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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.

rs1859009

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:24334032 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.494809 (130971/264690, TOPMED)
T=0.479318 (67046/139878, GnomAD)
C=0.25083 (7088/28258, 14KJPN) (+ 15 more)
T=0.45548 (8604/18890, ALFA)
C=0.25009 (4191/16758, 8.3KJPN)
C=0.4708 (3015/6404, 1000G_30x)
C=0.4760 (2384/5008, 1000G)
T=0.4551 (2039/4480, Estonian)
T=0.3980 (1534/3854, ALSPAC)
T=0.4153 (1540/3708, TWINSUK)
C=0.3137 (919/2930, KOREAN)
T=0.395 (394/998, GoNL)
T=0.442 (265/600, NorthernSweden)
C=0.305 (131/430, SGDP_PRJ)
T=0.394 (85/216, Qatari)
C=0.322 (69/214, Vietnamese)
T=0.25 (10/40, GENOME_DK)
C=0.30 (12/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107986777 : Intron 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 C=0.54452 T=0.45548
European Sub 14286 C=0.57525 T=0.42475
African Sub 2946 C=0.4318 T=0.5682
African Others Sub 114 C=0.412 T=0.588
African American Sub 2832 C=0.4326 T=0.5674
Asian Sub 112 C=0.312 T=0.688
East Asian Sub 86 C=0.33 T=0.67
Other Asian Sub 26 C=0.27 T=0.73
Latin American 1 Sub 146 C=0.521 T=0.479
Latin American 2 Sub 610 C=0.472 T=0.528
South Asian Sub 98 C=0.51 T=0.49
Other Sub 692 C=0.501 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=0.505191 T=0.494809
gnomAD - Genomes Global Study-wide 139878 C=0.520682 T=0.479318
gnomAD - Genomes European Sub 75790 C=0.58736 T=0.41264
gnomAD - Genomes African Sub 41894 C=0.42319 T=0.57681
gnomAD - Genomes American Sub 13608 C=0.45944 T=0.54056
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.6329 T=0.3671
gnomAD - Genomes East Asian Sub 3122 C=0.3680 T=0.6320
gnomAD - Genomes Other Sub 2146 C=0.5061 T=0.4939
14KJPN JAPANESE Study-wide 28258 C=0.25083 T=0.74917
Allele Frequency Aggregator Total Global 18890 C=0.54452 T=0.45548
Allele Frequency Aggregator European Sub 14286 C=0.57525 T=0.42475
Allele Frequency Aggregator African Sub 2946 C=0.4318 T=0.5682
Allele Frequency Aggregator Other Sub 692 C=0.501 T=0.499
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.472 T=0.528
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.521 T=0.479
Allele Frequency Aggregator Asian Sub 112 C=0.312 T=0.688
Allele Frequency Aggregator South Asian Sub 98 C=0.51 T=0.49
8.3KJPN JAPANESE Study-wide 16758 C=0.25009 T=0.74991
1000Genomes_30x Global Study-wide 6404 C=0.4708 T=0.5292
1000Genomes_30x African Sub 1786 C=0.4143 T=0.5857
1000Genomes_30x Europe Sub 1266 C=0.5798 T=0.4202
1000Genomes_30x South Asian Sub 1202 C=0.5441 T=0.4559
1000Genomes_30x East Asian Sub 1170 C=0.3624 T=0.6376
1000Genomes_30x American Sub 980 C=0.472 T=0.528
1000Genomes Global Study-wide 5008 C=0.4760 T=0.5240
1000Genomes African Sub 1322 C=0.4168 T=0.5832
1000Genomes East Asian Sub 1008 C=0.3681 T=0.6319
1000Genomes Europe Sub 1006 C=0.5875 T=0.4125
1000Genomes South Asian Sub 978 C=0.555 T=0.445
1000Genomes American Sub 694 C=0.473 T=0.527
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5449 T=0.4551
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6020 T=0.3980
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5847 T=0.4153
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3137 A=0.0000, T=0.6863
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.605 T=0.395
Northern Sweden ACPOP Study-wide 600 C=0.558 T=0.442
SGDP_PRJ Global Study-wide 430 C=0.305 T=0.695
Qatari Global Study-wide 216 C=0.606 T=0.394
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.322 T=0.678
The Danish reference pan genome Danish Study-wide 40 C=0.75 T=0.25
Siberian Global Study-wide 40 C=0.30 T=0.70
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 7 NC_000007.14:g.24334032C>A
GRCh38.p14 chr 7 NC_000007.14:g.24334032C>T
GRCh37.p13 chr 7 NC_000007.13:g.24373651C>A
GRCh37.p13 chr 7 NC_000007.13:g.24373651C>T
Gene: LOC107986777, uncharacterized LOC107986777 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107986777 transcript variant X3 XR_001745121.2:n. N/A Intron Variant
LOC107986777 transcript variant X7 XR_001745122.2:n. N/A Intron Variant
LOC107986777 transcript variant X8 XR_001745123.2:n. N/A Intron Variant
LOC107986777 transcript variant X10 XR_001745124.2:n. N/A Intron Variant
LOC107986777 transcript variant X11 XR_001745125.2:n. N/A Intron Variant
LOC107986777 transcript variant X13 XR_001745127.2:n. N/A Intron Variant
LOC107986777 transcript variant X9 XR_001745129.2:n. N/A Intron Variant
LOC107986777 transcript variant X4 XR_001745130.2:n. N/A Intron Variant
LOC107986777 transcript variant X14 XR_001745131.2:n. N/A Intron Variant
LOC107986777 transcript variant X15 XR_001745132.2:n. N/A Intron Variant
LOC107986777 transcript variant X1 XR_007060254.1:n. N/A Intron Variant
LOC107986777 transcript variant X2 XR_007060255.1:n. N/A Intron Variant
LOC107986777 transcript variant X5 XR_007060256.1:n. N/A Intron Variant
LOC107986777 transcript variant X6 XR_007060257.1:n. N/A Intron Variant
LOC107986777 transcript variant X12 XR_001745128.2:n. N/A Genic Upstream Transcript Variant
LOC107986777 transcript variant X16 XR_007060258.1:n. 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 C= A T
GRCh38.p14 chr 7 NC_000007.14:g.24334032= NC_000007.14:g.24334032C>A NC_000007.14:g.24334032C>T
GRCh37.p13 chr 7 NC_000007.13:g.24373651= NC_000007.13:g.24373651C>A NC_000007.13:g.24373651C>T
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#.

65 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2732587 Jan 12, 2001 (92)
2 SC_JCM ss3844820 Sep 28, 2001 (100)
3 SC_JCM ss5874946 Feb 20, 2003 (111)
4 CSHL-HAPMAP ss20309925 Feb 27, 2004 (120)
5 ABI ss42903318 Mar 14, 2006 (126)
6 HGSV ss78045603 Dec 06, 2007 (129)
7 HGSV ss84222041 Dec 14, 2007 (130)
8 HUMANGENOME_JCVI ss98240204 Feb 04, 2009 (130)
9 BGI ss104409902 Dec 01, 2009 (131)
10 1000GENOMES ss111684632 Jan 25, 2009 (130)
11 GMI ss154522882 Dec 01, 2009 (131)
12 BUSHMAN ss203084151 Jul 04, 2010 (132)
13 1000GENOMES ss212008650 Jul 14, 2010 (132)
14 1000GENOMES ss222966078 Jul 14, 2010 (132)
15 1000GENOMES ss233892377 Jul 15, 2010 (132)
16 1000GENOMES ss240864615 Jul 15, 2010 (132)
17 BL ss254124374 May 09, 2011 (134)
18 GMI ss279227537 May 04, 2012 (137)
19 PJP ss294031589 May 09, 2011 (134)
20 TISHKOFF ss559872785 Apr 25, 2013 (138)
21 SSMP ss654225959 Apr 25, 2013 (138)
22 EVA-GONL ss984059106 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1074447624 Aug 21, 2014 (142)
24 1000GENOMES ss1324328908 Aug 21, 2014 (142)
25 DDI ss1431060030 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1582114580 Apr 01, 2015 (144)
27 EVA_DECODE ss1593627953 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1617784674 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1660778707 Apr 01, 2015 (144)
30 HAMMER_LAB ss1804914946 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1927304421 Feb 12, 2016 (147)
32 GENOMED ss1970650485 Jul 19, 2016 (147)
33 JJLAB ss2024328922 Sep 14, 2016 (149)
34 USC_VALOUEV ss2152525126 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2292490178 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2626653491 Nov 08, 2017 (151)
37 GRF ss2708182011 Nov 08, 2017 (151)
38 GNOMAD ss2850881078 Nov 08, 2017 (151)
39 SWEGEN ss3000787237 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3025958712 Nov 08, 2017 (151)
41 CSHL ss3347485993 Nov 08, 2017 (151)
42 URBANLAB ss3648585033 Oct 12, 2018 (152)
43 EGCUT_WGS ss3668715636 Jul 13, 2019 (153)
44 EVA_DECODE ss3719295833 Jul 13, 2019 (153)
45 ACPOP ss3734447838 Jul 13, 2019 (153)
46 EVA ss3766311216 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3809478620 Jul 13, 2019 (153)
48 EVA ss3830468090 Apr 26, 2020 (154)
49 EVA ss3838721371 Apr 26, 2020 (154)
50 EVA ss3844172588 Apr 26, 2020 (154)
51 SGDP_PRJ ss3866844030 Apr 26, 2020 (154)
52 KRGDB ss3913881885 Apr 26, 2020 (154)
53 TOPMED ss4739030266 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5182250582 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5272177381 Oct 14, 2022 (156)
56 HUGCELL_USP ss5469427071 Oct 14, 2022 (156)
57 EVA ss5508883883 Oct 14, 2022 (156)
58 1000G_HIGH_COVERAGE ss5559995598 Oct 14, 2022 (156)
59 SANFORD_IMAGENETICS ss5642547914 Oct 14, 2022 (156)
60 TOMMO_GENOMICS ss5721827596 Oct 14, 2022 (156)
61 YY_MCH ss5808423398 Oct 14, 2022 (156)
62 EVA ss5822544856 Oct 14, 2022 (156)
63 EVA ss5855807628 Oct 14, 2022 (156)
64 EVA ss5858105912 Oct 14, 2022 (156)
65 EVA ss5971747651 Oct 14, 2022 (156)
66 1000Genomes NC_000007.13 - 24373651 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000007.14 - 24334032 Oct 14, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 24373651 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000007.13 - 24373651 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000007.13 - 24373651 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000007.14 - 24334032 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000007.13 - 24373651 Apr 26, 2020 (154)
73 KOREAN population from KRGDB NC_000007.13 - 24373651 Apr 26, 2020 (154)
74 Northern Sweden NC_000007.13 - 24373651 Jul 13, 2019 (153)
75 Qatari NC_000007.13 - 24373651 Apr 26, 2020 (154)
76 SGDP_PRJ NC_000007.13 - 24373651 Apr 26, 2020 (154)
77 Siberian NC_000007.13 - 24373651 Apr 26, 2020 (154)
78 8.3KJPN NC_000007.13 - 24373651 Apr 26, 2021 (155)
79 14KJPN NC_000007.14 - 24334032 Oct 14, 2022 (156)
80 TopMed NC_000007.14 - 24334032 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000007.13 - 24373651 Oct 12, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000007.13 - 24373651 Jul 13, 2019 (153)
83 ALFA NC_000007.14 - 24334032 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)
rs57213923 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
21059279, ss3913881885 NC_000007.13:24373650:C:A NC_000007.14:24334031:C:A (self)
ss78045603, ss84222041 NC_000007.11:24146890:C:T NC_000007.14:24334031:C:T (self)
ss111684632, ss203084151, ss212008650, ss254124374, ss279227537, ss294031589, ss1593627953 NC_000007.12:24340175:C:T NC_000007.14:24334031:C:T (self)
36270270, 20219656, 14453884, 8279519, 9014853, 21059279, 7732703, 9346351, 18861010, 5041480, 40219889, 20219656, 4505339, ss222966078, ss233892377, ss240864615, ss559872785, ss654225959, ss984059106, ss1074447624, ss1324328908, ss1431060030, ss1582114580, ss1617784674, ss1660778707, ss1804914946, ss1927304421, ss1970650485, ss2024328922, ss2152525126, ss2626653491, ss2708182011, ss2850881078, ss3000787237, ss3347485993, ss3668715636, ss3734447838, ss3766311216, ss3830468090, ss3838721371, ss3866844030, ss3913881885, ss5182250582, ss5508883883, ss5642547914, ss5822544856, ss5971747651 NC_000007.13:24373650:C:T NC_000007.14:24334031:C:T (self)
47521533, 255748917, 55664700, 576407825, 2206007815, ss2292490178, ss3025958712, ss3648585033, ss3719295833, ss3809478620, ss3844172588, ss4739030266, ss5272177381, ss5469427071, ss5559995598, ss5721827596, ss5808423398, ss5855807628, ss5858105912 NC_000007.14:24334031:C:T NC_000007.14:24334031:C:T (self)
ss20309925 NT_007819.14:23667258:C:T NC_000007.14:24334031:C:T (self)
ss2732587, ss3844820, ss5874946, ss42903318, ss98240204, ss104409902, ss154522882 NT_007819.17:24363650:C:T NC_000007.14:24334031: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 rs1859009

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