Variant report

Variant	rs11142467
Chromosome Location	chr9:73095886-73095887
allele	A/C
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:73030761..73038680-chr9:73091043..73101036,27	MCF-7	breast:
2	chr9:73026617..73037908-chr9:73091853..73102499,30	K562	blood:
3	chr9:73023348..73025257-chr9:73094505..73097293,2	K562	blood:
4	chr9:73030963..73039331-chr9:73089885..73101071,36	MCF-7	breast:
5	chr9:73025336..73030126-chr9:73090773..73099381,13	MCF-7	breast:
6	chr9:73094287..73096539-chr9:73098438..73101365,3	K562	blood:
7	chr9:73094687..73096290-chr9:73106130..73108014,2	MCF-7	breast:
8	chr9:73093971..73096517-chr9:73098061..73099840,2	MCF-7	breast:
9	chr9:73089437..73091298-chr9:73095044..73096704,2	K562	blood:
10	chr9:73025505..73030167-chr9:73091131..73097285,11	MCF-7	breast:
11	chr9:73032264..73037880-chr9:73093717..73104954,17	K562	blood:
12	chr9:73094287..73096782-chr9:73098912..73101911,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000119138	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11142431	0.82[EUR][1000 genomes]
rs11142434	0.82[EUR][1000 genomes]
rs11142435	0.81[EUR][1000 genomes]
rs11142441	0.85[EUR][1000 genomes]
rs11142443	0.85[EUR][1000 genomes]
rs11142451	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11142452	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142453	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142454	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142462	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11142464	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11142465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12238429	0.85[EUR][1000 genomes]
rs13291393	0.81[EUR][1000 genomes]
rs13298975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1556739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744598	0.85[EUR][1000 genomes]
rs4745011	0.85[EUR][1000 genomes]
rs4745012	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9644995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv428219	chr9:73006269-73192535	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv831616	chr9:73077855-73220928	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11142467	C9orf85	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73086600-73097400	Enhancers	Left Ventricle	heart
2	chr9:73087200-73097000	Enhancers	Right Atrium	heart
3	chr9:73088600-73107200	Weak transcription	Gastric	stomach
4	chr9:73092600-73096800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:73093000-73096800	Enhancers	Stomach Mucosa	stomach
6	chr9:73093000-73097600	Enhancers	Ovary	ovary
7	chr9:73093600-73100800	Enhancers	Brain Substantia Nigra	brain
8	chr9:73093800-73096000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:73093800-73096000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:73093800-73096200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:73093800-73096200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:73093800-73096200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr9:73093800-73096200	Enhancers	HMEC	breast
14	chr9:73093800-73096800	Enhancers	Small Intestine	intestine
15	chr9:73093800-73096800	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:73093800-73097000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr9:73093800-73097000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:73094000-73096000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:73094000-73096200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:73094000-73096200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:73094000-73096200	Enhancers	NHEK	skin
22	chr9:73094000-73096600	Enhancers	Fetal Stomach	stomach
23	chr9:73094000-73096800	Enhancers	HUVEC	blood vessel
24	chr9:73094200-73096000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr9:73094200-73096200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:73094200-73096200	Enhancers	NHLF	lung
27	chr9:73094200-73098000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:73094400-73096000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr9:73094400-73103600	Weak transcription	Aorta	Aorta
30	chr9:73094600-73096000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr9:73094600-73096200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:73094600-73096400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:73094800-73096200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:73094800-73096200	Flanking Active TSS	HSMM	muscle
35	chr9:73094800-73096400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr9:73094800-73096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr9:73095000-73096000	Enhancers	Fetal Muscle Leg	muscle
38	chr9:73095000-73096400	Enhancers	Fetal Intestine Large	intestine
39	chr9:73095000-73100200	Weak transcription	Spleen	Spleen
40	chr9:73095200-73096000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr9:73095200-73096000	Enhancers	Fetal Heart	heart
42	chr9:73095200-73096000	Enhancers	Fetal Intestine Small	intestine
43	chr9:73095200-73096600	Weak transcription	Esophagus	oesophagus
44	chr9:73095200-73096600	Weak transcription	Lung	lung
45	chr9:73095400-73096000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:73095400-73096000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:73095400-73096000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr9:73095400-73096000	Flanking Active TSS	Osteobl	bone
49	chr9:73095400-73096200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:73095400-73097400	Enhancers	Colon Smooth Muscle	Colon

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