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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.

rs7617400

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:79554914 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.24540 (30815/125568, TOPMED)
T=0.2332 (7191/30842, GnomAD)
T=0.222 (1111/5008, 1000G) (+ 2 more)
T=0.197 (759/3854, ALSPAC)
T=0.187 (692/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ROBO1 : 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.p7 chr 3 NC_000003.12:g.79554914C>A
GRCh38.p7 chr 3 NC_000003.12:g.79554914C>T
GRCh37.p13 chr 3 NC_000003.11:g.79604064C>A
GRCh37.p13 chr 3 NC_000003.11:g.79604064C>T
ROBO1 RefSeqGene NG_011729.1:g.217996G>T
ROBO1 RefSeqGene NG_011729.1:g.217996G>A
Gene: ROBO1, roundabout guidance receptor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ROBO1 transcript variant 1 NM_002941.3:c. N/A Intron Variant
ROBO1 transcript variant 4 NM_001145845.1:c. N/A Genic Upstream Transcript Variant
ROBO1 transcript variant 2 NM_133631.3:c. N/A Genic Upstream Transcript Variant
ROBO1 transcript variant X1 XM_011533976.1:c. N/A Intron Variant
ROBO1 transcript variant X2 XM_011533977.2:c. N/A Intron Variant
ROBO1 transcript variant X3 XM_011533978.1:c. N/A Intron Variant
ROBO1 transcript variant X7 XM_011533979.1:c. N/A Intron Variant
ROBO1 transcript variant X9 XM_011533980.1:c. N/A Intron Variant
ROBO1 transcript variant X4 XM_017006982.1:c. N/A Intron Variant
ROBO1 transcript variant X8 XM_017006984.1:c. N/A Intron Variant
ROBO1 transcript variant X5 XM_006713277.2:c. N/A Genic Upstream Transcript Variant
ROBO1 transcript variant X6 XM_017006983.1:c. N/A Genic Upstream Transcript Variant
ROBO1 transcript variant X10 XM_017006985.1: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

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
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.75460 T=0.24540
The Genome Aggregation Database Global Study-wide 30842 C=0.7668 T=0.2332
The Genome Aggregation Database European Sub 18438 C=0.8210 T=0.1790
The Genome Aggregation Database African Sub 8700 C=0.630 T=0.370
The Genome Aggregation Database East Asian Sub 1598 C=0.824 T=0.176
The Genome Aggregation Database Other Sub 974 C=0.81 T=0.19
The Genome Aggregation Database American Sub 830 C=0.86 T=0.14
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.71 T=0.29
1000Genomes Global Study-wide 5008 C=0.778 T=0.222
1000Genomes African Sub 1322 C=0.624 T=0.376
1000Genomes East Asian Sub 1008 C=0.859 T=0.141
1000Genomes Europe Sub 1006 C=0.793 T=0.207
1000Genomes South Asian Sub 978 C=0.83 T=0.17
1000Genomes American Sub 694 C=0.86 T=0.14
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.803 T=0.197
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.813 T=0.187
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 Note
GRCh38.p7 chr 3 NC_000003.12:g.79...

NC_000003.12:g.79554914C=

NC_000003.12:g.79...

NC_000003.12:g.79554914C>A

NC_000003.12:g.79...

NC_000003.12:g.79554914C>T

GRCh37.p13 chr 3 NC_000003.11:g.79...

NC_000003.11:g.79604064C=

NC_000003.11:g.79...

NC_000003.11:g.79604064C>A

NC_000003.11:g.79...

NC_000003.11:g.79604064C>T

ROBO1 RefSeqGene NG_011729.1:g.217...

NG_011729.1:g.217996G=

NG_011729.1:g.217...

NG_011729.1:g.217996G>T

NG_011729.1:g.217...

NG_011729.1:g.217996G>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#.

80 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11543722 Jul 11, 2003 (116)
2 SSAHASNP ss22011820 Apr 05, 2004 (121)
3 ABI ss44473269 Mar 14, 2006 (126)
4 ILLUMINA ss67807612 Dec 02, 2006 (127)
5 ILLUMINA ss67976907 Dec 02, 2006 (127)
6 ILLUMINA ss68281546 Dec 12, 2006 (127)
7 ILLUMINA ss70938247 May 23, 2008 (130)
8 ILLUMINA ss71541414 May 18, 2007 (127)
9 ILLUMINA ss75839904 Dec 07, 2007 (129)
10 HGSV ss84529112 Dec 14, 2007 (130)
11 KRIBB_YJKIM ss84691896 Dec 14, 2007 (130)
12 HUMANGENOME_JCVI ss96027019 Feb 04, 2009 (130)
13 BGI ss106274010 Feb 04, 2009 (130)
14 1000GENOMES ss110425443 Jan 24, 2009 (130)
15 1000GENOMES ss112022767 Jan 25, 2009 (130)
16 ILLUMINA-UK ss117152332 Feb 14, 2009 (130)
17 ILLUMINA ss154434980 Dec 01, 2009 (131)
18 ILLUMINA ss159610008 Dec 01, 2009 (131)
19 ILLUMINA ss160895786 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162319429 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss163617991 Jul 04, 2010 (132)
22 ILLUMINA ss174454020 Jul 04, 2010 (132)
23 1000GENOMES ss220243592 Jul 14, 2010 (132)
24 1000GENOMES ss231898365 Jul 14, 2010 (132)
25 1000GENOMES ss239296956 Jul 15, 2010 (132)
26 GMI ss277211997 May 04, 2012 (137)
27 PJP ss292837580 May 09, 2011 (134)
28 ILLUMINA ss481618376 May 04, 2012 (137)
29 ILLUMINA ss481648550 May 04, 2012 (137)
30 ILLUMINA ss482616269 Sep 08, 2015 (146)
31 ILLUMINA ss485604011 May 04, 2012 (137)
32 ILLUMINA ss537491455 Sep 08, 2015 (146)
33 TISHKOFF ss556737017 Apr 25, 2013 (138)
34 SSMP ss650428129 Apr 25, 2013 (138)
35 ILLUMINA ss778608882 Sep 08, 2015 (146)
36 ILLUMINA ss783247619 Sep 08, 2015 (146)
37 ILLUMINA ss784201284 Sep 08, 2015 (146)
38 ILLUMINA ss832508288 Sep 08, 2015 (146)
39 ILLUMINA ss834066263 Sep 08, 2015 (146)
40 EVA-GONL ss978797774 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1070563219 Aug 21, 2014 (142)
42 1000GENOMES ss1304784116 Aug 21, 2014 (142)
43 DDI ss1429481129 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1580041918 Apr 01, 2015 (144)
45 EVA_DECODE ss1588270813 Apr 01, 2015 (144)
46 EVA_UK10K_ALSPAC ss1607487868 Apr 01, 2015 (144)
47 EVA_UK10K_TWINSUK ss1650481901 Apr 01, 2015 (144)
48 EVA_SVP ss1712590846 Apr 01, 2015 (144)
49 ILLUMINA ss1752484897 Sep 08, 2015 (146)
50 HAMMER_LAB ss1799567521 Sep 08, 2015 (146)
51 WEILL_CORNELL_DGM ss1922033723 Feb 12, 2016 (147)
52 GENOMED ss1969439591 Jul 19, 2016 (147)
53 JJLAB ss2021578634 Sep 14, 2016 (149)
54 USC_VALOUEV ss2149666841 Dec 20, 2016 (150)
55 HUMAN_LONGEVITY ss2253168140 Dec 20, 2016 (150)
56 TOPMED ss2420280088 Dec 20, 2016 (150)
57 TOPMED ss2420280089 Dec 20, 2016 (150)
58 SYSTEMSBIOZJU ss2625291203 Nov 08, 2017 (151)
59 ILLUMINA ss2633975165 Nov 08, 2017 (151)
60 GRF ss2705057027 Nov 08, 2017 (151)
61 GNOMAD ss2795170303 Nov 08, 2017 (151)
62 SWEGEN ss2992636105 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3024553927 Nov 08, 2017 (151)
64 CSHL ss3345109135 Nov 08, 2017 (151)
65 TOPMED ss3395689169 Nov 08, 2017 (151)
66 TOPMED ss3395689170 Nov 08, 2017 (151)
67 ILLUMINA ss3628706419 Jul 20, 2018 (151)
68 ILLUMINA ss3631920023 Jul 20, 2018 (151)
69 ILLUMINA ss3633299087 Jul 20, 2018 (151)
70 ILLUMINA ss3634016390 Jul 20, 2018 (151)
71 ILLUMINA ss3634904254 Jul 20, 2018 (151)
72 ILLUMINA ss3635700189 Jul 20, 2018 (151)
73 ILLUMINA ss3636600148 Jul 20, 2018 (151)
74 ILLUMINA ss3637452564 Jul 20, 2018 (151)
75 ILLUMINA ss3638425667 Jul 20, 2018 (151)
76 ILLUMINA ss3639216171 Jul 20, 2018 (151)
77 ILLUMINA ss3639908802 Jul 20, 2018 (151)
78 ILLUMINA ss3640611555 Jul 20, 2018 (151)
79 ILLUMINA ss3643381845 Jul 20, 2018 (151)
80 ILLUMINA ss3643955614 Jul 20, 2018 (151)
81 1000Genomes NC_000003.11 - 79604064 Jul 20, 2018 (151)
82 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 79604064 Jul 20, 2018 (151)
83 The Genome Aggregation Database NC_000003.11 - 79604064 Jul 20, 2018 (151)
84 Trans-Omics for Precision Medicine NC_000003.12 - 79554914 Jul 20, 2018 (151)
85 UK 10K study - Twins NC_000003.11 - 79604064 Jul 20, 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)
rs57107035 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss84529112, ss3639216171, ss3639908802, ss3643955614 NC_000003.9:79686753:C= NC_000003.12:79554913:C= (self)
ss110425443, ss112022767, ss117152332, ss162319429, ss163617991, ss277211997, ss292837580, ss481618376, ss1588270813, ss1712590846, ss3643381845 NC_000003.10:79686753:C= NC_000003.12:79554913:C= (self)
15997719, 8906203, 135798057, 8906203, ss220243592, ss231898365, ss239296956, ss481648550, ss482616269, ss485604011, ss537491455, ss556737017, ss650428129, ss778608882, ss783247619, ss784201284, ss832508288, ss834066263, ss978797774, ss1070563219, ss1304784116, ss1429481129, ss1580041918, ss1607487868, ss1650481901, ss1752484897, ss1799567521, ss1922033723, ss1969439591, ss2021578634, ss2149666841, ss2420280088, ss2420280089, ss2625291203, ss2633975165, ss2705057027, ss2795170303, ss2992636105, ss3345109135, ss3628706419, ss3631920023, ss3633299087, ss3634016390, ss3634904254, ss3635700189, ss3636600148, ss3637452564, ss3638425667, ss3640611555 NC_000003.11:79604063:C= NC_000003.12:79554913:C= (self)
255462136, ss2253168140, ss3024553927, ss3395689169, ss3395689170 NC_000003.12:79554913:C= NC_000003.12:79554913:C= (self)
ss11543722 NT_022459.12:13285901:C= NC_000003.12:79554913:C= (self)
ss22011820 NT_022459.13:13298751:C= NC_000003.12:79554913:C= (self)
ss44473269, ss67807612, ss67976907, ss68281546, ss70938247, ss71541414, ss75839904, ss84691896, ss96027019, ss106274010, ss154434980, ss159610008, ss160895786, ss174454020 NT_022459.15:13333793:C= NC_000003.12:79554913:C= (self)
ss2420280088 NC_000003.11:79604063:C>A NC_000003.12:79554913:C>A (self)
ss2253168140, ss3395689169 NC_000003.12:79554913:C>A NC_000003.12:79554913:C>A (self)
ss84529112, ss3639216171, ss3639908802, ss3643955614 NC_000003.9:79686753:C>T NC_000003.12:79554913:C>T (self)
ss110425443, ss112022767, ss117152332, ss162319429, ss163617991, ss277211997, ss292837580, ss481618376, ss1588270813, ss1712590846, ss3643381845 NC_000003.10:79686753:C>T NC_000003.12:79554913:C>T (self)
15997719, 8906203, 135798057, 8906203, ss220243592, ss231898365, ss239296956, ss481648550, ss482616269, ss485604011, ss537491455, ss556737017, ss650428129, ss778608882, ss783247619, ss784201284, ss832508288, ss834066263, ss978797774, ss1070563219, ss1304784116, ss1429481129, ss1580041918, ss1607487868, ss1650481901, ss1752484897, ss1799567521, ss1922033723, ss1969439591, ss2021578634, ss2149666841, ss2420280089, ss2625291203, ss2633975165, ss2705057027, ss2795170303, ss2992636105, ss3345109135, ss3628706419, ss3631920023, ss3633299087, ss3634016390, ss3634904254, ss3635700189, ss3636600148, ss3637452564, ss3638425667, ss3640611555 NC_000003.11:79604063:C>T NC_000003.12:79554913:C>T (self)
255462136, ss2253168140, ss3024553927, ss3395689170 NC_000003.12:79554913:C>T NC_000003.12:79554913:C>T (self)
ss11543722 NT_022459.12:13285901:C>T NC_000003.12:79554913:C>T (self)
ss22011820 NT_022459.13:13298751:C>T NC_000003.12:79554913:C>T (self)
ss44473269, ss67807612, ss67976907, ss68281546, ss70938247, ss71541414, ss75839904, ss84691896, ss96027019, ss106274010, ss154434980, ss159610008, ss160895786, ss174454020 NT_022459.15:13333793:C>T NC_000003.12:79554913: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 rs7617400

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