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  • General Information
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10p15.1

General Information: Available

Organism	Human
Points of Interest	rs947474; rs11258747
Karyotype Band Location	10p15.1
Chromosomal Location (GRCh37)	Chr10:6435374-6545104
Region Size	0.11 Mb
Orthologous Regions	Mouse: Human 10p15.1 Orthologous Region Rat: Human 10p15.1 Orthologous Region
Genes in Region (1)	PRKCQ

View this region in the Human T1D Regions table.

Non-Synonymous SNPs in region dbSNP134:

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs143285381	dbSNP_134	6470255	+	D/N	PRKCQ	5588	679
rs142951028	dbSNP_134	6472792	+	P/S	PRKCQ	5588	649
rs147040074	dbSNP_134	6472833	+	R/Q	PRKCQ	5588	635
rs144073871	dbSNP_134	6483886	+		PRKCQ	5588	602
rs34663609	dbSNP_134	6483892	+	R/Q	PRKCQ	5588	600
rs78855257	dbSNP_134	6506284	+	S/C	PRKCQ	5588	479
rs34524148	dbSNP_134	6525521	+	D/N	PRKCQ	5588	354
rs139296268	dbSNP_134	6527125	+	P/L	PRKCQ	5588	336
rs2236379	dbSNP_134	6527143	-	P/L	PRKCQ	5588	330
rs45590231	dbSNP_134	6527215	+	D/V	PRKCQ	5588	306
rs142220465	dbSNP_134	6527221	+	L/S	PRKCQ	5588	304
rs148789784	dbSNP_134	6539017	+	I/V	PRKCQ	5588	214
rs141631625	dbSNP_134	6540431	+	V/I	PRKCQ	5588	157
rs138291602	dbSNP_134	6540487	+	G/A	PRKCQ	5588	138

(Human) GRCh37 - chr10:6435374..6545104 (109.73 kb)  View in Genome Browser

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
Immune Disease Associated Variants	Variants shown to be associated with different auto-immune diseases
P-values, -log(p)	1 degree of freedom p-values, stratified by geographic location. Generated using snpMatrix with data from the T1DGC Meta-analysis study.
HapMap Recobination Data	Genome-wide recombination rate from Phase 2 HapMap estimated from phased haplotypes in HapMap Release 22 (NCBI 36). Units are in cM/Mb, coordinates have been projected to the current build.

Genes in LD Region: Available

Summary data derived from GWA meta analysis Barrett et al. LD regions were calculated using different r² and D' threshold values, and these regions were then examined for genes. The definition of a gene location includes a 3kb flanking region either side of the gene.

Marker Data		Region Data					Links
		r2 Threshold	D' Threshold	Region	Genes
Marker rs947474 Chr 10 Position 6390450 Strand P-Value 5.63e-06		N/A	0.5	chr10: 6388928..6436034	DKFZp667F0711		LD Region Feature File LD File
		0.4	N/A	chr10: 6390192..6436034	DKFZp667F0711
		0.8	N/A	chr10: 6390192..6390450
		1	N/A
Marker rs11258747 Chr 10 Position 6472891 Strand P-Value 1.16e-07		N/A	0.5	chr10: 6437064..6522908	PRKCQ		LD Region Feature File LD File
		0.4	N/A	chr10: 6440578..6522908	PRKCQ
		0.8	N/A	chr10: 6448881..6498723	PRKCQ
		1	N/A	chr10: 6460644..6498723	PRKCQ

Publications: 4

• Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
  Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, The Type 1 Diabetes Genetics Consortium
  Nat Genet. 2009
  PubMed ID: 19430480
   
  
• Shared and distinct genetic variants in type 1 diabetes and celiac disease.
  Smyth DJ, Plagnol V, Walker NM, Cooper JD, Downes K, Yang JH, Howson JM, Stevens H, McManus R, Wijmenga C, Heap GA, Dubois PC, Clayton DG, Hunt KA, van Heel DA, Todd JA
  N Engl J Med. 2008
  PubMed ID: 19073967
   
  
• Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
  Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, Allen JE, Downes K, Barrett JC, Healy BC, Mychaleckyj JC, Warram JH, Todd JA
  Nat Genet. 2008
  PubMed ID: 18978792
   
  
• Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes.
  Lowe CE, Cooper JD, Brusko T, Walker NM, Smyth DJ, Bailey R, Bourget K, Plagnol V, Field S, Atkinson M, Clayton DG, Wicker LS, Todd JA
  Nat Genet. 2007
  PubMed ID: 17676041
   
  

Signal Clouds: Available

Genotype data for collections is plotted to give a visual sense of the quality of clustering. The two homozygous and the heterozygous genotypes are represented by different colours; a clear separation between the clouds is indicative of good clustering.

Source: ImmunoChip

Source: T1DGC 4K-4K Study - 2008

Source: US NIMH-GAIN Study - 2008

Source: WTCCC

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Printed on Fri February 10, 2012