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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.

rs1294421

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:6742916 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.38468 (48303/125568, TOPMED)
T=0.3748 (11584/30904, GnomAD)
T=0.473 (2369/5008, 1000G) (+ 3 more)
T=0.394 (1763/4480, Estonian)
T=0.397 (1530/3854, ALSPAC)
T=0.391 (1450/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101928004 : Intron Variant
Publications
7 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.6742916T>A
GRCh38.p12 chr 6 NC_000006.12:g.6742916T>C
GRCh38.p12 chr 6 NC_000006.12:g.6742916T>G
GRCh37.p13 chr 6 NC_000006.11:g.6743149T>A
GRCh37.p13 chr 6 NC_000006.11:g.6743149T>C
GRCh37.p13 chr 6 NC_000006.11:g.6743149T>G
Gene: LOC101928004, uncharacterized LOC101928004 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928004 transcript variant X2 XR_001743942.1:n. N/A Intron Variant
LOC101928004 transcript variant X5 XR_001743943.2:n. N/A Intron Variant
LOC101928004 transcript variant X7 XR_001743945.1:n. N/A Intron Variant
LOC101928004 transcript variant X8 XR_001743946.1:n. N/A Intron Variant
LOC101928004 transcript variant X1 XR_926420.2:n. N/A Intron Variant
LOC101928004 transcript variant X6 XR_001743944.1:n. N/A Genic Upstream Transcript Variant
LOC101928004 transcript variant X9 XR_001743947.1:n. N/A Genic Upstream Transcript Variant
LOC101928004 transcript variant X10 XR_001743948.1:n. N/A Genic Upstream Transcript Variant
LOC101928004 transcript variant X4 XR_926424.2:n. N/A Genic Upstream Transcript Variant
LOC101928004 transcript variant X3 XR_926425.3: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

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 T=0.38468 G=0.61532
gnomAD - Genomes Global Study-wide 30904 T=0.3748 G=0.6252
gnomAD - Genomes European Sub 18450 T=0.3881 G=0.6119
gnomAD - Genomes African Sub 8718 T=0.255 G=0.745
gnomAD - Genomes East Asian Sub 1620 T=0.765 G=0.235
gnomAD - Genomes Other Sub 976 T=0.42 G=0.58
gnomAD - Genomes American Sub 838 T=0.52 G=0.48
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.38 G=0.62
1000Genomes Global Study-wide 5008 T=0.473 G=0.527
1000Genomes African Sub 1322 T=0.228 G=0.772
1000Genomes East Asian Sub 1008 T=0.736 G=0.264
1000Genomes Europe Sub 1006 T=0.387 G=0.613
1000Genomes South Asian Sub 978 T=0.60 G=0.40
1000Genomes American Sub 694 T=0.50 G=0.50
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.394 G=0.606
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.397 G=0.603
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.391 G=0.609
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 T= A C G Note
GRCh38.p12 chr 6 NC_000006.12:...

NC_000006.12:g.6742916T=

NC_000006.12:...

NC_000006.12:g.6742916T>A

NC_000006.12:...

NC_000006.12:g.6742916T>C

NC_000006.12:...

NC_000006.12:g.6742916T>G

GRCh37.p13 chr 6 NC_000006.11:...

NC_000006.11:g.6743149T=

NC_000006.11:...

NC_000006.11:g.6743149T>A

NC_000006.11:...

NC_000006.11:g.6743149T>C

NC_000006.11:...

NC_000006.11:g.6743149T>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#.

77 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss2057401 Oct 18, 2000 (87)
2 SC_JCM ss2646013 Nov 09, 2000 (92)
3 BCM_SSAHASNP ss10272450 Jul 11, 2003 (116)
4 SC_SNP ss13155534 Dec 05, 2003 (119)
5 WI_SSAHASNP ss14685814 Dec 05, 2003 (119)
6 SC_SNP ss14801045 Dec 05, 2003 (119)
7 AFFY ss66089256 Nov 30, 2006 (127)
8 AFFY ss76041026 Dec 07, 2007 (129)
9 HGSV ss78079527 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss81459144 Dec 14, 2007 (130)
11 HGSV ss81469592 Dec 15, 2007 (130)
12 BCMHGSC_JDW ss93380647 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss98470806 Feb 06, 2009 (130)
14 1000GENOMES ss109725939 Jan 24, 2009 (130)
15 1000GENOMES ss113852500 Jan 25, 2009 (130)
16 ENSEMBL ss142930416 Dec 01, 2009 (131)
17 ENSEMBL ss143711023 Dec 01, 2009 (131)
18 ILLUMINA ss160308479 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss163104188 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss166089519 Jul 04, 2010 (132)
21 AFFY ss170737891 Jul 04, 2010 (132)
22 BUSHMAN ss201377870 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss207713153 Jul 04, 2010 (132)
24 1000GENOMES ss222190169 Jul 14, 2010 (132)
25 1000GENOMES ss233309797 Jul 14, 2010 (132)
26 1000GENOMES ss240398085 Jul 15, 2010 (132)
27 GMI ss278639224 May 04, 2012 (137)
28 GMI ss285333013 Apr 25, 2013 (138)
29 PJP ss293670575 May 09, 2011 (134)
30 ILLUMINA ss410902889 Sep 17, 2011 (135)
31 ILLUMINA ss480450596 Sep 08, 2015 (146)
32 EXOME_CHIP ss491377339 May 04, 2012 (137)
33 TISHKOFF ss558982081 Apr 25, 2013 (138)
34 SSMP ss652891506 Apr 25, 2013 (138)
35 ILLUMINA ss780681652 Aug 21, 2014 (142)
36 ILLUMINA ss783354980 Aug 21, 2014 (142)
37 EVA-GONL ss982548335 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1073354618 Aug 21, 2014 (142)
39 1000GENOMES ss1318835891 Aug 21, 2014 (142)
40 DDI ss1430626691 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1581517589 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1614876863 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1657870896 Apr 01, 2015 (144)
44 EVA_SVP ss1712832981 Apr 01, 2015 (144)
45 ILLUMINA ss1752644928 Sep 08, 2015 (146)
46 HAMMER_LAB ss1804265139 Sep 08, 2015 (146)
47 ILLUMINA ss1917798959 Feb 12, 2016 (147)
48 WEILL_CORNELL_DGM ss1925807036 Feb 12, 2016 (147)
49 ILLUMINA ss1946166559 Feb 12, 2016 (147)
50 ILLUMINA ss1958859760 Feb 12, 2016 (147)
51 GENOMED ss1970302153 Jul 19, 2016 (147)
52 JJLAB ss2023518791 Sep 14, 2016 (149)
53 USC_VALOUEV ss2151681050 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2281500466 Dec 20, 2016 (150)
55 TOPMED ss2449850671 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2626247264 Nov 08, 2017 (151)
57 ILLUMINA ss2634395312 Nov 08, 2017 (151)
58 ILLUMINA ss2634395313 Nov 08, 2017 (151)
59 GRF ss2707266650 Nov 08, 2017 (151)
60 GNOMAD ss2835411432 Nov 08, 2017 (151)
61 AFFY ss2985352474 Nov 08, 2017 (151)
62 AFFY ss2985980518 Nov 08, 2017 (151)
63 SWEGEN ss2998460546 Nov 08, 2017 (151)
64 ILLUMINA ss3022571327 Nov 08, 2017 (151)
65 BIOINF_KMB_FNS_UNIBA ss3025543588 Nov 08, 2017 (151)
66 CSHL ss3346820313 Nov 08, 2017 (151)
67 TOPMED ss3489275703 Nov 08, 2017 (151)
68 TOPMED ss3489275704 Nov 08, 2017 (151)
69 TOPMED ss3489275705 Nov 08, 2017 (151)
70 ILLUMINA ss3629436062 Oct 12, 2018 (152)
71 ILLUMINA ss3635042694 Oct 12, 2018 (152)
72 ILLUMINA ss3636757357 Oct 12, 2018 (152)
73 ILLUMINA ss3640749989 Oct 12, 2018 (152)
74 ILLUMINA ss3644899620 Oct 12, 2018 (152)
75 URBANLAB ss3648261087 Oct 12, 2018 (152)
76 ILLUMINA ss3653079231 Oct 12, 2018 (152)
77 ILLUMINA ss3654120760 Oct 12, 2018 (152)
78 1000Genomes NC_000006.11 - 6743149 Oct 12, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 6743149 Oct 12, 2018 (152)
80 Genetic variation in the Estonian population NC_000006.11 - 6743149 Oct 12, 2018 (152)
81 gnomAD - Genomes NC_000006.11 - 6743149 Oct 12, 2018 (152)
82 TopMed NC_000006.12 - 6742916 Oct 12, 2018 (152)
83 UK 10K study - Twins NC_000006.11 - 6743149 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).

Associated ID History Updated (Build)
rs1782306 Jan 18, 2001 (92)
rs57719131 Feb 27, 2009 (130)
rs60351814 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss2281500466, ss3489275703 NC_000006.12:6742915:T:A NC_000006.12:6742915:T:A (self)
ss3489275704 NC_000006.12:6742915:T:C NC_000006.12:6742915:T:C (self)
ss78079527, ss81469592 NC_000006.9:6688147:T:G NC_000006.12:6742915:T:G (self)
ss93380647, ss109725939, ss113852500, ss160308479, ss163104188, ss166089519, ss201377870, ss207713153, ss278639224, ss285333013, ss293670575, ss410902889, ss1712832981 NC_000006.10:6688147:T:G NC_000006.12:6742915:T:G (self)
30573369, 17021150, 12122521, 176039189, 17021150, ss222190169, ss233309797, ss240398085, ss480450596, ss491377339, ss558982081, ss652891506, ss780681652, ss783354980, ss982548335, ss1073354618, ss1318835891, ss1430626691, ss1581517589, ss1614876863, ss1657870896, ss1752644928, ss1804265139, ss1917798959, ss1925807036, ss1946166559, ss1958859760, ss1970302153, ss2023518791, ss2151681050, ss2449850671, ss2626247264, ss2634395312, ss2634395313, ss2707266650, ss2835411432, ss2985352474, ss2985980518, ss2998460546, ss3022571327, ss3346820313, ss3629436062, ss3635042694, ss3636757357, ss3640749989, ss3644899620, ss3653079231, ss3654120760 NC_000006.11:6743148:T:G NC_000006.12:6742915:T:G (self)
331368414, ss2281500466, ss3025543588, ss3489275705, ss3648261087 NC_000006.12:6742915:T:G NC_000006.12:6742915:T:G (self)
ss2057401, ss2646013, ss66089256, ss76041026, ss81459144, ss98470806, ss142930416, ss143711023, ss170737891 NT_007592.15:6683148:T:G NC_000006.12:6742915:T:G (self)
ss10272450, ss13155534 NT_034880.2:6683147:T:G NC_000006.12:6742915:T:G (self)
ss14685814, ss14801045 NT_034880.3:6683147:T:G NC_000006.12:6742915:T:G (self)
Help

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

7 citations for rs1294421
PMID Title Author Year Journal
20935629 Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Heid IM et al. 2010 Nature genetics
21466928 Genetics and epigenetics of obesity. Herrera BM et al. 2011 Maturitas
22651247 Sex differences in human adipose tissues - the biology of pear shape. Karastergiou K et al. 2012 Biology of sex differences
23221025 Replication study of 15 recently published Loci for body fat distribution in the Japanese population. Hotta K et al. 2013 Journal of atherosclerosis and thrombosis
27104953 Effects of Genetic Loci Associated with Central Obesity on Adipocyte Lipolysis. Strawbridge RJ et al. 2016 PloS one
27195708 Investigation of Genetic Variation Underlying Central Obesity amongst South Asians. Scott WR et al. 2016 PloS one
27427429 Commentary: Two-sample Mendelian randomization: opportunities and challenges. Lawlor DA et al. 2016 International journal of epidemiology

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.post104+4a6ee9c