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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.

rs11574637

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:31357553 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.20163 (25318/125568, TOPMED)
C=0.1963 (6064/30892, GnomAD)
C=0.201 (1005/5008, 1000G) (+ 2 more)
C=0.155 (599/3854, ALSPAC)
C=0.164 (608/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ITGAX : Intron Variant
Publications
7 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.p7 chr 16 NC_000016.10:g.31357553T>C
GRCh37.p13 chr 16 NC_000016.9:g.31368874T>C
ITGAX RefSeqGene NG_011451.1:g.7366T>C
Gene: ITGAX, integrin subunit alpha X (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ITGAX transcript variant 2 NM_000887.4:c. N/A Intron Variant
ITGAX transcript variant 1 NM_001286375.1:c. N/A Intron Variant
ITGAX transcript variant X3 XM_011545852.1:c. N/A Intron Variant
ITGAX transcript variant X4 XM_011545854.1:c. N/A Intron Variant
ITGAX transcript variant X1 XR_950797.2: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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.79837 C=0.20163
The Genome Aggregation Database Global Study-wide 30892 T=0.8037 C=0.1963
The Genome Aggregation Database European Sub 18452 T=0.8297 C=0.1703
The Genome Aggregation Database African Sub 8708 T=0.708 C=0.292
The Genome Aggregation Database East Asian Sub 1618 T=0.992 C=0.008
The Genome Aggregation Database Other Sub 976 T=0.82 C=0.18
The Genome Aggregation Database American Sub 836 T=0.87 C=0.13
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.71 C=0.29
1000Genomes Global Study-wide 5008 T=0.799 C=0.201
1000Genomes African Sub 1322 T=0.690 C=0.310
1000Genomes East Asian Sub 1008 T=0.985 C=0.015
1000Genomes Europe Sub 1006 T=0.800 C=0.200
1000Genomes South Asian Sub 978 T=0.72 C=0.28
1000Genomes American Sub 694 T=0.85 C=0.15
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.845 C=0.155
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.836 C=0.164
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= C Note
GRCh38.p7 chr 16 NC_000016.10:g.31357553T= NC_000016.10:g.31357553T>C
GRCh37.p13 chr 16 NC_000016.9:g.31368874T= NC_000016.9:g.31368874T>C
ITGAX RefSeqGene NG_011451.1:g.7366T= NG_011451.1:g.7366T>C
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, 92 SubSNP submissions
No Submitter Submission ID Date (Build)
1 FHCRC ss16360086 Feb 28, 2004 (120)
2 PERLEGEN ss23763673 Sep 20, 2004 (123)
3 AFFY ss66280319 Nov 29, 2006 (127)
4 ILLUMINA ss66931912 Nov 29, 2006 (127)
5 ILLUMINA ss67091832 Nov 29, 2006 (127)
6 ILLUMINA ss68106380 Dec 12, 2006 (127)
7 ILLUMINA ss70529912 May 24, 2008 (130)
8 ILLUMINA ss71060454 May 16, 2007 (127)
9 ILLUMINA ss75541547 Dec 06, 2007 (129)
10 AFFY ss75936357 Dec 08, 2007 (130)
11 KRIBB_YJKIM ss85099570 Dec 15, 2007 (130)
12 HUMANGENOME_JCVI ss96712749 Feb 05, 2009 (130)
13 1000GENOMES ss115029370 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118236610 Feb 14, 2009 (130)
15 ENSEMBL ss132475243 Dec 01, 2009 (131)
16 ILLUMINA ss152994791 Dec 01, 2009 (131)
17 ILLUMINA ss159176402 Dec 01, 2009 (131)
18 ILLUMINA ss159981763 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss169578855 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss171174666 Jul 04, 2010 (132)
21 ILLUMINA ss171302480 Jul 04, 2010 (132)
22 BUSHMAN ss201612990 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss207617432 Jul 04, 2010 (132)
24 1000GENOMES ss227215373 Jul 14, 2010 (132)
25 1000GENOMES ss237005278 Jul 15, 2010 (132)
26 BL ss255621872 May 09, 2011 (134)
27 ILLUMINA ss479529703 May 04, 2012 (137)
28 ILLUMINA ss479533532 May 04, 2012 (137)
29 ILLUMINA ss479992875 Sep 08, 2015 (146)
30 ILLUMINA ss484563818 May 04, 2012 (137)
31 EXOME_CHIP ss491507548 May 04, 2012 (137)
32 ILLUMINA ss536699344 Sep 08, 2015 (146)
33 TISHKOFF ss564871314 Apr 25, 2013 (138)
34 SSMP ss660626286 Apr 25, 2013 (138)
35 ILLUMINA ss778384143 Sep 08, 2015 (146)
36 ILLUMINA ss780681072 Sep 08, 2015 (146)
37 ILLUMINA ss782728615 Sep 08, 2015 (146)
38 ILLUMINA ss783354372 Sep 08, 2015 (146)
39 ILLUMINA ss783695881 Sep 08, 2015 (146)
40 ILLUMINA ss831980330 Sep 08, 2015 (146)
41 ILLUMINA ss833839155 Sep 08, 2015 (146)
42 EVA-GONL ss992434045 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1080589853 Aug 21, 2014 (142)
44 1000GENOMES ss1355984228 Aug 21, 2014 (142)
45 DDI ss1427824251 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1577895343 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1634307872 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1677301905 Apr 01, 2015 (144)
49 EVA_DECODE ss1696468497 Apr 01, 2015 (144)
50 EVA_SVP ss1713536125 Apr 01, 2015 (144)
51 ILLUMINA ss1752190521 Sep 08, 2015 (146)
52 ILLUMINA ss1752190522 Sep 08, 2015 (146)
53 HAMMER_LAB ss1808489573 Sep 08, 2015 (146)
54 ILLUMINA ss1917906954 Feb 12, 2016 (147)
55 WEILL_CORNELL_DGM ss1935859022 Feb 12, 2016 (147)
56 ILLUMINA ss1946413751 Feb 12, 2016 (147)
57 ILLUMINA ss1959673739 Feb 12, 2016 (147)
58 JJLAB ss2028716438 Sep 14, 2016 (149)
59 ILLUMINA ss2094799674 Dec 20, 2016 (150)
60 ILLUMINA ss2095066345 Dec 20, 2016 (150)
61 USC_VALOUEV ss2157130813 Dec 20, 2016 (150)
62 HUMAN_LONGEVITY ss2211752968 Dec 20, 2016 (150)
63 TOPMED ss2376549687 Dec 20, 2016 (150)
64 ILLUMINA ss2633311987 Nov 08, 2017 (151)
65 ILLUMINA ss2633311988 Nov 08, 2017 (151)
66 ILLUMINA ss2633311989 Nov 08, 2017 (151)
67 GNOMAD ss2942142097 Nov 08, 2017 (151)
68 AFFY ss2985067173 Nov 08, 2017 (151)
69 AFFY ss2985703225 Nov 08, 2017 (151)
70 SWEGEN ss3014338313 Nov 08, 2017 (151)
71 ILLUMINA ss3021700202 Nov 08, 2017 (151)
72 BIOINF_KMB_FNS_UNIBA ss3028181058 Nov 08, 2017 (151)
73 TOPMED ss3244284419 Nov 08, 2017 (151)
74 CSHL ss3351409141 Nov 08, 2017 (151)
75 ILLUMINA ss3627511460 Jul 20, 2018 (151)
76 ILLUMINA ss3627511461 Jul 20, 2018 (151)
77 ILLUMINA ss3631298774 Jul 20, 2018 (151)
78 ILLUMINA ss3633119217 Jul 20, 2018 (151)
79 ILLUMINA ss3633825204 Jul 20, 2018 (151)
80 ILLUMINA ss3634640052 Jul 20, 2018 (151)
81 ILLUMINA ss3634640053 Jul 20, 2018 (151)
82 ILLUMINA ss3635513543 Jul 20, 2018 (151)
83 ILLUMINA ss3636330621 Jul 20, 2018 (151)
84 ILLUMINA ss3637264971 Jul 20, 2018 (151)
85 ILLUMINA ss3638122359 Jul 20, 2018 (151)
86 ILLUMINA ss3639072879 Jul 20, 2018 (151)
87 ILLUMINA ss3639845350 Jul 20, 2018 (151)
88 ILLUMINA ss3640347371 Jul 20, 2018 (151)
89 ILLUMINA ss3640347372 Jul 20, 2018 (151)
90 ILLUMINA ss3643103665 Jul 20, 2018 (151)
91 ILLUMINA ss3643895159 Jul 20, 2018 (151)
92 ILLUMINA ss3644666816 Jul 20, 2018 (151)
93 1000Genomes NC_000016.9 - 31368874 Jul 20, 2018 (151)
94 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 31368874 Jul 20, 2018 (151)
95 The Genome Aggregation Database NC_000016.9 - 31368874 Jul 20, 2018 (151)
96 Trans-Omics for Precision Medicine NC_000016.10 - 31357553 Jul 20, 2018 (151)
97 UK 10K study - Twins NC_000016.9 - 31368874 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)
rs56622927 May 24, 2008 (130)
rs58681810 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss115029370, ss118236610, ss169578855, ss171174666, ss201612990, ss207617432, ss255621872, ss479529703, ss1696468497, ss1713536125, ss3639072879, ss3639845350, ss3643103665, ss3643895159 NC_000016.8:31276374:T= NC_000016.10:31357552:T= (self)
69139473, 38373830, 75843624, 38373830, ss227215373, ss237005278, ss479533532, ss479992875, ss484563818, ss491507548, ss536699344, ss564871314, ss660626286, ss778384143, ss780681072, ss782728615, ss783354372, ss783695881, ss831980330, ss833839155, ss992434045, ss1080589853, ss1355984228, ss1427824251, ss1577895343, ss1634307872, ss1677301905, ss1752190521, ss1752190522, ss1808489573, ss1917906954, ss1935859022, ss1946413751, ss1959673739, ss2028716438, ss2094799674, ss2095066345, ss2157130813, ss2376549687, ss2633311987, ss2633311988, ss2633311989, ss2942142097, ss2985067173, ss2985703225, ss3014338313, ss3021700202, ss3351409141, ss3627511460, ss3627511461, ss3631298774, ss3633119217, ss3633825204, ss3634640052, ss3634640053, ss3635513543, ss3636330621, ss3637264971, ss3638122359, ss3640347371, ss3640347372, ss3644666816 NC_000016.9:31368873:T= NC_000016.10:31357552:T= (self)
142724189, ss2211752968, ss3028181058, ss3244284419 NC_000016.10:31357552:T= NC_000016.10:31357552:T= (self)
ss16360086, ss23763673, ss66280319, ss66931912, ss67091832, ss68106380, ss70529912, ss71060454, ss75541547, ss75936357, ss85099570, ss96712749, ss132475243, ss152994791, ss159176402, ss159981763, ss171302480 NT_010393.16:31308873:T= NC_000016.10:31357552:T= (self)
ss115029370, ss118236610, ss169578855, ss171174666, ss201612990, ss207617432, ss255621872, ss479529703, ss1696468497, ss1713536125, ss3639072879, ss3639845350, ss3643103665, ss3643895159 NC_000016.8:31276374:T>C NC_000016.10:31357552:T>C (self)
69139473, 38373830, 75843624, 38373830, ss227215373, ss237005278, ss479533532, ss479992875, ss484563818, ss491507548, ss536699344, ss564871314, ss660626286, ss778384143, ss780681072, ss782728615, ss783354372, ss783695881, ss831980330, ss833839155, ss992434045, ss1080589853, ss1355984228, ss1427824251, ss1577895343, ss1634307872, ss1677301905, ss1752190521, ss1752190522, ss1808489573, ss1917906954, ss1935859022, ss1946413751, ss1959673739, ss2028716438, ss2094799674, ss2095066345, ss2157130813, ss2376549687, ss2633311987, ss2633311988, ss2633311989, ss2942142097, ss2985067173, ss2985703225, ss3014338313, ss3021700202, ss3351409141, ss3627511460, ss3627511461, ss3631298774, ss3633119217, ss3633825204, ss3634640052, ss3634640053, ss3635513543, ss3636330621, ss3637264971, ss3638122359, ss3640347371, ss3640347372, ss3644666816 NC_000016.9:31368873:T>C NC_000016.10:31357552:T>C (self)
142724189, ss2211752968, ss3028181058, ss3244284419 NC_000016.10:31357552:T>C NC_000016.10:31357552:T>C (self)
ss16360086, ss23763673, ss66280319, ss66931912, ss67091832, ss68106380, ss70529912, ss71060454, ss75541547, ss75936357, ss85099570, ss96712749, ss132475243, ss152994791, ss159176402, ss159981763, ss171302480 NT_010393.16:31308873:T>C NC_000016.10:31357552:T>C (self)
Help

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

7 citations for rs11574637
PMID Title Author Year Journal
18204098 Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. Hom G et al. 2008 The New England journal of medicine
19129174 Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Han S et al. 2009 Human molecular genetics
19286673 ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Yang W et al. 2009 Human molecular genetics
19997561 Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE). Hellquist A et al. 2009 PloS one
20629846 Association of ITGAM polymorphism with systemic lupus erythematosus: a meta-analysis. Fan Y et al. 2011 Journal of the European Academy of Dermatology and Venereology
21151989 Polymorphisms of the ITGAM gene confer higher risk of discoid cutaneous than of systemic lupus erythematosus. Järvinen TM et al. 2010 PloS one
21362770 Association study of ITGAM, ITGAX, and CD58 autoimmune risk loci in systemic sclerosis: results from 2 large European Caucasian cohorts. Coustet B et al. 2011 The Journal of rheumatology

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