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1q31.2

General Information: Available

Organism	Human
Points of Interest	rs2816316
Karyotype Band Location	1q31.2
Chromosomal Location (GRCh37)	Chr1:192461456-192549912
Region Size	0.09 Mb
Orthologous Regions	Mouse: Human 1q31.2 Orthologous Region Rat: Human 1q31.2 Orthologous Region
Genes in Region (1)	RGS1

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
rs140779829	dbSNP_134	192544927	+	R/L	RGS1	5996	2
rs146894683	dbSNP_134	192544998	+	L/M	RGS1	5996	26
rs11370469	dbSNP_134	192545048	+	R/S	RGS1	5996	42
rs144803737	dbSNP_134	192545450	+	I/N	RGS1	5996	58
rs113607203	dbSNP_134	192545936	+	Q/R	RGS1	5996	84
rs113660313	dbSNP_134	192547447	+	S/T	RGS1	5996	126
rs141227492	dbSNP_134	192548283	+	R/H	RGS1	5996	154
rs150745219	dbSNP_134	192548289	+	R/Q	RGS1	5996	156
rs34270164	dbSNP_134	192548346	+		RGS1	5996	175
rs139987236	dbSNP_134	192548388	+	R/T	RGS1	5996	189

(Human) GRCh37 - chr1:192461456..192549912 (88.46 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 rs2816316 Chr 1 Position 192536813 Strand P-Value 3.13e-05		N/A	0.5	chr1: 192477882..192597872	RGS1		LD Region Feature File LD File
		0.4	N/A	chr1: 192489724..192545099	RGS1
		0.8	N/A	chr1: 192519865..192545099	RGS1
		1	N/A	chr1: 192535553..192541472

Publications: 4

• IL12A, MPHOSPH9/CDK2AP1 and RGS1 are novel multiple sclerosis susceptibility loci.
  International Multiple Sclerosis Genetics Conssortium (IMSGC)
  Genes Immun. 2010
  PubMed ID: 20555355
   
  
• Multiple common variants for celiac disease influencing immune gene expression.
  Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adány R, Aromaa A, Bardella MT, van den Berg LH, Bockett NA, de la Concha EG, Dema B, Fehrmann RS, Fernández-Arquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwen RH, Hunt SE, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Mäki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Núñez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters VM, Urcelay E, Cukrowska B, Greco L, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, van Heel DA
  Nat Genet. 2010
  PubMed ID: 20190752
   
  
• 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
   
  

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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