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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.

rs10399931

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:203186952 (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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.267128 (70706/264690, TOPMED)
T=0.254149 (38224/150400, ALFA)
T=0.29226 (22964/78574, PAGE_STUDY) (+ 3 more)
T=0.26023 (7353/28256, 14KJPN)
T=0.2762 (1769/6404, 1000G_30x)
T=0.2820 (525/1862, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHI3L1 : 2KB Upstream Variant
Publications
14 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 3110 T=0.4781 A=0.0000, C=0.5219
European Sub 2618 T=0.4102 A=0.0000, C=0.5898
African Sub 318 T=0.843 A=0.000, C=0.157
African Others Sub 14 T=0.79 A=0.00, C=0.21
African American Sub 304 T=0.845 A=0.000, C=0.155
Asian Sub 26 T=0.88 A=0.00, C=0.12
East Asian Sub 20 T=0.95 A=0.00, C=0.05
Other Asian Sub 6 T=0.7 A=0.0, C=0.3
Latin American 1 Sub 10 T=1.0 A=0.0, C=0.0
Latin American 2 Sub 72 T=1.00 A=0.00, C=0.00
South Asian Sub 10 T=0.6 A=0.0, C=0.4
Other Sub 56 T=0.61 A=0.00, C=0.39


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=0.267128 C=0.732872
Allele Frequency Aggregator Total Global 150400 T=0.254149 A=0.000000, C=0.745851
Allele Frequency Aggregator European Sub 130130 T=0.246991 A=0.000000, C=0.753009
Allele Frequency Aggregator African Sub 6702 T=0.3205 A=0.0000, C=0.6795
Allele Frequency Aggregator Other Sub 6516 T=0.2520 A=0.0000, C=0.7480
Allele Frequency Aggregator Latin American 2 Sub 5742 T=0.3276 A=0.0000, C=0.6724
Allele Frequency Aggregator Asian Sub 612 T=0.359 A=0.000, C=0.641
Allele Frequency Aggregator Latin American 1 Sub 596 T=0.270 A=0.000, C=0.730
Allele Frequency Aggregator South Asian Sub 102 T=0.304 A=0.000, C=0.696
The PAGE Study Global Study-wide 78574 T=0.29226 C=0.70774
The PAGE Study AfricanAmerican Sub 32458 T=0.28649 C=0.71351
The PAGE Study Mexican Sub 10794 T=0.33185 C=0.66815
The PAGE Study Asian Sub 8310 T=0.2662 C=0.7338
The PAGE Study PuertoRican Sub 7910 T=0.2379 C=0.7621
The PAGE Study NativeHawaiian Sub 4524 T=0.4191 C=0.5809
The PAGE Study Cuban Sub 4222 T=0.2579 C=0.7421
The PAGE Study Dominican Sub 3824 T=0.2626 C=0.7374
The PAGE Study CentralAmerican Sub 2444 T=0.3130 C=0.6870
The PAGE Study SouthAmerican Sub 1974 T=0.3105 C=0.6895
The PAGE Study NativeAmerican Sub 1260 T=0.3000 C=0.7000
The PAGE Study SouthAsian Sub 854 T=0.286 C=0.714
14KJPN JAPANESE Study-wide 28256 T=0.26023 C=0.73977
1000Genomes_30x Global Study-wide 6404 T=0.2762 C=0.7238
1000Genomes_30x African Sub 1786 T=0.2872 C=0.7128
1000Genomes_30x Europe Sub 1266 T=0.2141 C=0.7859
1000Genomes_30x South Asian Sub 1202 T=0.2646 C=0.7354
1000Genomes_30x East Asian Sub 1170 T=0.3333 C=0.6667
1000Genomes_30x American Sub 980 T=0.283 C=0.717
HapMap Global Study-wide 1862 T=0.2820 C=0.7180
HapMap American Sub 756 T=0.272 C=0.728
HapMap African Sub 684 T=0.303 C=0.697
HapMap Asian Sub 248 T=0.298 C=0.702
HapMap Europe Sub 174 T=0.218 C=0.782
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.203186952T>A
GRCh38.p14 chr 1 NC_000001.11:g.203186952T>C
GRCh37.p13 chr 1 NC_000001.10:g.203156080T>A
GRCh37.p13 chr 1 NC_000001.10:g.203156080T>C
CHI3L1 RefSeqGene NG_013056.1:g.4843A>T
CHI3L1 RefSeqGene NG_013056.1:g.4843A>G
Gene: CHI3L1, chitinase 3 like 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CHI3L1 transcript NM_001276.4:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X1 XM_047442840.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X2 XM_047442841.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X3 XM_047442846.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X4 XM_047442847.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X5 XM_047442848.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X6 XM_047442873.1:c. N/A Upstream Transcript Variant
CHI3L1 transcript variant X7 XM_047442879.1:c. N/A 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= A C
GRCh38.p14 chr 1 NC_000001.11:g.203186952= NC_000001.11:g.203186952T>A NC_000001.11:g.203186952T>C
GRCh37.p13 chr 1 NC_000001.10:g.203156080= NC_000001.10:g.203156080T>A NC_000001.10:g.203156080T>C
CHI3L1 RefSeqGene NG_013056.1:g.4843= NG_013056.1:g.4843A>T NG_013056.1:g.4843A>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#.

16 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 HUMAN_LONGEVITY ss2169321178 Dec 20, 2016 (150)
2 BIOINF_KMB_FNS_UNIBA ss3023837838 Nov 08, 2017 (151)
3 URBANLAB ss3646866329 Oct 11, 2018 (152)
4 EVA_DECODE ss3688442999 Jul 12, 2019 (153)
5 ILLUMINA ss3725096424 Jul 12, 2019 (153)
6 PAGE_CC ss3770864830 Jul 12, 2019 (153)
7 KHV_HUMAN_GENOMES ss3800225606 Jul 12, 2019 (153)
8 EVA ss3842108774 Apr 25, 2020 (154)
9 TOPMED ss4480289988 Apr 25, 2021 (155)
10 1000G_HIGH_COVERAGE ss5245467699 Oct 12, 2022 (156)
11 HUGCELL_USP ss5445937766 Oct 12, 2022 (156)
12 1000G_HIGH_COVERAGE ss5519401628 Oct 12, 2022 (156)
13 TOMMO_GENOMICS ss5675642275 Oct 12, 2022 (156)
14 YY_MCH ss5801555487 Oct 12, 2022 (156)
15 EVA ss5849244341 Oct 12, 2022 (156)
16 EVA ss5911594845 Oct 12, 2022 (156)
17 1000Genomes_30x NC_000001.11 - 203186952 Oct 12, 2022 (156)
18 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 36875632 (NC_000001.11:203186951:T:A 4/140038)
Row 36875633 (NC_000001.11:203186951:T:C 102802/139988)

- Apr 25, 2021 (155)
19 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 36875632 (NC_000001.11:203186951:T:A 4/140038)
Row 36875633 (NC_000001.11:203186951:T:C 102802/139988)

- Apr 25, 2021 (155)
20 HapMap NC_000001.11 - 203186952 Apr 25, 2020 (154)
21 The PAGE Study NC_000001.11 - 203186952 Jul 12, 2019 (153)
22 14KJPN NC_000001.11 - 203186952 Oct 12, 2022 (156)
23 TopMed NC_000001.11 - 203186952 Apr 25, 2021 (155)
24 ALFA NC_000001.11 - 203186952 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3155123218 NC_000001.11:203186951:T:A NC_000001.11:203186951:T:A (self)
6927563, 247106, 86299, 9479379, 43896323, 3155123218, ss2169321178, ss3023837838, ss3646866329, ss3688442999, ss3725096424, ss3770864830, ss3800225606, ss3842108774, ss4480289988, ss5245467699, ss5445937766, ss5519401628, ss5675642275, ss5801555487, ss5849244341, ss5911594845 NC_000001.11:203186951:T:C NC_000001.11:203186951:T:C (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss79057093 NC_000001.8:199887736:T:C NC_000001.11:203186951:T:C rs2100230404
30582, ss87939584, ss108874658, ss119176954, ss159889043, ss165695474, ss167440829, ss199495472, ss205131922, ss210717890, ss276180628, ss284211930, ss290715071, ss479255580, ss1397269426, ss1585438680, ss1712397138, ss2635006093, ss3642814994 NC_000001.9:201422702:T:C NC_000001.11:203186951:T:C rs2100230415
3172352, ss2765159800, ss3895994958 NC_000001.10:203156079:T:A NC_000001.11:203186951:T:A rs2100230426
5115840, 2815266, 1992861, 1846168, 1229566, 3172352, 1064121, 71433, 19582, 1313201, 2720503, 700676, 5975425, 2815266, 608465, ss218832254, ss230864395, ss238483975, ss479258485, ss479622045, ss484428493, ss536601285, ss555059075, ss648635502, ss778730270, ss782660705, ss783629749, ss831911208, ss834189751, ss976043817, ss1068528181, ss1294274484, ss1426083214, ss1574614281, ss1601936281, ss1644930314, ss1751892479, ss1795594892, ss1919271271, ss1946020243, ss1958348059, ss1966949712, ss2020155912, ss2094995495, ss2148184322, ss2331919443, ss2624586016, ss2632616905, ss2698174490, ss2710690883, ss2765159800, ss2984890961, ss2985535925, ss2988295187, ss3021169981, ss3343867663, ss3625558941, ss3626285357, ss3630647360, ss3632921824, ss3633617692, ss3634367573, ss3635310869, ss3636046615, ss3637061397, ss3637807912, ss3640074927, ss3644516233, ss3646251491, ss3651512848, ss3653660593, ss3656254613, ss3727779256, ss3744059150, ss3744668416, ss3747217866, ss3772169399, ss3783662418, ss3789278807, ss3794151040, ss3826595805, ss3836697614, ss3850703523, ss3895994958, ss3984470264, ss3984845506, ss5148006118 NC_000001.10:203156079:T:C NC_000001.11:203186951:T:C rs2100230426
3172352, ss3895994958 NC_000001.10:203156079:T:G NC_000001.11:203186951:T:G rs2100230426
ss35075590, ss35075592, ss43987519, ss68789793, ss74856011, ss102814168, ss119620293, ss138138632, ss139096861, ss156174208, ss170019431 NT_004487.19:54644721:T:C NC_000001.11:203186951:T:C rs2100230448
ss14687713, ss20582791 NT_004671.15:14511063:T:C NC_000001.11:203186951:T:C rs2100230453
Help

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

14 citations for rs10399931
PMID Title Author Year Journal
19421404 Variation in CHI3LI in relation to type 2 diabetes and related quantitative traits. Rathcke CN et al. 2009 PloS one
19568425 Association of polymorphisms of the CHI3L1 gene with asthma and atopy: a populations-based study of 6514 Danish adults. Rathcke CN et al. 2009 PloS one
20300754 Lack of evidence for association of two functional SNPs of CHI3L1 gene (HC-gp39) with rheumatoid arthritis. Srivastava SK et al. 2011 Rheumatology international
21257319 Genetic polymorphisms in chitinase 3-like 1 (CHI3L1) are associated with circulating YKL-40 levels, but not with angiographic coronary artery disease in a Chinese population. Zheng JL et al. 2011 Cytokine
21714862 Promoter polymorphisms in the chitinase 3-like 1 gene influence the serum concentration of YKL-40 in Danish patients with rheumatoid arthritis and in healthy subjects. Nielsen KR et al. 2011 Arthritis research & therapy
22433444 Chitinase 3-like 1 gene-329G/A polymorphism, plasma concentration and risk of coronary heart disease in a Chinese population. Xie F et al. 2012 Gene
22937056 Variations of CHI3L1, levels of the encoded glycoprotein YKL-40 and prediction of fatal and non-fatal ischemic stroke. Rathcke CN et al. 2012 PloS one
23071724 The Association between genetic variations of CHI3L1, levels of the encoded glycoprotein YKL-40 and the lipid profile in a Danish population. Thomsen SB et al. 2012 PloS one
27193312 CHI3L1 polymorphisms, cord blood YKL-40 levels and later asthma development. Usemann J et al. 2016 BMC pulmonary medicine
28739286 Genetic and epigenetic regulation of YKL-40 in childhood. Guerra S et al. 2018 The Journal of allergy and clinical immunology
30988078 Functional study of the association of CHI3L1 polymorphisms with asthma susceptibility in the Southwest Chinese Han population. Chen G et al. 2019 Bioscience reports
32367614 Chitinase 3-like 1 polymorphisms and risk of chronic obstructive pulmonary disease and asthma in a Chinese population. Yu T et al. 2020 The journal of gene medicine
33280245 Association of CHI3L1 gene variants with YKL-40 levels and hypertension incidence: A population-based nested case-control study in China. Xu T et al. 2021 Journal of cellular and molecular medicine
35340006 Assessment of the Association between Genetic Polymorphisms in the CHI3L1 Gene and Asthma Risk. Huang QP et al. 2022 International archives of allergy and immunology
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