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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.

rs9442371

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1083182 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.498587 (131971/264690, TOPMED)
T=0.488474 (68361/139948, GnomAD)
C=0.49303 (8913/18078, ALFA) (+ 15 more)
C=0.18702 (3133/16752, 8.3KJPN)
C=0.4698 (2353/5008, 1000G)
C=0.4911 (2200/4480, Estonian)
C=0.4154 (1601/3854, ALSPAC)
C=0.4215 (1563/3708, TWINSUK)
C=0.2068 (606/2930, KOREAN)
C=0.439 (438/998, GoNL)
C=0.473 (284/600, NorthernSweden)
C=0.252 (114/452, SGDP_PRJ)
T=0.485 (159/328, HapMap)
T=0.384 (83/216, Qatari)
C=0.159 (34/214, Vietnamese)
C=0.40 (17/42, Siberian)
C=0.50 (20/40, GENOME_DK)
T=0.50 (20/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : 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.1083182C>A
GRCh38.p13 chr 1 NC_000001.11:g.1083182C>T
GRCh37.p13 chr 1 NC_000001.10:g.1018562C>A
GRCh37.p13 chr 1 NC_000001.10:g.1018562C>T
Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C1orf159 transcript variant 1 NM_001330306.2:c.1049-195…

NM_001330306.2:c.1049-195G>T

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.941-195G…

NM_001363525.2:c.941-195G>T

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.503-195G>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 18078 C=0.49303 A=0.00000, T=0.50697
European Sub 13750 C=0.45593 A=0.00000, T=0.54407
African Sub 2674 C=0.7364 A=0.0000, T=0.2636
African Others Sub 100 C=0.80 A=0.00, T=0.20
African American Sub 2574 C=0.7339 A=0.0000, T=0.2661
Asian Sub 112 C=0.223 A=0.000, T=0.777
East Asian Sub 86 C=0.19 A=0.00, T=0.81
Other Asian Sub 26 C=0.35 A=0.00, T=0.65
Latin American 1 Sub 146 C=0.459 A=0.000, T=0.541
Latin American 2 Sub 610 C=0.330 A=0.000, T=0.670
South Asian Sub 98 C=0.38 A=0.00, T=0.62
Other Sub 688 C=0.501 A=0.000, T=0.499


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=0.498587 T=0.501413
gnomAD - Genomes Global Study-wide 139948 C=0.511526 T=0.488474
gnomAD - Genomes European Sub 75790 C=0.45092 T=0.54908
gnomAD - Genomes African Sub 41922 C=0.70464 T=0.29536
gnomAD - Genomes American Sub 13642 C=0.35229 T=0.64771
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.4061 T=0.5939
gnomAD - Genomes East Asian Sub 3124 C=0.2270 T=0.7730
gnomAD - Genomes Other Sub 2146 C=0.4692 T=0.5308
8.3KJPN JAPANESE Study-wide 16752 C=0.18702 T=0.81298
1000Genomes Global Study-wide 5008 C=0.4698 T=0.5302
1000Genomes African Sub 1322 C=0.7648 T=0.2352
1000Genomes East Asian Sub 1008 C=0.2103 T=0.7897
1000Genomes Europe Sub 1006 C=0.4414 T=0.5586
1000Genomes South Asian Sub 978 C=0.457 T=0.543
1000Genomes American Sub 694 C=0.344 T=0.656
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.4911 T=0.5089
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4154 T=0.5846
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4215 T=0.5785
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2068 T=0.7932
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.439 T=0.561
Northern Sweden ACPOP Study-wide 600 C=0.473 T=0.527
SGDP_PRJ Global Study-wide 452 C=0.252 T=0.748
HapMap Global Study-wide 328 C=0.515 T=0.485
HapMap American Sub 120 C=0.408 T=0.592
HapMap African Sub 118 C=0.847 T=0.153
HapMap Asian Sub 90 C=0.22 T=0.78
Qatari Global Study-wide 216 C=0.616 T=0.384
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.159 T=0.841
Siberian Global Study-wide 42 C=0.40 T=0.60
The Danish reference pan genome Danish Study-wide 40 C=0.50 T=0.50
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= A T
GRCh38.p13 chr 1 NC_000001.11:g.1083182= NC_000001.11:g.1083182C>A NC_000001.11:g.1083182C>T
GRCh37.p13 chr 1 NC_000001.10:g.1018562= NC_000001.10:g.1018562C>A NC_000001.10:g.1018562C>T
C1orf159 transcript variant 1 NM_001330306.2:c.1049-195= NM_001330306.2:c.1049-195G>T NM_001330306.2:c.1049-195G>A
C1orf159 transcript variant 3 NM_001363525.2:c.941-195= NM_001363525.2:c.941-195G>T NM_001363525.2:c.941-195G>A
C1orf159 transcript variant 2 NM_017891.4:c.503-195= NM_017891.4:c.503-195G>T NM_017891.4:c.503-195G>A
C1orf159 transcript variant 2 NM_017891.5:c.503-195= NM_017891.5:c.503-195G>T NM_017891.5:c.503-195G>A
C1orf159 transcript variant X1 XM_005244764.1:c.1049-195= XM_005244764.1:c.1049-195G>T XM_005244764.1:c.1049-195G>A
C1orf159 transcript variant X16 XM_005244765.1:c.941-195= XM_005244765.1:c.941-195G>T XM_005244765.1:c.941-195G>A
C1orf159 transcript variant X3 XM_005244766.1:c.611-195= XM_005244766.1:c.611-195G>T XM_005244766.1:c.611-195G>A
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#.

62 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13052165 Dec 05, 2003 (119)
2 ABI ss44052656 Mar 13, 2006 (126)
3 PERLEGEN ss68756310 May 17, 2007 (127)
4 HGSV ss82183208 Dec 16, 2007 (130)
5 HGSV ss82523184 Dec 16, 2007 (130)
6 BCMHGSC_JDW ss87158094 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss99179683 Feb 06, 2009 (130)
8 ENSEMBL ss131630212 Dec 01, 2009 (131)
9 ENSEMBL ss137754346 Dec 01, 2009 (131)
10 GMI ss154527275 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss163706936 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss165982076 Jul 04, 2010 (132)
13 BUSHMAN ss197888366 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss205287801 Jul 04, 2010 (132)
15 1000GENOMES ss210446518 Jul 14, 2010 (132)
16 1000GENOMES ss218191727 Jul 14, 2010 (132)
17 1000GENOMES ss230396317 Jul 14, 2010 (132)
18 1000GENOMES ss238115881 Jul 15, 2010 (132)
19 BL ss252866233 May 09, 2011 (134)
20 GMI ss275682300 May 04, 2012 (137)
21 GMI ss283987993 Apr 25, 2013 (138)
22 PJP ss290494291 May 09, 2011 (134)
23 TISHKOFF ss553713105 Apr 25, 2013 (138)
24 SSMP ss647518188 Apr 25, 2013 (138)
25 EVA-GONL ss974771683 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1067613474 Aug 21, 2014 (142)
27 1000GENOMES ss1289348961 Aug 21, 2014 (142)
28 DDI ss1425685719 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1573851883 Apr 01, 2015 (144)
30 EVA_DECODE ss1584131578 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1599381895 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1642375928 Apr 01, 2015 (144)
33 HAMMER_LAB ss1793716478 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1917963551 Feb 12, 2016 (147)
35 GENOMED ss1966667709 Jul 19, 2016 (147)
36 JJLAB ss2019499654 Sep 14, 2016 (149)
37 USC_VALOUEV ss2147486326 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2159383408 Dec 20, 2016 (150)
39 TOPMED ss2321522743 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624265439 Nov 08, 2017 (151)
41 GRF ss2697377273 Nov 08, 2017 (151)
42 GNOMAD ss2750668045 Nov 08, 2017 (151)
43 SWEGEN ss2986153818 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3023514215 Nov 08, 2017 (151)
45 TOPMED ss3066463946 Nov 08, 2017 (151)
46 CSHL ss3343274057 Nov 08, 2017 (151)
47 URBANLAB ss3646581832 Oct 11, 2018 (152)
48 EGCUT_WGS ss3654264919 Jul 12, 2019 (153)
49 EVA_DECODE ss3685997298 Jul 12, 2019 (153)
50 ACPOP ss3726718422 Jul 12, 2019 (153)
51 EVA ss3745723891 Jul 12, 2019 (153)
52 PACBIO ss3783303001 Jul 12, 2019 (153)
53 PACBIO ss3788980789 Jul 12, 2019 (153)
54 PACBIO ss3793853338 Jul 12, 2019 (153)
55 KHV_HUMAN_GENOMES ss3798746534 Jul 12, 2019 (153)
56 EVA ss3825982472 Apr 25, 2020 (154)
57 EVA ss3836378995 Apr 25, 2020 (154)
58 EVA ss3841783022 Apr 25, 2020 (154)
59 SGDP_PRJ ss3848003069 Apr 25, 2020 (154)
60 KRGDB ss3892845608 Apr 25, 2020 (154)
61 TOPMED ss4436510328 Apr 25, 2021 (155)
62 TOMMO_GENOMICS ss5142065325 Apr 25, 2021 (155)
63 1000Genomes NC_000001.10 - 1018562 Oct 11, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1018562 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 1018562 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 1018562 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 1083182 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 1018562 Apr 25, 2020 (154)
69 HapMap NC_000001.11 - 1083182 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000001.10 - 1018562 Apr 25, 2020 (154)
71 Northern Sweden NC_000001.10 - 1018562 Jul 12, 2019 (153)
72 Qatari NC_000001.10 - 1018562 Apr 25, 2020 (154)
73 SGDP_PRJ NC_000001.10 - 1018562 Apr 25, 2020 (154)
74 Siberian NC_000001.10 - 1018562 Apr 25, 2020 (154)
75 8.3KJPN NC_000001.10 - 1018562 Apr 25, 2021 (155)
76 TopMed NC_000001.11 - 1083182 Apr 25, 2021 (155)
77 UK 10K study - Twins NC_000001.10 - 1018562 Oct 11, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000001.10 - 1018562 Jul 12, 2019 (153)
79 ALFA NC_000001.11 - 1083182 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)
rs61276853 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14533873258 NC_000001.11:1083181:C:A NC_000001.11:1083181:C:A
ss82183208, ss82523184 NC_000001.8:1058484:C:T NC_000001.11:1083181:C:T (self)
ss87158094, ss163706936, ss165982076, ss197888366, ss205287801, ss210446518, ss252866233, ss275682300, ss283987993, ss290494291, ss1584131578 NC_000001.9:1008424:C:T NC_000001.11:1083181:C:T (self)
14050, 4240, 3167, 1359117, 2054, 23002, 3287, 5481, 20049, 2680, 34632, 4240, 975, ss218191727, ss230396317, ss238115881, ss553713105, ss647518188, ss974771683, ss1067613474, ss1289348961, ss1425685719, ss1573851883, ss1599381895, ss1642375928, ss1793716478, ss1917963551, ss1966667709, ss2019499654, ss2147486326, ss2321522743, ss2624265439, ss2697377273, ss2750668045, ss2986153818, ss3343274057, ss3654264919, ss3726718422, ss3745723891, ss3783303001, ss3788980789, ss3793853338, ss3825982472, ss3836378995, ss3848003069, ss3892845608, ss5142065325 NC_000001.10:1018561:C:T NC_000001.11:1083181:C:T (self)
132899, 181, 65172, 116663, 14533873258, ss2159383408, ss3023514215, ss3066463946, ss3646581832, ss3685997298, ss3798746534, ss3841783022, ss4436510328 NC_000001.11:1083181:C:T NC_000001.11:1083181:C:T (self)
ss44052656, ss68756310, ss99179683, ss131630212, ss137754346, ss154527275 NT_004350.19:497193:C:T NC_000001.11:1083181:C:T (self)
ss13052165 NT_077960.1:90047:C:T NC_000001.11:1083181: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 rs9442371

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