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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.

rs203674

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:196715495 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.324119 (85791/264690, TOPMED)
G=0.350363 (49034/139952, GnomAD)
G=0.39514 (22064/55838, ALFA) (+ 17 more)
G=0.06689 (1121/16760, 8.3KJPN)
G=0.2454 (1229/5008, 1000G)
G=0.4408 (1975/4480, Estonian)
G=0.4183 (1612/3854, ALSPAC)
G=0.4272 (1584/3708, TWINSUK)
G=0.0795 (233/2930, KOREAN)
G=0.0759 (139/1832, Korea1K)
G=0.2309 (412/1784, HapMap)
G=0.391 (390/998, GoNL)
G=0.082 (64/784, PRJEB37584)
G=0.467 (280/600, NorthernSweden)
T=0.169 (90/534, MGP)
G=0.161 (83/516, SGDP_PRJ)
G=0.231 (50/216, Qatari)
G=0.046 (10/216, Vietnamese)
G=0.17 (7/42, Siberian)
G=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CFH : Intron Variant
Publications
8 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 1 NC_000001.11:g.196715495G>T
GRCh37.p13 chr 1 NC_000001.10:g.196684625G>T
CFH RefSeqGene (LRG_47) NG_007259.1:g.68485G>T
Gene: CFH, complement factor H (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CFH transcript variant 1 NM_000186.4:c.1520-98G>T N/A Intron Variant
CFH transcript variant 2 NM_001014975.3:c. N/A Genic Downstream Transcript Variant
CFH transcript variant X2 XM_017001108.2:c. N/A Genic Downstream Transcript Variant
CFH transcript variant X1 XR_001737134.2: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

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 55838 G=0.39514 T=0.60486
European Sub 44812 G=0.41748 T=0.58252
African Sub 5770 G=0.2589 T=0.7411
African Others Sub 206 G=0.238 T=0.762
African American Sub 5564 G=0.2597 T=0.7403
Asian Sub 162 G=0.093 T=0.907
East Asian Sub 126 G=0.079 T=0.921
Other Asian Sub 36 G=0.14 T=0.86
Latin American 1 Sub 502 G=0.329 T=0.671
Latin American 2 Sub 726 G=0.202 T=0.798
South Asian Sub 144 G=0.340 T=0.660
Other Sub 3722 G=0.3992 T=0.6008


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 G=0.324119 T=0.675881
gnomAD - Genomes Global Study-wide 139952 G=0.350363 T=0.649637
gnomAD - Genomes European Sub 75782 G=0.42769 T=0.57231
gnomAD - Genomes African Sub 41976 G=0.26606 T=0.73394
gnomAD - Genomes American Sub 13594 G=0.25813 T=0.74187
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.3336 T=0.6664
gnomAD - Genomes East Asian Sub 3126 G=0.0483 T=0.9517
gnomAD - Genomes Other Sub 2150 G=0.3191 T=0.6809
Allele Frequency Aggregator Total Global 55838 G=0.39514 T=0.60486
Allele Frequency Aggregator European Sub 44812 G=0.41748 T=0.58252
Allele Frequency Aggregator African Sub 5770 G=0.2589 T=0.7411
Allele Frequency Aggregator Other Sub 3722 G=0.3992 T=0.6008
Allele Frequency Aggregator Latin American 2 Sub 726 G=0.202 T=0.798
Allele Frequency Aggregator Latin American 1 Sub 502 G=0.329 T=0.671
Allele Frequency Aggregator Asian Sub 162 G=0.093 T=0.907
Allele Frequency Aggregator South Asian Sub 144 G=0.340 T=0.660
8.3KJPN JAPANESE Study-wide 16760 G=0.06689 T=0.93311
1000Genomes Global Study-wide 5008 G=0.2454 T=0.7546
1000Genomes African Sub 1322 G=0.2436 T=0.7564
1000Genomes East Asian Sub 1008 G=0.0486 T=0.9514
1000Genomes Europe Sub 1006 G=0.3966 T=0.6034
1000Genomes South Asian Sub 978 G=0.293 T=0.707
1000Genomes American Sub 694 G=0.248 T=0.752
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4408 T=0.5592
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4183 T=0.5817
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4272 T=0.5728
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0795 T=0.9205
Korean Genome Project KOREAN Study-wide 1832 G=0.0759 T=0.9241
HapMap Global Study-wide 1784 G=0.2309 T=0.7691
HapMap African Sub 688 G=0.215 T=0.785
HapMap American Sub 666 G=0.275 T=0.725
HapMap Asian Sub 254 G=0.071 T=0.929
HapMap Europe Sub 176 G=0.358 T=0.642
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.391 T=0.609
CNV burdens in cranial meningiomas Global Study-wide 784 G=0.082 T=0.918
CNV burdens in cranial meningiomas CRM Sub 784 G=0.082 T=0.918
Northern Sweden ACPOP Study-wide 600 G=0.467 T=0.533
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.831 T=0.169
SGDP_PRJ Global Study-wide 516 G=0.161 T=0.839
Qatari Global Study-wide 216 G=0.231 T=0.769
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.046 T=0.954
Siberian Global Study-wide 42 G=0.17 T=0.83
The Danish reference pan genome Danish Study-wide 40 G=0.38 T=0.62
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
GRCh38.p13 chr 1 NC_000001.11:g.196715495= NC_000001.11:g.196715495G>T
GRCh37.p13 chr 1 NC_000001.10:g.196684625= NC_000001.10:g.196684625G>T
CFH RefSeqGene (LRG_47) NG_007259.1:g.68485= NG_007259.1:g.68485G>T
CFH transcript variant 1 NM_000186.3:c.1520-98= NM_000186.3:c.1520-98G>T
CFH transcript variant 1 NM_000186.4:c.1520-98= NM_000186.4:c.1520-98G>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#.

99 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss267200 Jul 12, 2000 (79)
2 SC_JCM ss471082 Jul 16, 2000 (80)
3 KWOK ss1006671 Oct 04, 2000 (86)
4 KWOK ss1007007 Oct 04, 2000 (86)
5 KWOK ss2047274 Oct 18, 2000 (87)
6 KWOK ss2047523 Oct 18, 2000 (87)
7 TSC-CSHL ss3288652 Sep 28, 2001 (100)
8 SC_JCM ss6059314 Feb 20, 2003 (111)
9 WI_SSAHASNP ss6411783 Feb 20, 2003 (111)
10 BCM_SSAHASNP ss9873772 Jul 11, 2003 (116)
11 SC_SNP ss13010950 Dec 05, 2003 (119)
12 CSHL-HAPMAP ss17369482 Feb 27, 2004 (120)
13 SSAHASNP ss20491495 Apr 05, 2004 (121)
14 ABI ss43861946 Mar 13, 2006 (126)
15 PGA-UW-FHCRC ss48532135 Mar 13, 2006 (126)
16 ILLUMINA ss65758202 Oct 15, 2006 (127)
17 ILLUMINA ss74855128 Dec 07, 2007 (129)
18 CGM_KYOTO ss76864738 Dec 07, 2007 (129)
19 SI_EXO ss76890413 Dec 07, 2007 (129)
20 HGSV ss80921077 Dec 15, 2007 (130)
21 BCMHGSC_JDW ss87925765 Mar 23, 2008 (129)
22 HUMANGENOME_JCVI ss99275741 Feb 06, 2009 (130)
23 1000GENOMES ss108838835 Jan 23, 2009 (130)
24 1000GENOMES ss111591423 Jan 25, 2009 (130)
25 ILLUMINA-UK ss119164518 Feb 15, 2009 (130)
26 KRIBB_YJKIM ss119344054 Dec 01, 2009 (131)
27 ENSEMBL ss138131729 Dec 01, 2009 (131)
28 ENSEMBL ss139109354 Dec 01, 2009 (131)
29 GMI ss156119985 Dec 01, 2009 (131)
30 ILLUMINA ss160492068 Dec 01, 2009 (131)
31 COMPLETE_GENOMICS ss164842265 Jul 04, 2010 (132)
32 ILLUMINA ss173060162 Jul 04, 2010 (132)
33 BUSHMAN ss199446352 Jul 04, 2010 (132)
34 1000GENOMES ss218809902 Jul 14, 2010 (132)
35 1000GENOMES ss230847758 Jul 14, 2010 (132)
36 1000GENOMES ss238470311 Jul 15, 2010 (132)
37 ILLUMINA ss244286346 Jul 04, 2010 (132)
38 GMI ss276163350 May 04, 2012 (137)
39 GMI ss284204627 Apr 25, 2013 (138)
40 PJP ss290697450 May 09, 2011 (134)
41 ILLUMINA ss480404403 May 04, 2012 (137)
42 ILLUMINA ss481182922 Sep 08, 2015 (146)
43 ILLUMINA ss537026771 Sep 08, 2015 (146)
44 SSMP ss648606966 Apr 25, 2013 (138)
45 ILLUMINA ss832198674 Sep 08, 2015 (146)
46 EVA-GONL ss975995682 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1068496370 Aug 21, 2014 (142)
48 1000GENOMES ss1294098646 Aug 21, 2014 (142)
49 DDI ss1426070092 Apr 01, 2015 (144)
50 EVA_GENOME_DK ss1574589576 Apr 01, 2015 (144)
51 EVA_DECODE ss1585390843 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1601841141 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1644835174 Apr 01, 2015 (144)
54 EVA_MGP ss1710937095 Apr 01, 2015 (144)
55 EVA_SVP ss1712393635 Apr 01, 2015 (144)
56 HAMMER_LAB ss1795525631 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1919226853 Feb 12, 2016 (147)
58 GENOMED ss1966938940 Jul 19, 2016 (147)
59 JJLAB ss2020132128 Sep 14, 2016 (149)
60 USC_VALOUEV ss2148159183 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2168971950 Dec 20, 2016 (150)
62 TOPMED ss2331547968 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2624573897 Nov 08, 2017 (151)
64 GRF ss2698147130 Nov 08, 2017 (151)
65 GNOMAD ss2764655499 Nov 08, 2017 (151)
66 SWEGEN ss2988222874 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3023825995 Nov 08, 2017 (151)
68 TOPMED ss3099811872 Nov 08, 2017 (151)
69 CSHL ss3343847703 Nov 08, 2017 (151)
70 ILLUMINA ss3626274846 Oct 11, 2018 (152)
71 ILLUMINA ss3632920214 Oct 11, 2018 (152)
72 ILLUMINA ss3633615973 Oct 11, 2018 (152)
73 ILLUMINA ss3636044229 Oct 11, 2018 (152)
74 ILLUMINA ss3637805040 Oct 11, 2018 (152)
75 ILLUMINA ss3640990339 Oct 11, 2018 (152)
76 ILLUMINA ss3641284428 Oct 11, 2018 (152)
77 ILLUMINA ss3642812498 Oct 11, 2018 (152)
78 OMUKHERJEE_ADBS ss3646250442 Oct 11, 2018 (152)
79 URBANLAB ss3646857002 Oct 11, 2018 (152)
80 EGCUT_WGS ss3656183391 Jul 12, 2019 (153)
81 EVA_DECODE ss3688355387 Jul 12, 2019 (153)
82 ACPOP ss3727740328 Jul 12, 2019 (153)
83 EVA ss3747165055 Jul 12, 2019 (153)
84 PACBIO ss3783650253 Jul 12, 2019 (153)
85 PACBIO ss3789268534 Jul 12, 2019 (153)
86 PACBIO ss3794140709 Jul 12, 2019 (153)
87 KHV_HUMAN_GENOMES ss3800171840 Jul 12, 2019 (153)
88 EVA ss3826574054 Apr 25, 2020 (154)
89 EVA ss3836685868 Apr 25, 2020 (154)
90 EVA ss3842096797 Apr 25, 2020 (154)
91 SGDP_PRJ ss3850612251 Apr 25, 2020 (154)
92 KRGDB ss3895891152 Apr 25, 2020 (154)
93 KOGIC ss3946215155 Apr 25, 2020 (154)
94 FSA-LAB ss3983957331 Apr 25, 2021 (155)
95 EVA ss3984469474 Apr 25, 2021 (155)
96 EVA ss3986151941 Apr 25, 2021 (155)
97 EVA ss4016954045 Apr 25, 2021 (155)
98 TOPMED ss4478736242 Apr 25, 2021 (155)
99 TOMMO_GENOMICS ss5147803882 Apr 25, 2021 (155)
100 1000Genomes NC_000001.10 - 196684625 Oct 11, 2018 (152)
101 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 196684625 Oct 11, 2018 (152)
102 Genetic variation in the Estonian population NC_000001.10 - 196684625 Oct 11, 2018 (152)
103 The Danish reference pan genome NC_000001.10 - 196684625 Apr 25, 2020 (154)
104 gnomAD - Genomes NC_000001.11 - 196715495 Apr 25, 2021 (155)
105 Genome of the Netherlands Release 5 NC_000001.10 - 196684625 Apr 25, 2020 (154)
106 HapMap NC_000001.11 - 196715495 Apr 25, 2020 (154)
107 KOREAN population from KRGDB NC_000001.10 - 196684625 Apr 25, 2020 (154)
108 Korean Genome Project NC_000001.11 - 196715495 Apr 25, 2020 (154)
109 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 196684625 Apr 25, 2020 (154)
110 Northern Sweden NC_000001.10 - 196684625 Jul 12, 2019 (153)
111 CNV burdens in cranial meningiomas NC_000001.10 - 196684625 Apr 25, 2021 (155)
112 Qatari NC_000001.10 - 196684625 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000001.10 - 196684625 Apr 25, 2020 (154)
114 Siberian NC_000001.10 - 196684625 Apr 25, 2020 (154)
115 8.3KJPN NC_000001.10 - 196684625 Apr 25, 2021 (155)
116 TopMed NC_000001.11 - 196715495 Apr 25, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 196684625 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000001.10 - 196684625 Jul 12, 2019 (153)
119 ALFA NC_000001.11 - 196715495 Apr 25, 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)
rs60812505 May 26, 2008 (130)
rs386553937 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80921077 NC_000001.8:193416281:G:T NC_000001.11:196715494:G:T (self)
ss87925765, ss108838835, ss111591423, ss119164518, ss164842265, ss199446352, ss276163350, ss284204627, ss290697450, ss1585390843, ss1712393635, ss3642812498 NC_000001.9:194951247:G:T NC_000001.11:196715494:G:T (self)
4933248, 2709873, 1921639, 1829175, 1183051, 3068546, 53847, 1025193, 18792, 1268783, 2629231, 675537, 5773189, 2709873, 585933, ss218809902, ss230847758, ss238470311, ss480404403, ss481182922, ss537026771, ss648606966, ss832198674, ss975995682, ss1068496370, ss1294098646, ss1426070092, ss1574589576, ss1601841141, ss1644835174, ss1710937095, ss1795525631, ss1919226853, ss1966938940, ss2020132128, ss2148159183, ss2331547968, ss2624573897, ss2698147130, ss2764655499, ss2988222874, ss3343847703, ss3626274846, ss3632920214, ss3633615973, ss3636044229, ss3637805040, ss3640990339, ss3641284428, ss3646250442, ss3656183391, ss3727740328, ss3747165055, ss3783650253, ss3789268534, ss3794140709, ss3826574054, ss3836685868, ss3850612251, ss3895891152, ss3983957331, ss3984469474, ss3986151941, ss4016954045, ss5147803882 NC_000001.10:196684624:G:T NC_000001.11:196715494:G:T (self)
35588018, 237838, 2593156, 26603274, 42342577, 594728806, ss2168971950, ss3023825995, ss3099811872, ss3646857002, ss3688355387, ss3800171840, ss3842096797, ss3946215155, ss4478736242 NC_000001.11:196715494:G:T NC_000001.11:196715494:G:T (self)
ss76890413 NT_004487.18:47174978:G:T NC_000001.11:196715494:G:T (self)
ss267200, ss471082, ss1006671, ss1007007, ss2047274, ss2047523, ss3288652, ss6059314, ss6411783, ss43861946, ss48532135, ss65758202, ss74855128, ss76864738, ss99275741, ss119344054, ss138131729, ss139109354, ss156119985, ss160492068, ss173060162, ss244286346 NT_004487.19:48173266:G:T NC_000001.11:196715494:G:T (self)
ss9873772, ss13010950, ss17369482, ss20491495 NT_004671.15:8039610:G:T NC_000001.11:196715494: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.

8 citations for rs203674
PMID Title Author Year Journal
18043728 Haplotypes in the complement factor H (CFH) gene: associations with drusen and advanced age-related macular degeneration. Francis PJ et al. 2007 PloS one
18541031 The NEI/NCBI dbGAP database: genotypes and haplotypes that may specifically predispose to risk of neovascular age-related macular degeneration. Zhang H et al. 2008 BMC medical genetics
19796758 Comprehensive analysis of complement factor H and LOC387715/ARMS2/HTRA1 variants with respect to phenotype in advanced age-related macular degeneration. Andreoli MT et al. 2009 American journal of ophthalmology
21197116 Genome-wide association analyses of genetic, phenotypic, and environmental risks in the age-related eye disease study. Ryu E et al. 2010 Molecular vision
22035603 Plasma biomarkers of oxidative stress and genetic variants in age-related macular degeneration. Brantley MA Jr et al. 2012 American journal of ophthalmology
22059990 The major risk alleles of age-related macular degeneration (AMD) in CFH do not play a major role in rheumatoid arthritis (RA). Trouw LA et al. 2011 Clinical and experimental immunology
26152901 CFH polymorphisms in a Northern Spanish population with neovascular and dry forms of age-related macular degeneration. GarcĂ­a M et al. 2015 Acta ophthalmologica
27239600 Complement factor H and LOC387715/ARMS2/HTRA1 variant's frequencies and phenotypic associations in neovascular age-related macular degeneration, a pilot study. Karkhane R et al. 2016 Journal of current ophthalmology
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