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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.

rs6002626

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:42121985 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.342831 (90744/264690, TOPMED)
C=0.345492 (48371/140006, GnomAD)
C=0.39857 (7112/17844, ALFA) (+ 14 more)
C=0.45704 (7660/16760, 8.3KJPN)
C=0.3243 (1624/5008, 1000G)
C=0.4471 (2003/4480, Estonian)
C=0.4600 (1773/3854, ALSPAC)
C=0.4679 (1735/3708, TWINSUK)
C=0.3618 (1060/2930, KOREAN)
C=0.468 (467/998, GoNL)
C=0.482 (289/600, NorthernSweden)
C=0.253 (114/450, SGDP_PRJ)
C=0.297 (98/330, HapMap)
C=0.352 (76/216, Qatari)
C=0.282 (61/216, Vietnamese)
G=0.45 (18/40, GENOME_DK)
C=0.30 (12/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NDUFA6-DT : Intron Variant
LOC102723722 : 2KB Upstream Variant
LOC105373047 : 500B Downstream Variant (+ 1 more)
LOC107987476 : 500B Downstream 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.p13 chr 22 NC_000022.11:g.42121985C>G
GRCh38.p13 chr 22 NC_000022.11:g.42121985C>T
GRCh37.p13 chr 22 NC_000022.10:g.42517989C>G
GRCh37.p13 chr 22 NC_000022.10:g.42517989C>T
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG1 NW_003315971.2:g.44330C>G
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG1 NW_003315971.2:g.44330C>T
GRCh38.p13 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.44328G>C
GRCh38.p13 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.44328G>T
chr 22 novel patch HSCHR22_4_CTG1 NW_009646207.1:g.36947G>C
chr 22 novel patch HSCHR22_4_CTG1 NW_009646207.1:g.36947G>T
chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.15575G>C
chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.15575G>T
chr 22 novel patch HSCHR22_6_CTG1 NW_014040930.1:g.26704C>G
chr 22 novel patch HSCHR22_6_CTG1 NW_014040930.1:g.26704C>T
chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.7552G>C
chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.7552G>T
GRCh38.p13 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.44313G>C
GRCh38.p13 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.44313G>T
Gene: NDUFA6-DT, NDUFA6 divergent transcript (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NDUFA6-DT transcript NR_034118.2:n. N/A Intron Variant
Gene: LOC105373047, uncharacterized LOC105373047 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105373047 transcript XR_001755569.1:n. N/A 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

ALFA Allele Frequency
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 17844 C=0.39857 G=0.60143, T=0.00000
European Sub 13764 C=0.44914 G=0.55086, T=0.00000
African Sub 2426 C=0.0919 G=0.9081, T=0.0000
African Others Sub 90 C=0.03 G=0.97, T=0.00
African American Sub 2336 C=0.0942 G=0.9058, T=0.0000
Asian Sub 112 C=0.268 G=0.732, T=0.000
East Asian Sub 86 C=0.28 G=0.72, T=0.00
Other Asian Sub 26 C=0.23 G=0.77, T=0.00
Latin American 1 Sub 146 C=0.349 G=0.651, T=0.000
Latin American 2 Sub 610 C=0.562 G=0.438, T=0.000
South Asian Sub 98 C=0.41 G=0.59, T=0.00
Other Sub 688 C=0.353 G=0.647, T=0.000


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=0.342831 G=0.657169
gnomAD - Genomes Global Study-wide 140006 C=0.345492 G=0.654508
gnomAD - Genomes European Sub 75814 C=0.45813 G=0.54187
gnomAD - Genomes African Sub 41974 C=0.09420 G=0.90580
gnomAD - Genomes American Sub 13634 C=0.49098 G=0.50902
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.3603 G=0.6397
gnomAD - Genomes East Asian Sub 3122 C=0.3190 G=0.6810
gnomAD - Genomes Other Sub 2140 C=0.3724 G=0.6276
8.3KJPN JAPANESE Study-wide 16760 C=0.45704 G=0.54296
1000Genomes Global Study-wide 5008 C=0.3243 G=0.6757
1000Genomes African Sub 1322 C=0.0265 G=0.9735
1000Genomes East Asian Sub 1008 C=0.3065 G=0.6935
1000Genomes Europe Sub 1006 C=0.4583 G=0.5417
1000Genomes South Asian Sub 978 C=0.485 G=0.515
1000Genomes American Sub 694 C=0.497 G=0.503
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.4471 G=0.5529
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4600 G=0.5400
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4679 G=0.5321
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3618 G=0.6382, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.468 G=0.532
Northern Sweden ACPOP Study-wide 600 C=0.482 G=0.518
SGDP_PRJ Global Study-wide 450 C=0.253 G=0.747
HapMap Global Study-wide 330 C=0.297 G=0.703
HapMap African Sub 120 C=0.000 G=1.000
HapMap American Sub 120 C=0.450 G=0.550
HapMap Asian Sub 90 C=0.49 G=0.51
Qatari Global Study-wide 216 C=0.352 G=0.648
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.282 G=0.718
The Danish reference pan genome Danish Study-wide 40 C=0.55 G=0.45
Siberian Global Study-wide 40 C=0.30 G=0.70
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= G T
GRCh38.p13 chr 22 NC_000022.11:g.42121985= NC_000022.11:g.42121985C>G NC_000022.11:g.42121985C>T
GRCh37.p13 chr 22 NC_000022.10:g.42517989= NC_000022.10:g.42517989C>G NC_000022.10:g.42517989C>T
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG1 NW_003315971.2:g.44330= NW_003315971.2:g.44330C>G NW_003315971.2:g.44330C>T
GRCh38.p13 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.44328G>C NT_187682.1:g.44328= NT_187682.1:g.44328G>T
chr 22 novel patch HSCHR22_4_CTG1 NW_009646207.1:g.36947G>C NW_009646207.1:g.36947= NW_009646207.1:g.36947G>T
chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.15575G>C NW_014040931.1:g.15575= NW_014040931.1:g.15575G>T
chr 22 novel patch HSCHR22_6_CTG1 NW_014040930.1:g.26704= NW_014040930.1:g.26704C>G NW_014040930.1:g.26704C>T
chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.7552G>C NW_009646208.1:g.7552= NW_009646208.1:g.7552G>T
GRCh38.p13 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.44313G>C NW_004504305.1:g.44313= NW_004504305.1:g.44313G>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#.

75 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8298747 Apr 21, 2003 (114)
2 SC_SNP ss13362372 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss16930773 Feb 27, 2004 (120)
4 ABI ss41518414 Mar 14, 2006 (126)
5 HGSV ss77317148 Dec 06, 2007 (129)
6 HGSV ss82254540 Dec 15, 2007 (130)
7 HUMANGENOME_JCVI ss96102575 Feb 05, 2009 (130)
8 BGI ss103867147 Dec 01, 2009 (131)
9 1000GENOMES ss112671793 Jan 25, 2009 (130)
10 ENSEMBL ss143074298 Dec 01, 2009 (131)
11 ILLUMINA ss152536345 Dec 01, 2009 (131)
12 ILLUMINA ss159100354 Dec 01, 2009 (131)
13 ILLUMINA ss159102625 Dec 01, 2009 (131)
14 ILLUMINA ss159524406 Dec 01, 2009 (131)
15 ILLUMINA ss159846002 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168007979 Jul 04, 2010 (132)
17 ILLUMINA ss168870799 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss172010077 Jul 04, 2010 (132)
19 BUSHMAN ss204099745 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss208821094 Jul 04, 2010 (132)
21 1000GENOMES ss238081948 Jul 15, 2010 (132)
22 1000GENOMES ss244197281 Jul 15, 2010 (132)
23 GMI ss283649224 May 04, 2012 (137)
24 GMI ss287575132 Apr 25, 2013 (138)
25 PJP ss292767903 May 09, 2011 (134)
26 ILLUMINA ss479154441 Sep 08, 2015 (146)
27 ILLUMINA ss532727815 Sep 08, 2015 (146)
28 TISHKOFF ss566667038 Apr 25, 2013 (138)
29 SSMP ss662596324 Apr 25, 2013 (138)
30 ILLUMINA ss832615421 Aug 21, 2014 (142)
31 ILLUMINA ss833035674 Aug 21, 2014 (142)
32 ILLUMINA ss833206110 Aug 21, 2014 (142)
33 ILLUMINA ss833626502 Aug 21, 2014 (142)
34 EVA-GONL ss995393752 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1082687821 Aug 21, 2014 (142)
36 1000GENOMES ss1367335898 Aug 21, 2014 (142)
37 DDI ss1429268103 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1579767130 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1640083652 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1683077685 Apr 01, 2015 (144)
41 HAMMER_LAB ss1809806549 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1938961215 Feb 12, 2016 (147)
43 GENOMED ss1969279588 Jul 19, 2016 (147)
44 JJLAB ss2030253464 Sep 14, 2016 (149)
45 USC_VALOUEV ss2158873685 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2247688418 Dec 20, 2016 (150)
47 TOPMED ss2414676025 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2629622749 Nov 08, 2017 (151)
49 GRF ss2704626545 Nov 08, 2017 (151)
50 SWEGEN ss3019375385 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3028962562 Nov 08, 2017 (151)
52 CSHL ss3352855473 Nov 08, 2017 (151)
53 TOPMED ss3378339672 Nov 08, 2017 (151)
54 TOPMED ss3378339673 Nov 08, 2017 (151)
55 ILLUMINA ss3628544554 Oct 12, 2018 (152)
56 ILLUMINA ss3636565836 Oct 12, 2018 (152)
57 ILLUMINA ss3638385688 Oct 12, 2018 (152)
58 EGCUT_WGS ss3685867754 Jul 13, 2019 (153)
59 EVA_DECODE ss3708287292 Jul 13, 2019 (153)
60 ACPOP ss3743969230 Jul 13, 2019 (153)
61 EVA ss3759434260 Jul 13, 2019 (153)
62 PACBIO ss3788837884 Jul 13, 2019 (153)
63 PACBIO ss3793701116 Jul 13, 2019 (153)
64 PACBIO ss3798587592 Jul 13, 2019 (153)
65 KHV_HUMAN_GENOMES ss3822593646 Jul 13, 2019 (153)
66 EVA ss3836012207 Apr 27, 2020 (154)
67 EVA ss3841634466 Apr 27, 2020 (154)
68 EVA ss3847149693 Apr 27, 2020 (154)
69 SGDP_PRJ ss3890637514 Apr 27, 2020 (154)
70 KRGDB ss3941034844 Apr 27, 2020 (154)
71 VINODS ss4034711764 Apr 26, 2021 (155)
72 VINODS ss4034712597 Apr 26, 2021 (155)
73 VINODS ss4034758223 Apr 26, 2021 (155)
74 TOPMED ss5110778967 Apr 26, 2021 (155)
75 TOMMO_GENOMICS ss5232836830 Apr 26, 2021 (155)
76 1000Genomes NC_000022.10 - 42517989 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 42517989 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000022.10 - 42517989 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000022.10 - 42517989 Apr 27, 2020 (154)
80 gnomAD - Genomes NC_000022.11 - 42121985 Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000022.10 - 42517989 Apr 27, 2020 (154)
82 HapMap NC_000022.11 - 42121985 Apr 27, 2020 (154)
83 KOREAN population from KRGDB NC_000022.10 - 42517989 Apr 27, 2020 (154)
84 Northern Sweden NC_000022.10 - 42517989 Jul 13, 2019 (153)
85 Qatari NC_000022.10 - 42517989 Apr 27, 2020 (154)
86 SGDP_PRJ NC_000022.10 - 42517989 Apr 27, 2020 (154)
87 Siberian NC_000022.10 - 42517989 Apr 27, 2020 (154)
88 8.3KJPN NC_000022.10 - 42517989 Apr 26, 2021 (155)
89 TopMed NC_000022.11 - 42121985 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000022.10 - 42517989 Oct 12, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000022.10 - 42517989 Jul 13, 2019 (153)
92 ALFA NC_000022.11 - 42121985 Apr 26, 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)
rs58803690 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77317148, ss82254540 NC_000022.8:40842486:G:G NC_000022.11:42121984:C:G (self)
ss112671793, ss159846002, ss168007979, ss172010077, ss204099745, ss208821094, ss283649224, ss287575132, ss292767903 NC_000022.9:40847932:G:G NC_000022.11:42121984:C:G (self)
80894307, 44747497, 31606002, 5932069, 19935822, 48212238, 17254095, 21003137, 42654494, 11390039, 90806137, 44747497, 9868416, ss238081948, ss244197281, ss479154441, ss532727815, ss566667038, ss662596324, ss832615421, ss833035674, ss833206110, ss833626502, ss995393752, ss1082687821, ss1367335898, ss1429268103, ss1579767130, ss1640083652, ss1683077685, ss1809806549, ss1938961215, ss1969279588, ss2030253464, ss2158873685, ss2414676025, ss2629622749, ss2704626545, ss3019375385, ss3352855473, ss3628544554, ss3636565836, ss3638385688, ss3685867754, ss3743969230, ss3759434260, ss3788837884, ss3793701116, ss3798587592, ss3836012207, ss3841634466, ss3890637514, ss3941034844, ss5232836830 NC_000022.10:42517988:C:G NC_000022.11:42121984:C:G (self)
571268464, 2263460, 241058884, 385887914, 2197640273, ss2247688418, ss3028962562, ss3378339672, ss3708287292, ss3822593646, ss3847149693, ss5110778967 NC_000022.11:42121984:C:G NC_000022.11:42121984:C:G (self)
ss13362372, ss16930773 NT_011520.9:21827042:C:G NC_000022.11:42121984:C:G (self)
ss8298747, ss41518414, ss96102575, ss103867147, ss143074298, ss152536345, ss159100354, ss159102625, ss159524406, ss168870799 NT_011520.12:21908557:C:G NC_000022.11:42121984:C:G (self)
ss4034758223 NT_187682.1:44327:G:G NC_000022.11:42121984:C:G
ss4034711764 NW_003315971.2:44329:C:G NC_000022.11:42121984:C:G
ss4034712597 NW_004504305.1:44312:G:G NC_000022.11:42121984:C:G
48212238, ss3941034844 NC_000022.10:42517988:C:T NC_000022.11:42121984:C:T (self)
2197640273, ss3378339673 NC_000022.11:42121984:C:T NC_000022.11:42121984: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 rs6002626

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