Variant report

Variant	rs2292293
Chromosome Location	chr11:119548698-119548699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr11:119548593-119548876	K562	blood:	n/a	n/a
2	KAP1	chr11:119548404-119548981	HEK293	kidney:	n/a	n/a
3	CBX3	chr11:119548611-119548864	K562	blood:	n/a	n/a
4	SETDB1	chr11:119548500-119548959	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119548530..119557660-chr11:119596856..119602607,12	MCF-7	breast:

Variant related genes	Relation type
PVRL1	TF binding region
ENSG00000254854	Chromatin interaction
ENSG00000110400	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	0.80[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10790331	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10790332	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs10790335	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10892433	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10892434	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1110166	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs11217414	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217415	0.88[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs11825206	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1467051	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533051	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2015078	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3902806	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3935405	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935406	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4459318	0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4623916	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4936492	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4936493	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4936494	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4936495	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4938704	0.83[EUR][1000 genomes]
rs4938708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938709	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938710	0.84[EUR][1000 genomes]
rs4938711	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6589769	0.88[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs7110874	0.88[CEU][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7111290	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs7118532	0.86[EUR][1000 genomes]
rs7122134	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs715849	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7924573	0.88[CEU][hapmap]
rs7932832	0.91[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs7933848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7945395	0.88[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7945424	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950059	0.88[CEU][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs885429	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs885430	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs906830	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]

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
rs2292293	BACE1	cis	cerebellum	SCAN
rs2292293	UPK2	cis	cerebellum	SCAN
rs2292293	RPS25	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119535200-119552600	Weak transcription	HepG2	liver
2	chr11:119541800-119548800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:119541800-119549000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:119542200-119551400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:119543000-119548800	Weak transcription	Ovary	ovary
6	chr11:119543000-119551400	Weak transcription	Fetal Heart	heart
7	chr11:119543000-119551400	Weak transcription	Right Atrium	heart
8	chr11:119543200-119551600	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:119543400-119551000	Weak transcription	Stomach Mucosa	stomach
10	chr11:119543600-119549400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:119543600-119551400	Weak transcription	Fetal Brain Male	brain
12	chr11:119543800-119549400	Strong transcription	Gastric	stomach
13	chr11:119544000-119549200	Strong transcription	Brain Cingulate Gyrus	brain
14	chr11:119544000-119549400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:119544200-119549400	Strong transcription	Right Ventricle	heart
16	chr11:119544400-119549600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:119544600-119549400	Strong transcription	Brain Angular Gyrus	brain
18	chr11:119544800-119549000	Strong transcription	Placenta	Placenta
19	chr11:119545000-119549400	Strong transcription	Brain Substantia Nigra	brain
20	chr11:119545000-119551200	Weak transcription	Aorta	Aorta
21	chr11:119545200-119549200	Strong transcription	Adipose Nuclei	Adipose
22	chr11:119545600-119549400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:119545800-119549600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr11:119545800-119551000	Weak transcription	Primary B cells from cord blood	blood
25	chr11:119545800-119551400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:119545800-119551800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:119546000-119549600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:119546800-119549600	Strong transcription	Pancreas	Pancrea
29	chr11:119547000-119548800	Strong transcription	Brain Anterior Caudate	brain
30	chr11:119547000-119549400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr11:119547200-119549200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:119547200-119549400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:119547200-119549600	Strong transcription	Colonic Mucosa	Colon
34	chr11:119547400-119549000	Strong transcription	Fetal Lung	lung
35	chr11:119547400-119549000	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:119547600-119549000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr11:119547600-119549200	Strong transcription	Liver	Liver
38	chr11:119547800-119549000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:119547800-119549400	Strong transcription	Fetal Kidney	kidney
40	chr11:119547800-119549600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:119547800-119549600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr11:119547800-119549600	Strong transcription	Brain Hippocampus Middle	brain
43	chr11:119547800-119549800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:119547800-119551200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:119547800-119554800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:119547800-119555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr11:119548000-119549000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr11:119548000-119549000	ZNF genes & repeats	A549	lung
49	chr11:119548000-119549200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:119548000-119549400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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