Variant report

Variant	rs6479445
Chromosome Location	chr9:95766471-95766472
allele	A/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95719185..95719752-chr9:95765738..95766670,2	MCF-7	breast:
2	chr9:95718780..95720145-chr9:95765787..95766663,4	MCF-7	breast:
3	chr9:95613255..95613805-chr9:95765967..95766514,2	MCF-7	breast:
4	chr9:95739140..95740868-chr9:95765712..95767872,2	MCF-7	breast:
5	chr9:95765944..95766668-chr9:95869207..95869714,2	MCF-7	breast:
6	chr9:95764914..95766688-chr9:95768707..95770560,2	MCF-7	breast:
7	chr9:95761527..95763076-chr9:95764735..95767676,2	K562	blood:
8	chr9:95764926..95767414-chr9:95782606..95784200,2	MCF-7	breast:
9	chr9:95766021..95766601-chr9:95883577..95884469,2	MCF-7	breast:
10	chr9:95764397..95768278-chr9:95771729..95773311,3	K562	blood:
11	chr9:95765905..95766638-chr9:95918506..95919335,2	MCF-7	breast:
12	chr9:95765841..95768225-chr9:95860926..95862448,2	MCF-7	breast:
13	chr9:95765978..95766635-chr9:95868909..95869887,2	MCF-7	breast:
14	chr9:95766003..95766670-chr9:96067179..96067717,2	MCF-7	breast:
15	chr9:95766059..95768538-chr9:95781716..95783313,2	MCF-7	breast:

No data

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10739940	0.95[JPT][hapmap]
rs10761189	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821046	1.00[YRI][hapmap]
rs10992564	0.95[JPT][hapmap]
rs12685670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13300085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3936098	1.00[YRI][hapmap]
rs3936099	1.00[YRI][hapmap]
rs4237217	1.00[YRI][hapmap]
rs4744163	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023321	1.00[YRI][hapmap]
rs7026624	1.00[YRI][hapmap]
rs7030160	0.95[JPT][hapmap]
rs7869421	0.95[JPT][hapmap]
rs9942903	0.95[JPT][hapmap]
rs9942965	0.95[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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6479445	C9orf3	cis	cerebellum	SCAN
rs6479445	ZNF484	cis	parietal	SCAN
rs6479445	SUSD3	cis	multi-tissue	Pritchard
rs6479445	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95761600-95785800	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:95761600-95785800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:95762000-95767800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr9:95762000-95786400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr9:95762200-95767400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr9:95762600-95790200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:95763000-95767200	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr9:95763000-95773400	Strong transcription	Primary B cells from cord blood	blood
9	chr9:95763600-95787200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:95763800-95766600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:95763800-95766800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:95763800-95767400	Genic enhancers	Primary T cells from cord blood	blood
13	chr9:95763800-95789400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:95764000-95767000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:95764000-95773000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:95764000-95777000	Strong transcription	Dnd41	blood
17	chr9:95764400-95768200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr9:95764400-95774000	Strong transcription	Thymus	Thymus
19	chr9:95764600-95766800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:95764600-95767200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr9:95765000-95767200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:95765200-95767000	Genic enhancers	Fetal Thymus	thymus
23	chr9:95765800-95766600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:95765800-95766600	Active TSS	A549	lung
25	chr9:95765800-95767200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr9:95765800-95768400	Strong transcription	Brain Germinal Matrix	brain
27	chr9:95766000-95766600	Enhancers	Fetal Lung	lung
28	chr9:95766000-95766800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr9:95766000-95766800	Flanking Active TSS	K562	blood
30	chr9:95766000-95767000	Enhancers	Fetal Muscle Trunk	muscle
31	chr9:95766000-95767200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:95766000-95771200	Strong transcription	GM12878-XiMat	blood
33	chr9:95766000-95772200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr9:95766200-95766600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:95766200-95766600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:95766200-95766600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr9:95766200-95766600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:95766200-95766600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:95766200-95766600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr9:95766200-95766600	Flanking Active TSS	Liver	Liver
41	chr9:95766200-95766600	Active TSS	Brain Hippocampus Middle	brain
42	chr9:95766200-95766600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr9:95766200-95766600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:95766200-95766600	Flanking Active TSS	Colonic Mucosa	Colon
45	chr9:95766200-95766600	Enhancers	Colon Smooth Muscle	Colon
46	chr9:95766200-95766600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr9:95766200-95766600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr9:95766200-95766600	Genic enhancers	Fetal Intestine Large	intestine
49	chr9:95766200-95766600	Genic enhancers	Fetal Intestine Small	intestine
50	chr9:95766200-95766600	Flanking Active TSS	Placenta	Placenta

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