Variant report

Variant	rs10961923
Chromosome Location	chr9:15229797-15229798
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15180910..15183220-chr9:15227592..15229851,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10217576	0.87[EUR][1000 genomes]
rs10961915	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs10961918	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10961924	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1215123	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1215124	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12343442	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs12377170	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2146864	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2488958	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480635	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs513270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs591647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs654202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68152174	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7033069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv521191	chr9:15218947-15246652	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2761504	chr9:15227680-15237785	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10961923	PLIN2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15163000-15233000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:15193400-15249600	Weak transcription	Colonic Mucosa	Colon
3	chr9:15210000-15231800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:15221200-15242200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:15221800-15231200	Weak transcription	Fetal Intestine Small	intestine
6	chr9:15221800-15233000	Weak transcription	Osteobl	bone
7	chr9:15221800-15242800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:15222600-15230200	Weak transcription	Left Ventricle	heart
9	chr9:15223400-15258200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:15223600-15232000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:15223600-15232600	Weak transcription	Fetal Stomach	stomach
12	chr9:15223800-15235200	Weak transcription	Fetal Lung	lung
13	chr9:15224400-15242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:15224600-15231200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:15224600-15231800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:15224600-15232200	Weak transcription	Fetal Intestine Large	intestine
17	chr9:15224600-15235200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:15224600-15243600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:15224600-15244400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:15224800-15232800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:15224800-15235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:15225000-15231800	Weak transcription	Primary T cells from cord blood	blood
23	chr9:15225400-15231800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:15228400-15230600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:15228800-15230000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:15229200-15229800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr9:15229200-15229800	Enhancers	Aorta	Aorta
28	chr9:15229200-15229800	Enhancers	Duodenum Mucosa	Duodenum
29	chr9:15229200-15229800	Enhancers	Fetal Kidney	kidney
30	chr9:15229200-15229800	Enhancers	Gastric	stomach
31	chr9:15229200-15229800	Enhancers	Ovary	ovary
32	chr9:15229200-15229800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:15229200-15229800	Enhancers	Small Intestine	intestine
34	chr9:15229200-15230000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:15229200-15230200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:15229600-15229800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links