 (149)
16	ILLUMINA	ss2094816747	Dec 20, 2016 (150)
17	ILLUMINA	ss2095149853	Dec 20, 2016 (150)
18	USC_VALOUEV	ss2150647496	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2266737837	Dec 20, 2016 (150)
20	GNOMAD	ss2814688151	Nov 08, 2017 (151)
21	SWEGEN	ss2995473891	Nov 08, 2017 (151)
22	BIOINF_KMB_FNS_UNIBA	ss3025035314	Nov 08, 2017 (151)
23	CSHL	ss3345938008	Nov 08, 2017 (151)
24	ILLUMINA	ss3629057072	Oct 12, 2018 (152)
25	URBANLAB	ss3647837894	Oct 12, 2018 (152)
26	ILLUMINA	ss3652901304	Oct 12, 2018 (152)
27	EGCUT_WGS	ss3663376558	Jul 13, 2019 (153)
28	EVA_DECODE	ss3712967541	Jul 13, 2019 (153)
29	ACPOP	ss3731565144	Jul 13, 2019 (153)
30	EVA	ss3762352451	Jul 13, 2019 (153)
31	SGDP_PRJ	ss3859949349	Apr 26, 2020 (154)
32	TOPMED	ss4630269592	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5260848291	Oct 17, 2022 (156)
34	HUGCELL_USP	ss5459424283	Oct 17, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5542814235	Oct 17, 2022 (156)
36	SANFORD_IMAGENETICS	ss5624566488	Oct 17, 2022 (156)
37	SANFORD_IMAGENETICS	ss5635989395	Oct 17, 2022 (156)
38	EVA	ss5844643279	Oct 17, 2022 (156)
39	EVA	ss5847250251	Oct 17, 2022 (156)
40	EVA	ss5848023868	Oct 17, 2022 (156)
41	EVA	ss5865308974	Oct 17, 2022 (156)
42	EVA	ss5964392198	Oct 17, 2022 (156)
43	EVA	ss5979713261	Oct 17, 2022 (156)
44	1000Genomes	NC_000004.11 - 123597171	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000004.12 - 122676016	Oct 17, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 123597171	Oct 12, 2018 (152)
47	Genome-wide autozygosity in Daghestan	NC_000004.10 - 123816621	Apr 26, 2020 (154)
48	Genetic variation in the Estonian population	NC_000004.11 - 123597171	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000004.11 - 123597171	Apr 26, 2020 (154)
50	gnomAD - Genomes	NC_000004.12 - 122676016	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000004.11 - 123597171	Apr 26, 2020 (154)
52	HapMap	NC_000004.12 - 122676016	Apr 26, 2020 (154)
53	Northern Sweden	NC_000004.11 - 123597171	Jul 13, 2019 (153)
54	Qatari	NC_000004.11 - 123597171	Apr 26, 2020 (154)
55	SGDP_PRJ	NC_000004.11 - 123597171	Apr 26, 2020 (154)
56	Siberian	NC_000004.11 - 123597171	Apr 26, 2020 (154)
57	TopMed	NC_000004.12 - 122676016	Apr 26, 2021 (155)
58	UK 10K study - Twins	NC_000004.11 - 123597171	Oct 12, 2018 (152)
59	ALFA	NC_000004.12 - 122676016	Apr 26, 2021 (155)

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
363159, ss206400107, ss1397387814, ss1590131163	NC_000004.10:123816620:T:C	NC_000004.12:122676015:T:C	(self)
23083903, 12842462, 9114806, 6920198, 5682732, 4850009, 5908066, 11966329, 3163850, 12842462, ss232578779, ss536499398, ss980623345, ss1311616589, ss1580755259, ss1611072932, ss1654066965, ss1923866136, ss2022516397, ss2094816747, ss2095149853, ss2150647496, ss2814688151, ss2995473891, ss3345938008, ss3629057072, ss3652901304, ss3663376558, ss3731565144, ss3762352451, ss3859949349, ss5624566488, ss5635989395, ss5844643279, ss5847250251, ss5848023868, ss5964392198, ss5979713261	NC_000004.11:123597170:T:C	NC_000004.12:122676015:T:C	(self)
30340170, 163521574, 2701114, 467647148, 11500152052, ss2266737837, ss3025035314, ss3647837894, ss3712967541, ss4630269592, ss5260848291, ss5459424283, ss5542814235, ss5865308974	NC_000004.12:122676015:T:C	NC_000004.12:122676015:T:C	(self)
ss22198421	NT_016354.16:48092301:T:C	NC_000004.12:122676015:T:C	(self)
ss44582037, ss120248426	NT_016354.19:48144891:T:C	NC_000004.12:122676015:T:C	(self)

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

1 citation for rs13147359

PMID	Title	Author	Year	Journal
21425124	Fine-mapping and transethnic genotyping establish IL2/IL21 genetic association with lupus and localize this genetic effect to IL21.	Hughes T et al.	2011	Arthritis and rheumatism

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs13147359