Variant report

Variant	rs906830
Chromosome Location	chr11:119549825-119549826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:119545626..119547284-chr11:119549130..119552080,2	K562	blood:
2	chr11:119549707..119551883-chr11:119554689..119557483,2	K562	blood:
3	chr11:119548530..119557660-chr11:119596856..119602607,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction
ENSG00000254854	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10790330	0.82[TSI][hapmap]
rs10790331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10790332	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10790335	0.82[AMR][1000 genomes]
rs10892433	0.88[CEU][hapmap]
rs10892434	0.88[CEU][hapmap]
rs1110166	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217414	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs11217415	0.88[CEU][hapmap]
rs11825206	0.81[AMR][1000 genomes]
rs1467051	0.88[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1533051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006949	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2015078	0.82[AMR][1000 genomes]
rs2292293	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3902806	0.82[AMR][1000 genomes]
rs3935406	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs4459318	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs4623916	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4936492	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4936493	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4936494	0.81[AMR][1000 genomes]
rs4936495	0.81[AMR][1000 genomes]
rs4938705	0.84[EUR][1000 genomes]
rs4938706	0.84[EUR][1000 genomes]
rs4938708	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs4938709	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938710	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938711	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6589769	0.88[CEU][hapmap]
rs7110874	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7111290	0.84[CEU][hapmap]
rs7122134	0.92[CEU][hapmap]
rs715849	0.88[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs7924573	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7932832	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs7933848	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7945395	0.88[CEU][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs7945424	0.88[CEU][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs7950059	0.88[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs885429	0.81[AMR][1000 genomes]
rs885430	0.88[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv984471	chr11:119505802-119568473	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs906830	RPS25	cis	parietal	SCAN
rs906830	UPK2	cis	cerebellum	SCAN
rs906830	BACE1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119535200-119552600	Weak transcription	HepG2	liver
2	chr11:119542200-119551400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:119543000-119551400	Weak transcription	Fetal Heart	heart
4	chr11:119543000-119551400	Weak transcription	Right Atrium	heart
5	chr11:119543200-119551600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:119543400-119551000	Weak transcription	Stomach Mucosa	stomach
7	chr11:119543600-119551400	Weak transcription	Fetal Brain Male	brain
8	chr11:119545000-119551200	Weak transcription	Aorta	Aorta
9	chr11:119545800-119551000	Weak transcription	Primary B cells from cord blood	blood
10	chr11:119545800-119551400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:119545800-119551800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:119547800-119551200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:119547800-119554800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:119547800-119555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:119548000-119551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:119548000-119555000	Weak transcription	Osteobl	bone
17	chr11:119548200-119550000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr11:119548200-119550400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:119548200-119554600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr11:119548400-119550400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr11:119548600-119550000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr11:119548600-119550600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
23	chr11:119548800-119550200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:119548800-119551200	Weak transcription	Brain Anterior Caudate	brain
25	chr11:119548800-119551200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:119548800-119551400	Weak transcription	Lung	lung
27	chr11:119548800-119551400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:119548800-119554600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:119549000-119550000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:119549000-119550000	Weak transcription	Placenta	Placenta
31	chr11:119549000-119550800	Weak transcription	Fetal Lung	lung
32	chr11:119549000-119550800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:119549000-119550800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:119549000-119551400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:119549000-119551400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:119549000-119551600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:119549000-119554600	Weak transcription	A549	lung
38	chr11:119549000-119554800	Weak transcription	NHLF	lung
39	chr11:119549000-119555400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:119549200-119550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:119549200-119550400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:119549200-119551200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:119549200-119551200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:119549200-119551400	Weak transcription	Adipose Nuclei	Adipose
45	chr11:119549200-119551600	Weak transcription	Liver	Liver
46	chr11:119549200-119554800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:119549400-119550800	Weak transcription	Fetal Kidney	kidney
48	chr11:119549400-119550800	Weak transcription	Fetal Stomach	stomach
49	chr11:119549400-119550800	Weak transcription	Spleen	Spleen
50	chr11:119549400-119550800	Strong transcription	HMEC	breast

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