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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.

rs10861279

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr12:104821412 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.08595 (10793/125568, TOPMED)
C=0.0903 (2791/30924, GnomAD)
C=0.082 (413/5008, 1000G) (+ 2 more)
C=0.091 (351/3854, ALSPAC)
C=0.085 (314/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC41A2 : Intron Variant
Publications
1 citation
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 12 NC_000012.12:g.104821412A>C
GRCh38.p7 chr 12 NC_000012.12:g.104821412A>G
GRCh37.p13 chr 12 NC_000012.11:g.105215190A>C
GRCh37.p13 chr 12 NC_000012.11:g.105215190A>G
Gene: SLC41A2, solute carrier family 41 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC41A2 transcript NM_032148.3:c. N/A Intron Variant
SLC41A2 transcript variant X1 XM_005269176.1:c. N/A Intron Variant
SLC41A2 transcript variant X3 XM_005269178.1:c. N/A Intron Variant
SLC41A2 transcript variant X5 XM_005269179.1:c. N/A Intron Variant
SLC41A2 transcript variant X2 XM_006719630.2:c. N/A Intron Variant
SLC41A2 transcript variant X4 XM_011538807.2:c. N/A Intron Variant
SLC41A2 transcript variant X2 XM_011538808.1:c. N/A Intron Variant
SLC41A2 transcript variant X5 XM_011538809.1:c. N/A Intron Variant
SLC41A2 transcript variant X3 XM_011538810.2:c. N/A Intron Variant
SLC41A2 transcript variant X4 XM_011538811.2:c. N/A Intron Variant
SLC41A2 transcript variant X11 XM_011538813.2:c. N/A Intron Variant
SLC41A2 transcript variant X6 XM_017020013.1:c. N/A Intron Variant
SLC41A2 transcript variant X7 XM_017020014.1:c. N/A Intron Variant
SLC41A2 transcript variant X13 XM_017020016.1:c. N/A Intron Variant
SLC41A2 transcript variant X10 XM_017020017.1:c. N/A Intron Variant
SLC41A2 transcript variant X8 XM_017020015.1: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 A=0.91405 C=0.08595
The Genome Aggregation Database Global Study-wide 30924 A=0.8968 G=0.0129, C=0.0903
The Genome Aggregation Database European Sub 18464 A=0.9040 G=0.0000, C=0.0960
The Genome Aggregation Database African Sub 8718 A=0.869 G=0.046, C=0.086
The Genome Aggregation Database East Asian Sub 1620 A=0.933 G=0.000, C=0.067
The Genome Aggregation Database Other Sub 982 A=0.90 G=0.00, C=0.09
The Genome Aggregation Database American Sub 838 A=0.94 G=0.00, C=0.06
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.93 G=0.00, C=0.07
1000Genomes Global Study-wide 5008 A=0.904 C=0.082, G=0.014
1000Genomes African Sub 1322 A=0.887 C=0.063, G=0.050
1000Genomes East Asian Sub 1008 A=0.912 C=0.088, G=0.000
1000Genomes Europe Sub 1006 A=0.914 C=0.086, G=0.000
1000Genomes South Asian Sub 978 A=0.89 C=0.11, G=0.00
1000Genomes American Sub 694 A=0.93 C=0.07, G=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.909 C=0.091
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.915 C=0.085
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 A= C G Note
GRCh38.p7 chr 12 NC_000012.12:g.10...

NC_000012.12:g.104821412A=

NC_000012.12:g.10...

NC_000012.12:g.104821412A>C

NC_000012.12:g.10...

NC_000012.12:g.104821412A>G

GRCh37.p13 chr 12 NC_000012.11:g.10...

NC_000012.11:g.105215190A=

NC_000012.11:g.10...

NC_000012.11:g.105215190A>C

NC_000012.11:g.10...

NC_000012.11:g.105215190A>G

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#.

46 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15827578 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17459423 Feb 27, 2004 (120)
3 SC_SNP ss18972471 Feb 27, 2004 (120)
4 PERLEGEN ss69119557 May 16, 2007 (127)
5 KRIBB_YJKIM ss82785344 Dec 15, 2007 (130)
6 1000GENOMES ss225940164 Jul 14, 2010 (132)
7 1000GENOMES ss236073919 Jul 15, 2010 (132)
8 1000GENOMES ss242603883 Jul 15, 2010 (132)
9 GMI ss281534387 May 04, 2012 (137)
10 ILLUMINA ss482665713 May 04, 2012 (137)
11 ILLUMINA ss482961124 May 04, 2012 (137)
12 ILLUMINA ss534738055 Sep 08, 2015 (146)
13 SSMP ss658962241 Apr 25, 2013 (138)
14 ILLUMINA ss780046985 Sep 08, 2015 (146)
15 ILLUMINA ss781836987 Sep 08, 2015 (146)
16 ILLUMINA ss835527810 Sep 08, 2015 (146)
17 EVA-GONL ss989916664 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1078740481 Aug 21, 2014 (142)
19 1000GENOMES ss1346472633 Aug 21, 2014 (142)
20 1000GENOMES ss1346472634 Aug 21, 2014 (142)
21 DDI ss1427042212 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1576501001 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1629355451 Apr 01, 2015 (144)
24 EVA_DECODE ss1642019862 Apr 01, 2015 (144)
25 EVA_DECODE ss1642019863 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1672349484 Apr 01, 2015 (144)
27 EVA_SVP ss1713354958 Apr 01, 2015 (144)
28 HAMMER_LAB ss1807401216 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1933270588 Feb 12, 2016 (147)
30 GENOMED ss1967673200 Jul 19, 2016 (147)
31 JJLAB ss2027392457 Sep 14, 2016 (149)
32 CSHL ss2136801810 Nov 08, 2017 (151)
33 USC_VALOUEV ss2155739295 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2192836992 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2628177295 Nov 08, 2017 (151)
36 ILLUMINA ss2633003490 Nov 08, 2017 (151)
37 GRF ss2700096573 Nov 08, 2017 (151)
38 GNOMAD ss2914705777 Nov 08, 2017 (151)
39 SWEGEN ss3010281038 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3027506572 Nov 08, 2017 (151)
41 TOPMED ss3180575285 Nov 08, 2017 (151)
42 TOPMED ss3180575286 Nov 08, 2017 (151)
43 CSHL ss3350231374 Nov 08, 2017 (151)
44 ILLUMINA ss3626958910 Jul 20, 2018 (151)
45 ILLUMINA ss3631010220 Jul 20, 2018 (151)
46 ILLUMINA ss3641809593 Jul 20, 2018 (151)
47 1000Genomes NC_000012.11 - 105215190 Jul 20, 2018 (151)
48 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 105215190 Jul 20, 2018 (151)
49 The Genome Aggregation Database NC_000012.11 - 105215190 Jul 20, 2018 (151)
50 Trans-Omics for Precision Medicine NC_000012.12 - 104821412 Jul 20, 2018 (151)
51 UK 10K study - Twins NC_000012.11 - 105215190 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)
rs56528828 May 25, 2008 (130)
rs60533715 Feb 27, 2009 (130)
rs116875443 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss281534387, ss482961124, ss1642019862, ss1642019863, ss1713354958, ss2136801810 NC_000012.10:103739319:A= NC_000012.12:104821411:A= (self)
59277329, 32917341, 48407300, 32917341, ss225940164, ss236073919, ss242603883, ss482665713, ss534738055, ss658962241, ss780046985, ss781836987, ss835527810, ss989916664, ss1078740481, ss1346472633, ss1346472634, ss1427042212, ss1576501001, ss1629355451, ss1672349484, ss1807401216, ss1933270588, ss1967673200, ss2027392457, ss2155739295, ss2628177295, ss2633003490, ss2700096573, ss2914705777, ss3010281038, ss3350231374, ss3626958910, ss3631010220, ss3641809593 NC_000012.11:105215189:A= NC_000012.12:104821411:A= (self)
91889765, ss2192836992, ss3027506572, ss3180575285, ss3180575286 NC_000012.12:104821411:A= NC_000012.12:104821411:A= (self)
ss15827578, ss17459423, ss18972471 NT_019546.15:28697379:A= NC_000012.12:104821411:A= (self)
ss69119557, ss82785344 NT_029419.12:67358495:A= NC_000012.12:104821411:A= (self)
ss281534387, ss482961124, ss1642019862, ss1713354958, ss2136801810 NC_000012.10:103739319:A>C NC_000012.12:104821411:A>C (self)
59277329, 32917341, 48407300, 32917341, ss225940164, ss236073919, ss242603883, ss482665713, ss534738055, ss658962241, ss780046985, ss781836987, ss835527810, ss989916664, ss1078740481, ss1346472633, ss1427042212, ss1576501001, ss1629355451, ss1672349484, ss1807401216, ss1933270588, ss1967673200, ss2027392457, ss2155739295, ss2628177295, ss2633003490, ss2700096573, ss2914705777, ss3010281038, ss3350231374, ss3626958910, ss3631010220, ss3641809593 NC_000012.11:105215189:A>C NC_000012.12:104821411:A>C (self)
91889765, ss2192836992, ss3027506572, ss3180575285 NC_000012.12:104821411:A>C NC_000012.12:104821411:A>C (self)
ss15827578, ss17459423, ss18972471 NT_019546.15:28697379:A>C NC_000012.12:104821411:A>C (self)
ss69119557, ss82785344 NT_029419.12:67358495:A>C NC_000012.12:104821411:A>C (self)
ss1642019863 NC_000012.10:103739319:A>G NC_000012.12:104821411:A>G (self)
59277329, 48407300, ss1346472634, ss2914705777 NC_000012.11:105215189:A>G NC_000012.12:104821411:A>G (self)
ss2192836992, ss3180575286 NC_000012.12:104821411:A>G NC_000012.12:104821411:A>G (self)
Help

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

1 citation for rs10861279
PMID Title Author Year Journal
25733456 Genetic variations in magnesium-related ion channels may affect diabetes risk among African American and Hispanic American women. Chan KH et al. 2015 The Journal of nutrition

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