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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs6678176

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99535271 (GRCh38.p13) 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=0.374041 (99005/264690, TOPMED)
T=0.296218 (59352/200366, ALFA)
T=0.38568 (6464/16760, 8.3KJPN) (+ 16 more)
T=0.3928 (1967/5008, 1000G)
T=0.3801 (1703/4480, Estonian)
T=0.2942 (1134/3854, ALSPAC)
T=0.2770 (1027/3708, TWINSUK)
T=0.4270 (1251/2930, KOREAN)
T=0.3584 (747/2084, HGDP_Stanford)
T=0.4619 (873/1890, HapMap)
T=0.307 (306/998, GoNL)
T=0.273 (171/626, Chileans)
T=0.418 (251/600, NorthernSweden)
C=0.378 (124/328, SGDP_PRJ)
T=0.333 (72/216, Qatari)
T=0.332 (71/214, Vietnamese)
T=0.35 (14/40, GENOME_DK)
C=0.36 (13/36, Siberian)
T=0.14 (4/28, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 1 NC_000001.11:g.99535271C>A
GRCh38.p13 chr 1 NC_000001.11:g.99535271C>T
GRCh37.p13 chr 1 NC_000001.10:g.100000827C>A
GRCh37.p13 chr 1 NC_000001.10:g.100000827C>T
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

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 200366 C=0.703782 A=0.000000, T=0.296218
European Sub 172510 C=0.711947 A=0.000000, T=0.288053
African Sub 5544 C=0.5256 A=0.0000, T=0.4744
African Others Sub 186 C=0.435 A=0.000, T=0.565
African American Sub 5358 C=0.5287 A=0.0000, T=0.4713
Asian Sub 684 C=0.681 A=0.000, T=0.319
East Asian Sub 518 C=0.645 A=0.000, T=0.355
Other Asian Sub 166 C=0.795 A=0.000, T=0.205
Latin American 1 Sub 914 C=0.694 A=0.000, T=0.306
Latin American 2 Sub 8710 C=0.6815 A=0.0000, T=0.3185
South Asian Sub 4998 C=0.6829 A=0.0000, T=0.3171
Other Sub 7006 C=0.6898 A=0.0000, T=0.3102


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 264690 C=0.625959 T=0.374041
8.3KJPN JAPANESE Study-wide 16760 C=0.61432 T=0.38568
1000Genomes Global Study-wide 5008 C=0.6072 T=0.3928
1000Genomes African Sub 1322 C=0.4470 T=0.5530
1000Genomes East Asian Sub 1008 C=0.6200 T=0.3800
1000Genomes Europe Sub 1006 C=0.6948 T=0.3052
1000Genomes South Asian Sub 978 C=0.667 T=0.333
1000Genomes American Sub 694 C=0.683 T=0.317
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6199 T=0.3801
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7058 T=0.2942
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7230 T=0.2770
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5730 T=0.4270
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.6416 T=0.3584
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.598 T=0.402
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.650 T=0.350
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.706 T=0.294
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.728 T=0.272
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.306 T=0.694
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.764 T=0.236
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.94 T=0.06
HapMap Global Study-wide 1890 C=0.5381 T=0.4619
HapMap American Sub 768 C=0.624 T=0.376
HapMap African Sub 692 C=0.373 T=0.627
HapMap Asian Sub 254 C=0.618 T=0.382
HapMap Europe Sub 176 C=0.699 T=0.301
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.693 T=0.307
Chileans Chilean Study-wide 626 C=0.727 T=0.273
Northern Sweden ACPOP Study-wide 600 C=0.582 T=0.418
SGDP_PRJ Global Study-wide 328 C=0.378 T=0.622
Qatari Global Study-wide 216 C=0.667 T=0.333
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.668 T=0.332
The Danish reference pan genome Danish Study-wide 40 C=0.65 T=0.35
Siberian Global Study-wide 36 C=0.36 T=0.64
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 28 C=0.86 T=0.14
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
GRCh38.p13 chr 1 NC_000001.11:g.99535271= NC_000001.11:g.99535271C>A NC_000001.11:g.99535271C>T
GRCh37.p13 chr 1 NC_000001.10:g.100000827= NC_000001.10:g.100000827C>A NC_000001.10:g.100000827C>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#.

98 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9852599 Jul 11, 2003 (116)
2 PERLEGEN ss23842239 Sep 20, 2004 (123)
3 ILLUMINA ss66847267 Dec 02, 2006 (127)
4 ILLUMINA ss67483735 Dec 02, 2006 (127)
5 ILLUMINA ss67841207 Dec 02, 2006 (127)
6 ILLUMINA ss70879061 May 24, 2008 (130)
7 ILLUMINA ss71469359 May 18, 2007 (127)
8 ILLUMINA ss75880003 Dec 06, 2007 (129)
9 AFFY ss76675109 Dec 06, 2007 (129)
10 ILLUMINA ss79229444 Dec 15, 2007 (130)
11 KRIBB_YJKIM ss84521865 Dec 15, 2007 (130)
12 BGI ss102767752 Dec 01, 2009 (131)
13 1000GENOMES ss108453310 Jan 23, 2009 (130)
14 1000GENOMES ss110890348 Jan 25, 2009 (130)
15 ILLUMINA-UK ss118918889 Feb 15, 2009 (130)
16 ILLUMINA ss122592026 Dec 01, 2009 (131)
17 ILLUMINA ss154374668 Dec 01, 2009 (131)
18 ILLUMINA ss159550583 Dec 01, 2009 (131)
19 ILLUMINA ss160797043 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss163738280 Jul 04, 2010 (132)
21 ILLUMINA ss172169675 Jul 04, 2010 (132)
22 ILLUMINA ss174065547 Jul 04, 2010 (132)
23 BUSHMAN ss198832196 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss205365472 Jul 04, 2010 (132)
25 1000GENOMES ss218548429 Jul 14, 2010 (132)
26 1000GENOMES ss230656564 Jul 14, 2010 (132)
27 1000GENOMES ss238323590 Jul 15, 2010 (132)
28 GMI ss275945205 May 04, 2012 (137)
29 GMI ss284105596 Apr 25, 2013 (138)
30 ILLUMINA ss481314195 May 04, 2012 (137)
31 ILLUMINA ss481339333 May 04, 2012 (137)
32 ILLUMINA ss482321346 Sep 08, 2015 (146)
33 ILLUMINA ss485452294 May 04, 2012 (137)
34 ILLUMINA ss537377318 Sep 08, 2015 (146)
35 TISHKOFF ss554480170 Apr 25, 2013 (138)
36 SSMP ss648253663 Apr 25, 2013 (138)
37 ILLUMINA ss778947459 Sep 08, 2015 (146)
38 ILLUMINA ss783171598 Sep 08, 2015 (146)
39 ILLUMINA ss784127124 Sep 08, 2015 (146)
40 ILLUMINA ss825559962 Apr 01, 2015 (144)
41 ILLUMINA ss832431146 Sep 08, 2015 (146)
42 ILLUMINA ss833061756 Jul 12, 2019 (153)
43 ILLUMINA ss834409268 Sep 08, 2015 (146)
44 EVA-GONL ss975482626 Aug 21, 2014 (142)
45 JMKIDD_LAB ss1068127410 Aug 21, 2014 (142)
46 1000GENOMES ss1292106341 Aug 21, 2014 (142)
47 DDI ss1425910898 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1574271249 Apr 01, 2015 (144)
49 EVA_DECODE ss1584860895 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1600816162 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1643810195 Apr 01, 2015 (144)
52 EVA_SVP ss1712357115 Apr 01, 2015 (144)
53 ILLUMINA ss1751859097 Sep 08, 2015 (146)
54 HAMMER_LAB ss1794806881 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1918682256 Feb 12, 2016 (147)
56 GENOMED ss1966820697 Jul 19, 2016 (147)
57 JJLAB ss2019862566 Sep 14, 2016 (149)
58 USC_VALOUEV ss2147881293 Dec 20, 2016 (150)
59 HUMAN_LONGEVITY ss2165028387 Dec 20, 2016 (150)
60 TOPMED ss2327379173 Dec 20, 2016 (150)
61 SYSTEMSBIOZJU ss2624442774 Nov 08, 2017 (151)
62 ILLUMINA ss2632553589 Nov 08, 2017 (151)
63 GRF ss2697808653 Nov 08, 2017 (151)
64 GNOMAD ss2758634225 Nov 08, 2017 (151)
65 SWEGEN ss2987305200 Nov 08, 2017 (151)
66 BIOINF_KMB_FNS_UNIBA ss3023694882 Nov 08, 2017 (151)
67 TOPMED ss3084641761 Nov 08, 2017 (151)
68 TOPMED ss3084641762 Nov 08, 2017 (151)
69 CSHL ss3343595748 Nov 08, 2017 (151)
70 ILLUMINA ss3626165227 Oct 11, 2018 (152)
71 ILLUMINA ss3630587763 Oct 11, 2018 (152)
72 ILLUMINA ss3632903269 Oct 11, 2018 (152)
73 ILLUMINA ss3633598267 Oct 11, 2018 (152)
74 ILLUMINA ss3634339241 Oct 11, 2018 (152)
75 ILLUMINA ss3635291879 Oct 11, 2018 (152)
76 ILLUMINA ss3636016795 Oct 11, 2018 (152)
77 ILLUMINA ss3637042334 Oct 11, 2018 (152)
78 ILLUMINA ss3637775435 Oct 11, 2018 (152)
79 ILLUMINA ss3638905820 Oct 11, 2018 (152)
80 ILLUMINA ss3639450865 Oct 11, 2018 (152)
81 ILLUMINA ss3640046601 Oct 11, 2018 (152)
82 ILLUMINA ss3640984518 Oct 11, 2018 (152)
83 ILLUMINA ss3641278506 Oct 11, 2018 (152)
84 ILLUMINA ss3642785621 Oct 11, 2018 (152)
85 EGCUT_WGS ss3655390201 Jul 12, 2019 (153)
86 EVA_DECODE ss3687366475 Jul 12, 2019 (153)
87 ACPOP ss3727313774 Jul 12, 2019 (153)
88 ILLUMINA ss3744640210 Jul 12, 2019 (153)
89 EVA ss3746573709 Jul 12, 2019 (153)
90 ILLUMINA ss3772141447 Jul 12, 2019 (153)
91 KHV_HUMAN_GENOMES ss3799574456 Jul 12, 2019 (153)
92 EVA ss3826326368 Apr 25, 2020 (154)
93 HGDP ss3847343727 Apr 25, 2020 (154)
94 SGDP_PRJ ss3849476904 Apr 25, 2020 (154)
95 KRGDB ss3894554885 Apr 25, 2020 (154)
96 EVA ss3984814943 Apr 25, 2021 (155)
97 TOPMED ss4460686378 Apr 25, 2021 (155)
98 TOMMO_GENOMICS ss5145311921 Apr 25, 2021 (155)
99 1000Genomes NC_000001.10 - 100000827 Oct 11, 2018 (152)
100 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100000827 Oct 11, 2018 (152)
101 Chileans NC_000001.10 - 100000827 Apr 25, 2020 (154)
102 Genetic variation in the Estonian population NC_000001.10 - 100000827 Oct 11, 2018 (152)
103 The Danish reference pan genome NC_000001.10 - 100000827 Apr 25, 2020 (154)
104 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 20287928 (NC_000001.11:99535270:C:A 2/140014)
Row 20287929 (NC_000001.11:99535270:C:T 53493/139964)

- Apr 25, 2021 (155)
105 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 20287928 (NC_000001.11:99535270:C:A 2/140014)
Row 20287929 (NC_000001.11:99535270:C:T 53493/139964)

- Apr 25, 2021 (155)
106 Genome of the Netherlands Release 5 NC_000001.10 - 100000827 Apr 25, 2020 (154)
107 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99773415 Apr 25, 2020 (154)
108 HapMap NC_000001.11 - 99535271 Apr 25, 2020 (154)
109 KOREAN population from KRGDB NC_000001.10 - 100000827 Apr 25, 2020 (154)
110 Northern Sweden NC_000001.10 - 100000827 Jul 12, 2019 (153)
111 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100000827 Apr 25, 2021 (155)
112 Qatari NC_000001.10 - 100000827 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000001.10 - 100000827 Apr 25, 2020 (154)
114 Siberian NC_000001.10 - 100000827 Apr 25, 2020 (154)
115 8.3KJPN NC_000001.10 - 100000827 Apr 25, 2021 (155)
116 TopMed NC_000001.11 - 99535271 Apr 25, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 100000827 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000001.10 - 100000827 Jul 12, 2019 (153)
119 ALFA NC_000001.11 - 99535271 Apr 25, 2021 (155)
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)
rs58293179 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2758634225 NC_000001.10:100000826:C:A NC_000001.11:99535270:C:A (self)
2525519208, ss3084641761 NC_000001.11:99535270:C:A NC_000001.11:99535270:C:A (self)
ss3638905820, ss3639450865 NC_000001.8:99712847:C:T NC_000001.11:99535270:C:T (self)
21619, ss108453310, ss110890348, ss118918889, ss163738280, ss198832196, ss205365472, ss275945205, ss284105596, ss481314195, ss825559962, ss1584860895, ss1712357115, ss3642785621, ss3847343727 NC_000001.9:99773414:C:T NC_000001.11:99535270:C:T (self)
2869860, 1583023, 16650, 1128449, 1628799, 686726, 1732279, 598639, 40870, 724186, 1493884, 397647, 3281228, 1583023, 341010, ss218548429, ss230656564, ss238323590, ss481339333, ss482321346, ss485452294, ss537377318, ss554480170, ss648253663, ss778947459, ss783171598, ss784127124, ss832431146, ss833061756, ss834409268, ss975482626, ss1068127410, ss1292106341, ss1425910898, ss1574271249, ss1600816162, ss1643810195, ss1751859097, ss1794806881, ss1918682256, ss1966820697, ss2019862566, ss2147881293, ss2327379173, ss2624442774, ss2632553589, ss2697808653, ss2758634225, ss2987305200, ss3343595748, ss3626165227, ss3630587763, ss3632903269, ss3633598267, ss3634339241, ss3635291879, ss3636016795, ss3637042334, ss3637775435, ss3640046601, ss3640984518, ss3641278506, ss3655390201, ss3727313774, ss3744640210, ss3746573709, ss3772141447, ss3826326368, ss3849476904, ss3894554885, ss3984814943, ss5145311921 NC_000001.10:100000826:C:T NC_000001.11:99535270:C:T (self)
136458, 15300119, 24292713, 2525519208, ss2165028387, ss3023694882, ss3084641762, ss3687366475, ss3799574456, ss4460686378 NC_000001.11:99535270:C:T NC_000001.11:99535270:C:T (self)
ss9852599 NT_028050.12:874497:C:T NC_000001.11:99535270:C:T (self)
ss23842239, ss66847267, ss67483735, ss67841207, ss70879061, ss71469359, ss75880003, ss76675109, ss79229444, ss84521865, ss102767752, ss122592026, ss154374668, ss159550583, ss160797043, ss172169675, ss174065547 NT_032977.9:69972744:C:T NC_000001.11:99535270: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 rs6678176

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad