2q11.2

Sections: General Information - Query T1DMart for overlapping human marker information - Region Overview - Genes in LD Region - Signal Clouds - Publications

General Information Top Help

General Information: Available

Organism	Human
Points of Interest	rs9653442, rs1160542
Karyotype Band Location	2q11.2
Chromosomal Location (NCBI36)	Chr2:99883121-100415547
Region Size	0.53 Mb
Genes in Region (4)	AFF3, CHST10, LOC150577, LONRF2

Query T1DMart for overlapping human marker information from T1DMart Top Help

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs72819180	dbSNP_130	100112150	+	R/Q	LOC648405	648405	101
rs17023563	dbSNP_130	100125462	+	R/Q	LOC648405	648405	56
rs17023571	dbSNP_130	100126296	+	P/S	LOC648405	648405	25
rs11123814	dbSNP_130	100133514	+	P/L	LOC648405	648405	15
rs4851287	dbSNP_130	100282204	+	L/P	LONRF2	164832	426
rs74177694	dbSNP_130	100304658	+	D/E	LONRF2	164832	110
rs74177696	dbSNP_130	100304913	+	Q/H	LONRF2	164832	25
rs3748932	dbSNP_130	100376438	-	D/N	CHST10	9486	258
rs12476171	dbSNP_130	100376537	+	Y/N	CHST10	9486	225
rs57227647	dbSNP_130	100378500	+	S/P	CHST10	9486	146
rs35177621	dbSNP_130	100389512	-	V/L	CHST10	9486	20

Non-Synonymous SNPs in region dbSNP_130:

Region Overview Top Help

GBrowse Image: Available

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
D' (black) and r-squared (red) with genotyped SNP	Calculated using the HapMap CEU Founders population. D' data has been limited to those values where LOD score > 3
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.
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.

Genes in LD Region Top Help

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	rs9653442
Chr	2
Position	100191799
Strand	+
P-Value	7.04e-07

N/A

0.5

chr2: 99943239..100251325

LOC150577 AFF3

LD Region Feature File

LD File

0.4

N/A

chr2: 99943239..100237294

LOC150577 AFF3

0.8

N/A

chr2: 100126604..100203999

LOC150577

N/A

chr2: 100172946..100198587

LOC150577

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2