Variant report

Variant	rs10116369
Chromosome Location	chr9:96946670-96946671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96943921..96946821-chr9:96947982..96950934,2	MCF-7	breast:
2	chr9:96945873..96948322-chr9:96948466..96951194,2	MCF-7	breast:
3	chr9:96927843..96930054-chr9:96943540..96946724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10081759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10116630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123498	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10821312	0.81[MKK][hapmap]
rs12335636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12338528	1.00[EUR][1000 genomes]
rs12341848	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12345658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28493183	1.00[EUR][1000 genomes]
rs4744321	0.81[MKK][hapmap]
rs6479524	1.00[MEX][hapmap]
rs6479531	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024817	1.00[MEX][hapmap]
rs7030026	1.00[CEU][hapmap]
rs7036037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7038156	0.83[MKK][hapmap]
rs7039624	1.00[MEX][hapmap]
rs7046683	1.00[EUR][1000 genomes]
rs7851345	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7852992	1.00[MEX][hapmap]
rs7866977	1.00[MEX][hapmap]

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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10116369	POMZP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:96937200-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:96938200-96949000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:96938400-96947400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:96939400-96948400	Weak transcription	Brain Germinal Matrix	brain
7	chr9:96939600-96947200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:96939600-96947600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:96939600-96948000	Weak transcription	Fetal Brain Female	brain
10	chr9:96939600-96949400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:96939600-96950600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:96939800-96946800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:96939800-96946800	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr9:96939800-96947200	Weak transcription	Esophagus	oesophagus
15	chr9:96939800-96947400	Strong transcription	Osteobl	bone
16	chr9:96939800-96948400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:96939800-96960800	Weak transcription	NHDF-Ad	bronchial
18	chr9:96940000-96946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:96940000-96949200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:96940400-96947800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:96940400-96955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:96940600-96947200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:96940800-96950400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:96941200-96946800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:96941400-96959400	Weak transcription	Spleen	Spleen
26	chr9:96941600-96947600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr9:96941800-96947200	Weak transcription	Dnd41	blood
28	chr9:96941800-96947200	Strong transcription	HSMM	muscle
29	chr9:96941800-96947600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:96942000-96947200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:96942200-96950000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr9:96942200-96950600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:96942400-96947400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:96942400-96947600	Weak transcription	HepG2	liver
35	chr9:96942400-96948400	Weak transcription	Fetal Lung	lung
36	chr9:96942400-96949400	Weak transcription	A549	lung
37	chr9:96942400-96949800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:96942400-96953200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:96942400-96957600	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:96942400-96964000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:96943000-96948600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr9:96943000-96952200	Weak transcription	HMEC	breast
43	chr9:96943400-96949400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:96943800-96947200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:96944200-96947600	Weak transcription	HUVEC	blood vessel
46	chr9:96944200-96949200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr9:96944400-96946800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:96944400-96959400	Weak transcription	Psoas Muscle	Psoas
49	chr9:96944800-96946800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:96944800-96946800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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