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10q23.31

General Information: Available

Organism	Human
Points of Interest	rs10509540
Karyotype Band Location	10q23.31
Chromosomal Location (GRCh37)	Chr10:90008047-90278380
Region Size	0.27 Mb
Orthologous Regions	Mouse: Human 10q23.31 Orthologous Region Rat: Human 10q23.31 Orthologous Region
Genes in Region (1)	RNLS

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
rs148477675	dbSNP_134	90034737	+	A/V	RNLS	55328	310
rs146268123	dbSNP_134	90074351	+	F/L	RNLS	55328	250
rs138921267	dbSNP_134	90074372	+	V/M	RNLS	55328	243
rs149300466	dbSNP_134	90074381	+	P/S	RNLS	55328	240
rs148749882	dbSNP_134	90074396	+	S/P	RNLS	55328	235
rs117446494	dbSNP_134	90122314	+	N/S	RNLS	55328	232
rs143744963	dbSNP_134	90122333	+	I/V	RNLS	55328	226
rs151245420	dbSNP_134	90122360	+	S/G	RNLS	55328	217
rs116376263	dbSNP_134	90122388	+	D/E	RNLS	55328	207
rs112858030	dbSNP_134	90122437	+	S/F	RNLS	55328	191
rs78525460	dbSNP_134	90122468	+	Q/K	RNLS	55328	181

(Human) GRCh37 - chr10:90008047..90278380 (270.33 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 rs10509540 Chr 10 Position 90023033 Strand P-Value 6.92e-09		N/A	0.5	chr10: 90013189..90139756	RNLS		LD Region Feature File LD File
		0.4	N/A	chr10: 90013189..90052348	RNLS
		0.8	N/A	chr10: 90015401..90051317	RNLS
		1	N/A

Publications: 1

• 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
   
  

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

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Printed on Fri February 10, 2012