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dbSNP Short Genetic Variations

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.

rs10456100

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:39215694 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.20416 (25636/125568, TOPMED)
T=0.2045 (6320/30908, GnomAD)
T=0.181 (908/5008, 1000G) (+ 3 more)
T=0.263 (1180/4480, Estonian)
T=0.285 (1098/3854, ALSPAC)
T=0.273 (1011/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KCNK5 : 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.p12 chr 6 NC_000006.12:g.39215694C>T
GRCh37.p13 chr 6 NC_000006.11:g.39183470C>T
Gene: KCNK5, potassium two pore domain channel subfamily K member 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KCNK5 transcript NM_003740.3:c. N/A Intron Variant
KCNK5 transcript variant X1 XM_005249456.1:c. N/A Intron Variant
KCNK5 transcript variant X2 XM_006715235.2: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
TopMed Global Study-wide 125568 C=0.79584 T=0.20416
gnomAD - Genomes Global Study-wide 30908 C=0.7955 T=0.2045
gnomAD - Genomes European Sub 18458 C=0.7361 T=0.2639
gnomAD - Genomes African Sub 8720 C=0.933 T=0.067
gnomAD - Genomes East Asian Sub 1612 C=0.805 T=0.195
gnomAD - Genomes Other Sub 978 C=0.76 T=0.24
gnomAD - Genomes American Sub 838 C=0.72 T=0.28
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.74 T=0.26
1000Genomes Global Study-wide 5008 C=0.819 T=0.181
1000Genomes African Sub 1322 C=0.977 T=0.023
1000Genomes East Asian Sub 1008 C=0.831 T=0.169
1000Genomes Europe Sub 1006 C=0.745 T=0.255
1000Genomes South Asian Sub 978 C=0.70 T=0.30
1000Genomes American Sub 694 C=0.78 T=0.22
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.737 T=0.263
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.715 T=0.285
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.727 T=0.273
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= T Note
GRCh38.p12 chr 6 NC_000006.12:g.39215694C= NC_000006.12:g.39215694C>T
GRCh37.p13 chr 6 NC_000006.11:g.39183470C= NC_000006.11:g.39183470C>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#.

64 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14794456 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss20291494 Feb 27, 2004 (120)
3 PERLEGEN ss68974310 May 17, 2007 (127)
4 BCMHGSC_JDW ss93446031 Mar 24, 2008 (129)
5 BGI ss104305018 Dec 01, 2009 (131)
6 ILLUMINA ss159895234 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss162266256 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss207706846 Jul 04, 2010 (132)
9 1000GENOMES ss233438117 Jul 14, 2010 (132)
10 1000GENOMES ss240502117 Jul 15, 2010 (132)
11 BL ss254260076 May 09, 2011 (134)
12 GMI ss278763105 May 04, 2012 (137)
13 ILLUMINA ss479270926 May 04, 2012 (137)
14 ILLUMINA ss479273771 May 04, 2012 (137)
15 ILLUMINA ss479646754 Sep 08, 2015 (146)
16 ILLUMINA ss484436069 May 04, 2012 (137)
17 ILLUMINA ss536606410 Sep 08, 2015 (146)
18 TISHKOFF ss559153099 Apr 25, 2013 (138)
19 SSMP ss653090974 Apr 25, 2013 (138)
20 ILLUMINA ss778356331 Sep 08, 2015 (146)
21 ILLUMINA ss782664502 Sep 08, 2015 (146)
22 ILLUMINA ss783633339 Sep 08, 2015 (146)
23 ILLUMINA ss831915065 Sep 08, 2015 (146)
24 ILLUMINA ss833811076 Sep 08, 2015 (146)
25 EVA-GONL ss982841045 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1073549973 Aug 21, 2014 (142)
27 1000GENOMES ss1319786558 Aug 21, 2014 (142)
28 DDI ss1430695193 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1581637702 Apr 01, 2015 (144)
30 EVA_DECODE ss1592375886 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1615396308 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1658390341 Apr 01, 2015 (144)
33 ILLUMINA ss1752635717 Sep 08, 2015 (146)
34 HAMMER_LAB ss1804391118 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1926098305 Feb 12, 2016 (147)
36 ILLUMINA ss1946177216 Feb 12, 2016 (147)
37 ILLUMINA ss1958902183 Feb 12, 2016 (147)
38 JJLAB ss2023687222 Sep 14, 2016 (149)
39 USC_VALOUEV ss2151865348 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2283373392 Dec 20, 2016 (150)
41 TOPMED ss2451749757 Dec 20, 2016 (150)
42 ILLUMINA ss2634442448 Nov 08, 2017 (151)
43 GRF ss2707463056 Nov 08, 2017 (151)
44 ILLUMINA ss2711076436 Nov 08, 2017 (151)
45 GNOMAD ss2838036123 Nov 08, 2017 (151)
46 SWEGEN ss2998927123 Nov 08, 2017 (151)
47 ILLUMINA ss3022613579 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3025635570 Nov 08, 2017 (151)
49 CSHL ss3346923069 Nov 08, 2017 (151)
50 TOPMED ss3495219661 Nov 08, 2017 (151)
51 ILLUMINA ss3625901322 Oct 12, 2018 (152)
52 ILLUMINA ss3629528603 Oct 12, 2018 (152)
53 ILLUMINA ss3632359666 Oct 12, 2018 (152)
54 ILLUMINA ss3633419301 Oct 12, 2018 (152)
55 ILLUMINA ss3634142082 Oct 12, 2018 (152)
56 ILLUMINA ss3635063837 Oct 12, 2018 (152)
57 ILLUMINA ss3635822953 Oct 12, 2018 (152)
58 ILLUMINA ss3636786921 Oct 12, 2018 (152)
59 ILLUMINA ss3637575764 Oct 12, 2018 (152)
60 ILLUMINA ss3640771136 Oct 12, 2018 (152)
61 ILLUMINA ss3641194071 Oct 12, 2018 (152)
62 ILLUMINA ss3641491219 Oct 12, 2018 (152)
63 ILLUMINA ss3644910259 Oct 12, 2018 (152)
64 ILLUMINA ss3653130065 Oct 12, 2018 (152)
65 1000Genomes NC_000006.11 - 39183470 Oct 12, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 39183470 Oct 12, 2018 (152)
67 Genetic variation in the Estonian population NC_000006.11 - 39183470 Oct 12, 2018 (152)
68 gnomAD - Genomes NC_000006.11 - 39183470 Oct 12, 2018 (152)
69 TopMed NC_000006.12 - 39215694 Oct 12, 2018 (152)
70 UK 10K study - Twins NC_000006.11 - 39183470 Oct 12, 2018 (152)
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
ss93446031, ss162266256, ss207706846, ss254260076, ss278763105, ss479270926, ss1592375886 NC_000006.10:39291447:C= NC_000006.12:39215693:C= (self)
31562878, 17599154, 12554743, 178663880, 17599154, ss233438117, ss240502117, ss479273771, ss479646754, ss484436069, ss536606410, ss559153099, ss653090974, ss778356331, ss782664502, ss783633339, ss831915065, ss833811076, ss982841045, ss1073549973, ss1319786558, ss1430695193, ss1581637702, ss1615396308, ss1658390341, ss1752635717, ss1804391118, ss1926098305, ss1946177216, ss1958902183, ss2023687222, ss2151865348, ss2451749757, ss2634442448, ss2707463056, ss2711076436, ss2838036123, ss2998927123, ss3022613579, ss3346923069, ss3625901322, ss3629528603, ss3632359666, ss3633419301, ss3634142082, ss3635063837, ss3635822953, ss3636786921, ss3637575764, ss3640771136, ss3641194071, ss3641491219, ss3644910259, ss3653130065 NC_000006.11:39183469:C= NC_000006.12:39215693:C= (self)
336096945, ss2283373392, ss3025635570, ss3495219661 NC_000006.12:39215693:C= NC_000006.12:39215693:C= (self)
ss14794456, ss20291494 NT_007592.13:29980596:C= NC_000006.12:39215693:C= (self)
ss68974310, ss104305018, ss159895234 NT_007592.15:39123469:C= NC_000006.12:39215693:C= (self)
ss93446031, ss162266256, ss207706846, ss254260076, ss278763105, ss479270926, ss1592375886 NC_000006.10:39291447:C>T NC_000006.12:39215693:C>T (self)
31562878, 17599154, 12554743, 178663880, 17599154, ss233438117, ss240502117, ss479273771, ss479646754, ss484436069, ss536606410, ss559153099, ss653090974, ss778356331, ss782664502, ss783633339, ss831915065, ss833811076, ss982841045, ss1073549973, ss1319786558, ss1430695193, ss1581637702, ss1615396308, ss1658390341, ss1752635717, ss1804391118, ss1926098305, ss1946177216, ss1958902183, ss2023687222, ss2151865348, ss2451749757, ss2634442448, ss2707463056, ss2711076436, ss2838036123, ss2998927123, ss3022613579, ss3346923069, ss3625901322, ss3629528603, ss3632359666, ss3633419301, ss3634142082, ss3635063837, ss3635822953, ss3636786921, ss3637575764, ss3640771136, ss3641194071, ss3641491219, ss3644910259, ss3653130065 NC_000006.11:39183469:C>T NC_000006.12:39215693:C>T (self)
336096945, ss2283373392, ss3025635570, ss3495219661 NC_000006.12:39215693:C>T NC_000006.12:39215693:C>T (self)
ss14794456, ss20291494 NT_007592.13:29980596:C>T NC_000006.12:39215693:C>T (self)
ss68974310, ss104305018, ss159895234 NT_007592.15:39123469:C>T NC_000006.12:39215693: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 rs10456100

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.post58+e54ea20