• About T1DBase
• Regions
  • Human T1D Regions
  • Mouse T1D Regions
    • Linkage Regions
    • Orthologous Regions
  • Rat T1D Regions
    • Linkage Regions
    • Orthologous Regions
    • QTL Regions
• Genome Browser
  • Human GBrowse
  • Mouse GBrowse
  • Rat GBrowse
• Tools
  • Gene Dossier
  • Beta Cell Gene Atlas
  • Batch Query
  • Sequence Search
  • HaemAtlas Search
  • Mouse Strain Search
• Data
  • Poster Pages
  • Downloads
  • Data Submission
• Help
  • FAQ
  • T1DBase Tutorial
• Contact Us

• Page Sections
  • General Information
  • Regions of Interest Overlapping this feature
  • Query T1DMart for overlapping human marker information
  • Region Overview
  • Genes in LD Region
  • Publications
  • Signal Clouds

10q22.3

General Information: Available

Organism	Human
Points of Interest	rs1250550; rs1250558
Karyotype Band Location	10q22.3
Chromosomal Location (GRCh37)	Chr10:81012071-81091563
Region Size	0.08 Mb
Orthologous Regions	Mouse: Human 10q22.3 Orthologous Region Rat: Human 10q22.3 Orthologous Region
Genes in Region (1)	ZMIZ1

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
rs139894250	dbSNP_134	81036957	+	C/W	ZMIZ1	57178	100
rs113298541	dbSNP_134	81037034	+	Q/L	ZMIZ1	57178	126
rs113562619	dbSNP_134	81037082	+	S/N	ZMIZ1	57178	142
rs148262266	dbSNP_134	81051959	+	P/L	ZMIZ1	57178	268
rs142880335	dbSNP_134	81052048	+		ZMIZ1	57178	298
rs140387368	dbSNP_134	81053214	+	S/T	ZMIZ1	57178	345
rs143127715	dbSNP_134	81053331	+	R/Q	ZMIZ1	57178	384
rs147476107	dbSNP_134	81056240	+	N/H	ZMIZ1	57178	415
rs147952022	dbSNP_134	81056259	+		ZMIZ1	57178	421
rs138149224	dbSNP_134	81056307	+	P/L	ZMIZ1	57178	437
rs146714955	dbSNP_134	81057383	+	N/S	ZMIZ1	57178	476
rs144230790	dbSNP_134	81057413	+	S/T	ZMIZ1	57178	486
rs148810329	dbSNP_134	81057446	+	R/K	ZMIZ1	57178	497
rs35162012	dbSNP_134	81058840	+	P/P	ZMIZ1	57178	567
rs144052949	dbSNP_134	81058931	+	H/Q	ZMIZ1	57178	597
rs4264113	dbSNP_134	81060501	+	E/D	ZMIZ1	57178	607
rs12767060	dbSNP_134	81061903	+	V/L	ZMIZ1	57178	687
rs12767074	dbSNP_134	81061921	+	G/R	ZMIZ1	57178	693
rs142913980	dbSNP_134	81066039	+	P/L	ZMIZ1	57178	869
rs148650342	dbSNP_134	81066086	+	D/N	ZMIZ1	57178	885
rs145299702	dbSNP_134	81070813	+	P/S	ZMIZ1	57178	990
rs145555506	dbSNP_134	81070850	+	P/L	ZMIZ1	57178	1002
rs149174704	dbSNP_134	81070858	+	D/N	ZMIZ1	57178	1005
rs143270296	dbSNP_134	81070939	+	D/N	ZMIZ1	57178	1032

(Human) GRCh37 - chr10:81012071..81091563 (79.49 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 rs1250558 Chr 10 Position 81065201 Strand P-Value 9.66e-05		N/A	0.5	chr10: 80959973..81071087	ZMIZ1		LD Region Feature File LD File
		0.4	N/A	chr10: 81032532..81069413	ZMIZ1
		0.8	N/A	chr10: 81059335..81067480	ZMIZ1
		1	N/A	chr10: 81065201..81067040	ZMIZ1
Marker rs1250550 Chr 10 Position 81060317 Strand P-Value 7.98e-04		N/A	0.5	chr10: 80971456..81071087	ZMIZ1		LD Region Feature File LD File
		0.4	N/A	chr10: 81032885..81069413	ZMIZ1
		0.8	N/A	chr10: 81059335..81067040	ZMIZ1
		1	N/A

Publications: 2

• Common variants at five new loci associated with early-onset inflammatory bowel disease.
  Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, Western Regional Alliance for Pediatric IBD, Silber G, Wrobel I, Quiros A, International IBD Genetics Consortium, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Belgian-French IBD Consortium, Wellcome Trust Case Control Consortium, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwillam R, Tremelling M, Delukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ, Heyman MB, Ferry GD, Kirschner B, Lee J, Essers J, Grand R, Stephens M, Levine A, Piccoli D, Van Limbergen J, Cucchiara S, Monos DS, Guthery SL, Denson L, Wilson DC, Grant SF, Daly M, Silverberg MS, Satsangi J, Hakonarson H
  Nat Genet. 2009
  PubMed ID: 19915574
   
  
• 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

Comment on this Page
Privacy Statement  |   Copyright, Warranty & Disclaimer  |   Contact Us
Copyright © 2001-2011, T1DBase | Version 4.8 | PMID:20937630
Printed on Fri February 10, 2012