Variant report

Variant	rs9556466
Chromosome Location	chr13:95900071-95900072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95893721..95895916-chr13:95898093..95900583,2	K562	blood:
2	chr13:95898930..95900924-chr13:95902230..95904877,2	K562	blood:
3	chr13:95898278..95901890-chr13:95902438..95906069,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10508018	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874657	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892715	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892716	0.87[CEU][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4148436	0.88[CEU][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4148437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148438	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148446	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148447	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773858	0.85[ASN][1000 genomes]
rs4773859	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561814	0.88[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832689	chr13:95759073-95921308	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9556466	OSBPL5	trans	parietal	SCAN
rs9556466	ABCC4	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95859000-95901000	Weak transcription	Aorta	Aorta
2	chr13:95859200-95901400	Weak transcription	Primary T cells from cord blood	blood
3	chr13:95859200-95902200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:95861600-95906200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:95879200-95907400	Weak transcription	Small Intestine	intestine
6	chr13:95879200-95914000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:95880600-95922600	Weak transcription	Psoas Muscle	Psoas
8	chr13:95880800-95902400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:95881600-95904000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:95884200-95901200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:95884800-95906400	Weak transcription	Hela-S3	cervix
12	chr13:95887000-95918800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:95888000-95909000	Weak transcription	Fetal Stomach	stomach
14	chr13:95888400-95906800	Weak transcription	Gastric	stomach
15	chr13:95890000-95907600	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:95890800-95906400	Weak transcription	Osteobl	bone
17	chr13:95891800-95908000	Weak transcription	Esophagus	oesophagus
18	chr13:95892600-95905400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr13:95893000-95905400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:95896000-95902000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:95896200-95923400	Weak transcription	Ovary	ovary
22	chr13:95897000-95900400	Genic enhancers	GM12878-XiMat	blood
23	chr13:95897000-95927400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr13:95897400-95900600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr13:95897600-95901200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:95897800-95900600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:95898200-95900200	Genic enhancers	K562	blood
28	chr13:95898800-95906200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:95898800-95906600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:95898800-95908000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr13:95898800-95919600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:95899000-95901000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:95899000-95901600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:95899000-95903200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr13:95899000-95906000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:95899000-95910000	Weak transcription	Fetal Intestine Large	intestine
37	chr13:95899000-95919600	Weak transcription	Fetal Lung	lung
38	chr13:95899400-95900200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:95899400-95900400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:95899400-95900600	Enhancers	HUVEC	blood vessel
41	chr13:95899400-95901400	Weak transcription	HepG2	liver
42	chr13:95899400-95907000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr13:95899600-95901200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr13:95899600-95902400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr13:95899600-95903200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr13:95899600-95903600	Weak transcription	HSMMtube	muscle
47	chr13:95899800-95900200	Weak transcription	Pancreas	Pancrea
48	chr13:95899800-95906000	Weak transcription	NHEK	skin
49	chr13:95899800-95919600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr13:95900000-95900600	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links