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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.

rs1867749

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:119256336 (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
G=0.347119 (91879/264690, TOPMED)
G=0.34027 (5703/16760, 8.3KJPN)
G=0.25401 (2979/11728, ALFA) (+ 14 more)
G=0.3067 (1536/5008, 1000G)
G=0.4208 (1885/4480, Estonian)
G=0.4414 (1701/3854, ALSPAC)
G=0.4364 (1618/3708, TWINSUK)
G=0.3270 (958/2930, KOREAN)
G=0.3376 (628/1860, HapMap)
G=0.3313 (607/1832, Korea1K)
G=0.475 (474/998, GoNL)
G=0.432 (259/600, NorthernSweden)
C=0.397 (115/290, SGDP_PRJ)
G=0.431 (93/216, Qatari)
G=0.394 (85/216, Vietnamese)
G=0.47 (19/40, GENOME_DK)
C=0.37 (11/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STEAP3 : 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.p13 chr 2 NC_000002.12:g.119256336C>G
GRCh38.p13 chr 2 NC_000002.12:g.119256336C>T
GRCh37.p13 chr 2 NC_000002.11:g.120013912C>G
GRCh37.p13 chr 2 NC_000002.11:g.120013912C>T
STEAP3 RefSeqGene NG_042823.1:g.37529C>G
STEAP3 RefSeqGene NG_042823.1:g.37529C>T
Gene: STEAP3, STEAP3 metalloreductase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
STEAP3 transcript variant 3 NM_001008410.2:c.1185+148…

NM_001008410.2:c.1185+1488C>G

N/A Intron Variant
STEAP3 transcript variant 2 NM_018234.3:c.1185+1488C>G N/A Intron Variant
STEAP3 transcript variant 4 NM_138637.3:c.1186-1121C>G N/A Intron Variant
STEAP3 transcript variant 1 NM_182915.3:c.1215+1488C>G N/A Intron Variant
STEAP3 transcript variant X2 XM_006712614.3:c.1185+148…

XM_006712614.3:c.1185+1488C>G

N/A Intron Variant
STEAP3 transcript variant X3 XM_006712615.1:c.1185+148…

XM_006712615.1:c.1185+1488C>G

N/A Intron Variant
STEAP3 transcript variant X1 XM_011511403.1:c.1185+148…

XM_011511403.1:c.1185+1488C>G

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 11728 C=0.74599 G=0.25401, T=0.00000
European Sub 9096 C=0.6854 G=0.3146, T=0.0000
African Sub 1706 C=0.9830 G=0.0170, T=0.0000
African Others Sub 76 C=0.99 G=0.01, T=0.00
African American Sub 1630 C=0.9828 G=0.0172, T=0.0000
Asian Sub 62 C=0.97 G=0.03, T=0.00
East Asian Sub 44 C=0.98 G=0.02, T=0.00
Other Asian Sub 18 C=0.94 G=0.06, T=0.00
Latin American 1 Sub 56 C=1.00 G=0.00, T=0.00
Latin American 2 Sub 342 C=1.000 G=0.000, T=0.000
South Asian Sub 42 C=0.95 G=0.05, T=0.00
Other Sub 424 C=0.802 G=0.198, 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=0.652881 G=0.347119
8.3KJPN JAPANESE Study-wide 16760 C=0.65973 G=0.34027
1000Genomes Global Study-wide 5008 C=0.6933 G=0.3067
1000Genomes African Sub 1322 C=0.7723 G=0.2277
1000Genomes East Asian Sub 1008 C=0.6964 G=0.3036
1000Genomes Europe Sub 1006 C=0.5537 G=0.4463
1000Genomes South Asian Sub 978 C=0.711 G=0.289
1000Genomes American Sub 694 C=0.716 G=0.284
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5792 G=0.4208
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5586 G=0.4414
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5636 G=0.4364
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6730 G=0.3270
HapMap Global Study-wide 1860 C=0.6624 G=0.3376
HapMap American Sub 762 C=0.640 G=0.360
HapMap African Sub 672 C=0.716 G=0.284
HapMap Asian Sub 250 C=0.692 G=0.308
HapMap Europe Sub 176 C=0.511 G=0.489
Korean Genome Project KOREAN Study-wide 1832 C=0.6687 G=0.3313
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.525 G=0.475
Northern Sweden ACPOP Study-wide 600 C=0.568 G=0.432
SGDP_PRJ Global Study-wide 290 C=0.397 G=0.603
Qatari Global Study-wide 216 C=0.569 G=0.431
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.606 G=0.394
The Danish reference pan genome Danish Study-wide 40 C=0.53 G=0.47
Siberian Global Study-wide 30 C=0.37 G=0.63
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 2 NC_000002.12:g.119256336= NC_000002.12:g.119256336C>G NC_000002.12:g.119256336C>T
GRCh37.p13 chr 2 NC_000002.11:g.120013912= NC_000002.11:g.120013912C>G NC_000002.11:g.120013912C>T
STEAP3 RefSeqGene NG_042823.1:g.37529= NG_042823.1:g.37529C>G NG_042823.1:g.37529C>T
STEAP3 transcript variant 3 NM_001008410.1:c.1185+1488= NM_001008410.1:c.1185+1488C>G NM_001008410.1:c.1185+1488C>T
STEAP3 transcript variant 3 NM_001008410.2:c.1185+1488= NM_001008410.2:c.1185+1488C>G NM_001008410.2:c.1185+1488C>T
STEAP3 transcript variant 2 NM_018234.2:c.1185+1488= NM_018234.2:c.1185+1488C>G NM_018234.2:c.1185+1488C>T
STEAP3 transcript variant 2 NM_018234.3:c.1185+1488= NM_018234.3:c.1185+1488C>G NM_018234.3:c.1185+1488C>T
STEAP3 transcript variant 4 NM_138637.3:c.1186-1121= NM_138637.3:c.1186-1121C>G NM_138637.3:c.1186-1121C>T
STEAP3 transcript variant 1 NM_182915.2:c.1215+1488= NM_182915.2:c.1215+1488C>G NM_182915.2:c.1215+1488C>T
STEAP3 transcript variant 1 NM_182915.3:c.1215+1488= NM_182915.3:c.1215+1488C>G NM_182915.3:c.1215+1488C>T
STEAP3 transcript variant X1 XM_005263696.1:c.1186-1121= XM_005263696.1:c.1186-1121C>G XM_005263696.1:c.1186-1121C>T
STEAP3 transcript variant X2 XM_006712614.3:c.1185+1488= XM_006712614.3:c.1185+1488C>G XM_006712614.3:c.1185+1488C>T
STEAP3 transcript variant X3 XM_006712615.1:c.1185+1488= XM_006712615.1:c.1185+1488C>G XM_006712615.1:c.1185+1488C>T
STEAP3 transcript variant X1 XM_011511403.1:c.1185+1488= XM_011511403.1:c.1185+1488C>G XM_011511403.1:c.1185+1488C>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#.

76 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2743194 Jan 12, 2001 (92)
2 YUSUKE ss4917596 Aug 28, 2002 (108)
3 SC_JCM ss5863100 Feb 20, 2003 (111)
4 WI_SSAHASNP ss6698425 Feb 20, 2003 (111)
5 CSHL-HAPMAP ss16852614 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss20099780 Feb 27, 2004 (120)
7 PERLEGEN ss24309656 Sep 20, 2004 (123)
8 ABI ss44345314 Mar 13, 2006 (126)
9 ILLUMINA ss65716838 Oct 16, 2006 (127)
10 CSHL-HAPMAP ss68401827 Jan 12, 2007 (127)
11 PERLEGEN ss68825766 May 18, 2007 (127)
12 AFFY ss76821682 Dec 07, 2007 (129)
13 HGSV ss85436783 Dec 15, 2007 (130)
14 BGI ss103570920 Dec 01, 2009 (131)
15 KRIBB_YJKIM ss104855190 Feb 06, 2009 (130)
16 1000GENOMES ss110814225 Jan 25, 2009 (130)
17 ILLUMINA ss120244547 Dec 01, 2009 (131)
18 ENSEMBL ss161173414 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss164046697 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss165085071 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss167087526 Jul 04, 2010 (132)
22 1000GENOMES ss219463790 Jul 14, 2010 (132)
23 1000GENOMES ss231328728 Jul 14, 2010 (132)
24 1000GENOMES ss238844791 Jul 15, 2010 (132)
25 GMI ss276641678 May 04, 2012 (137)
26 GMI ss284421474 Apr 25, 2013 (138)
27 PJP ss292351058 May 09, 2011 (134)
28 ILLUMINA ss481139529 May 04, 2012 (137)
29 ILLUMINA ss483891011 May 04, 2012 (137)
30 ILLUMINA ss534153599 Sep 08, 2015 (146)
31 TISHKOFF ss555821691 Apr 25, 2013 (138)
32 SSMP ss649443188 Apr 25, 2013 (138)
33 ILLUMINA ss779832921 Aug 21, 2014 (142)
34 ILLUMINA ss781406538 Aug 21, 2014 (142)
35 ILLUMINA ss835309526 Aug 21, 2014 (142)
36 EVA-GONL ss977272066 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1069430463 Aug 21, 2014 (142)
38 1000GENOMES ss1298979418 Aug 21, 2014 (142)
39 DDI ss1428709700 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1579051895 Apr 01, 2015 (144)
41 EVA_DECODE ss1586696924 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1604394984 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1647389017 Apr 01, 2015 (144)
44 EVA_SVP ss1712484685 Apr 01, 2015 (144)
45 HAMMER_LAB ss1797371984 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1920522701 Feb 12, 2016 (147)
47 GENOMED ss1968867356 Jul 19, 2016 (147)
48 JJLAB ss2020788897 Sep 14, 2016 (149)
49 USC_VALOUEV ss2148845036 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2233658702 Dec 20, 2016 (150)
51 TOPMED ss2399915676 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2624899631 Nov 08, 2017 (151)
53 ILLUMINA ss2633663614 Nov 08, 2017 (151)
54 GRF ss2703457395 Nov 08, 2017 (151)
55 GNOMAD ss2778666405 Nov 08, 2017 (151)
56 SWEGEN ss2990274839 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3024156392 Nov 08, 2017 (151)
58 TOPMED ss3320730026 Nov 08, 2017 (151)
59 TOPMED ss3320730027 Nov 08, 2017 (151)
60 CSHL ss3344434283 Nov 08, 2017 (151)
61 ILLUMINA ss3628149955 Oct 11, 2018 (152)
62 ILLUMINA ss3631627734 Oct 11, 2018 (152)
63 ILLUMINA ss3642119328 Oct 11, 2018 (152)
64 EGCUT_WGS ss3658148309 Jul 13, 2019 (153)
65 EVA_DECODE ss3704730284 Jul 13, 2019 (153)
66 ACPOP ss3728795925 Jul 13, 2019 (153)
67 EVA ss3757277338 Jul 13, 2019 (153)
68 KHV_HUMAN_GENOMES ss3801644462 Jul 13, 2019 (153)
69 EVA ss3827178872 Apr 25, 2020 (154)
70 EVA ss3837004178 Apr 25, 2020 (154)
71 EVA ss3842422811 Apr 25, 2020 (154)
72 SGDP_PRJ ss3853221833 Apr 25, 2020 (154)
73 KRGDB ss3898738611 Apr 25, 2020 (154)
74 KOGIC ss3948788144 Apr 25, 2020 (154)
75 TOPMED ss4521024334 Apr 26, 2021 (155)
76 TOMMO_GENOMICS ss5153467039 Apr 26, 2021 (155)
77 1000Genomes NC_000002.11 - 120013912 Oct 11, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 120013912 Oct 11, 2018 (152)
79 Genetic variation in the Estonian population NC_000002.11 - 120013912 Oct 11, 2018 (152)
80 The Danish reference pan genome NC_000002.11 - 120013912 Apr 25, 2020 (154)
81 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 71304204 (NC_000002.12:119256335:C:G 50689/139936)
Row 71304205 (NC_000002.12:119256335:C:T 51/140002)

- Apr 26, 2021 (155)
82 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 71304204 (NC_000002.12:119256335:C:G 50689/139936)
Row 71304205 (NC_000002.12:119256335:C:T 51/140002)

- Apr 26, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000002.11 - 120013912 Apr 25, 2020 (154)
84 HapMap NC_000002.12 - 119256336 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000002.11 - 120013912 Apr 25, 2020 (154)
86 Korean Genome Project NC_000002.12 - 119256336 Apr 25, 2020 (154)
87 Northern Sweden NC_000002.11 - 120013912 Jul 13, 2019 (153)
88 Qatari NC_000002.11 - 120013912 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000002.11 - 120013912 Apr 25, 2020 (154)
90 Siberian NC_000002.11 - 120013912 Apr 25, 2020 (154)
91 8.3KJPN NC_000002.11 - 120013912 Apr 26, 2021 (155)
92 TopMed NC_000002.12 - 119256336 Apr 26, 2021 (155)
93 UK 10K study - Twins NC_000002.11 - 120013912 Oct 11, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000002.11 - 120013912 Jul 13, 2019 (153)
95 ALFA NC_000002.12 - 119256336 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)
rs3731605 Oct 09, 2002 (108)
rs17805393 Oct 07, 2004 (123)
rs60877239 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85436783 NC_000002.9:119730141:C:G NC_000002.12:119256335:C:G (self)
ss76821682, ss110814225, ss164046697, ss165085071, ss167087526, ss276641678, ss284421474, ss292351058, ss483891011, ss1586696924, ss1712484685 NC_000002.10:119730381:C:G NC_000002.12:119256335:C:G (self)
9983653, 5510635, 3886557, 5217707, 2421911, 5916005, 2080790, 2564631, 5238813, 1361390, 11436346, 5510635, 1193585, ss219463790, ss231328728, ss238844791, ss481139529, ss534153599, ss555821691, ss649443188, ss779832921, ss781406538, ss835309526, ss977272066, ss1069430463, ss1298979418, ss1428709700, ss1579051895, ss1604394984, ss1647389017, ss1797371984, ss1920522701, ss1968867356, ss2020788897, ss2148845036, ss2399915676, ss2624899631, ss2633663614, ss2703457395, ss2778666405, ss2990274839, ss3344434283, ss3628149955, ss3631627734, ss3642119328, ss3658148309, ss3728795925, ss3757277338, ss3827178872, ss3837004178, ss3853221833, ss3898738611, ss5153467039 NC_000002.11:120013911:C:G NC_000002.12:119256335:C:G (self)
1877921, 5166145, 202668191, 324847213, 13150146376, ss2233658702, ss3024156392, ss3320730026, ss3704730284, ss3801644462, ss3842422811, ss3948788144, ss4521024334 NC_000002.12:119256335:C:G NC_000002.12:119256335:C:G (self)
ss16852614, ss20099780 NT_022135.13:8721653:C:G NC_000002.12:119256335:C:G (self)
ss2743194, ss4917596, ss5863100, ss6698425, ss24309656, ss44345314, ss65716838, ss68401827, ss68825766, ss103570920, ss104855190, ss120244547, ss161173414 NT_022135.16:9762574:C:G NC_000002.12:119256335:C:G (self)
ss2778666405 NC_000002.11:120013911:C:T NC_000002.12:119256335:C:T (self)
13150146376, ss2233658702, ss3320730027 NC_000002.12:119256335:C:T NC_000002.12:119256335: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.

1 citation for rs1867749
PMID Title Author Year Journal
23386860 Exploring genome-wide - dietary heme iron intake interactions and the risk of type 2 diabetes. Pasquale LR et al. 2013 Frontiers in 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