6q23.3

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	rs6920220,rs10499194
Karyotype Band Location	6q23.3
Chromosomal Location (NCBI36)	Chr6:137915383-138379949
Region Size	0.46 Mb
Orthologous Regions	Mouse: Human 6q23.3 Ortholgous Region Rat: Human 6q23.3 Ortholgous Region
Genes in Region (2)	LOC100130476, TNFAIP3

Query T1DMart for overlapping human marker information from T1DMart Top Help

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	rs6920220
Chr	6
Position	138048197
Strand	+
P-Value	7.99e-04

N/A

0.5

chr6: 138001747..138064935

LD Region Feature File

LD File

0.4

N/A

chr6: 138014761..138048197

0.8

N/A

chr6: 138014761..138048197

N/A

chr6: 138014761..138048197

Marker	rs10499194
Chr	6
Position	138044330
Strand	+
P-Value	0.000

N/A

0.5

chr6: 138001148..138064935

LD Region Feature File

LD File

0.4

N/A

chr6: 138002706..138055358

0.8

N/A

chr6: 138002706..138052844

N/A

chr6: 138002706..138044330

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2