7p15.2

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	rs7804356
Karyotype Band Location	7p15.2
Chromosomal Location (NCBI36)	Chr7:26624487-27171807
Region Size	0.55 Mb
Genes in Region (12)	C7orf71, HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, LOC100133311, LOC285943, SKAP2

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
rs17154402	dbSNP_130	26731610	+	S/T	SKAP2	8935	253
rs1129771	dbSNP_130	26732121	-	A/S	SKAP2	8935	202
rs71698762	dbSNP_130	26857422	+		SKAP2	8935	23
rs41311760	dbSNP_130	27100670	+	E/X	HOXA1	3198	308
rs41303378	dbSNP_130	27100697	+	T/S	HOXA1	3198	299
rs41311763	dbSNP_130	27100795	+	L/P	HOXA1	3198	266
rs17500494	dbSNP_130	27101491	+	E/A	HOXA1	3198	189
rs45571645	dbSNP_130	27101621	+	H/N	HOXA1	3198	146
rs10951154	dbSNP_130	27101839	+	H/R	HOXA1	3198	73
rs41303375	dbSNP_130	27107121	+	V/L	HOXA2	3199	294
rs941002	dbSNP_130	27107415	-	M/L	HOXA2	3199	196
rs71554077	dbSNP_130	27114132	+	T/H	HOXA3	3200	420
rs35614593	dbSNP_130	27116644	+	R/R	HOXA3	3200	47
rs17500757	dbSNP_130	27135383	+	P/S	HOXA4	3201	317
rs66569027	dbSNP_130	27135407	+	P/P	HOXA4	3201	308
rs41305924	dbSNP_130	27135524	+	W/R	HOXA4	3201	270
rs6976847	dbSNP_130	27135581	+	T/P	HOXA4	3201	251
rs13246088	dbSNP_130	27136346	+	L/F	HOXA4	3201	178
rs10251056	dbSNP_130	27136459	+	L/P	HOXA4	3201	140
rs6944345	dbSNP_130	27136670	+	T/P	HOXA4	3201	70
rs6962314	dbSNP_130	27136684	+	G/D	HOXA4	3201	65
rs61236211	dbSNP_130	27145557	+	G/R	LOC100133311	100133311	45
rs17500835	dbSNP_130	27145564	+	Q/P	LOC100133311	100133311	47
rs35281041	dbSNP_130	27149353	+	G/G	HOXA5	3202	133
rs62454418	dbSNP_130	27153554	+	D/Y	HOXA6	3203	114
rs35510017	dbSNP_130	27162382	+	K/R	HOXA7	3204	103
rs2301721	dbSNP_130	27162638	+	A/T	HOXA7	3204	18
rs35991882	dbSNP_130	27169898	-	K/T	HOXA9	3205	223
rs11978680	dbSNP_130	27171390	+	H/P	HOXA9	3205	71

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	rs7804356
Chr	7
Position	26858190
Strand	+
P-Value	3.27e-08

N/A

0.5

chr7: 26661451..27316480

LOC100129463 LOC100133311 EVX1 HOXA11AS LOC285943 HOXA1 HOXA2 HOXA3 HOXA4 HOXA5 HOXA6 HOXA7 HOXA9 HOXA10 HOXA11 HOXA13 LOC392008 SKAP2

LD Region Feature File

LD File

0.4

N/A

chr7: 26661451..27092849

SKAP2

0.8

N/A

chr7: 26661451..26873648

SKAP2

N/A

chr7: 26785990..26868265

SKAP2

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 1