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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.

rs1800891

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:206775221 (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=0.061600 (16305/264690, TOPMED)
C=0.062479 (8745/139966, GnomAD)
C=0.05813 (1098/18890, ALFA) (+ 10 more)
C=0.0439 (281/6404, 1000G_30x)
C=0.0399 (200/5008, 1000G)
C=0.0511 (197/3854, ALSPAC)
C=0.0604 (224/3708, TWINSUK)
C=0.058 (58/998, GoNL)
C=0.088 (53/600, NorthernSweden)
C=0.083 (18/216, Qatari)
T=0.46 (21/46, SGDP_PRJ)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IL19 : 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 18890 T=0.94187 C=0.05813
European Sub 14286 T=0.94155 C=0.05845
African Sub 2946 T=0.9382 C=0.0618
African Others Sub 114 T=0.939 C=0.061
African American Sub 2832 T=0.9382 C=0.0618
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=0.918 C=0.082
Latin American 2 Sub 610 T=0.966 C=0.034
South Asian Sub 98 T=0.99 C=0.01
Other Sub 692 T=0.932 C=0.068


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=0.938400 C=0.061600
gnomAD - Genomes Global Study-wide 139966 T=0.937521 C=0.062479
gnomAD - Genomes European Sub 75828 T=0.93887 C=0.06113
gnomAD - Genomes African Sub 41896 T=0.92901 C=0.07099
gnomAD - Genomes American Sub 13642 T=0.94664 C=0.05336
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.9160 C=0.0840
gnomAD - Genomes East Asian Sub 3132 T=0.9994 C=0.0006
gnomAD - Genomes Other Sub 2148 T=0.9409 C=0.0591
Allele Frequency Aggregator Total Global 18890 T=0.94187 C=0.05813
Allele Frequency Aggregator European Sub 14286 T=0.94155 C=0.05845
Allele Frequency Aggregator African Sub 2946 T=0.9382 C=0.0618
Allele Frequency Aggregator Other Sub 692 T=0.932 C=0.068
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.966 C=0.034
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.918 C=0.082
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=0.99 C=0.01
1000Genomes_30x Global Study-wide 6404 T=0.9561 C=0.0439
1000Genomes_30x African Sub 1786 T=0.9222 C=0.0778
1000Genomes_30x Europe Sub 1266 T=0.9400 C=0.0600
1000Genomes_30x South Asian Sub 1202 T=0.9884 C=0.0116
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.947 C=0.053
1000Genomes Global Study-wide 5008 T=0.9601 C=0.0399
1000Genomes African Sub 1322 T=0.9251 C=0.0749
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9404 C=0.0596
1000Genomes South Asian Sub 978 T=0.989 C=0.011
1000Genomes American Sub 694 T=0.957 C=0.043
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9489 C=0.0511
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9396 C=0.0604
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.942 C=0.058
Northern Sweden ACPOP Study-wide 600 T=0.912 C=0.088
Qatari Global Study-wide 216 T=0.917 C=0.083
SGDP_PRJ Global Study-wide 46 T=0.46 C=0.54
Siberian Global Study-wide 6 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 1 NC_000001.11:g.206775221T>C
GRCh37.p13 chr 1 NC_000001.10:g.206948566T>C
IL10 RefSeqGene (LRG_1230) NG_012088.1:g.2274A>G
Gene: IL19, interleukin 19 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
IL19 transcript variant 4 NM_001393490.1:c.-149+439…

NM_001393490.1:c.-149+4391T>C

N/A Intron Variant
IL19 transcript variant 1 NM_153758.5:c.-149+4143T>C N/A Intron Variant
IL19 transcript variant 3 NM_001369605.1:c. N/A Genic Upstream Transcript Variant
IL19 transcript variant 5 NM_001393491.1:c. N/A Genic Upstream Transcript Variant
IL19 transcript variant 2 NM_013371.5:c. N/A Genic Upstream Transcript Variant
IL19 transcript variant X1 XM_011509450.3:c. N/A Genic Upstream 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 T= C
GRCh38.p14 chr 1 NC_000001.11:g.206775221= NC_000001.11:g.206775221T>C
GRCh37.p13 chr 1 NC_000001.10:g.206948566= NC_000001.10:g.206948566T>C
IL10 RefSeqGene (LRG_1230) NG_012088.1:g.2274= NG_012088.1:g.2274A>G
IL19 transcript variant 4 NM_001393490.1:c.-149+4391= NM_001393490.1:c.-149+4391T>C
IL19 transcript variant 1 NM_153758.5:c.-149+4143= NM_153758.5:c.-149+4143T>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#.

42 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss11111829 Jul 11, 2003 (130)
2 SC_SNP ss15441413 Feb 27, 2004 (130)
3 CSHL-HAPMAP ss16399416 Feb 27, 2004 (130)
4 SSAHASNP ss20572650 Apr 05, 2004 (130)
5 ABI ss41087964 Mar 13, 2006 (130)
6 HGSV ss81164917 Dec 14, 2007 (130)
7 HUMANGENOME_JCVI ss99281624 Feb 04, 2009 (130)
8 ILLUMINA-UK ss119184739 Dec 01, 2009 (131)
9 ENSEMBL ss131739061 Dec 01, 2009 (131)
10 PJP ss290719932 May 09, 2011 (134)
11 1000GENOMES ss329178003 May 09, 2011 (134)
12 TISHKOFF ss555087300 Apr 25, 2013 (138)
13 SSMP ss648651812 Apr 25, 2013 (138)
14 EVA-GONL ss976069368 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1068546094 Aug 21, 2014 (142)
16 1000GENOMES ss1294370540 Aug 21, 2014 (142)
17 EVA_UK10K_ALSPAC ss1601987574 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1644981607 Apr 01, 2015 (144)
19 HAMMER_LAB ss1795631736 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1919296264 Feb 12, 2016 (147)
21 JJLAB ss2020168996 Sep 14, 2016 (149)
22 USC_VALOUEV ss2148198602 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2169516670 Dec 20, 2016 (150)
24 GNOMAD ss2765435084 Nov 08, 2017 (151)
25 SWEGEN ss2988336526 Nov 08, 2017 (151)
26 CSHL ss3343879324 Nov 08, 2017 (151)
27 URBANLAB ss3646871873 Oct 11, 2018 (152)
28 EVA_DECODE ss3688492963 Jul 12, 2019 (153)
29 ACPOP ss3727800718 Jul 12, 2019 (153)
30 EVA ss3747248002 Jul 12, 2019 (153)
31 KHV_HUMAN_GENOMES ss3800254955 Jul 12, 2019 (153)
32 EVA ss3826607889 Apr 25, 2020 (154)
33 SGDP_PRJ ss3850754934 Apr 25, 2020 (154)
34 TOPMED ss4481131971 Apr 25, 2021 (155)
35 1000G_HIGH_COVERAGE ss5245556322 Oct 12, 2022 (156)
36 EVA ss5324348174 Oct 12, 2022 (156)
37 HUGCELL_USP ss5446015869 Oct 12, 2022 (156)
38 1000G_HIGH_COVERAGE ss5519530230 Oct 12, 2022 (156)
39 SANFORD_IMAGENETICS ss5627310572 Oct 12, 2022 (156)
40 EVA ss5833164526 Oct 12, 2022 (156)
41 EVA ss5911692253 Oct 12, 2022 (156)
42 EVA ss5939139894 Oct 12, 2022 (156)
43 1000Genomes NC_000001.10 - 206948566 Oct 11, 2018 (152)
44 1000Genomes_30x NC_000001.11 - 206775221 Oct 12, 2022 (156)
45 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 206948566 Oct 11, 2018 (152)
46 gnomAD - Genomes NC_000001.11 - 206775221 Apr 25, 2021 (155)
47 Genome of the Netherlands Release 5 NC_000001.10 - 206948566 Apr 25, 2020 (154)
48 Northern Sweden NC_000001.10 - 206948566 Jul 12, 2019 (153)
49 Qatari NC_000001.10 - 206948566 Apr 25, 2020 (154)
50 SGDP_PRJ NC_000001.10 - 206948566 Apr 25, 2020 (154)
51 Siberian NC_000001.10 - 206948566 Apr 25, 2020 (154)
52 TopMed NC_000001.11 - 206775221 Apr 25, 2021 (155)
53 UK 10K study - Twins NC_000001.10 - 206948566 Oct 11, 2018 (152)
54 ALFA NC_000001.11 - 206775221 Apr 25, 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)
rs7349077 May 23, 2008 (130)
rs57133400 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81164917 NC_000001.8:203336960:T:C NC_000001.11:206775220:T:C (self)
ss119184739, ss290719932 NC_000001.9:205015188:T:C NC_000001.11:206775220:T:C (self)
5215181, 2871920, 1254245, 1085583, 1338194, 2771914, 714956, 2871920, ss329178003, ss555087300, ss648651812, ss976069368, ss1068546094, ss1294370540, ss1601987574, ss1644981607, ss1795631736, ss1919296264, ss2020168996, ss2148198602, ss2765435084, ss2988336526, ss3343879324, ss3727800718, ss3747248002, ss3826607889, ss3850754934, ss5324348174, ss5627310572, ss5833164526, ss5939139894 NC_000001.10:206948565:T:C NC_000001.11:206775220:T:C (self)
7056165, 37583604, 44738306, 11160869068, ss2169516670, ss3646871873, ss3688492963, ss3800254955, ss4481131971, ss5245556322, ss5446015869, ss5519530230, ss5911692253 NC_000001.11:206775220:T:C NC_000001.11:206775220:T:C (self)
ss16399416, ss20572650 NT_021877.16:411672:T:C NC_000001.11:206775220:T:C (self)
ss11111829, ss15441413, ss41087964, ss99281624, ss131739061 NT_167186.1:466344:T:C NC_000001.11:206775220: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 rs1800891
PMID Title Author Year Journal
18479293 Evaluation of IL10, IL19 and IL20 gene polymorphisms and chronic hepatitis B infection outcome. Truelove AL et al. 2008 International journal of immunogenetics
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