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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1167998

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:62465961 (GRCh38.p7) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.43261 (54322/125568, TOPMED)
C=0.4214 (13023/30904, GnomAD)
C=0.440 (2203/5008, 1000G) (+ 2 more)
C=0.373 (1439/3854, ALSPAC)
C=0.368 (1365/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DOCK7 : Intron Variant
Publications
8 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.p7 chr 1 NC_000001.11:g.62465961C>A
GRCh37.p13 chr 1 NC_000001.10:g.62931632C>A
DOCK7 RefSeqGene NG_033073.1:g.227408G>T
Gene: DOCK7, dedicator of cytokinesis 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DOCK7 transcript variant 1 NM_001271999.1:c. N/A Intron Variant
DOCK7 transcript variant 3 NM_001272000.1:c. N/A Intron Variant
DOCK7 transcript variant 4 NM_001272001.1:c. N/A Intron Variant
DOCK7 transcript variant 2 NM_033407.3:c. N/A Intron Variant
DOCK7 transcript variant 5 NM_001272002.1:c. N/A Genic Downstream Transcript Variant
DOCK7 transcript variant X4 XM_005271292.2:c. N/A Intron Variant
DOCK7 transcript variant X1 XM_011542326.2:c. N/A Intron Variant
DOCK7 transcript variant X2 XM_011542327.2:c. N/A Intron Variant
DOCK7 transcript variant X3 XM_011542328.2:c. N/A Intron Variant
DOCK7 transcript variant X4 XM_017002639.1:c. N/A Intron Variant
DOCK7 transcript variant X6 XM_011542330.2:c. N/A Genic Downstream Transcript Variant
DOCK7 transcript variant X5 XM_017002640.1:c. N/A Genic Downstream 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

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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.43261 A=0.56739
The Genome Aggregation Database Global Study-wide 30904 C=0.4214 A=0.5786
The Genome Aggregation Database European Sub 18470 C=0.3279 A=0.6721
The Genome Aggregation Database African Sub 8706 C=0.666 A=0.334
The Genome Aggregation Database East Asian Sub 1610 C=0.248 A=0.752
The Genome Aggregation Database Other Sub 978 C=0.35 A=0.65
The Genome Aggregation Database American Sub 838 C=0.41 A=0.59
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.28 A=0.72
1000Genomes Global Study-wide 5008 C=0.440 A=0.560
1000Genomes African Sub 1322 C=0.689 A=0.311
1000Genomes East Asian Sub 1008 C=0.234 A=0.766
1000Genomes Europe Sub 1006 C=0.313 A=0.687
1000Genomes South Asian Sub 978 C=0.48 A=0.52
1000Genomes American Sub 694 C=0.40 A=0.60
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.373 A=0.627
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.368 A=0.632
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 Note
GRCh38.p7 chr 1 NC_000001.11:g.62465961C= NC_000001.11:g.62465961C>A
GRCh37.p13 chr 1 NC_000001.10:g.62931632C= NC_000001.10:g.62931632C>A
DOCK7 RefSeqGene NG_033073.1:g.227408G= NG_033073.1:g.227408G>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#.

90 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1591200 Oct 18, 2000 (87)
2 SC_JCM ss2644465 Nov 09, 2000 (126)
3 BCM_SSAHASNP ss9836575 Jul 11, 2003 (116)
4 SSAHASNP ss20549592 Apr 05, 2004 (123)
5 ABI ss41254520 Mar 11, 2006 (126)
6 ILLUMINA ss66668561 Dec 02, 2006 (127)
7 ILLUMINA ss66944159 Dec 02, 2006 (127)
8 ILLUMINA ss67105833 Dec 02, 2006 (127)
9 ILLUMINA ss70397158 May 18, 2007 (127)
10 ILLUMINA ss70536233 May 25, 2008 (130)
11 ILLUMINA ss71067619 May 18, 2007 (127)
12 ILLUMINA ss75603664 Dec 06, 2007 (129)
13 HGSV ss78075425 Dec 06, 2007 (129)
14 KRIBB_YJKIM ss83694205 Dec 15, 2007 (130)
15 HUMANGENOME_JCVI ss97941792 Feb 05, 2009 (130)
16 BGI ss106570339 Feb 05, 2009 (130)
17 1000GENOMES ss108249262 Jan 23, 2009 (130)
18 ILLUMINA ss121490724 Dec 01, 2009 (131)
19 ENSEMBL ss138924258 Dec 01, 2009 (131)
20 ILLUMINA ss153028401 Dec 01, 2009 (131)
21 GMI ss155073775 Dec 01, 2009 (131)
22 ILLUMINA ss159183098 Dec 01, 2009 (131)
23 ILLUMINA ss161054352 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss164405322 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss166601492 Jul 04, 2010 (132)
26 ILLUMINA ss169915854 Jul 04, 2010 (132)
27 ILLUMINA ss171433720 Jul 04, 2010 (132)
28 BUSHMAN ss198526652 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss205240425 Jul 04, 2010 (132)
30 1000GENOMES ss210538141 Jul 14, 2010 (132)
31 1000GENOMES ss218414443 Jul 14, 2010 (132)
32 1000GENOMES ss230556288 Jul 14, 2010 (132)
33 1000GENOMES ss238246796 Jul 15, 2010 (132)
34 ILLUMINA ss244273678 Jul 04, 2010 (132)
35 BL ss253132638 May 09, 2011 (134)
36 GMI ss275847573 May 04, 2012 (137)
37 GMI ss284060023 Apr 25, 2013 (138)
38 PJP ss290522093 May 09, 2011 (134)
39 ILLUMINA ss479444005 Sep 08, 2015 (146)
40 EXOME_CHIP ss491294887 May 04, 2012 (137)
41 ILLUMINA ss536711797 Sep 08, 2015 (146)
42 TISHKOFF ss554172704 Apr 25, 2013 (138)
43 SSMP ss648030036 Apr 25, 2013 (138)
44 ILLUMINA ss780681134 Sep 08, 2015 (146)
45 ILLUMINA ss783354435 Sep 08, 2015 (146)
46 ILLUMINA ss825366553 Apr 01, 2015 (144)
47 EVA-GONL ss975215911 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1067929859 Aug 21, 2014 (142)
49 1000GENOMES ss1291105471 Aug 21, 2014 (142)
50 HAMMER_LAB ss1397247332 Sep 08, 2015 (146)
51 DDI ss1425826674 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1574098539 Apr 01, 2015 (144)
53 EVA_DECODE ss1584583971 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1600287234 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1643281267 Apr 01, 2015 (144)
56 EVA_SVP ss1712337647 Apr 01, 2015 (144)
57 ILLUMINA ss1751928471 Sep 08, 2015 (146)
58 HAMMER_LAB ss1794449366 Sep 08, 2015 (146)
59 ILLUMINA ss1917729616 Feb 12, 2016 (147)
60 WEILL_CORNELL_DGM ss1918424429 Feb 12, 2016 (147)
61 ILLUMINA ss1945996931 Feb 12, 2016 (147)
62 ILLUMINA ss1958277811 Feb 12, 2016 (147)
63 GENOMED ss1966758340 Jul 19, 2016 (147)
64 JJLAB ss2019728646 Sep 14, 2016 (149)
65 USC_VALOUEV ss2147744351 Dec 20, 2016 (150)
66 HUMAN_LONGEVITY ss2162944792 Dec 20, 2016 (150)
67 TOPMED ss2325194204 Dec 20, 2016 (150)
68 SYSTEMSBIOZJU ss2624378038 Nov 08, 2017 (151)
69 ILLUMINA ss2632522991 Nov 08, 2017 (151)
70 ILLUMINA ss2632522992 Nov 08, 2017 (151)
71 GRF ss2697660039 Nov 08, 2017 (151)
72 GNOMAD ss2755741125 Nov 08, 2017 (151)
73 AFFY ss2984861344 Nov 08, 2017 (151)
74 AFFY ss2985513540 Nov 08, 2017 (151)
75 SWEGEN ss2986901989 Nov 08, 2017 (151)
76 ILLUMINA ss3021092887 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3023625114 Nov 08, 2017 (151)
78 TOPMED ss3078010267 Nov 08, 2017 (151)
79 CSHL ss3343478672 Nov 08, 2017 (151)
80 ILLUMINA ss3625541243 Jul 19, 2018 (151)
81 ILLUMINA ss3626110563 Jul 19, 2018 (151)
82 ILLUMINA ss3626110564 Jul 19, 2018 (151)
83 ILLUMINA ss3634327468 Jul 19, 2018 (151)
84 ILLUMINA ss3636003063 Jul 19, 2018 (151)
85 ILLUMINA ss3637760243 Jul 19, 2018 (151)
86 ILLUMINA ss3638899019 Jul 19, 2018 (151)
87 ILLUMINA ss3639447074 Jul 19, 2018 (151)
88 ILLUMINA ss3640034829 Jul 19, 2018 (151)
89 ILLUMINA ss3642772067 Jul 19, 2018 (151)
90 ILLUMINA ss3644492854 Jul 19, 2018 (151)
91 1000Genomes NC_000001.10 - 62931632 Jul 19, 2018 (151)
92 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 62931632 Jul 19, 2018 (151)
93 The Genome Aggregation Database NC_000001.10 - 62931632 Jul 19, 2018 (151)
94 Trans-Omics for Precision Medicine NC_000001.11 - 62465961 Jul 19, 2018 (151)
95 UK 10K study - Twins NC_000001.10 - 62931632 Jul 19, 2018 (151)
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)
rs1781213 Mar 11, 2006 (126)
rs12747715 Sep 24, 2004 (123)
rs60029621 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78075425, ss3638899019, ss3639447074 NC_000001.8:62643652:C= NC_000001.11:62465960:C= (self)
ss108249262, ss164405322, ss166601492, ss198526652, ss205240425, ss210538141, ss253132638, ss275847573, ss284060023, ss290522093, ss825366553, ss1397247332, ss1584583971, ss1712337647, ss3642772067 NC_000001.9:62704219:C= NC_000001.11:62465960:C= (self)
1831122, 1000778, 5140324, 1000778, ss218414443, ss230556288, ss238246796, ss479444005, ss491294887, ss536711797, ss554172704, ss648030036, ss780681134, ss783354435, ss975215911, ss1067929859, ss1291105471, ss1425826674, ss1574098539, ss1600287234, ss1643281267, ss1751928471, ss1794449366, ss1917729616, ss1918424429, ss1945996931, ss1958277811, ss1966758340, ss2019728646, ss2147744351, ss2325194204, ss2624378038, ss2632522991, ss2632522992, ss2697660039, ss2755741125, ss2984861344, ss2985513540, ss2986901989, ss3021092887, ss3343478672, ss3625541243, ss3626110563, ss3626110564, ss3634327468, ss3636003063, ss3637760243, ss3640034829, ss3644492854 NC_000001.10:62931631:C= NC_000001.11:62465960:C= (self)
9569529, ss2162944792, ss3023625114, ss3078010267 NC_000001.11:62465960:C= NC_000001.11:62465960:C= (self)
ss9836575 NT_032977.5:15380542:C= NC_000001.11:62465960:C= (self)
ss20549592 NT_032977.6:24494701:C= NC_000001.11:62465960:C= (self)
ss1591200, ss2644465, ss41254520, ss66668561, ss66944159, ss67105833, ss70397158, ss70536233, ss71067619, ss75603664, ss83694205, ss97941792, ss106570339, ss121490724, ss138924258, ss153028401, ss155073775, ss159183098, ss161054352, ss169915854, ss171433720, ss244273678 NT_032977.9:32903549:C= NC_000001.11:62465960:C= (self)
ss78075425, ss3638899019, ss3639447074 NC_000001.8:62643652:C>A NC_000001.11:62465960:C>A (self)
ss108249262, ss164405322, ss166601492, ss198526652, ss205240425, ss210538141, ss253132638, ss275847573, ss284060023, ss290522093, ss825366553, ss1397247332, ss1584583971, ss1712337647, ss3642772067 NC_000001.9:62704219:C>A NC_000001.11:62465960:C>A (self)
1831122, 1000778, 5140324, 1000778, ss218414443, ss230556288, ss238246796, ss479444005, ss491294887, ss536711797, ss554172704, ss648030036, ss780681134, ss783354435, ss975215911, ss1067929859, ss1291105471, ss1425826674, ss1574098539, ss1600287234, ss1643281267, ss1751928471, ss1794449366, ss1917729616, ss1918424429, ss1945996931, ss1958277811, ss1966758340, ss2019728646, ss2147744351, ss2325194204, ss2624378038, ss2632522991, ss2632522992, ss2697660039, ss2755741125, ss2984861344, ss2985513540, ss2986901989, ss3021092887, ss3343478672, ss3625541243, ss3626110563, ss3626110564, ss3634327468, ss3636003063, ss3637760243, ss3640034829, ss3644492854 NC_000001.10:62931631:C>A NC_000001.11:62465960:C>A (self)
9569529, ss2162944792, ss3023625114, ss3078010267 NC_000001.11:62465960:C>A NC_000001.11:62465960:C>A (self)
ss9836575 NT_032977.5:15380542:C>A NC_000001.11:62465960:C>A (self)
ss20549592 NT_032977.6:24494701:C>A NC_000001.11:62465960:C>A (self)
ss1591200, ss2644465, ss41254520, ss66668561, ss66944159, ss67105833, ss70397158, ss70536233, ss71067619, ss75603664, ss83694205, ss97941792, ss106570339, ss121490724, ss138924258, ss153028401, ss155073775, ss159183098, ss161054352, ss169915854, ss171433720, ss244273678 NT_032977.9:32903549:C>A NC_000001.11:62465960:C>A (self)
Help

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

8 citations for rs1167998
PMID Title Author Year Journal
19060910 Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Sabatti C et al. 2009 Nature genetics
19060911 Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Aulchenko YS et al. 2009 Nature genetics
19185284 Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Ferrucci L et al. 2009 American journal of human genetics
19435741 Common lipid-altering gene variants are associated with therapeutic intervention thresholds of lipid levels in older people. Murray A et al. 2009 European heart journal
20833654 Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes. Murphy A et al. 2010 Human molecular genetics
21860704 Implications of discoveries from genome-wide association studies in current cardiovascular practice. Jeemon P et al. 2011 World journal of cardiology
26744084 Association between the DOCK7, PCSK9 and GALNT2 Gene Polymorphisms and Serum Lipid levels. Guo T et al. 2016 Scientific reports
28577571 Genetic determinants of inherited susceptibility to hypercholesterolemia - a comprehensive literature review. Paththinige CS et al. 2017 Lipids in health and disease

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: 0.1.4.post833+d3ba21e