6q25.3

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	rs1738074
Karyotype Band Location	6q25.3
Chromosomal Location (NCBI36)	Chr6:159237500-159446677
Region Size	0.21 Mb
Genes in Region (4)	C6orf99, LOC100130967, RSPH3, TAGAP

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
rs3756987	dbSNP_130	159318688	-	G/D	RSPH3	83861	518
rs12204826	dbSNP_130	159318791	+	E/K	RSPH3	83861	484
rs768994	dbSNP_130	159319336	-	M/T	RSPH3	83861	439
rs10455840	dbSNP_130	159321886	+	R/Q	RSPH3	83861	398
rs41267751	dbSNP_130	159327404	+	R/Q	RSPH3	83861	223
rs34582178	dbSNP_130	159327434	-	R/Q	RSPH3	83861	213
rs41267753	dbSNP_130	159327435	+	R/W	RSPH3	83861	213
rs16889320	dbSNP_130	159334887	+	N/S	RSPH3	83861	201
rs61750776	dbSNP_130	159340533	+	P/R	RSPH3	83861	155
rs61750777	dbSNP_130	159340536	+	A/D	RSPH3	83861	154
rs41267755	dbSNP_130	159340723	+	P/S	RSPH3	83861	92
rs35263580	dbSNP_130	159378006	-	G/D	TAGAP	117289	346
rs61753626	dbSNP_130	159378012	+	S/T	TAGAP	117289	344
rs34649601	dbSNP_130	159380278	+	V/G	TAGAP	117289	213
rs41267765	dbSNP_130	159382412	+	E/K	TAGAP	117289	147
rs34834201	dbSNP_130	159384657	+	H/H	TAGAP	117289	33

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	rs1738074
Chr	6
Position	159385965
Strand	-
P-Value	6.02e-03

N/A

0.5

chr6: 159258007..159435297

TAGAP RSPH3

LD Region Feature File

LD File

0.4

N/A

chr6: 159260013..159405199

TAGAP RSPH3

0.8

N/A

chr6: 159385965..159389562

TAGAP

N/A

chr6: 159385965..159389562

TAGAP

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2