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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.

rs6119471

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr20:34197406 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.17820 (22376/125568, TOPMED)
G=0.2797 (21997/78646, PAGE_STUDY)
G=0.1661 (5209/31366, GnomAD) (+ 3 more)
G=0.191 (956/5008, 1000G)
G=0.001 (4/3854, ALSPAC)
G=0.001 (5/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ASIP : Intron Variant
Publications
2 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 20 NC_000020.11:g.34197406C>G
GRCh37.p13 chr 20 NC_000020.10:g.32785212C>G
Gene: ASIP, agouti signaling protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ASIP transcript NM_001672.2:c. N/A Genic Upstream Transcript Variant
ASIP transcript variant X3 XM_011528821.1:c. N/A Intron Variant
ASIP transcript variant X1 XM_005260412.3:c. N/A Genic Upstream Transcript Variant
ASIP transcript variant X2 XM_011528820.2:c. 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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.82180 G=0.17820
The PAGE Study Global Study-wide 78646 C=0.7203 G=0.2797
The PAGE Study AfricanAmerican Sub 32488 C=0.4394 G=0.5606
The PAGE Study Mexican Sub 10804 C=0.9711 G=0.0289
The PAGE Study Asian Sub 8314 C=0.999 G=0.001
The PAGE Study PuertoRican Sub 7910 C=0.817 G=0.183
The PAGE Study NativeHawaiian Sub 4534 C=0.992 G=0.008
The PAGE Study Cuban Sub 4228 C=0.904 G=0.096
The PAGE Study Dominican Sub 3826 C=0.715 G=0.285
The PAGE Study CentralAmerican Sub 2446 C=0.894 G=0.106
The PAGE Study SouthAmerican Sub 1980 C=0.946 G=0.054
The PAGE Study NativeAmerican Sub 1260 C=0.903 G=0.097
The PAGE Study SouthAsian Sub 856 C=1.00 G=0.00
gnomAD - Genomes Global Study-wide 31366 C=0.8339 G=0.1661
gnomAD - Genomes European Sub 18898 C=0.9988 G=0.0012
gnomAD - Genomes African Sub 8686 C=0.412 G=0.588
gnomAD - Genomes East Asian Sub 1558 C=1.000 G=0.000
gnomAD - Genomes Other Sub 1088 C=0.959 G=0.041
gnomAD - Genomes American Sub 848 C=0.96 G=0.04
gnomAD - Genomes Ashkenazi Jewish Sub 288 C=1.00 G=0.00
1000Genomes Global Study-wide 5008 C=0.809 G=0.191
1000Genomes African Sub 1322 C=0.314 G=0.686
1000Genomes East Asian Sub 1008 C=1.000 G=0.000
1000Genomes Europe Sub 1006 C=0.999 G=0.001
1000Genomes South Asian Sub 978 C=1.00 G=0.00
1000Genomes American Sub 694 C=0.93 G=0.07
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.999 G=0.001
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.999 G=0.001
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 Note
GRCh38.p12 chr 20 NC_000020.11:g.34197406= NC_000020.11:g.34197406C>G
GRCh37.p13 chr 20 NC_000020.10:g.32785212= NC_000020.10:g.32785212C>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#.

34 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8447690 Apr 21, 2003 (114)
2 PERLEGEN ss23567041 Sep 20, 2004 (123)
3 AFFY ss65949668 Dec 02, 2006 (127)
4 HGSV ss78515715 Dec 06, 2007 (129)
5 1000GENOMES ss113284226 Jan 25, 2009 (130)
6 ILLUMINA-UK ss117532317 Feb 14, 2009 (130)
7 ILLUMINA ss161067009 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss169499578 Jul 04, 2010 (132)
9 BUSHMAN ss203877146 Jul 04, 2010 (132)
10 1000GENOMES ss228333724 Jul 14, 2010 (132)
11 PJP ss292644542 May 09, 2011 (134)
12 ILLUMINA ss479257756 Sep 08, 2015 (146)
13 TISHKOFF ss566224384 Apr 25, 2013 (138)
14 EVA-GONL ss994683650 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1082178163 Aug 21, 2014 (142)
16 1000GENOMES ss1364624777 Aug 21, 2014 (142)
17 EVA_UK10K_ALSPAC ss1638701974 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1681696007 Apr 01, 2015 (144)
19 HAMMER_LAB ss1809486001 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1938197103 Feb 12, 2016 (147)
21 ILLUMINA ss1959911451 Feb 12, 2016 (147)
22 JJLAB ss2029880903 Sep 14, 2016 (149)
23 HUMAN_LONGEVITY ss2242444096 Dec 20, 2016 (150)
24 TOPMED ss2408971724 Dec 20, 2016 (150)
25 GNOMAD ss2966998360 Nov 08, 2017 (151)
26 SWEGEN ss3018126354 Nov 08, 2017 (151)
27 ILLUMINA ss3022115066 Nov 08, 2017 (151)
28 TOPMED ss3359473980 Nov 08, 2017 (151)
29 ILLUMINA ss3636525831 Oct 12, 2018 (152)
30 ILLUMINA ss3652570078 Oct 12, 2018 (152)
31 EVA_DECODE ss3706873952 Jul 13, 2019 (153)
32 ILLUMINA ss3725911655 Jul 13, 2019 (153)
33 PAGE_CC ss3772045083 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3821766102 Jul 13, 2019 (153)
35 1000Genomes NC_000020.10 - 32785212 Oct 12, 2018 (152)
36 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 32785212 Oct 12, 2018 (152)
37 gnomAD - Genomes NC_000020.10 - 32785212 Jul 13, 2019 (153)
38 The PAGE Study NC_000020.11 - 34197406 Jul 13, 2019 (153)
39 TopMed NC_000020.11 - 34197406 Oct 12, 2018 (152)
40 UK 10K study - Twins NC_000020.10 - 32785212 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78515715, ss113284226, ss117532317, ss161067009, ss169499578, ss203877146, ss292644542 NC_000020.9:32248872:C:G NC_000020.11:34197405:C:G (self)
78082960, 43221893, 213099824, 43221893, ss228333724, ss479257756, ss566224384, ss994683650, ss1082178163, ss1364624777, ss1638701974, ss1681696007, ss1809486001, ss1938197103, ss1959911451, ss2029880903, ss2408971724, ss2966998360, ss3018126354, ss3022115066, ss3636525831, ss3652570078 NC_000020.10:32785211:C:G NC_000020.11:34197405:C:G (self)
1266552, 226311890, ss2242444096, ss3359473980, ss3706873952, ss3725911655, ss3772045083, ss3821766102 NC_000020.11:34197405:C:G NC_000020.11:34197405:C:G (self)
ss23567041, ss65949668 NT_011362.10:2981303:C:G NC_000020.11:34197405:C:G (self)
ss8447690 NT_028392.4:2951979:C:G NC_000020.11:34197405:C:G (self)
Help

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

2 citations for rs6119471
PMID Title Author Year Journal
23771755 Improved eye- and skin-color prediction based on 8 SNPs. Hart KL et al. 2013 Croatian medical journal
26690364 Genetic differences among ethnic groups. Huang T et al. 2015 BMC genomics

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