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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.

rs7554246

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99610139 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.296449 (78467/264690, TOPMED)
C=0.392797 (79623/202708, ALFA)
C=0.316206 (44291/140070, GnomAD) (+ 19 more)
C=0.19423 (15286/78702, PAGE_STUDY)
C=0.00495 (83/16760, 8.3KJPN)
C=0.1857 (930/5008, 1000G)
C=0.4420 (1980/4480, Estonian)
C=0.4185 (1613/3854, ALSPAC)
C=0.4164 (1544/3708, TWINSUK)
C=0.0068 (20/2922, KOREAN)
C=0.1934 (403/2084, HGDP_Stanford)
C=0.0055 (10/1832, Korea1K)
C=0.1809 (326/1802, HapMap)
C=0.2637 (298/1130, Daghestan)
C=0.436 (435/998, GoNL)
C=0.387 (232/600, NorthernSweden)
C=0.273 (59/216, Qatari)
C=0.019 (4/216, Vietnamese)
T=0.412 (70/170, SGDP_PRJ)
C=0.40 (16/40, GENOME_DK)
T=0.43 (12/28, Ancient Sardinia)
T=0.33 (6/18, Siberian)
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.99610139T>C
GRCh37.p13 chr 1 NC_000001.10:g.100075695T>C
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 202708 T=0.607203 C=0.392797
European Sub 174762 T=0.580550 C=0.419450
African Sub 7526 T=0.8424 C=0.1576
African Others Sub 264 T=0.924 C=0.076
African American Sub 7262 T=0.8394 C=0.1606
Asian Sub 736 T=0.985 C=0.015
East Asian Sub 590 T=0.988 C=0.012
Other Asian Sub 146 T=0.973 C=0.027
Latin American 1 Sub 844 T=0.675 C=0.325
Latin American 2 Sub 6902 T=0.7650 C=0.2350
South Asian Sub 5048 T=0.8374 C=0.1626
Other Sub 6890 T=0.6509 C=0.3491


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 T=0.703551 C=0.296449
gnomAD - Genomes Global Study-wide 140070 T=0.683794 C=0.316206
gnomAD - Genomes European Sub 75824 T=0.58663 C=0.41337
gnomAD - Genomes African Sub 42014 T=0.84826 C=0.15174
gnomAD - Genomes American Sub 13632 T=0.68097 C=0.31903
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.5512 C=0.4488
gnomAD - Genomes East Asian Sub 3134 T=0.9850 C=0.0150
gnomAD - Genomes Other Sub 2146 T=0.6799 C=0.3201
The PAGE Study Global Study-wide 78702 T=0.80577 C=0.19423
The PAGE Study AfricanAmerican Sub 32516 T=0.83909 C=0.16091
The PAGE Study Mexican Sub 10810 T=0.76586 C=0.23414
The PAGE Study Asian Sub 8318 T=0.9903 C=0.0097
The PAGE Study PuertoRican Sub 7918 T=0.6918 C=0.3082
The PAGE Study NativeHawaiian Sub 4534 T=0.8333 C=0.1667
The PAGE Study Cuban Sub 4230 T=0.6260 C=0.3740
The PAGE Study Dominican Sub 3828 T=0.7288 C=0.2712
The PAGE Study CentralAmerican Sub 2450 T=0.7518 C=0.2482
The PAGE Study SouthAmerican Sub 1982 T=0.7462 C=0.2538
The PAGE Study NativeAmerican Sub 1260 T=0.6841 C=0.3159
The PAGE Study SouthAsian Sub 856 T=0.863 C=0.137
8.3KJPN JAPANESE Study-wide 16760 T=0.99505 C=0.00495
1000Genomes Global Study-wide 5008 T=0.8143 C=0.1857
1000Genomes African Sub 1322 T=0.8994 C=0.1006
1000Genomes East Asian Sub 1008 T=0.9812 C=0.0188
1000Genomes Europe Sub 1006 T=0.5636 C=0.4364
1000Genomes South Asian Sub 978 T=0.865 C=0.135
1000Genomes American Sub 694 T=0.702 C=0.298
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5580 C=0.4420
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5815 C=0.4185
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5836 C=0.4164
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9932 C=0.0068
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.8066 C=0.1934
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.955 C=0.045
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.855 C=0.145
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.594 C=0.406
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.619 C=0.381
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.934 C=0.066
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.884 C=0.116
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.76 C=0.24
Korean Genome Project KOREAN Study-wide 1832 T=0.9945 C=0.0055
HapMap Global Study-wide 1802 T=0.8191 C=0.1809
HapMap American Sub 768 T=0.781 C=0.219
HapMap African Sub 690 T=0.880 C=0.120
HapMap Asian Sub 172 T=0.983 C=0.017
HapMap Europe Sub 172 T=0.581 C=0.419
Genome-wide autozygosity in Daghestan Global Study-wide 1130 T=0.7363 C=0.2637
Genome-wide autozygosity in Daghestan Daghestan Sub 626 T=0.725 C=0.275
Genome-wide autozygosity in Daghestan Near_East Sub 142 T=0.732 C=0.268
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.820 C=0.180
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.593 C=0.407
Genome-wide autozygosity in Daghestan South Asian Sub 96 T=0.90 C=0.10
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.67 C=0.33
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.564 C=0.436
Northern Sweden ACPOP Study-wide 600 T=0.613 C=0.387
Qatari Global Study-wide 216 T=0.727 C=0.273
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.981 C=0.019
SGDP_PRJ Global Study-wide 170 T=0.412 C=0.588
The Danish reference pan genome Danish Study-wide 40 T=0.60 C=0.40
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 28 T=0.43 C=0.57
Siberian Global Study-wide 18 T=0.33 C=0.67
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= C
GRCh38.p13 chr 1 NC_000001.11:g.99610139= NC_000001.11:g.99610139T>C
GRCh37.p13 chr 1 NC_000001.10:g.100075695= NC_000001.10:g.100075695T>C
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#.

103 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11427364 Jul 11, 2003 (116)
2 ILLUMINA ss67797697 Dec 01, 2006 (127)
3 ILLUMINA ss67970885 Dec 01, 2006 (127)
4 ILLUMINA ss68279593 Dec 12, 2006 (127)
5 ILLUMINA ss70933278 May 26, 2008 (130)
6 ILLUMINA ss71535389 May 18, 2007 (127)
7 ILLUMINA ss74944878 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss84677740 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss87656660 Mar 23, 2008 (129)
10 1000GENOMES ss108453861 Jan 23, 2009 (130)
11 ENSEMBL ss138045134 Dec 01, 2009 (131)
12 ILLUMINA ss154429750 Dec 01, 2009 (131)
13 ILLUMINA ss159604859 Dec 01, 2009 (131)
14 ILLUMINA ss160887848 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss164869544 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss166904968 Jul 04, 2010 (132)
17 ILLUMINA ss174414543 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205437191 Jul 04, 2010 (132)
19 1000GENOMES ss218548747 Jul 14, 2010 (132)
20 1000GENOMES ss230656812 Jul 14, 2010 (132)
21 BL ss253316075 May 09, 2011 (134)
22 GMI ss275945383 May 04, 2012 (137)
23 GMI ss284105717 Apr 25, 2013 (138)
24 PJP ss290580538 May 09, 2011 (134)
25 ILLUMINA ss481592536 May 04, 2012 (137)
26 ILLUMINA ss481622521 May 04, 2012 (137)
27 ILLUMINA ss482592353 Sep 08, 2015 (146)
28 ILLUMINA ss485591210 May 04, 2012 (137)
29 ILLUMINA ss537481711 Sep 08, 2015 (146)
30 TISHKOFF ss554480809 Apr 25, 2013 (138)
31 SSMP ss648254068 Apr 25, 2013 (138)
32 ILLUMINA ss778977361 Aug 21, 2014 (142)
33 ILLUMINA ss783241201 Aug 21, 2014 (142)
34 ILLUMINA ss784195017 Aug 21, 2014 (142)
35 ILLUMINA ss832501780 Apr 01, 2015 (144)
36 ILLUMINA ss833115849 Aug 21, 2014 (142)
37 ILLUMINA ss833706677 Aug 21, 2014 (142)
38 ILLUMINA ss834439476 Aug 21, 2014 (142)
39 EVA-GONL ss975483187 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1068127840 Aug 21, 2014 (142)
41 1000GENOMES ss1292108422 Aug 21, 2014 (142)
42 HAMMER_LAB ss1397255158 Sep 08, 2015 (146)
43 DDI ss1425911046 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1574271761 Apr 01, 2015 (144)
45 EVA_DECODE ss1584861496 Apr 01, 2015 (144)
46 EVA_UK10K_ALSPAC ss1600817364 Apr 01, 2015 (144)
47 EVA_UK10K_TWINSUK ss1643811397 Apr 01, 2015 (144)
48 EVA_SVP ss1712357162 Apr 01, 2015 (144)
49 ILLUMINA ss1751859123 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1918682768 Feb 12, 2016 (147)
51 ILLUMINA ss1958296800 Feb 12, 2016 (147)
52 GENOMED ss1966820828 Jul 19, 2016 (147)
53 JJLAB ss2019862906 Sep 14, 2016 (149)
54 USC_VALOUEV ss2147881598 Dec 20, 2016 (150)
55 HUMAN_LONGEVITY ss2165032723 Dec 20, 2016 (150)
56 TOPMED ss2327383529 Dec 20, 2016 (150)
57 ILLUMINA ss2632553647 Nov 08, 2017 (151)
58 GRF ss2697808942 Nov 08, 2017 (151)
59 GNOMAD ss2758639862 Nov 08, 2017 (151)
60 SWEGEN ss2987305958 Nov 08, 2017 (151)
61 ILLUMINA ss3021113806 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3023695046 Nov 08, 2017 (151)
63 TOPMED ss3084654843 Nov 08, 2017 (151)
64 CSHL ss3343596019 Nov 08, 2017 (151)
65 ILLUMINA ss3626165323 Oct 11, 2018 (152)
66 ILLUMINA ss3630587823 Oct 11, 2018 (152)
67 ILLUMINA ss3632903293 Oct 11, 2018 (152)
68 ILLUMINA ss3633598291 Oct 11, 2018 (152)
69 ILLUMINA ss3634339265 Oct 11, 2018 (152)
70 ILLUMINA ss3635291901 Oct 11, 2018 (152)
71 ILLUMINA ss3636016820 Oct 11, 2018 (152)
72 ILLUMINA ss3637042357 Oct 11, 2018 (152)
73 ILLUMINA ss3637775462 Oct 11, 2018 (152)
74 ILLUMINA ss3638905839 Oct 11, 2018 (152)
75 ILLUMINA ss3639765064 Oct 11, 2018 (152)
76 ILLUMINA ss3640046625 Oct 11, 2018 (152)
77 ILLUMINA ss3642785647 Oct 11, 2018 (152)
78 ILLUMINA ss3643818614 Oct 11, 2018 (152)
79 ILLUMINA ss3651444589 Oct 11, 2018 (152)
80 EGCUT_WGS ss3655391073 Jul 12, 2019 (153)
81 EVA_DECODE ss3687367480 Jul 12, 2019 (153)
82 ILLUMINA ss3725048147 Jul 12, 2019 (153)
83 ACPOP ss3727314240 Jul 12, 2019 (153)
84 ILLUMINA ss3744640234 Jul 12, 2019 (153)
85 EVA ss3746574356 Jul 12, 2019 (153)
86 PAGE_CC ss3770828007 Jul 12, 2019 (153)
87 ILLUMINA ss3772141471 Jul 12, 2019 (153)
88 PACBIO ss3783495949 Jul 12, 2019 (153)
89 PACBIO ss3789140980 Jul 12, 2019 (153)
90 PACBIO ss3794013824 Jul 12, 2019 (153)
91 KHV_HUMAN_GENOMES ss3799575125 Jul 12, 2019 (153)
92 EVA ss3826326685 Apr 25, 2020 (154)
93 EVA ss3836553620 Apr 25, 2020 (154)
94 EVA ss3841961616 Apr 25, 2020 (154)
95 HGDP ss3847343749 Apr 25, 2020 (154)
96 SGDP_PRJ ss3849477951 Apr 25, 2020 (154)
97 KRGDB ss3894556009 Apr 25, 2020 (154)
98 KOGIC ss3945091680 Apr 25, 2020 (154)
99 EVA ss3984814987 Apr 25, 2021 (155)
100 EVA ss4016927702 Apr 25, 2021 (155)
101 TOPMED ss4460704533 Apr 25, 2021 (155)
102 TOMMO_GENOMICS ss5145314040 Apr 25, 2021 (155)
103 EVA ss5237270833 Apr 25, 2021 (155)
104 1000Genomes NC_000001.10 - 100075695 Oct 11, 2018 (152)
105 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100075695 Oct 11, 2018 (152)
106 Genome-wide autozygosity in Daghestan NC_000001.9 - 99848283 Apr 25, 2020 (154)
107 Genetic variation in the Estonian population NC_000001.10 - 100075695 Oct 11, 2018 (152)
108 The Danish reference pan genome NC_000001.10 - 100075695 Apr 25, 2020 (154)
109 gnomAD - Genomes NC_000001.11 - 99610139 Apr 25, 2021 (155)
110 Genome of the Netherlands Release 5 NC_000001.10 - 100075695 Apr 25, 2020 (154)
111 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99848283 Apr 25, 2020 (154)
112 HapMap NC_000001.11 - 99610139 Apr 25, 2020 (154)
113 KOREAN population from KRGDB NC_000001.10 - 100075695 Apr 25, 2020 (154)
114 Korean Genome Project NC_000001.11 - 99610139 Apr 25, 2020 (154)
115 Northern Sweden NC_000001.10 - 100075695 Jul 12, 2019 (153)
116 The PAGE Study NC_000001.11 - 99610139 Jul 12, 2019 (153)
117 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100075695 Apr 25, 2021 (155)
118 Qatari NC_000001.10 - 100075695 Apr 25, 2020 (154)
119 SGDP_PRJ NC_000001.10 - 100075695 Apr 25, 2020 (154)
120 Siberian NC_000001.10 - 100075695 Apr 25, 2020 (154)
121 8.3KJPN NC_000001.10 - 100075695 Apr 25, 2021 (155)
122 TopMed NC_000001.11 - 99610139 Apr 25, 2021 (155)
123 UK 10K study - Twins NC_000001.10 - 100075695 Oct 11, 2018 (152)
124 A Vietnamese Genetic Variation Database NC_000001.10 - 100075695 Jul 12, 2019 (153)
125 ALFA NC_000001.11 - 99610139 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)
rs60766798 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638905839, ss3639765064, ss3643818614 NC_000001.8:99787715:T:C NC_000001.11:99610138:T:C (self)
16460, 21641, ss87656660, ss108453861, ss160887848, ss164869544, ss166904968, ss205437191, ss253316075, ss275945383, ss284105717, ss290580538, ss481592536, ss1397255158, ss1584861496, ss1712357162, ss3642785647, ss3847343749 NC_000001.9:99848282:T:C NC_000001.11:99610138:T:C (self)
2872014, 1584326, 1129321, 1629032, 687281, 1733403, 599105, 40914, 724698, 1494931, 397952, 3283347, 1584326, 341295, ss218548747, ss230656812, ss481622521, ss482592353, ss485591210, ss537481711, ss554480809, ss648254068, ss778977361, ss783241201, ss784195017, ss832501780, ss833115849, ss833706677, ss834439476, ss975483187, ss1068127840, ss1292108422, ss1425911046, ss1574271761, ss1600817364, ss1643811397, ss1751859123, ss1918682768, ss1958296800, ss1966820828, ss2019862906, ss2147881598, ss2327383529, ss2632553647, ss2697808942, ss2758639862, ss2987305958, ss3021113806, ss3343596019, ss3626165323, ss3630587823, ss3632903293, ss3633598291, ss3634339265, ss3635291901, ss3636016820, ss3637042357, ss3637775462, ss3640046625, ss3651444589, ss3655391073, ss3727314240, ss3744640234, ss3746574356, ss3772141471, ss3783495949, ss3789140980, ss3794013824, ss3826326685, ss3836553620, ss3849477951, ss3894556009, ss3984814987, ss4016927702, ss5145314040, ss5237270833 NC_000001.10:100075694:T:C NC_000001.11:99610138:T:C (self)
20302332, 136612, 1469681, 49476, 15311701, 24310868, 4564992484, ss2165032723, ss3023695046, ss3084654843, ss3687367480, ss3725048147, ss3770828007, ss3799575125, ss3841961616, ss3945091680, ss4460704533 NC_000001.11:99610138:T:C NC_000001.11:99610138:T:C (self)
ss11427364 NT_028050.12:949365:T:C NC_000001.11:99610138:T:C (self)
ss67797697, ss67970885, ss68279593, ss70933278, ss71535389, ss74944878, ss84677740, ss138045134, ss154429750, ss159604859, ss174414543 NT_032977.9:70047612:T:C NC_000001.11:99610138:T:C (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 rs7554246

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