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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs3006142

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chrX:33978185 (GRCh38.p7) 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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.21122 (26523/125568, TOPMED)
G=0.2199 (4676/21269, GnomAD)
G=0.241 (908/3775, 1000G) (+ 2 more)
G=0.231 (855/3708, TWINSUK)
G=0.235 (680/2889, ALSPAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105373153 : Intron 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.p7 chr X NC_000023.11:g.33978185G>T
GRCh37.p13 chr X NC_000023.10:g.33996302G>T
Gene: LOC105373153, uncharacterized LOC105373153 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105373153 transcript XR_950542.2: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
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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.21122 T=0.78878
The Genome Aggregation Database Global Study-wide 21269 G=0.2199 T=0.7801
The Genome Aggregation Database European Sub 13003 G=0.2321 T=0.7679
The Genome Aggregation Database African Sub 5766 G=0.168 T=0.832
The Genome Aggregation Database East Asian Sub 986 G=0.44 T=0.56
The Genome Aggregation Database Other Sub 716 G=0.23 T=0.77
The Genome Aggregation Database American Sub 614 G=0.13 T=0.87
The Genome Aggregation Database Ashkenazi Jewish Sub 184 G=0.08 T=0.92
1000Genomes Global Study-wide 3775 G=0.241 T=0.759
1000Genomes African Sub 1003 G=0.136 T=0.864
1000Genomes Europe Sub 766 G=0.19 T=0.81
1000Genomes East Asian Sub 764 G=0.46 T=0.54
1000Genomes South Asian Sub 718 G=0.25 T=0.75
1000Genomes American Sub 524 G=0.17 T=0.83
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.231 T=0.769
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 G=0.235 T=0.765
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 G= T Note
GRCh38.p7 chr X NC_000023.11:g.33978185G= NC_000023.11:g.33978185G>T
GRCh37.p13 chr X NC_000023.10:g.33996302G= NC_000023.10:g.33996302G>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#.

5 Frequency, 49 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4231468 Nov 05, 2001 (101)
2 SC_SNP ss8206688 Apr 21, 2003 (114)
3 WI_SSAHASNP ss12045382 Jul 11, 2003 (116)
4 BCM_SSAHASNP ss14252142 Dec 05, 2003 (119)
5 PERLEGEN ss24234289 Sep 20, 2004 (123)
6 ABI ss43612507 Mar 14, 2006 (126)
7 ILLUMINA ss65810274 Oct 14, 2006 (127)
8 AFFY ss66153543 Nov 29, 2006 (127)
9 ILLUMINA ss75059489 Dec 06, 2007 (129)
10 AFFY ss76186226 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss81926511 Dec 16, 2007 (130)
12 1000GENOMES ss112848768 Jan 25, 2009 (130)
13 1000GENOMES ss114599183 Jan 25, 2009 (130)
14 ILLUMINA-UK ss115605552 Feb 06, 2009 (130)
15 ENSEMBL ss143330940 Dec 01, 2009 (131)
16 GMI ss157423475 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss163083378 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss164720456 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss166173815 Jul 04, 2010 (132)
20 ILLUMINA ss173550645 Jul 04, 2010 (132)
21 BUSHMAN ss204206617 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208861400 Jul 04, 2010 (132)
23 BL ss255964881 May 09, 2011 (134)
24 GMI ss283728772 May 04, 2012 (137)
25 GMI ss287603901 Apr 25, 2013 (138)
26 PJP ss294542073 May 09, 2011 (134)
27 1000GENOMES ss341411839 May 09, 2011 (134)
28 ILLUMINA ss537156735 Sep 08, 2015 (146)
29 TISHKOFF ss566827516 Apr 25, 2013 (138)
30 SSMP ss662760077 Apr 25, 2013 (138)
31 JMKIDD_LAB ss1082867545 Aug 21, 2014 (142)
32 DDI ss1432026488 Apr 01, 2015 (144)
33 1000GENOMES ss1554040196 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1583366636 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1640582141 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1683576174 Apr 01, 2015 (144)
37 WEILL_CORNELL_DGM ss1939262549 Feb 12, 2016 (147)
38 GENOMED ss1971364723 Jul 19, 2016 (147)
39 USC_VALOUEV ss2159010891 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2316664090 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2629688176 Nov 08, 2017 (151)
42 GRF ss2710135788 Nov 08, 2017 (151)
43 GNOMAD ss2977813775 Nov 08, 2017 (151)
44 SWEGEN ss3019822906 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3029032225 Nov 08, 2017 (151)
46 TOPMED ss3608502847 Nov 08, 2017 (151)
47 ILLUMINA ss3630418527 Jul 20, 2018 (151)
48 ILLUMINA ss3638853674 Jul 20, 2018 (151)
49 ILLUMINA ss3643778106 Jul 20, 2018 (151)
50 1000Genomes NC_000023.10 - 33996302 Jul 20, 2018 (151)
51 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 33996302 Jul 20, 2018 (151)
52 The Genome Aggregation Database NC_000023.10 - 33996302 Jul 20, 2018 (151)
53 Trans-Omics for Precision Medicine NC_000023.11 - 33978185 Jul 20, 2018 (151)
54 UK 10K study - Twins NC_000023.10 - 33996302 Jul 20, 2018 (151)
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)
rs17339257 Oct 07, 2004 (123)
rs61656336 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss112848768, ss114599183, ss115605552, ss163083378, ss164720456, ss166173815, ss204206617, ss208861400, ss255964881, ss283728772, ss287603901, ss294542073, ss3643778106 NC_000023.9:33906222:G= NC_000023.11:33978184:G= (self)
82018811, 45296394, 227212991, 45296394, ss341411839, ss537156735, ss566827516, ss662760077, ss1082867545, ss1432026488, ss1554040196, ss1583366636, ss1640582141, ss1683576174, ss1939262549, ss1971364723, ss2159010891, ss2629688176, ss2710135788, ss2977813775, ss3019822906, ss3630418527, ss3638853674 NC_000023.10:33996301:G= NC_000023.11:33978184:G= (self)
426521216, ss2316664090, ss3029032225, ss3608502847 NC_000023.11:33978184:G= NC_000023.11:33978184:G= (self)
ss12045382 NT_011757.12:20910768:G= NC_000023.11:33978184:G= (self)
ss14252142 NT_011757.13:29962866:G= NC_000023.11:33978184:G= (self)
ss4231468, ss8206688, ss24234289, ss43612507, ss65810274, ss66153543, ss75059489, ss76186226, ss81926511, ss143330940, ss157423475, ss173550645 NT_167197.1:31878063:G= NC_000023.11:33978184:G= (self)
ss112848768, ss114599183, ss115605552, ss163083378, ss164720456, ss166173815, ss204206617, ss208861400, ss255964881, ss283728772, ss287603901, ss294542073, ss3643778106 NC_000023.9:33906222:G>T NC_000023.11:33978184:G>T (self)
82018811, 45296394, 227212991, 45296394, ss341411839, ss537156735, ss566827516, ss662760077, ss1082867545, ss1432026488, ss1554040196, ss1583366636, ss1640582141, ss1683576174, ss1939262549, ss1971364723, ss2159010891, ss2629688176, ss2710135788, ss2977813775, ss3019822906, ss3630418527, ss3638853674 NC_000023.10:33996301:G>T NC_000023.11:33978184:G>T (self)
426521216, ss2316664090, ss3029032225, ss3608502847 NC_000023.11:33978184:G>T NC_000023.11:33978184:G>T (self)
ss12045382 NT_011757.12:20910768:G>T NC_000023.11:33978184:G>T (self)
ss14252142 NT_011757.13:29962866:G>T NC_000023.11:33978184:G>T (self)
ss4231468, ss8206688, ss24234289, ss43612507, ss65810274, ss66153543, ss75059489, ss76186226, ss81926511, ss143330940, ss157423475, ss173550645 NT_167197.1:31878063:G>T NC_000023.11:33978184:G>T (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 rs3006142
PMID Title Author Year Journal
22177906 Development of multiplex assay with 16 SNPs on X chromosome for degraded samples. Oki T et al. 2012 Legal medicine (Tokyo, Japan)

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: 0.1.4.post833+d3ba21e