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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.

rs1059232

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:137000265 (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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.258763 (68492/264690, TOPMED)
C=0.261307 (36584/140004, GnomAD)
C=0.06819 (1927/28258, 14KJPN) (+ 19 more)
C=0.27893 (5269/18890, ALFA)
C=0.07154 (1199/16760, 8.3KJPN)
C=0.2205 (1412/6404, 1000G_30x)
C=0.2188 (1096/5008, 1000G)
C=0.2638 (1182/4480, Estonian)
C=0.2981 (1149/3854, ALSPAC)
C=0.3047 (1130/3708, TWINSUK)
C=0.0818 (239/2922, KOREAN)
C=0.0884 (162/1832, Korea1K)
C=0.2633 (298/1132, Daghestan)
C=0.289 (288/998, GoNL)
C=0.267 (160/600, NorthernSweden)
C=0.264 (87/330, HapMap)
C=0.347 (75/216, Qatari)
C=0.074 (16/216, Vietnamese)
G=0.416 (84/202, SGDP_PRJ)
C=0.28 (11/40, GENOME_DK)
G=0.50 (15/30, Siberian)
C=0.50 (15/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IL20RA : 3 Prime UTR 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 18890 G=0.72107 C=0.27893
European Sub 14286 G=0.70622 C=0.29378
African Sub 2946 G=0.7556 C=0.2444
African Others Sub 114 G=0.798 C=0.202
African American Sub 2832 G=0.7539 C=0.2461
Asian Sub 112 G=0.902 C=0.098
East Asian Sub 86 G=0.91 C=0.09
Other Asian Sub 26 G=0.88 C=0.12
Latin American 1 Sub 146 G=0.760 C=0.240
Latin American 2 Sub 610 G=0.820 C=0.180
South Asian Sub 98 G=0.70 C=0.30
Other Sub 692 G=0.759 C=0.241


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=0.741237 C=0.258763
gnomAD - Genomes Global Study-wide 140004 G=0.738693 C=0.261307
gnomAD - Genomes European Sub 75832 G=0.71501 C=0.28499
gnomAD - Genomes African Sub 41938 G=0.75292 C=0.24708
gnomAD - Genomes American Sub 13642 G=0.78749 C=0.21251
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.7141 C=0.2859
gnomAD - Genomes East Asian Sub 3130 G=0.9396 C=0.0604
gnomAD - Genomes Other Sub 2146 G=0.7321 C=0.2679
14KJPN JAPANESE Study-wide 28258 G=0.93181 C=0.06819
Allele Frequency Aggregator Total Global 18890 G=0.72107 C=0.27893
Allele Frequency Aggregator European Sub 14286 G=0.70622 C=0.29378
Allele Frequency Aggregator African Sub 2946 G=0.7556 C=0.2444
Allele Frequency Aggregator Other Sub 692 G=0.759 C=0.241
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.820 C=0.180
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.760 C=0.240
Allele Frequency Aggregator Asian Sub 112 G=0.902 C=0.098
Allele Frequency Aggregator South Asian Sub 98 G=0.70 C=0.30
8.3KJPN JAPANESE Study-wide 16760 G=0.92846 C=0.07154
1000Genomes_30x Global Study-wide 6404 G=0.7795 C=0.2205
1000Genomes_30x African Sub 1786 G=0.7396 C=0.2604
1000Genomes_30x Europe Sub 1266 G=0.7038 C=0.2962
1000Genomes_30x South Asian Sub 1202 G=0.7512 C=0.2488
1000Genomes_30x East Asian Sub 1170 G=0.9308 C=0.0692
1000Genomes_30x American Sub 980 G=0.804 C=0.196
1000Genomes Global Study-wide 5008 G=0.7812 C=0.2188
1000Genomes African Sub 1322 G=0.7330 C=0.2670
1000Genomes East Asian Sub 1008 G=0.9296 C=0.0704
1000Genomes Europe Sub 1006 G=0.7087 C=0.2913
1000Genomes South Asian Sub 978 G=0.754 C=0.246
1000Genomes American Sub 694 G=0.801 C=0.199
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7362 C=0.2638
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7019 C=0.2981
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6953 C=0.3047
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9182 C=0.0818
Korean Genome Project KOREAN Study-wide 1832 G=0.9116 C=0.0884
Genome-wide autozygosity in Daghestan Global Study-wide 1132 G=0.7367 C=0.2633
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.745 C=0.255
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.729 C=0.271
Genome-wide autozygosity in Daghestan Central Asia Sub 120 G=0.775 C=0.225
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.713 C=0.287
Genome-wide autozygosity in Daghestan South Asian Sub 96 G=0.72 C=0.28
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.61 C=0.39
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.711 C=0.289
Northern Sweden ACPOP Study-wide 600 G=0.733 C=0.267
HapMap Global Study-wide 330 G=0.736 C=0.264
HapMap African Sub 120 G=0.700 C=0.300
HapMap American Sub 120 G=0.675 C=0.325
HapMap Asian Sub 90 G=0.87 C=0.13
Qatari Global Study-wide 216 G=0.653 C=0.347
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.926 C=0.074
SGDP_PRJ Global Study-wide 202 G=0.416 C=0.584
The Danish reference pan genome Danish Study-wide 40 G=0.72 C=0.28
Siberian Global Study-wide 30 G=0.50 C=0.50
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 6 NC_000006.12:g.137000265G>C
GRCh37.p13 chr 6 NC_000006.11:g.137321402G>C
Gene: IL20RA, interleukin 20 receptor subunit alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IL20RA transcript variant 2 NM_001278722.2:c.*1293= N/A 3 Prime UTR Variant
IL20RA transcript variant 1 NM_014432.4:c.*1293= N/A 3 Prime UTR Variant
IL20RA transcript variant 4 NM_001278724.4:c.*1293= N/A 3 Prime UTR Variant
IL20RA transcript variant 3 NM_001278723.3:c.*1293= N/A 3 Prime UTR Variant
IL20RA transcript variant X1 XM_017010954.3:c.*1293= N/A 3 Prime UTR 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 G= C
GRCh38.p14 chr 6 NC_000006.12:g.137000265= NC_000006.12:g.137000265G>C
GRCh37.p13 chr 6 NC_000006.11:g.137321402= NC_000006.11:g.137321402G>C
IL20RA transcript variant 1 NM_014432.4:c.*1293= NM_014432.4:c.*1293C>G
IL20RA transcript variant 1 NM_014432.3:c.*1293= NM_014432.3:c.*1293C>G
IL20RA transcript variant 4 NM_001278724.4:c.*1293= NM_001278724.4:c.*1293C>G
IL20RA transcript variant 4 NM_001278724.3:c.*1293= NM_001278724.3:c.*1293C>G
IL20RA transcript variant 4 NM_001278724.2:c.*1293= NM_001278724.2:c.*1293C>G
IL20RA transcript variant 4 NM_001278724.1:c.*1293= NM_001278724.1:c.*1293C>G
IL20RA transcript variant X1 XM_017010954.3:c.*1293= XM_017010954.3:c.*1293C>G
IL20RA transcript variant X1 XM_017010954.2:c.*1293= XM_017010954.2:c.*1293C>G
IL20RA transcript variant X1 XM_017010954.1:c.*1293= XM_017010954.1:c.*1293C>G
IL20RA transcript variant 3 NM_001278723.3:c.*1293= NM_001278723.3:c.*1293C>G
IL20RA transcript variant 3 NM_001278723.2:c.*1293= NM_001278723.2:c.*1293C>G
IL20RA transcript variant 3 NM_001278723.1:c.*1293= NM_001278723.1:c.*1293C>G
IL20RA transcript variant 2 NM_001278722.2:c.*1293= NM_001278722.2:c.*1293C>G
IL20RA transcript variant 2 NM_001278722.1:c.*1293= NM_001278722.1:c.*1293C>G
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#.

77 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1541489 Oct 05, 2000 (86)
2 LEE ss4398974 May 29, 2002 (106)
3 LEE ss4428263 May 29, 2002 (106)
4 SC_SNP ss13122020 Dec 05, 2003 (126)
5 CGAP-GAI ss16253019 Feb 27, 2004 (120)
6 PERLEGEN ss24426884 Sep 20, 2004 (123)
7 ABI ss44728458 Mar 14, 2006 (126)
8 SI_EXO ss52067750 Oct 16, 2006 (127)
9 HGSV ss83697896 Dec 15, 2007 (130)
10 HUMANGENOME_JCVI ss98544545 Feb 06, 2009 (130)
11 1000GENOMES ss115178973 Jan 25, 2009 (130)
12 ENSEMBL ss143876860 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162846423 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss164675240 Jul 04, 2010 (132)
15 BUSHMAN ss202467537 Jul 04, 2010 (132)
16 1000GENOMES ss222703236 Jul 14, 2010 (132)
17 1000GENOMES ss233702767 Jul 15, 2010 (132)
18 1000GENOMES ss240713010 Jul 15, 2010 (132)
19 GMI ss279040350 May 04, 2012 (137)
20 GMI ss285512297 Apr 25, 2013 (138)
21 PJP ss293733649 May 09, 2011 (134)
22 ILLUMINA ss533310983 Sep 08, 2015 (146)
23 TISHKOFF ss559557380 Apr 25, 2013 (138)
24 SSMP ss653843970 Apr 25, 2013 (138)
25 EVA-GONL ss983554567 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1074074448 Aug 21, 2014 (142)
27 1000GENOMES ss1322482725 Aug 21, 2014 (142)
28 HAMMER_LAB ss1397472532 Sep 08, 2015 (146)
29 DDI ss1430909281 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1581916859 Apr 01, 2015 (144)
31 EVA_DECODE ss1593126003 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1616809448 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1659803481 Apr 01, 2015 (144)
34 WEILL_CORNELL_DGM ss1926800209 Feb 12, 2016 (147)
35 GENOMED ss1970537383 Jul 19, 2016 (147)
36 JJLAB ss2024057272 Sep 14, 2016 (149)
37 USC_VALOUEV ss2152250294 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2288834028 Dec 20, 2016 (150)
39 ILLUMINA ss2635162357 Nov 08, 2017 (151)
40 GRF ss2707882947 Nov 08, 2017 (151)
41 GNOMAD ss2845725040 Nov 08, 2017 (151)
42 SWEGEN ss3000033508 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3025820485 Nov 08, 2017 (151)
44 CSHL ss3347250947 Nov 08, 2017 (151)
45 ILLUMINA ss3629667085 Oct 12, 2018 (152)
46 URBANLAB ss3648481045 Oct 12, 2018 (152)
47 EGCUT_WGS ss3667957031 Jul 13, 2019 (153)
48 EVA_DECODE ss3718380740 Jul 13, 2019 (153)
49 ACPOP ss3734027905 Jul 13, 2019 (153)
50 EVA ss3765732525 Jul 13, 2019 (153)
51 PACBIO ss3785634715 Jul 13, 2019 (153)
52 PACBIO ss3790960283 Jul 13, 2019 (153)
53 PACBIO ss3795839586 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3808890824 Jul 13, 2019 (153)
55 EVA ss3825708090 Apr 26, 2020 (154)
56 EVA ss3830217452 Apr 26, 2020 (154)
57 EVA ss3838595682 Apr 26, 2020 (154)
58 EVA ss3844045564 Apr 26, 2020 (154)
59 SGDP_PRJ ss3865819000 Apr 26, 2020 (154)
60 KRGDB ss3912781917 Apr 26, 2020 (154)
61 KOGIC ss3960168599 Apr 26, 2020 (154)
62 FSA-LAB ss3984349925 Apr 26, 2021 (155)
63 TOPMED ss4723693358 Apr 26, 2021 (155)
64 TOMMO_GENOMICS ss5180165805 Apr 26, 2021 (155)
65 1000G_HIGH_COVERAGE ss5270534433 Oct 13, 2022 (156)
66 EVA ss5369347485 Oct 13, 2022 (156)
67 HUGCELL_USP ss5467960882 Oct 13, 2022 (156)
68 EVA ss5508726740 Oct 13, 2022 (156)
69 1000G_HIGH_COVERAGE ss5557572676 Oct 13, 2022 (156)
70 SANFORD_IMAGENETICS ss5641596207 Oct 13, 2022 (156)
71 TOMMO_GENOMICS ss5719117294 Oct 13, 2022 (156)
72 YY_MCH ss5808003472 Oct 13, 2022 (156)
73 EVA ss5843062008 Oct 13, 2022 (156)
74 EVA ss5855605332 Oct 13, 2022 (156)
75 EVA ss5886167753 Oct 13, 2022 (156)
76 EVA ss5970362746 Oct 13, 2022 (156)
77 EVA ss5970362747 Oct 13, 2022 (156)
78 1000Genomes NC_000006.11 - 137321402 Oct 12, 2018 (152)
79 1000Genomes_30x NC_000006.12 - 137000265 Oct 13, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 137321402 Oct 12, 2018 (152)
81 Genome-wide autozygosity in Daghestan NC_000006.10 - 137363095 Apr 26, 2020 (154)
82 Genetic variation in the Estonian population NC_000006.11 - 137321402 Oct 12, 2018 (152)
83 The Danish reference pan genome NC_000006.11 - 137321402 Apr 26, 2020 (154)
84 gnomAD - Genomes NC_000006.12 - 137000265 Apr 26, 2021 (155)
85 Genome of the Netherlands Release 5 NC_000006.11 - 137321402 Apr 26, 2020 (154)
86 HapMap NC_000006.12 - 137000265 Apr 26, 2020 (154)
87 KOREAN population from KRGDB NC_000006.11 - 137321402 Apr 26, 2020 (154)
88 Korean Genome Project NC_000006.12 - 137000265 Apr 26, 2020 (154)
89 Northern Sweden NC_000006.11 - 137321402 Jul 13, 2019 (153)
90 Qatari NC_000006.11 - 137321402 Apr 26, 2020 (154)
91 SGDP_PRJ NC_000006.11 - 137321402 Apr 26, 2020 (154)
92 Siberian NC_000006.11 - 137321402 Apr 26, 2020 (154)
93 8.3KJPN NC_000006.11 - 137321402 Apr 26, 2021 (155)
94 14KJPN NC_000006.12 - 137000265 Oct 13, 2022 (156)
95 TopMed NC_000006.12 - 137000265 Apr 26, 2021 (155)
96 UK 10K study - Twins NC_000006.11 - 137321402 Oct 12, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000006.11 - 137321402 Jul 13, 2019 (153)
98 ALFA NC_000006.12 - 137000265 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)
rs3173119 Jul 03, 2002 (106)
rs9483974 Oct 16, 2006 (127)
rs17250679 Oct 08, 2004 (123)
rs60303369 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83697896 NC_000006.9:137363094:G:C NC_000006.12:137000264:G:C (self)
446938, ss115178973, ss162846423, ss164675240, ss202467537, ss279040350, ss285512297, ss293733649, ss1397472532, ss1593126003, ss2635162357 NC_000006.10:137363094:G:C NC_000006.12:137000264:G:C (self)
34359689, 19152077, 13695279, 8081798, 8528182, 19959311, 7312770, 8842139, 17835980, 4766648, 38135112, 19152077, 4262712, ss222703236, ss233702767, ss240713010, ss533310983, ss559557380, ss653843970, ss983554567, ss1074074448, ss1322482725, ss1430909281, ss1581916859, ss1616809448, ss1659803481, ss1926800209, ss1970537383, ss2024057272, ss2152250294, ss2707882947, ss2845725040, ss3000033508, ss3347250947, ss3629667085, ss3667957031, ss3734027905, ss3765732525, ss3785634715, ss3790960283, ss3795839586, ss3825708090, ss3830217452, ss3838595682, ss3865819000, ss3912781917, ss3984349925, ss5180165805, ss5369347485, ss5508726740, ss5641596207, ss5843062008, ss5970362746, ss5970362747 NC_000006.11:137321401:G:C NC_000006.12:137000264:G:C (self)
45098611, 242652028, 3260649, 16546600, 52954398, 561070916, 14119956319, ss2288834028, ss3025820485, ss3648481045, ss3718380740, ss3808890824, ss3844045564, ss3960168599, ss4723693358, ss5270534433, ss5467960882, ss5557572676, ss5719117294, ss5808003472, ss5855605332, ss5886167753 NC_000006.12:137000264:G:C NC_000006.12:137000264:G:C (self)
ss13122020 NT_025741.12:41425830:G:C NC_000006.12:137000264:G:C (self)
ss52067750 NT_025741.13:41425830:G:C NC_000006.12:137000264:G:C (self)
ss1541489, ss4398974, ss4428263, ss16253019, ss24426884, ss44728458, ss98544545, ss143876860 NT_025741.15:41490858:G:C NC_000006.12:137000264:G:C (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 rs1059232

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