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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.

rs41306079

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr9:12710473 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.124213 (32878/264690, TOPMED)
G=0.122824 (17115/139346, GnomAD)
G=0.10492 (1982/18890, ALFA) (+ 15 more)
G=0.07792 (1306/16760, 8.3KJPN)
G=0.1214 (608/5008, 1000G)
G=0.0982 (440/4480, Estonian)
G=0.0851 (328/3854, ALSPAC)
G=0.0850 (315/3708, TWINSUK)
G=0.0856 (250/2922, KOREAN)
G=0.1097 (124/1130, Daghestan)
G=0.073 (73/998, GoNL)
G=0.072 (43/600, NorthernSweden)
G=0.185 (40/216, Qatari)
G=0.079 (17/214, Vietnamese)
T=0.49 (43/88, SGDP_PRJ)
G=0.07 (3/40, GENOME_DK)
T=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LURAP1L-AS1 : Intron Variant
TYRP1 : 500B Downstream 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.p13 chr 9 NC_000009.12:g.12710473T>G
GRCh37.p13 chr 9 NC_000009.11:g.12710473T>G
TYRP1 RefSeqGene NG_011705.1:g.22088T>G
Gene: TYRP1, tyrosinase related protein 1 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TYRP1 transcript NM_000550.3:c. N/A Downstream Transcript Variant
TYRP1 transcript variant X1 XR_001746372.2:n. N/A Downstream Transcript Variant
Gene: LURAP1L-AS1, LURAP1L antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LURAP1L-AS1 transcript NR_125775.1:n. N/A Intron 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 18890 T=0.89508 G=0.10492
European Sub 14286 T=0.91404 G=0.08596
African Sub 2946 T=0.7977 G=0.2023
African Others Sub 114 T=0.789 G=0.211
African American Sub 2832 T=0.7980 G=0.2020
Asian Sub 112 T=0.929 G=0.071
East Asian Sub 86 T=0.92 G=0.08
Other Asian Sub 26 T=0.96 G=0.04
Latin American 1 Sub 146 T=0.911 G=0.089
Latin American 2 Sub 610 T=0.921 G=0.079
South Asian Sub 98 T=0.92 G=0.08
Other Sub 692 T=0.883 G=0.117


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=0.875787 G=0.124213
gnomAD - Genomes Global Study-wide 139346 T=0.877176 G=0.122824
gnomAD - Genomes European Sub 75504 T=0.91606 G=0.08394
gnomAD - Genomes African Sub 41842 T=0.79929 G=0.20071
gnomAD - Genomes American Sub 13458 T=0.88260 G=0.11740
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.9053 G=0.0947
gnomAD - Genomes East Asian Sub 3092 T=0.9117 G=0.0883
gnomAD - Genomes Other Sub 2134 T=0.9007 G=0.0993
8.3KJPN JAPANESE Study-wide 16760 T=0.92208 G=0.07792
1000Genomes Global Study-wide 5008 T=0.8786 G=0.1214
1000Genomes African Sub 1322 T=0.7731 G=0.2269
1000Genomes East Asian Sub 1008 T=0.9246 G=0.0754
1000Genomes Europe Sub 1006 T=0.9145 G=0.0855
1000Genomes South Asian Sub 978 T=0.921 G=0.079
1000Genomes American Sub 694 T=0.901 G=0.099
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9018 G=0.0982
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9149 G=0.0851
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9150 G=0.0850
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9144 G=0.0856
Genome-wide autozygosity in Daghestan Global Study-wide 1130 T=0.8903 G=0.1097
Genome-wide autozygosity in Daghestan Daghestan Sub 624 T=0.877 G=0.123
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.875 G=0.125
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.869 G=0.131
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.944 G=0.056
Genome-wide autozygosity in Daghestan South Asian Sub 96 T=0.95 G=0.05
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.94 G=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.927 G=0.073
Northern Sweden ACPOP Study-wide 600 T=0.928 G=0.072
Qatari Global Study-wide 216 T=0.815 G=0.185
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.921 G=0.079
SGDP_PRJ Global Study-wide 88 T=0.49 G=0.51
The Danish reference pan genome Danish Study-wide 40 T=0.93 G=0.07
Siberian Global Study-wide 8 T=0.5 G=0.5
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= G
GRCh38.p13 chr 9 NC_000009.12:g.12710473= NC_000009.12:g.12710473T>G
GRCh37.p13 chr 9 NC_000009.11:g.12710473= NC_000009.11:g.12710473T>G
TYRP1 RefSeqGene NG_011705.1:g.22088= NG_011705.1:g.22088T>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#.

40 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss61708173 Oct 18, 2006 (127)
2 PERLEGEN ss69374773 May 18, 2007 (127)
3 BCMHGSC_JDW ss94014201 Mar 25, 2008 (130)
4 BUSHMAN ss200117467 Jul 04, 2010 (132)
5 1000GENOMES ss224132490 Jul 14, 2010 (132)
6 1000GENOMES ss234733854 Jul 15, 2010 (132)
7 1000GENOMES ss241526144 Jul 15, 2010 (132)
8 GMI ss280114564 May 04, 2012 (137)
9 SSMP ss655678929 Apr 25, 2013 (138)
10 EVA-GONL ss986330400 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1076127185 Aug 21, 2014 (142)
12 1000GENOMES ss1332968147 Aug 21, 2014 (142)
13 HAMMER_LAB ss1397548352 Sep 08, 2015 (146)
14 DDI ss1431756586 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1582995218 Apr 01, 2015 (144)
16 EVA_DECODE ss1595959658 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1622287035 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1665281068 Apr 01, 2015 (144)
19 HAMMER_LAB ss1805886267 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1929612512 Feb 12, 2016 (147)
21 JJLAB ss2025517076 Sep 14, 2016 (149)
22 USC_VALOUEV ss2153744479 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2309540098 Dec 20, 2016 (150)
24 TOPMED ss2479569541 Dec 20, 2016 (150)
25 GRF ss2709543385 Nov 08, 2017 (151)
26 GNOMAD ss2875611814 Nov 08, 2017 (151)
27 SWEGEN ss3004411661 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3026547484 Nov 08, 2017 (151)
29 TOPMED ss3582460250 Nov 08, 2017 (151)
30 URBANLAB ss3649074495 Oct 12, 2018 (152)
31 EGCUT_WGS ss3672151792 Jul 13, 2019 (153)
32 EVA_DECODE ss3723508961 Jul 13, 2019 (153)
33 ACPOP ss3736325126 Jul 13, 2019 (153)
34 EVA ss3768936659 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3812096459 Jul 13, 2019 (153)
36 EVA ss3831546334 Apr 26, 2020 (154)
37 SGDP_PRJ ss3871556480 Apr 26, 2020 (154)
38 KRGDB ss3919201678 Apr 26, 2020 (154)
39 TOPMED ss4813155680 Apr 26, 2021 (155)
40 TOMMO_GENOMICS ss5192156015 Apr 26, 2021 (155)
41 1000Genomes NC_000009.11 - 12710473 Oct 12, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 12710473 Oct 12, 2018 (152)
43 Genome-wide autozygosity in Daghestan NC_000009.10 - 12700473 Apr 26, 2020 (154)
44 Genetic variation in the Estonian population NC_000009.11 - 12710473 Oct 12, 2018 (152)
45 The Danish reference pan genome NC_000009.11 - 12710473 Apr 26, 2020 (154)
46 gnomAD - Genomes NC_000009.12 - 12710473 Apr 26, 2021 (155)
47 Genome of the Netherlands Release 5 NC_000009.11 - 12710473 Apr 26, 2020 (154)
48 KOREAN population from KRGDB NC_000009.11 - 12710473 Apr 26, 2020 (154)
49 Northern Sweden NC_000009.11 - 12710473 Jul 13, 2019 (153)
50 Qatari NC_000009.11 - 12710473 Apr 26, 2020 (154)
51 SGDP_PRJ NC_000009.11 - 12710473 Apr 26, 2020 (154)
52 Siberian NC_000009.11 - 12710473 Apr 26, 2020 (154)
53 8.3KJPN NC_000009.11 - 12710473 Apr 26, 2021 (155)
54 TopMed NC_000009.12 - 12710473 Apr 26, 2021 (155)
55 UK 10K study - Twins NC_000009.11 - 12710473 Oct 12, 2018 (152)
56 A Vietnamese Genetic Variation Database NC_000009.11 - 12710473 Jul 13, 2019 (153)
57 ALFA NC_000009.12 - 12710473 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)
rs62540178 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
521912, ss94014201, ss200117467, ss280114564, ss1397548352, ss1595959658 NC_000009.10:12700472:T:G NC_000009.12:12710472:T:G (self)
45198037, 25147347, 17890040, 9160155, 11217707, 26379072, 9609991, 11654442, 23573460, 6260833, 50125322, 25147347, 5585700, ss224132490, ss234733854, ss241526144, ss655678929, ss986330400, ss1076127185, ss1332968147, ss1431756586, ss1582995218, ss1622287035, ss1665281068, ss1805886267, ss1929612512, ss2025517076, ss2153744479, ss2479569541, ss2709543385, ss2875611814, ss3004411661, ss3672151792, ss3736325126, ss3768936659, ss3831546334, ss3871556480, ss3919201678, ss5192156015 NC_000009.11:12710472:T:G NC_000009.12:12710472:T:G (self)
318582750, 406353240, 650533241, 8185077071, ss2309540098, ss3026547484, ss3582460250, ss3649074495, ss3723508961, ss3812096459, ss4813155680 NC_000009.12:12710472:T:G NC_000009.12:12710472:T:G (self)
ss61708173 NT_008413.16:12700472:T:G NC_000009.12:12710472:T:G (self)
ss69374773 NT_008413.18:12700472:T:G NC_000009.12:12710472: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.

1 citation for rs41306079
PMID Title Author Year Journal
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
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