Variant report

Variant	rs533324
Chromosome Location	chr9:15213032-15213033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10961916	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1215128	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs473384	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552768	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs560767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs533324	TTC39B	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15163000-15233000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:15171000-15228600	Weak transcription	Stomach Mucosa	stomach
3	chr9:15179400-15221000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:15182200-15229200	Weak transcription	Gastric	stomach
5	chr9:15185600-15225800	Weak transcription	Pancreas	Pancrea
6	chr9:15192200-15229200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:15192400-15223200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:15193400-15249600	Weak transcription	Colonic Mucosa	Colon
9	chr9:15196000-15214200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:15197200-15223000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:15197200-15225000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:15202000-15217400	Weak transcription	Esophagus	oesophagus
13	chr9:15206000-15214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:15206000-15220800	Weak transcription	Lung	lung
15	chr9:15206000-15222800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:15206000-15223000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:15206000-15229200	Weak transcription	Ovary	ovary
18	chr9:15206400-15221000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:15207600-15225600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr9:15207800-15214400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:15207800-15223000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:15209600-15223000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:15210000-15231800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:15210600-15226200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:15211000-15222400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:15211200-15216000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:15211200-15222000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:15211400-15213400	Enhancers	HepG2	liver
29	chr9:15211400-15213800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:15211400-15216200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:15211400-15216400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:15211400-15222600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:15211400-15222600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:15211400-15229000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:15211400-15229000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr9:15211600-15214400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:15211600-15215200	Enhancers	Fetal Intestine Large	intestine
38	chr9:15211600-15216600	Weak transcription	Right Ventricle	heart
39	chr9:15211600-15223200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:15211600-15224600	Weak transcription	NHEK	skin
41	chr9:15211600-15226600	Weak transcription	HMEC	breast
42	chr9:15211800-15220800	Weak transcription	Adipose Nuclei	Adipose
43	chr9:15212000-15213200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:15212000-15214200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:15212000-15218800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:15212000-15219400	Weak transcription	Fetal Kidney	kidney
47	chr9:15212000-15220200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:15212000-15222400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:15212000-15222400	Weak transcription	Fetal Stomach	stomach
50	chr9:15212000-15222800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links