Variant report

Variant	rs2805831
Chromosome Location	chr9:100466636-100466637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100465773..100467417-chr9:100473375..100476124,2	MCF-7	breast:
2	chr9:100462976..100466831-chr9:100467484..100471759,4	K562	blood:
3	chr9:100466290..100468242-chr9:100471348..100474178,4	K562	blood:
4	chr9:100466474..100468807-chr9:100682892..100684747,2	MCF-7	breast:
5	chr9:100456256..100459810-chr9:100463870..100468057,7	MCF-7	breast:
6	chr9:100465031..100468402-chr9:100745252..100748120,3	MCF-7	breast:
7	chr9:100464367..100467056-chr9:100650913..100653289,2	K562	blood:
8	chr9:100458037..100462084-chr9:100463856..100467658,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000214417	Chromatin interaction
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10982745	0.85[CHD][hapmap]
rs16922598	1.00[JPT][hapmap]
rs1962592	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs2773343	1.00[CEU][hapmap];0.85[CHD][hapmap];0.90[TSI][hapmap]
rs2773344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2773349	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2773350	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.86[CEU][hapmap]
rs2805785	1.00[CEU][hapmap]
rs2805834	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2805835	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2808669	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808676	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808682	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2805831	C9orf89	cis	cerebellum	SCAN
rs2805831	TMOD1	cis	cerebellum	SCAN
rs2805831	ZNF367	cis	parietal	SCAN
rs2805831	TBC1D2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100460400-100467000	Weak transcription	Esophagus	oesophagus
2	chr9:100460400-100467800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:100461400-100467800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:100461600-100467200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr9:100462400-100472800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:100465000-100466800	Enhancers	Fetal Intestine Small	intestine
7	chr9:100465200-100467000	Enhancers	GM12878-XiMat	blood
8	chr9:100465200-100467200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr9:100465400-100466800	Flanking Active TSS	A549	lung
10	chr9:100465400-100467200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:100465400-100467200	Enhancers	Fetal Intestine Large	intestine
12	chr9:100465400-100469000	Enhancers	HMEC	breast
13	chr9:100465600-100466800	Flanking Active TSS	Hela-S3	cervix
14	chr9:100465600-100466800	Enhancers	NHDF-Ad	bronchial
15	chr9:100465600-100467000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:100465600-100467200	Enhancers	Pancreas	Pancrea
17	chr9:100465600-100468600	Enhancers	HUVEC	blood vessel
18	chr9:100465600-100468800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:100465600-100468800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:100465800-100466800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:100465800-100466800	Enhancers	NHLF	lung
22	chr9:100465800-100467000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:100465800-100467000	Enhancers	Stomach Mucosa	stomach
24	chr9:100465800-100467000	Flanking Active TSS	NH-A	brain
25	chr9:100465800-100467000	Flanking Active TSS	NHEK	skin
26	chr9:100465800-100467400	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:100466000-100466800	Enhancers	K562	blood
28	chr9:100466000-100467200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr9:100466000-100467200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:100466000-100467400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:100466000-100467800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:100466200-100466800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:100466200-100466800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:100466200-100466800	Enhancers	Colon Smooth Muscle	Colon
35	chr9:100466200-100466800	Enhancers	Fetal Heart	heart
36	chr9:100466200-100467200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:100466400-100466800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr9:100466400-100468000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:100466400-100468400	Enhancers	Osteobl	bone
40	chr9:100466600-100466800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:100466600-100466800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr9:100466600-100467000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:100466600-100467200	Enhancers	HSMM	muscle
44	chr9:100466600-100467200	Enhancers	HSMMtube	muscle
45	chr9:100466600-100467600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:100466600-100468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:100466600-100468000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr9:100466600-100468000	Enhancers	HepG2	liver
49	chr9:100466600-100468600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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