Variant report

Variant	rs11142465
Chromosome Location	chr9:73090916-73090917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112280225..112280976-chr9:73090788..73091346,2	HCT-116	colon:
2	chr9:73030963..73039331-chr9:73089885..73101071,36	MCF-7	breast:
3	chr9:73025336..73030126-chr9:73090773..73099381,13	MCF-7	breast:
4	chr9:73025306..73027654-chr9:73088271..73090967,2	K562	blood:
5	chr9:73034309..73037135-chr9:73089839..73091361,2	K562	blood:
6	chr9:73089437..73091298-chr9:73095044..73096704,2	K562	blood:

Variant related genes	Relation type
ENSG00000138459	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000144848	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11142420	0.81[EUR][1000 genomes]
rs11142431	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11142434	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11142435	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11142441	0.87[EUR][1000 genomes]
rs11142443	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11142451	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11142452	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11142453	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11142454	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11142462	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11142464	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11142467	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	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13291393	0.83[EUR][1000 genomes]
rs13298975	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556739	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34775197	0.81[EUR][1000 genomes]
rs4744598	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4745011	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4745012	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9644995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs11142465	C9orf85	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73082600-73091600	Weak transcription	HSMMtube	muscle
2	chr9:73082600-73092000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:73085000-73093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:73085800-73093000	Weak transcription	Aorta	Aorta
5	chr9:73086000-73091600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr9:73086000-73093000	Weak transcription	Ovary	ovary
7	chr9:73086000-73093800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:73086000-73094200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:73086200-73092800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:73086200-73094000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:73086400-73094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:73086600-73097400	Enhancers	Left Ventricle	heart
13	chr9:73086800-73095800	Enhancers	Pancreas	Pancrea
14	chr9:73087200-73097000	Enhancers	Right Atrium	heart
15	chr9:73087800-73094600	Weak transcription	Osteobl	bone
16	chr9:73088000-73091800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:73088000-73092200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:73088000-73092800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:73088000-73092800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:73088000-73093000	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:73088000-73093200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:73088600-73107200	Weak transcription	Gastric	stomach
23	chr9:73089200-73091200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:73089400-73091000	Enhancers	Colon Smooth Muscle	Colon
25	chr9:73089600-73091000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr9:73089600-73093800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:73089600-73094200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:73089800-73093000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:73090000-73091400	Enhancers	Psoas Muscle	Psoas
30	chr9:73090000-73091800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:73090200-73093000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:73090400-73092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:73090400-73092800	Weak transcription	Adipose Nuclei	Adipose
34	chr9:73090600-73091200	Enhancers	Lung	lung
35	chr9:73090600-73091200	Enhancers	Right Ventricle	heart
36	chr9:73090600-73091800	Weak transcription	HUVEC	blood vessel
37	chr9:73090600-73092000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:73090600-73094200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:73090800-73091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr9:73090800-73093000	Weak transcription	Stomach Mucosa	stomach
41	chr9:73090800-73093200	Weak transcription	Liver	Liver

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