Variant report

Variant	rs2494386
Chromosome Location	chr9:94090486-94090487
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94083958..94089590-chr9:94090031..94094657,6	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1082054	0.80[EUR][1000 genomes]
rs1105486	0.85[JPT][hapmap]
rs12551859	0.81[CHD][hapmap]
rs12552364	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs1397574	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972090	0.84[CEU][hapmap]
rs2457714	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2482338	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2482340	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298718	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036028	0.82[MEX][hapmap]
rs773506	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs773509	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs773513	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs773515	0.81[EUR][1000 genomes]
rs9299391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv893570	chr9:93973938-94148084	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS 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 target site	9 gene(s)	inside rSNPs	diseases
2	nsv482877	chr9:93979351-94157734	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv893571	chr9:94072113-94202927	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2494386	FAM120A	cis	parietal	SCAN
rs2494386	SPIN3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94033800-94096400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:94052000-94119200	Weak transcription	Small Intestine	intestine
3	chr9:94053400-94103800	Weak transcription	HSMMtube	muscle
4	chr9:94058800-94091800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:94059600-94103400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:94059800-94101400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:94065400-94101400	Weak transcription	K562	blood
8	chr9:94065600-94091400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:94065600-94102000	Weak transcription	Hela-S3	cervix
10	chr9:94066400-94103400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:94066800-94104000	Weak transcription	HSMM	muscle
12	chr9:94067800-94094400	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:94069200-94096200	Weak transcription	Psoas Muscle	Psoas
14	chr9:94072800-94101200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:94074600-94103800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:94075800-94104200	Weak transcription	NHEK	skin
17	chr9:94080800-94101000	Weak transcription	Fetal Kidney	kidney
18	chr9:94080800-94102400	Weak transcription	Colonic Mucosa	Colon
19	chr9:94081000-94101000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:94082200-94094800	Weak transcription	Fetal Heart	heart
21	chr9:94082200-94095000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:94082200-94104000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr9:94084400-94104200	Weak transcription	NHDF-Ad	bronchial
24	chr9:94087800-94103600	Weak transcription	A549	lung
25	chr9:94088000-94090600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:94088000-94090800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:94088000-94091000	Strong transcription	Primary T cells from cord blood	blood
28	chr9:94088200-94092600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:94088600-94099800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:94089200-94090600	Strong transcription	HepG2	liver
31	chr9:94089200-94090800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr9:94089200-94090800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr9:94089200-94090800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr9:94089200-94091000	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr9:94089200-94091800	Strong transcription	Fetal Lung	lung
36	chr9:94089200-94093600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:94089200-94093800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:94089200-94095000	Weak transcription	Stomach Mucosa	stomach
39	chr9:94089400-94090600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr9:94089400-94090600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:94089400-94090600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:94089400-94090600	ZNF genes & repeats	Fetal Thymus	thymus
43	chr9:94089400-94090600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr9:94089400-94090600	ZNF genes & repeats	Dnd41	blood
45	chr9:94089400-94090800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:94089400-94090800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:94089400-94090800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr9:94089400-94090800	ZNF genes & repeats	Liver	Liver
49	chr9:94089400-94090800	ZNF genes & repeats	Brain Substantia Nigra	brain
50	chr9:94089400-94090800	ZNF genes & repeats	Fetal Intestine Small	intestine

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